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<h1 class="title toc-ignore">Publications</h1>

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<p>Journal names have been intentionally excluded. Lab member names can be bolded through the publication overrides file. Shared first authors can be marked with a superscript * and corresponding authors with a superscript †. Click on a triangle for the article abstract.</p>
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<div id="preprints" class="section level3">
<h3>Preprints</h3>
<details>
<summary>
<a href="https://doi.org/10.64898/2026.02.26.708357">Bias in diversity estimators and neutrality tests induced by neutral polymorphic structural variants</a> [<a href="https://doi.org/10.64898/2026.02.26.708357">preprint</a>]<br />
S. E. Ramos-Onsins, <strong>J. Ross-Ibarra</strong>, M. Caceres, L. Ferretti
</summary>
<p style="margin-left: 30px">
Abstract Estimators of genetic diversity and neutrality tests derived from the site frequency spectrum (SFS), such as Watterson’s θ W , nucleotide diversity π , Tajima’s D , and Fay and Wu’s H , are designed to be interpreted relative to a baseline defined by the standard neutral SFS. In genomic regions strongly linked to a polymorphic structural variant (SV), deviations from these baselines occur even under strict neutrality: conditioning on an SV at known frequency partitions samples into SV and non-SV haplotypes and distorts the SFS for linked neutral mutations. These deviations are well understood for genomic inversions under long-term balancing selection. However, not all SVs are under strong selection, and the evolution of some SVs may be better approximated as neutral. Here we derive analytical expectations for the unfolded (and, when necessary, folded) SFS of single nucleotide polymorphisms conditional on neutral linked polymorphic SVs, including inversions, deletions, insertions, and introgressions. We use these expectations to quantify the resulting bias in standard diversity estimators and neutrality tests as a function of SV frequency and type. Finally, we discuss approaches to build corrected estimators of diversity and neutrality tests that are unbiased/centered after accounting for the presence and frequency of the SV.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.64898/2026.02.02.703385">Maize genetic diversity is largely unstructured by human ethnolinguistic diversity in its center of origin</a> [<a href="https://doi.org/10.64898/2026.02.02.703385">preprint</a>]<br />
<strong>S. Snodgrass<sup>*</sup><sup>†</sup></strong>, <strong>F. Li<sup>*</sup><sup>†</sup></strong>, <strong>S. Mambakkam</strong>, S. G. Medina-Muñoz, …[7 authors including <strong>L. Sparreo</strong>, <strong>M. Menon</strong>, <strong>C. Perez</strong>]…, A. Moreno-Estrada, D. Runcie, G. Coop, <strong>J. Ross-Ibarra<sup>†</sup></strong>
</summary>
<p style="margin-left: 30px">
Abstract Population structure and environmental features often capture major axes of genetic variation in many species. Yet the impacts of human activity often remain unquantified. For domesticated species that rely on human activity for survival and dispersal, human movements and cultural differences may play key roles patterning genetic diversity. Maize is a staple crop of enormous cultural importance to indigenous peoples of the Americas, but cannot survive or disperse without farmers. Using publicly available genotyping and passport data from almost 2,000 traditional maize varieties, more than 500 whole genome sequences of humans from Mexico, and indigenous linguistic maps, we quantify anthropogenic effects on maize genetic diversity in the Americas. Maize shows very little overall structure, highlighting the effectiveness of indigenous farmers in moving and mixing maize populations. While principal components of maize diversity show meaningful correlations to human genetic diversity, our linear modeling suggests little additional impact of human population structure beyond shared geography. Though differences in maize diversity are often patterned by language locally, we find only weak genome-wide effects at larger spatial scales. Despite the relatively weak global signal of anthropogenic effects, linguistic GWAS, outlier F ST analyses, and selection scans identified loci associated with specific languages. Leveraging landscape-level sequencing data, we highlight how anthropogenic factors have shaped patterns of maize genetic diversity across Mesoamerica.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.64898/2026.01.17.700095">The MexMAGIC population reveals the genetic architecture of clinal trait variation in Mexican native maize</a> [<a href="https://doi.org/10.64898/2026.01.17.700095">preprint</a>]<br />
S. Perez-Limón, A. L. Alonso-Nieves, M. R. Ramírez-Flores, G. C. Cintora-Martínez, …[10 authors including <strong>F. Li</strong>]…, <strong>J. Ross-Ibarra</strong>, C. S. Gillmor, R. Rellán-Álvarez, R. J. H. Sawers
</summary>
<p style="margin-left: 30px">
ABSTRACT Defining the genetic basis of local adaptation is fundamental to evolutionary biology and crop improvement. Theory predicts that when selective pressures track differences in the environment, a cline will be established. Such clines might be exploited to uncover adaptive variation by association of alleles with environmental stressors. However, monotonic phenotypic change over a cline is not necessarily mirrored by adaptive genetic variants. Furthermore, population structure can complicate the interpretation of genotype-environment association. To test the assumptions of genotype-environment association in a crop species, we developed a multi-parent advanced generation inter-cross (MAGIC) population using eight Mexican native maize varieties sourced from distinct agroecological zones. We mapped two clinal traits (tassel branching and flowering time) differing in genetic architecture. Variation in tassel branch number was dominated by a single QTL with allele effects that aligned well with a negative elevational cline. In contrast, we mapped 11 flowering time QTL with allele effects that were not consistently correlated with any one source environmental factor and distinct loci donated by highland and lowland early maturing varieties. Our observations support the theoretical result that genotype-environment association will be strongest under simple genetic architecture, although identification of adaptive alleles may still be confounded by population structure. Plain Language: Nine thousand years of careful selection and cultivation by indigenous farmers has generated a rich diversity of native Mexican maize (corn) varieties, grown from sea level to high mountains, and from jungle to semidesert. By crossing native varieties adapted to different locations, we can uncover important genetic variants conferring tolerance to environmental stressors.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1101/2025.11.25.690567">The origins and adaptive consequences of polyploidy in a dominant prairie grass</a> [<a href="https://doi.org/10.1101/2025.11.25.690567">preprint</a>]<br />
<strong>A. R. Phillips<sup>†</sup></strong>, T. AuBuchon-Elder, K. Barry, M. Stitzer, …[20 authors including <strong>E. Cryan</strong>, <strong>J. Porter</strong>, <strong>B. Solomon</strong>]…, S. Flint-Garcia, M. C. Romay, E. A. Kellogg, <strong>J. Ross-Ibarra<sup>†</sup></strong>
</summary>
<p style="margin-left: 30px">
Abstract Polyploidy is ubiquitous across North American prairies, which provide essential ecosystem services and rich soil for agriculture. Yet the mechanism driving polyploid abundance is unclear. Multiple hypotheses have been proposed including polyploid abundance is proportional to the opportunity for whole genome duplication (WGD), and WGD alters phenotypes that may increase fitness. We tested these two hypotheses together in the mixed-ploidy species Andropogon gerardi , a dominant grass species in endangered North American tallgrass prairies. Leveraging a novel, phased allopolyploid reference genome, we found the A. gerardi hexaploid arose after the C 4 grassland expansion in the early Pleistocene, when glacial cycles likely increased secondary contact between the diploid progenitors. We sequenced A. gerardi from 25 popula-tions and examined cytotype performance and morphology in a controlled environment to investigate the consequences of the contemporary mixed-ploidy populations. We found the 9 x A. gerardi cytotype is a neopolyploid and a result of recurrent WGD events. Further, we demonstrate the 9 x neopolyploids have greater growth and a decreased stomatal pore index, which is adaptive in xeric climates where the 9 x cy-totype is most common. Together, our results support both hypotheses for polyploid abundance in North America: WGD is a product of opportunity and can have immediate fitness consequences. Although the changes to fitness may provide an advantage to 9 x A. gerardi , the establishment of 9 x may lower overall population fitness due to the lower reproductive viability of 9 x individuals. Significance statement Polyploid species are abundant in North American prairies and make up many of the dominant species in the ecosystem. This prominence could be a result of whole genome duplication conferring an advantage that increases the frequency of polyploids or could simply indicate that the opportunity for whole genome duplication is higher in this ecosystem, or both. Through examining three polyploidization events in A. gerardi , the dominant species in endangered tallgrass North American prairies, we found whole genome duplication is both surprisingly common and confers traits that are beneficial in some environments.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1101/2025.11.03.686376">The dominance of gene expression controlled by trans -eQTL hotspots contributes to phenotypic heterosis in maize</a> [<a href="https://doi.org/10.1101/2025.11.03.686376">preprint</a>]<br />
G. Xu, X. Yang, M. Zhang, C. Kang, …[3 authors]…, P. Liu, <strong>J. Ross-Ibarra</strong>, J. Yang, H. Liu
</summary>
<p style="margin-left: 30px">
ABSTRACT Heterosis, or hybrid vigor, is a key phenomenon in genetics research and agricultural production, and has been primarily attributed to non-additive genetic effects such as dominance — a prevailing consensus shaped by decades of empirical research and theoretical debate. Although dominance may arguably arise from distal modifiers, their selective advantage is debated due to presumably small individual effects. To address this long-standing question, particularly how genetic dominance manifests at the transcriptomic level and contributes to phenotypic heterosis, we integrated transcriptomic and phenotypic data from a large population of maize hybrids and their inbred parents. We found that ∼ 30% of the expressed seedling genes in a significant proportion of hybrids exhibited expression patterns deviating from the average of the two parents, indicative of non-additivity. Further analysis suggests that while hybrid gene expression per se is primarily regulated by cis -eQTLs, expression dominance (or non-additivity) is disproportionately controlled by trans -eQTLs. These trans -eQTLs cluster into hotspots that regulate the non-additivity of hundreds of target genes, mostly within co-expression networks, and are notably enriched for transcription factors (TFs). Focusing on one such hotspot, we functionally validated a classical maize gene ZmR1 , a basic helix-loop-helix (bHLH) TF associated with multiple seedling trait heterosis, as a candidate regulator of expression dominance across hundreds of genes. Overexpression of ZmR1 enhances expression dominance of downstream genes and increases phenotypic heterosis in both seedling and adult traits. Further experiments confirmed its direct regulatory role in modulating genes involved in anthocyanin biosynthesis and lignin metabolism, driving transcriptome-level dominance. These results provide empirical support for the modifier hypothesis under an omnigenic model, suggesting that heterosis arises not from the modification of a single gene’s inheritance but through the coordinated regulation of hundreds of phenotype-associated genes, thereby helping to reconcile the long-standing debate over the genetic basis of dominance in heterosis.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1101/2025.09.16.676665">Genome-wide selection on transposable elements in maize</a> [<a href="https://doi.org/10.1101/2025.09.16.676665">preprint</a>]<br />
<strong>B. Liu<sup>†</sup></strong>, M. Munasinghe, R. A. Fairbanks, C. N. Hirsch, <strong>J. Ross-Ibarra<sup>†</sup></strong>
</summary>
<p style="margin-left: 30px">
ABSTRACT While most evolutionary research has focused on single nucleotide polymorphisms (SNPs), transposable elements (TEs) represent a major but understudied source of mutations that can influence organismal fitness. Previous studies on TEs often overlook the mechanisms and rates of transposition, rely on short-read sequencing that limits TE detection, or focus on small genomes such as Arabidopsis or Drosophila . In this study, we leveraged high-quality, long-read genome assemblies from 26 maize inbreds to investigate natural selection on TEs. We developed a novel and interpretable method, Φ SFS , which incorporates TE age and improves resolution for detecting selection. Using this approach, we identified key factors influencing selection on TEs: (1) the distance to the nearest gene, (2) the pre-insertion DNA methylation level at the insertion site, and (3) intrinsic TE characteristics, including copy number and expression level. This work represents the first application of long-read genome assemblies to study TE selection in a major crop species with a typical plant genome size. Our Φ SFS method offers a broadly applicable framework for detecting selection on TEs, and the factors uncovered provide new insights into the evolutionary dynamics and trade-offs between TEs and host genes.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1101/2025.09.10.675198">Heritability and QTL mapping of aerial roots and other yield component traits with implications for N2 fixation in Zea mays</a><br />
D. A. O’Donnell, <strong>J. Yang</strong>, P. Zamora, <strong>A. Lorant</strong>, C. Miao, A. Van Deynze, A. Bennett, <strong>J. Ross-Ibarra<sup>†</sup></strong>
</summary>
<p style="margin-left: 30px">
ABSTRACT Zea mays L. spp. mays (hereafter maize) populations from an indigenous community of Mexico have been reported to perform well using traditional cultivation practices that exclude industrial fertilizers despite low soil nitrate levels. The local maize cultivar is characterized by extended maturity, tall stature, and presence of thick aerial roots that secrete an abundance of polysaccharide-rich root exudate, or mucilage, that is implicated in the recruitment of diazotrophic microbes to facilitate biological nitrogen fixation. Here we estimate the broad sense heritability of traits related to nitrogen fixation in a panel of Zea entries spanning pre-domestication, post-domestication and post-improvement, and identify QTL via F2:F3 families for traits including aerial root node counts and various other yield related traits ( i.e. germination rate, time to reproductive maturity, total biomass and nitrogen content of shoot and grain). Across two separate field studies, aerial root node count (AR) demonstrates heritability of 64% and 73%, and genetic mapping reveals three distinct QTL distributed on chromosomes 1 and 9. Further, we report novel QTL for germination rate via stand counts after direct sowing (SC), Plant Total Nitrogen (PTN), Plant Dry Mass (PDM), and a joint QTL for Grain Total Nitrogen (GTN) and Grain Dry Mass (GDM). Finally, we identify overlap between QTL for multiple traits (including AR and SC) and regions of elevated introgression from wild Zea mays L. spp. mexicana (hereafter mexicana ) into Totontepec maize, with a greater degree of overlap than expected under a uniform genomic distribution suggesting adaptive introgression from mexicana . Given its pronounced aerial root morphology, we propose that mexicana is the ancestral source for prominent aerial roots and corresponding abundant mucilage production in Totontepec maize and other maize traditional varieties. ARTICLE SUMMARY Zea mays aerial roots (AR) and mucilage have been implicated in diazotrophic recruitment. This study estimates heritability and identifies QTL for AR and yield components via a diverse panel of Zea entries and F2:F3 mapping populations. Genetic mapping reveals three QTL for AR and several QTL for other yield traits, both novel and previously reported. This study also compares QTL and regions of elevated introgression from wild Zea mays L. spp. mexicana (hereafter mexicana ) into a native cultivar. For AR QTL, enrichment for mexicana -derived haplotypes is greater than expected under a uniform genomic distribution, suggesting adaptive introgression from mexicana .
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1101/2025.01.22.633974">Extensive genome evolution distinguishes maize within a stable tribe of grasses</a><br />
M. C. Stitzer, A. S. Seetharam, A. Scheben, S. K. Hsu, …[35 authors including <strong>A. R. Phillips</strong>, <strong>J. Ross-Ibarra</strong>]…, M. C. Romay, E. A. Kellogg, E. S. Buckler, M. B. Hufford
</summary>
<p style="margin-left: 30px">
Abstract Over the last 20 million years, the Andropogoneae tribe of grasses has evolved to dominate 17% of global land area. Domestication of these grasses in the last 10,000 years has yielded our most productive crops, including maize, sugarcane, and sorghum. The majority of Andropogoneae species, including maize, show a history of polyploidy – a condition that, while offering the evolutionary advantage of multiple gene copies, poses challenges to basic cellular processes, gene expression, and epigenetic regulation. Genomic studies of polyploidy have been limited by sparse sampling of taxa in groups with multiple polyploidy events. Here, we present 33 genome assemblies from 27 species, including chromosome-scale assemblies of maize relatives Zea and Tripsacum . In maize, the after-effects of polyploidy have been widely studied, showing reduced chromosome number, biased fractionation of duplicate genes, and transposable element (TE) expansions. While we observe these patterns within the genus Zea , 12 other polyploidy events deviate significantly. Those tetraploids and hexaploids retain elevated chromosome number, maintain nearly complete complements of duplicate genes, and have only stochastic TE amplifications. These genomes reveal variable outcomes of polyploidy, challenging simple predictions and providing a foundation for understanding its evolutionary implications in an ecologically and economically important clade.
</p>
</details>
<p>
</p>
</div>
<div id="section" class="section level3">
<h3>2026</h3>
<details>
<summary>
<a href="https://doi.org/10.1016/j.isci.2025.114062">Plant domestication revisited: Genomic insights into origins, mechanisms, and convergent evolution</a><br />
<strong>Y. Cao</strong>, J. Yan, <strong>J. Ross-Ibarra<sup>†</sup></strong>, N. Yang<sup>†</sup>
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p>
</details>
<p>
</p>
</div>
<div id="section-1" class="section level3">
<h3>2025</h3>
<details>
<summary>
<a href="https://doi.org/10.1038/s41588-025-02246-7">Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize</a> [<a href="https://doi.org/10.1101/2023.08.08.551183">preprint</a>]<br />
J. Engelhorn, S. J. Snodgrass, A. Kok, A. S. Seetharam, …[17 authors]…, B. Stich, W. B. Frommer, <strong>J. Ross-Ibarra</strong>, T. Hartwig
</summary>
<p style="margin-left: 30px">
Abstract Comprehensive maps of functional variation at transcription factor (TF) binding sites ( cis -elements) are crucial for elucidating how genotype shapes phenotype. Here, we report the construction of a pan-cistrome of the maize leaf under well-watered and drought conditions. We quantified haplotype-specific TF footprints across a pan-genome of 25 maize hybrids and mapped over 200,000 variants, genetic, epigenetic, or both (termed binding quantitative trait loci (bQTL)), linked to cis -element occupancy. Three lines of evidence support the functional significance of bQTL: (1) coincidence with causative loci that regulate traits, including vgt1 , ZmTRE1 and the MITE transposon near ZmNAC111 under drought; (2) bQTL allelic bias is shared between inbred parents and matches chromatin immunoprecipitation sequencing results; and (3) partitioning genetic variation across genomic regions demonstrates that bQTL capture the majority of heritable trait variation across ~72% of 143 phenotypes. Our study provides an auspicious approach to make functional cis -variation accessible at scale for genetic studies and targeted engineering of complex traits.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1073/pnas.2503748122">An ancient origin of the naked grains of maize</a> [<a href="https://doi.org/10.1101/2024.12.02.626434">preprint</a>]<br />
R. A. Fairbanks, <strong>J. Ross-Ibarra<sup>†</sup></strong>
</summary>
<p style="margin-left: 30px">
Adaptation to novel environments requires genetic variation, but whether adaptation typically acts upon preexisting genetic variation or must wait for new mutations remains a fundamental question in evolutionary biology. Selection during domestication has been long used as a model to understand evolutionary processes, providing information not only on the phenotypes selected but also, in many cases, an understanding of the causal loci. For each of the causal loci that have been identified in maize, the selected allele can be found segregating in natural populations, consistent with their origin as standing genetic variation. The sole exception to this pattern is the well-characterized domestication locus tga1 ( teosinte glume architecture1 ), which has long been thought to be an example of selection on a de novo mutation. Here, we use a large dataset of maize and teosinte genomes to reconstruct the origin and evolutionary history of tga1 . We first estimated the age of tga1-maize using a genealogy-based method, finding that the allele arose approximately 42,000 to 49,000 y ago, predating the beginning of maize domestication. We also identify tga1-maize in teosinte populations, indicating that the allele can survive in the wild. Finally, we compare observed patterns of haplotype structure and mutational age distributions near tga1 with simulations, finding that patterns near tga1 in maize better resemble those generated under simulated selective sweeps on standing variation. These multiple lines of evidence suggest that maize domestication likely drew upon standing genetic variation at tga1 and cement the importance of standing variation in driving adaptation during domestication.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1371/journal.pgen.1011714">Environmental data provide marginal benefit for predicting climate adaptation</a><br />
<strong>F. Li<sup>†</sup></strong>, <strong>D. J. Gates</strong>, E. S. Buckler, M. B. Hufford, …[7 authors]…, M. C. Willcox, S. J. Hearne, <strong>J. Ross-Ibarra<sup>†</sup></strong>, D. E. Runcie<sup>†</sup>
</summary>
<p style="margin-left: 30px">
Climate change poses a major challenge for both natural and cultivated species. Genomic tools are increasingly used in both conservation and breeding to identify adaptive loci that can be used to guide management in future climates. Here, we study the utility of climate and genomic data for identifying promising alleles using common gardens of a large, geographically diverse sample of traditional maize varieties to evaluate multiple approaches. First, we used genotype data to predict environmental characteristics of germplasm collections to identify varieties that may be pre-adapted to target environments. Second, we used environmental GWAS (envGWAS) to identify loci associated with historical divergence along climatic gradients. Finally, we compared the value of environmental data and envGWAS-prioritized loci to genomic data for prioritizing traditional varieties. We find that maize yield traits are best predicted by genome-wide relatedness and population structure, and that incorporating envGWAS-identified variants or environment-of-origin data provide little additional predictive information. While our results suggest that environmental data provide limited benefit in predicting fitness-related phenotypes, environmental GWAS is nonetheless a potentially powerful approach to identify individual novel loci associated with adaptation, especially when coupled with high density genotyping.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.7554/eLife.92405">The population genetics of convergent adaptation in maize and teosinte is not locally restricted</a> [<a href="https://doi.org/10.1101/2021.09.09.459637">preprint</a>]<br />
<strong>S. Tittes<sup>†</sup></strong>, <strong>A. Lorant</strong>, <strong>S. P. McGinty</strong>, J. B. Holland, J. de Jesus Sánchez-González, A. Seetharam, M. Tenaillon, <strong>J. Ross-Ibarra<sup>†</sup></strong>
</summary>
<p style="margin-left: 30px">
What is the genetic architecture of local adaptation and what is the geographic scale over which it operates? We investigated patterns of local and convergent adaptation in five sympatric population pairs of traditionally cultivated maize and its wild relative teosinte ( Zea mays subsp. parviglumis ). We found that signatures of local adaptation based on the inference of adaptive fixations and selective sweeps are frequently exclusive to individual populations, more so in teosinte compared to maize. However, for both maize and teosinte, selective sweeps are also frequently shared by several populations, and often between subspecies. We were further able to infer that selective sweeps were shared among populations most often via migration, though sharing via standing variation was also common. Our analyses suggest that teosinte has been a continued source of beneficial alleles for maize, even after domestication, and that maize populations have facilitated adaptation in teosinte by moving beneficial alleles across the landscape. Taken together, our results suggest local adaptation in maize and teosinte has an intermediate geographic scale, one that is larger than individual populations but smaller than the species range.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1093/genetics/iyaf085">Molecular evolution of a reproductive barrier in maize and related species</a><br />
<strong>E. Cryan<sup>†</sup></strong>, <strong>G. Phinney</strong>, A. S. Seetharam, M. M. S. Evans, E. A. Kellogg, J. Zhan, B. Meyers, D. J. Kliebenstein, <strong>J. Ross-Ibarra<sup>†</sup></strong>
</summary>
<p style="margin-left: 30px">
Abstract Three cross-incompatibility loci each control a distinct reproductive barrier in both domesticated maize (Zea mays ssp. mays) and its wild teosinte relatives. These 3 loci, Teosinte crossing barrier1 (Tcb1), Gametophytic factor1 (Ga1), and Ga2, each play a key role in preventing hybridization between incompatible populations and are proposed to maintain the barrier between domesticated and wild subspecies. Each locus encodes both a silk-active and a matching pollen-active pectin methylesterase (PMEs). To investigate the diversity and molecular evolution of these gametophytic factor loci, we identified existing and improved models of the responsible genes in a new genome assembly of maize line P8860 that contains active versions of all 3 loci. We then examined 52 assembled genomes from 17 species to classify haplotype diversity and identify sites under diversifying selection during the evolution of these genes. We show that Ga2, the oldest of these 3 loci, was duplicated to form Ga1 at least 12 million years ago. Tcb1, the youngest locus, arose as a duplicate of Ga1 before or around the time of diversification of the Zea genus. We find evidence of positive selection during evolution of the functional genes at an active site in the pollen-expressed PME and predicted surface sites in both the silk- and pollen-expressed PMEs. The most common allele at the Ga1 locus is a conserved ga1 allele (ga1-Off), which is specific haplotype containing 3 full-length PME gene copies, all of which are noncoding due to conserved stop codons and are between 610 thousand and 1.5 million years old. We show that the ga1-Off allele is associated with and likely generates 24-nt siRNAs in developing pollen-producing tissue, and these siRNAs map to functional Ga1 alleles. In previously published crosses, the ga1-Off allele was associated with reduced function of the typically dominant functional alleles for the Ga1 and Tcb1 barriers. Taken together, this seems to be an example of an allele at a reproductive barrier locus being associated with an as yet undetermined mechanism capable of silencing the reproductive barrier.
</p>
</details>
<p>
</p>
</div>
<div id="section-2" class="section level3">
<h3>2024</h3>
<details>
<summary>
<a href="https://doi.org/10.1038/s41586-024-07788-0">Teosinte Pollen Drive guides maize diversification and domestication by RNAi</a> [<a href="https://doi.org/10.1101/2023.07.12.548689">preprint</a>]<br />
B. Berube, E. Ernst, J. Cahn, B. Roche, …[4 authors]…, A. Siepel, <strong>J. Ross-Ibarra</strong>, J. Kermicle, R. A. Martienssen
</summary>
<p style="margin-left: 30px">
Abstract Selfish genetic elements contribute to hybrid incompatibility and bias or ‘drive’ their own transmission 1,2 . Chromosomal drive typically functions in asymmetric female meiosis, whereas gene drive is normally post-meiotic and typically found in males. Here, using single-molecule and single-pollen genome sequencing, we describe Teosinte Pollen Drive , an instance of gene drive in hybrids between maize ( Zea mays ssp. mays ) and teosinte mexicana ( Z. mays ssp. mexicana ) that depends on RNA interference (RNAi). 22-nucleotide small RNAs from a non-coding RNA hairpin in mexicana depend on Dicer-like 2 ( Dcl2 ) and target Teosinte Drive Responder 1 ( Tdr1 ), which encodes a lipase required for pollen viability. Dcl2 , Tdr1 and the hairpin are in tight pseudolinkage on chromosome 5, but only when transmitted through the male. Introgression of mexicana into early cultivated maize is thought to have been critical to its geographical dispersal throughout the Americas 3 , and a tightly linked inversion in mexicana spans a major domestication sweep in modern maize 4 . A survey of maize traditional varieties and sympatric populations of teosinte mexicana reveals correlated patterns of admixture among unlinked genes required for RNAi on at least four chromosomes that are also subject to gene drive in pollen from synthetic hybrids. Teosinte Pollen Drive probably had a major role in maize domestication and diversification, and offers an explanation for the widespread abundance of ‘self’ small RNAs in the germ lines of plants and animals.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1093/evolut/qpae130">Teosinte populations exhibit weak local adaptation to their rhizosphere biota despite strong effects of biota source on teosinte fitness and traits</a> [<a href="https://doi.org/10.1101/2021.04.20.440703">preprint</a>]<br />
A. M. O’Brien, R. J. H. Sawers, J. Gasca-Pineda, I. Baxter, L. E. Eguiarte, <strong>J. Ross-Ibarra</strong>, S. Y. Strauss
</summary>
<p style="margin-left: 30px">
Abstract While biotic interactions often impose selection, species and populations vary in whether they are locally adapted to biotic interactions. Evolutionary theory predicts that environmental conditions drive this variable local adaptation by altering the fitness impacts of species interactions. To investigate the influence of an environmental gradient on adaptation between a plant and its associated rhizosphere biota, we cross-combined teosinte (Zea mays ssp. mexicana) and rhizosphere biota collected across a gradient of decreasing temperature, precipitation, and nutrients in a greenhouse common garden experiment. We measured both fitness and phenotypes expected to be influenced by biota, including concentrations of nutrients in leaves. Independent, main effects of teosinte and biota source explained most variation in teosinte fitness and traits. For example, biota from warmer sites provided population-independent fitness benefits across teosinte hosts. Effects of biota that depended on teosinte genotype were often not specific to their local hosts, and most traits had similar relationships to fitness across biota treatments. However, we found weak patterns of local adaptation between teosinte and biota from colder sites, suggesting environmental gradients may alter the importance of local adaptation in teosinte–biota interactions, as evolutionary theory predicts.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1093/g3journal/jkae281">A unified VCF dataset from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize</a><br />
C. M. Andorf, <strong>J. Ross-Ibarra</strong>, A. S. Seetharam, M. B. Hufford, M. R. Woodhouse
</summary>
<p style="margin-left: 30px">
Abstract Efforts to capture and analyze maize nucleotide diversity have ranged widely in scope, but differences in reference genome version and software algorithms used in these efforts inhibit comparison, and these data are generally not available in an easy-to-use visualization platform for quick access and analysis. To address these issues, The Maize Genetics and Genomics Database has collaborated with maize researchers to offer variant data from a diverse set of 1,498 inbred lines, traditional varieties, and teosintes through a standardized variant-calling pipeline against version 5 of the B73 reference genome. The output was filtered for mapping quality, completeness, and linkage disequilibrium, and annotated based on variant effects relative to the B73 RefGen_v5 gene annotations. MaizeGDB has also updated a web tool, SNPversity 2.0, to filter, visualize, and download genotype sets based on genomic locations and accessions of interest, and added external datasets to demonstrate SNPversity 2.0’s broad usage. MaizeGDB plans to host annual updates of these resources as additional resequencing data become available, with plans to expand to all publicly available sequence data.
</p>
</details>
<p>
</p>
</div>
<div id="section-3" class="section level3">
<h3>2023</h3>
<details>
<summary>
<a href="https://doi.org/10.1126/science.adg8940">Two teosintes made modern maize</a> [<a href="https://doi.org/10.1101/2023.01.31.526540">preprint</a>]<br />
<strong>N. Yang<sup>*</sup><sup>†</sup></strong>, Y. Wang<sup>*</sup>, X. Liu<sup>*</sup>, M. Jin, …[22 authors including <strong>S. Mambakkam</strong>, <strong>M. Menon</strong>, <strong>S. Snodgrass</strong>]…, M. C. Stitzer, D. Runcie, J. Yan<sup>†</sup>, <strong>J. Ross-Ibarra<sup>†</sup></strong>
</summary>
<p style="margin-left: 30px">
The origins of maize were the topic of vigorous debate for nearly a century, but neither the current genetic model nor earlier archaeological models account for the totality of available data, and recent work has highlighted the potential contribution of a wild relative, Zea mays ssp. mexicana . Our population genetic analysis reveals that the origin of modern maize can be traced to an admixture between ancient maize and Zea mays ssp. mexicana in the highlands of Mexico some 4000 years after domestication began. We show that variation in admixture is a key component of maize diversity, both at individual loci and for additive genetic variation underlying agronomic traits. Our results clarify the origin of modern maize and raise new questions about the anthropogenic mechanisms underlying dispersal throughout the Americas.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1093/g3journal/jkad073">A happy accident: a novel turfgrass reference genome</a> [<a href="https://doi.org/10.1101/2022.03.08.483531">preprint</a>]<br />
<strong>A. R. Phillips<sup>†</sup></strong>, A. S. Seetharam, P. S. Albert, T. AuBuchon-Elder, …[5 authors]…, M. C. Romay, R. J. Soreng, E. A. Kellogg, <strong>J. Ross-Ibarra<sup>†</sup></strong>
</summary>
<p style="margin-left: 30px">
Abstract Poa pratensis, commonly known as Kentucky bluegrass, is a popular cool-season grass species used as turf in lawns and recreation areas globally. Despite its substantial economic value, a reference genome had not previously been assembled due to the genome’s relatively large size and biological complexity that includes apomixis, polyploidy, and interspecific hybridization. We report here a fortuitous de novo assembly and annotation of a P. pratensis genome. Instead of sequencing the genome of a C4 grass, we accidentally sampled and sequenced tissue from a weedy P. pratensis whose stolon was intertwined with that of the C4 grass. The draft assembly consists of 6.09 Gbp with an N50 scaffold length of 65.1 Mbp, and a total of 118 scaffolds, generated using PacBio long reads and Bionano optical map technology. We annotated 256K gene models and found 58% of the genome to be composed of transposable elements. To demonstrate the applicability of the reference genome, we evaluated population structure and estimated genetic diversity in P. pratensis collected from three North American prairies, two in Manitoba, Canada and one in Colorado, USA. Our results support previous studies that found high genetic diversity and population structure within the species. The reference genome and annotation will be an important resource for turfgrass breeding and study of bluegrasses.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1038/d41586-023-02895-w">Genetic modification can improve crop yields — but stop overselling it</a><br />
M. Khaipho-Burch, M. Cooper, J. Crossa, N. de Leon, …[5 authors]…, P. Ronald, <strong>J. Ross-Ibarra</strong>, D. Weigel, E. S. Buckler
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1371/journal.pbio.3002235">Diamonds in the not-so-rough: Wild relative diversity hidden in crop genomes</a><br />
S. Flint-Garcia, M. J. Feldmann, H. Dempewolf, P. L. Morrell, <strong>J. Ross-Ibarra<sup>†</sup></strong>
</summary>
<p style="margin-left: 30px">
Crop production is becoming an increasing challenge as the global population grows and the climate changes. Modern cultivated crop species are selected for productivity under optimal growth environments and have often lost genetic variants that could allow them to adapt to diverse, and now rapidly changing, environments. These genetic variants are often present in their closest wild relatives, but so are less desirable traits. How to preserve and effectively utilize the rich genetic resources that crop wild relatives offer while avoiding detrimental variants and maladaptive genetic contributions is a central challenge for ongoing crop improvement. This Essay explores this challenge and potential paths that could lead to a solution.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1093/molbev/msad170">Unraveling Prevalence and Effects of Deleterious Mutations in Maize Elite Lines across Decades of Modern Breeding</a><br />
S. Sun, B. Wang, C. Li, G. Xu, J. Yang, M. B. Hufford, <strong>J. Ross-Ibarra<sup>†</sup></strong>, H. Wang<sup>†</sup>, L. Wang<sup>†</sup>
</summary>
<p style="margin-left: 30px">
Abstract Future breeding is likely to involve the detection and removal of deleterious alleles, which are mutations that negatively affect crop fitness. However, little is known about the prevalence of such mutations and their effects on phenotypic traits in the context of modern crop breeding. To address this, we examined the number and frequency of deleterious mutations in 350 elite maize inbred lines developed over the past few decades in China and the United States. Our findings reveal an accumulation of weakly deleterious mutations and a decrease in strongly deleterious mutations, indicating the dominant effects of genetic drift and purifying selection for the two types of mutations, respectively. We also discovered that slightly deleterious mutations, when at lower frequencies, were more likely to be heterozygous in the developed hybrids. This is consistent with complementation as a potential explanation for heterosis. Subsequently, we found that deleterious mutations accounted for more of the variation in phenotypic traits than nondeleterious mutations with matched minor allele frequencies, especially for traits related to leaf angle and flowering time. Moreover, we detected fewer deleterious mutations in the promoter and gene body regions of differentially expressed genes across breeding eras than in nondifferentially expressed genes. Overall, our results provide a comprehensive assessment of the prevalence and impact of deleterious mutations in modern maize breeding and establish a useful baseline for future maize improvement efforts.
</p>
</details>
<p>
</p>
</div>
<div id="section-4" class="section level3">
<h3>2022</h3>
<details>
<summary>
<a href="https://doi.org/10.1093/g3journal/jkac013">Analysis of genotype-by-environment interactions in a maize mapping population</a> [<a href="https://doi.org/10.1101/2021.07.21.453280">preprint</a>]<br />
<strong>A. I. Hudson<sup>†</sup></strong>, <strong>S. G. Odell</strong>, P. Dubreuil, M. H. Tixier, S. Praud, D. E. Runcie, <strong>J. Ross-Ibarra</strong>
</summary>
<p style="margin-left: 30px">
Abstract Genotype-by-environment interactions are a significant challenge for crop breeding as well as being important for understanding the genetic basis of environmental adaptation. In this study, we analyzed genotype-by-environment interactions in a maize multiparent advanced generation intercross population grown across 5 environments. We found that genotype-by-environment interactions contributed as much as genotypic effects to the variation in some agronomically important traits. To understand how genetic correlations between traits change across environments, we estimated the genetic variance–covariance matrix in each environment. Changes in genetic covariances between traits across environments were common, even among traits that show low genotype-by-environment variance. We also performed a genome-wide association study to identify markers associated with genotype-by-environment interactions but found only a small number of significantly associated markers, possibly due to the highly polygenic nature of genotype-by-environment interactions in this population.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1038/s41588-022-01184-y">Genome sequencing reveals evidence of adaptive variation in the genus Zea</a> [<a href="https://doi.org/10.1101/2022.06.03.494450">preprint</a>]<br />
L. Chen, J. Luo, M. Jin, N. Yang<sup>†</sup>, …[27 authors]…, A. R. Fernie, M. L. Warburton, <strong>J. Ross-Ibarra<sup>†</sup></strong>, J. Yan<sup>†</sup>
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1093/molbev/msac239">Allele-specific Expression Reveals Multiple Paths to Highland Adaptation in Maize</a> [<a href="https://doi.org/10.1101/2022.07.15.500250">preprint</a>]<br />
H. Hu, T. Crow, S. Nojoomi, A. J. Schulz, …[3 authors]…, R. Sawers, R. Rellán-Álvarez, <strong>J. Ross-Ibarra</strong>, D. E. Runcie
</summary>
<p style="margin-left: 30px">
Abstract Maize is a staple food of smallholder farmers living in highland regions up to 4,000 m above sea level worldwide. Mexican and South American highlands are two major highland maize growing regions, and population genetic data suggest the maize’s adaptation to these regions occurred largely independently, providing a case study for convergent evolution. To better understand the mechanistic basis of highland adaptation, we crossed maize landraces from 108 highland and lowland sites of Mexico and South America with the inbred line B73 to produce F1 hybrids and grew them in both highland and lowland sites in Mexico. We identified thousands of genes with divergent expression between highland and lowland populations. Hundreds of these genes show patterns of convergent evolution between Mexico and South America. To dissect the genetic architecture of the divergent gene expression, we developed a novel allele–specific expression analysis pipeline to detect genes with divergent functional cis-regulatory variation between highland and lowland populations. We identified hundreds of genes with divergent cis-regulation between highland and lowland landrace alleles, with 20 in common between regions, further suggesting convergence in the genes underlying highland adaptation. Further analyses suggest multiple mechanisms contribute to this convergence in gene regulation. Although the vast majority of evolutionary changes associated with highland adaptation were region specific, our findings highlight an important role for convergence at the gene expression and gene regulation levels as well.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1093/gbe/evac016">Controlling for Variable Transposition Rate with an Age-Adjusted Site Frequency Spectrum</a> [<a href="https://doi.org/10.1101/2021.08.16.456262">preprint</a>]<br />
<strong>R. Horvath<sup>†</sup></strong>, <strong>M. Menon</strong>, M. Stitzer, <strong>J. Ross-Ibarra<sup>†</sup></strong>
</summary>
<p style="margin-left: 30px">
Abstract Recognition of the important role of transposable elements (TEs) in eukaryotic genomes quickly led to a burgeoning literature modeling and estimating the effects of selection on TEs. Much of the empirical work on selection has focused on analyzing the site frequency spectrum (SFS) of TEs. But TE evolution differs from standard models in a number of ways that can impact the power and interpretation of the SFS. For example, rather than mutating under a clock-like model, transposition often occurs in bursts which can inflate particular frequency categories compared with expectations under a standard neutral model. If a TE burst has been recent, the excess of low-frequency polymorphisms can mimic the effect of purifying selection. Here, we investigate how transposition bursts affect the frequency distribution of TEs and the correlation between age and allele frequency. Using information on the TE age distribution, we propose an age-adjusted SFS to compare TEs and neutral polymorphisms to more effectively evaluate whether TEs are under selective constraints. We show that our approach can minimize instances of false inference of selective constraint, remains robust to simple demographic changes, and allows for a correct identification of even weak selection affecting TEs which experienced a transposition burst. The results presented here will help researchers working on TEs to more reliably identify the effects of selection on TEs without having to rely on the assumption of a constant transposition rate.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1093/g3journal/jkab447">A B73×Palomero Toluqueño mapping population reveals local adaptation in Mexican highland maize</a> [<a href="https://doi.org/10.1101/2021.09.15.460568">preprint</a>]<br />
S. Perez-Limón, M. Li, G. C. Cintora-Martinez, M. R. Aguilar-Rangel, …[12 authors including <strong>J. Ross-Ibarra</strong>]…, S. Flint-Garcia, L. Diaz-Garcia, R. Rellán-Álvarez, R. J. H. Sawers
</summary>
<p style="margin-left: 30px">
Abstract Generations of farmer selection in the central Mexican highlands have produced unique maize varieties adapted to the challenges of the local environment. In addition to possessing great agronomic and cultural value, Mexican highland maize represents a good system for the study of local adaptation and acquisition of adaptive phenotypes under cultivation. In this study, we characterize a recombinant inbred line population derived from the B73 reference line and the Mexican highland maize variety Palomero Toluqueño. B73 and Palomero Toluqueño showed classic rank-changing differences in performance between lowland and highland field sites, indicative of local adaptation. Quantitative trait mapping identified genomic regions linked to effects on yield components that were conditionally expressed depending on the environment. For the principal genomic regions associated with ear weight and total kernel number, the Palomero Toluqueño allele conferred an advantage specifically in the highland site, consistent with local adaptation. We identified Palomero Toluqueño alleles associated with expression of characteristic highland traits, including reduced tassel branching, increased sheath pigmentation and the presence of sheath macrohairs. The oligogenic architecture of these three morphological traits supports their role in adaptation, suggesting they have arisen from consistent directional selection acting at distinct points across the genome. We discuss these results in the context of the origin of phenotypic novelty during selection, commenting on the role of de novo mutation and the acquisition of adaptive variation by gene flow from endemic wild relatives.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1093/g3journal/jkac011">Modeling allelic diversity of multiparent mapping populations affects detection of quantitative trait loci</a> [<a href="https://doi.org/10.1101/2021.07.14.452335">preprint</a>]<br />
<strong>S. G. Odell<sup>†</sup></strong>, <strong>A. I. Hudson</strong>, S. Praud, P. Dubreuil, M. H. Tixier, <strong>J. Ross-Ibarra</strong>, D. E. Runcie
</summary>
<p style="margin-left: 30px">
Abstract The search for quantitative trait loci that explain complex traits such as yield and drought tolerance has been ongoing in all crops. Methods such as biparental quantitative trait loci mapping and genome-wide association studies each have their own advantages and limitations. Multiparent advanced generation intercross populations contain more recombination events and genetic diversity than biparental mapping populations and are better able to estimate effect sizes of rare alleles than association mapping populations. Here, we discuss the results of using a multiparent advanced generation intercross population of doubled haploid maize lines created from 16 diverse founders to perform quantitative trait loci mapping. We compare 3 models that assume bi-allelic, founder, and ancestral haplotype allelic states for quantitative trait loci. The 3 methods have differing power to detect quantitative trait loci for a variety of agronomic traits. Although the founder approach finds the most quantitative trait loci, all methods are able to find unique quantitative trait loci, suggesting that each model has advantages for traits with different genetic architectures. A closer look at a well-characterized flowering time quantitative trait loci, qDTA8, which contains vgt1, highlights the strengths and weaknesses of each method and suggests a potential epistatic interaction. Overall, our results reinforce the importance of considering different approaches to analyzing genotypic datasets, and shows the limitations of binary SNP data for identifying multiallelic quantitative trait loci.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1073/pnas.2100036119">An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time</a> [<a href="https://doi.org/10.1101/2021.01.25.426574">preprint</a>]<br />
A. C. Barnes, F. Rodríguez-Zapata, K. A. Juárez-Núñez, D. J. Gates, …[22 authors]…, <strong>J. Ross-Ibarra</strong>, M. B. Hufford, R. J. H. Sawers, R. Rellán-Álvarez
</summary>
<p style="margin-left: 30px">
Native Americans domesticated maize ( Zea mays ssp. mays ) from lowland teosinte parviglumis ( Zea mays ssp. parviglumis) in the warm Mexican southwest and brought it to the highlands of Mexico and South America where it was exposed to lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites in plant responses to low-temperature and phosphorus availability and have been suggested to influence flowering time. Here, we combined linkage mapping with genome scans to identify High PhosphatidylCholine 1 ( HPC1 ), a gene that encodes a phospholipase A1 enzyme, as a major driver of phospholipid variation in highland maize. Common garden experiments demonstrated strong genotype-by-environment interactions associated with variation at HPC1, with the highland HPC1 allele leading to higher fitness in highlands, possibly by hastening flowering. The highland maize HPC1 variant resulted in impaired function of the encoded protein due to a polymorphism in a highly conserved sequence. A meta-analysis across HPC1 orthologs indicated a strong association between the identity of the amino acid at this position and optimal growth in prokaryotes. Mutagenesis of HPC1 via genome editing validated its role in regulating phospholipid metabolism. Finally, we showed that the highland HPC1 allele entered cultivated maize by introgression from the wild highland teosinte Zea mays ssp. mexicana and has been maintained in maize breeding lines from the Northern United States, Canada, and Europe. Thus, HPC1 introgressed from teosinte mexicana underlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1038/s41477-022-01190-2">Genomic insights into historical improvement of heterotic groups during modern hybrid maize breeding</a><br />
C. Li, H. Guan, X. Jing, Y. Li<sup>†</sup>, …[18 authors]…, <strong>J. Ross-Ibarra<sup>†</sup></strong>, Y. Li<sup>†</sup>, T. Wang<sup>†</sup>, H. Wang<sup>†</sup>
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1371/journal.pbio.3001814">Conflict over fertilization underlies the transient evolution of reinforcement</a> [<a href="https://doi.org/10.1101/2020.11.10.377481">preprint</a>]<br />
<strong>C. A. Rushworth</strong>, A. M. Wardlaw, <strong>J. Ross-Ibarra</strong>, Y. Brandvain
</summary>
<p style="margin-left: 30px">
When two species meet in secondary contact, the production of low fitness hybrids may be prevented by the adaptive evolution of increased prezygotic isolation, a process known as reinforcement. Theoretical challenges to the evolution of reinforcement are generally cast as a coordination problem, i.e., “how can statistical associations between traits and preferences be maintained in the face of recombination?” However, the evolution of reinforcement also poses a potential conflict between mates. For example, the opportunity costs to hybridization may differ between the sexes or species. This is particularly likely for reinforcement based on postmating prezygotic (PMPZ) incompatibilities, as the ability to fertilize both conspecific and heterospecific eggs is beneficial to male gametes, but heterospecific mating may incur a cost for female gametes. We develop a population genetic model of interspecific conflict over reinforcement inspired by “gametophytic factors”, which act as PMPZ barriers among Zea mays subspecies. We demonstrate that this conflict results in the transient evolution of reinforcement—after females adaptively evolve to reject gametes lacking a signal common in conspecific gametes, this gamete signal adaptively introgresses into the other population. Ultimately, the male gamete signal fixes in both species, and isolation returns to pre-reinforcement levels. We interpret geographic patterns of isolation among Z . mays subspecies considering these findings and suggest when and how this conflict can be resolved. Our results suggest that sexual conflict over fertilization may pose an understudied obstacle to the evolution of reinforcement.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1002/evl3.285">The genomic signature of wild-to-crop introgression during the domestication of scarlet runner bean ( Phaseolus coccineus L.)</a> [<a href="https://doi.org/10.1101/2021.02.03.429668">preprint</a>]<br />
A. Guerra-García, I. C. Rojas-Barrera, <strong>J. Ross-Ibarra</strong>, R. Papa, D. Piñero
</summary>
<p style="margin-left: 30px">
Abstract The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. It is cultivated in small-scale agriculture in the highlands of Mesoamerica for its dry seeds and immature pods, and unlike the other domesticated beans, P. coccineus is an open-pollinated legume. Contrasting with its close relative, the common bean, few studies focusing on its domestication history have been conducted. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 single-nucleotide variants) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even though there is evidence of a severe initial genetic bottleneck followed by a population expansion. Introgression from wild to domesticated populations was detected, which might contribute to the recovery of the genetic variation. Introgression has occurred at different times: constantly in the center of Mexico; recently in the North West; and anciently in the South. Several factors are acting together to increase and maintain genetic diversity in P. coccineus cultivars, such as demographic expansion and introgression. Wild relatives represent a valuable genetic resource and have played a key role in scarlet runner bean evolution via introgression into traditional varieties.
</p>
</details>
<p>
</p>
</div>
<div id="section-5" class="section level3">
<h3>2021</h3>
<details>
<summary>
<a href="https://doi.org/10.1126/science.abg5289">De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes</a> [<a href="https://doi.org/10.1101/2021.01.14.426684">preprint</a>]<br />
M. B. Hufford, A. S. Seetharam, M. R. Woodhouse, K. M. Chougule, …[38 authors including <strong>S. Tittes</strong>, <strong>A. I. Hudson</strong>, <strong>J. Ross-Ibarra</strong>]…, J. I. Gent, C. N. Hirsch, D. Ware, R. K. Dawe
</summary>
<p style="margin-left: 30px">
An a-maize-ing set of genomes Maize is an important crop cultivated worldwide. As maize spread across the world, selection for local environments resulted in variation, but the impact on differences between the genome has not been quantified. By producing high-quality genomic sequences of the 26 lines used in the maize nested association mapping panel, Hufford et al . map important traits and demonstrate the diversity of maize. Examining RNA and methylation of genes across accessions, the authors identified a core set of maize genes. Beyond this core set, comparative analysis across lines identified high levels of variation in the total set of genes, the maize pan-genome. The value of this resource was further exemplified by mapping quantitative traits of interest, including those related to pathogen resistance. —LMZ
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1371/journal.pgen.1009768">The genomic ecosystem of transposable elements in maize</a> [<a href="https://doi.org/10.1101/559922">preprint</a>]<br />
<strong>M. C. Stitzer<sup>†</sup></strong>, S. N. Anderson, N. M. Springer, <strong>J. Ross-Ibarra</strong>
</summary>
<p style="margin-left: 30px">
Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. Genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between attributes of the genomic environment and the survival of TE copies and families. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences reveal a diversity of survival strategies of TE families. Together these generate a rich ecology of the genome, with each TE family representing the evolution of a distinct ecological niche. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1038/s41477-020-00834-5">Comparative evolutionary genetics of deleterious load in sorghum and maize</a> [<a href="https://doi.org/10.1101/777623">preprint</a>]<br />
R. Lozano, E. Gazave, J. P. R. dos Santos, <strong>M. G. Stetter</strong>, …[7 authors]…, M. Taylor Perkins, E. S. Buckler, <strong>J. Ross-Ibarra<sup>†</sup></strong>, M. A. Gore<sup>†</sup>
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1371/journal.pgen.1009810">Selective sorting of ancestral introgression in maize and teosinte along an elevational cline</a> [<a href="https://doi.org/10.1101/2021.03.05.434040">preprint</a>]<br />
E. Calfee<sup>†</sup>, <strong>D. Gates</strong>, <strong>A. Lorant</strong>, <strong>M. T. Perkins</strong>, G. Coop<sup>†</sup>, <strong>J. Ross-Ibarra<sup>†</sup></strong>
</summary>
<p style="margin-left: 30px">
While often deleterious, hybridization can also be a key source of genetic variation and pre-adapted haplotypes, enabling rapid evolution and niche expansion. Here we evaluate these opposing selection forces on introgressed ancestry between maize ( Zea mays ssp. mays ) and its wild teosinte relative, mexicana ( Zea mays ssp. mexicana ). Introgression from ecologically diverse teosinte may have facilitated maize’s global range expansion, in particular to challenging high elevation regions (&gt; 1500 m). We generated low-coverage genome sequencing data for 348 maize and mexicana individuals to evaluate patterns of introgression in 14 sympatric population pairs, spanning the elevational range of mexicana , a teosinte endemic to the mountains of Mexico. While recent hybrids are commonly observed in sympatric populations and mexicana demonstrates fine-scale local adaptation, we find that the majority of mexicana ancestry tracts introgressed into maize over 1000 generations ago. This mexicana ancestry seems to have maintained much of its diversity and likely came from a common ancestral source, rather than contemporary sympatric populations, resulting in relatively low F ST between mexicana ancestry tracts sampled from geographically distant maize populations. Introgressed mexicana ancestry in maize is reduced in lower-recombination rate quintiles of the genome and around domestication genes, consistent with pervasive selection against introgression. However, we also find mexicana ancestry increases across the sampled elevational gradient and that high introgression peaks are most commonly shared among high-elevation maize populations, consistent with introgression from mexicana facilitating adaptation to the highland environment. In the other direction, we find patterns consistent with adaptive and clinal introgression of maize ancestry into sympatric mexicana at many loci across the genome, suggesting that maize also contributes to adaptation in mexicana , especially at the lower end of its elevational range. In sympatric maize, in addition to high introgression regions we find many genomic regions where selection for local adaptation maintains steep gradients in introgressed mexicana ancestry across elevation, including at least two inversions: the well-characterized 14 Mb Inv4m on chromosome 4 and a novel 3 Mb inversion Inv9f surrounding the macrohairless1 locus on chromosome 9. Most outlier loci with high mexicana introgression show no signals of sweeps or local sourcing from sympatric populations and so likely represent ancestral introgression sorted by selection, resulting in correlated but distinct outcomes of introgression in different contemporary maize populations.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1093/molbev/msab119">Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces</a> [<a href="https://doi.org/10.1101/2020.07.31.227629">preprint</a>]<br />
<strong>L. Wang<sup>†</sup></strong>, <strong>E. B. Josephs</strong>, K. M. Lee, L. M. Roberts, R. Rellán-Álvarez, <strong>J. Ross-Ibarra<sup>†</sup></strong>, M. B. Hufford<sup>†</sup>
</summary>
<p style="margin-left: 30px">
Abstract Convergent phenotypic evolution provides some of the strongest evidence for adaptation. However, the extent to which recurrent phenotypic adaptation has arisen via parallelism at the molecular level remains unresolved, as does the evolutionary origin of alleles underlying such adaptation. Here, we investigate genetic mechanisms of convergent highland adaptation in maize landrace populations and evaluate the genetic sources of recurrently selected alleles. Population branch excess statistics reveal substantial evidence of parallel adaptation at the level of individual single-nucleotide polymorphism (SNPs), genes, and pathways in four independent highland maize populations. The majority of convergently selected SNPs originated via migration from a single population, most likely in the Mesoamerican highlands, while standing variation introduced by ancient gene flow was also a contributor. Polygenic adaptation analyses of quantitative traits reveal that alleles affecting flowering time are significantly associated with elevation, indicating the flowering time pathway was targeted by highland adaptation. In addition, repeatedly selected genes were significantly enriched in the flowering time pathway, indicating their significance in adapting to highland conditions. Overall, our study system represents a promising model to study convergent evolution in plants with potential applications to crop adaptation across environmental gradients.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1093/genetics/iyab061">Gene body methylation is under selection in Arabidopsis thaliana</a> [<a href="https://doi.org/10.1101/2020.09.04.283333">preprint</a>]<br />
A. Muyle, <strong>J. Ross-Ibarra</strong>, D. K. Seymour, B. S. Gaut
</summary>
<p style="margin-left: 30px">
Abstract In plants, mammals and insects, some genes are methylated in the CG dinucleotide context, a phenomenon called gene body methylation (gbM). It has been controversial whether this phenomenon has any functional role. Here, we took advantage of the availability of 876 leaf methylomes in Arabidopsis thaliana to characterize the population frequency of methylation at the gene level and to estimate the site-frequency spectrum of allelic states. Using a population genetics model specifically designed for epigenetic data, we found that genes with ancestral gbM are under significant selection to remain methylated. Conversely, ancestrally unmethylated genes were under selection to remain unmethylated. Repeating the analyses at the level of individual cytosines confirmed these results. Estimated selection coefficients were small, on the order of 4 Nes = 1.4, which is similar to the magnitude of selection acting on codon usage. We also estimated that A. thaliana is losing gbM threefold more rapidly than gaining it, which could be due to a recent reduction in the efficacy of selection after a switch to selfing. Finally, we investigated the potential function of gbM through its link with gene expression. Across genes with polymorphic methylation states, the expression of gene body methylated alleles was consistently and significantly higher than unmethylated alleles. Although it is difficult to disentangle genetic from epigenetic effects, our work suggests that gbM has a small but measurable effect on fitness, perhaps due to its association to a phenotype-like gene expression.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1101/gr.266528.120">Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize</a><br />
B. Song, E. S. Buckler, H. Wang, Y. Wu, …[4 authors]…, P. J. Bradbury, <strong>J. Ross-Ibarra</strong>, M. B. Hufford, M. C. Romay
</summary>
<p style="margin-left: 30px">
Thousands of species will be sequenced in the next few years; however, understanding how their genomes work, without an unlimited budget, requires both molecular and novel evolutionary approaches. We developed a sensitive sequence alignment pipeline to identify conserved noncoding sequences (CNSs) in the Andropogoneae tribe (multiple crop species descended from a common ancestor ∼18 million years ago). The Andropogoneae share similar physiology while being tremendously genomically diverse, harboring a broad range of ploidy levels, structural variation, and transposons. These contribute to the potential of Andropogoneae as a powerful system for studying CNSs and are factors we leverage to understand the function of maize CNSs. We found that 86% of CNSs were comprised of annotated features, including introns, UTRs, putative cis -regulatory elements, chromatin loop anchors, noncoding RNA (ncRNA) genes, and several transposable element superfamilies. CNSs were enriched in active regions of DNA replication in the early S phase of the mitotic cell cycle and showed different DNA methylation ratios compared to the genome-wide background. More than half of putative cis -regulatory sequences (identified via other methods) overlapped with CNSs detected in this study. Variants in CNSs were associated with gene expression levels, and CNS absence contributed to loss of gene expression. Furthermore, the evolution of CNSs was associated with the functional diversification of duplicated genes in the context of maize subgenomes. Our results provide a quantitative understanding of the molecular processes governing the evolution of CNSs in maize.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1371/journal.pgen.1009797">Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte</a> [<a href="https://doi.org/10.1101/2021.09.01.458502">preprint</a>]<br />
L. F. Samayoa, B. A. Olukolu, C. J. Yang, Q. Chen, …[8 authors including <strong>M. G. Stetter</strong>, <strong>J. Yang</strong>]…, <strong>J. Ross-Ibarra</strong>, E. S. Buckler, J. F. Doebley, J. B. Holland
</summary>
<p style="margin-left: 30px">
Inbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. The extent to which the genetic load of mutations contributing to inbreeding depression is due to large-effect mutations versus variants with very small individual effects is unknown and may be affected by population history. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits, congruent with the greater segregating genetic load in the maize population that we predicted from sequence data. Parental breeding values were highly consistent between outcross and selfed offspring, indicating that additive effects determine most of the genetic value even in the presence of strong inbreeding depression. We developed a novel linkage scan to identify quantitative trait loci (QTL) representing large-effect rare variants carried by only a single parent, which were more important in teosinte than maize. Teosinte also carried more putative juvenile-acting lethal variants identified by segregation distortion. These results suggest a mixture of mostly polygenic, small-effect partially recessive effects in linkage disequilibrium underlying inbreeding depression, with an additional contribution from rare larger-effect variants that was more important in teosinte but depleted in maize following the domestication bottleneck. Purging associated with the maize domestication bottleneck may have selected against some large effect variants, but polygenic load is harder to purge and overall segregating mutational burden increased in maize compared to teosinte.
</p>
</details>
<p>
</p>
</div>
<div id="section-6" class="section level3">
<h3>2020</h3>
<details>
<summary>
<a href="https://doi.org/10.1016/j.pbi.2020.03.003">Evolutionary insights into plant breeding</a><br />
<strong>S. D. Turner-Hissong<sup>†</sup></strong>, M. E. Mabry, T. M. Beissinger, <strong>J. Ross-Ibarra</strong>, J. C. Pires
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p>
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<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1007/978-1-0716-0199-0_12">Genomics of Long- and Short-Term Adaptation in Maize and Teosintes</a><br />
<strong>A. Lorant</strong>, <strong>J. Ross-Ibarra</strong>, M. Tenaillon
</summary>
<p style="margin-left: 30px">
Abstract Maize is an excellent model for the study of plant adaptation. Indeed, post domestication maize quickly adapted to a host of new environments across the globe. And work over the last decade has begun to highlight the role of the wild relatives of maize—the teosintes Zea mays ssp. parviglumis and ssp. mexicana —as excellent models for dissecting long-term local adaptation. Although human-driven selection associated with maize domestication has been extensively studied, the genetic basis of natural variation is still poorly understood. Here we review studies on the genetic basis of adaptation and plasticity in maize and its wild relatives. We highlight a range of different processes that contribute to adaptation and discuss evidence from natural, cultivated, and experimental populations. From an applied perspective, understanding the genetic bases of adaptation and the contribution of plasticity will provide us with new tools to both better understand and mitigate the effect of climate changes on natural and cultivated populations.
</p>
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<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1038/s41588-020-0616-3">Genome-wide selection and genetic improvement during modern maize breeding</a><br />
B. Wang, Z. Lin, X. Li, Y. Zhao, …[19 authors]…, M. B. Hufford, <strong>J. Ross-Ibarra</strong>, H. He, H. Wang
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p>
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<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1534/genetics.119.302892">The Temporal Dynamics of Background Selection in Nonequilibrium Populations</a> [<a href="https://doi.org/10.1101/618389">preprint</a>]<br />
R. Torres<sup>*</sup>, M. G. Stetter<sup>*</sup>, R. D. Hernandez<sup>†</sup>, <strong>J. Ross-Ibarra<sup>†</sup></strong>
</summary>
<p style="margin-left: 30px">
Abstract Neutral genetic diversity across the genome is determined by the complex interplay of mutation, demographic history, and natural selection. While the direct action of natural selection is limited to functional loci across the genome, its impact can have effects on nearby neutral loci due to genetic linkage. These effects of selection at linked sites, referred to as genetic hitchhiking and background selection (BGS), are pervasive across natural populations. However, only recently has there been a focus on the joint consequences of demography and selection at linked sites, and some empirical studies have come to apparently contradictory conclusions as to their combined effects. To understand the relationship between demography and selection at linked sites, we conducted an extensive forward simulation study of BGS under a range of demographic models. We found that the relative levels of diversity in BGS and neutral regions vary over time and that the initial dynamics after a population size change are often in the opposite direction of the long-term expected trajectory. Our detailed observations of the temporal dynamics of neutral diversity in the context of selection at linked sites in nonequilibrium populations provide new intuition about why patterns of diversity under BGS vary through time in natural populations and help reconcile previously contradictory observations. Most notably, our results highlight that classical models of BGS are poorly suited for predicting diversity in nonequilibrium populations.
</p>
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<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1038/s41467-020-19333-4">Evolutionary and functional genomics of DNA methylation in maize domestication and improvement</a> [<a href="https://doi.org/10.1101/2020.03.13.991117">preprint</a>]<br />
G. Xu, J. Lyu, Q. Li, H. Liu, D. Wang, M. Zhang, N. M. Springer, <strong>J. Ross-Ibarra</strong>, J. Yang
</summary>
<p style="margin-left: 30px">
Abstract DNA methylation is a ubiquitous chromatin feature, present in 25% of cytosines in the maize genome, but variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here, we leverage whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) data on populations of modern maize, landrace, and teosinte ( Zea mays ssp. parviglumis) to estimate epimutation rates and selection coefficients. We find weak evidence for direct selection on DNA methylation in any context, but thousands of differentially methylated regions (DMRs) are identified population-wide that are correlated with recent selection. For two trait-associated DMRs, vgt1 -DMR and tb1 -DMR, HiChIP data indicate that the interactive loops between DMRs and respective downstream genes are present in B73, a modern maize line, but absent in teosinte. Our results enable a better understanding of the evolutionary forces acting on patterns of DNA methylation and suggest a role of methylation variation in adaptive evolution.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1371/journal.pgen.1008791">The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication</a><br />
Q. Chen, L. F. Samayoa, C. J. Yang, P. J. Bradbury, …[5 authors including <strong>A. Lorant</strong>]…, E. S. Buckler, <strong>J. Ross-Ibarra</strong>, J. B. Holland, J. F. Doebley
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1534/g3.120.401196">Selective Loss of Diversity in Doubled-Haploid Lines from European Maize Landraces</a> [<a href="https://doi.org/10.1101/817791">preprint</a>]<br />
<strong>L. Zeitler</strong>, <strong>J. Ross-Ibarra<sup>†</sup></strong>, <strong>M. G. Stetter<sup>†</sup></strong>
</summary>
<p style="margin-left: 30px">
Abstract Maize landraces are well adapted to their local environments and present valuable sources of genetic diversity for breeding and conservation. But the maintenance of open-pollinated landraces in ex-situ programs is challenging, as regeneration of seed can often lead to inbreeding depression and the loss of diversity due to genetic drift. Recent reports suggest that the production of doubled-haploid (DH) lines from landraces may serve as a convenient means to preserve genetic diversity in a homozygous form that is immediately useful for modern breeding. The production of doubled-haploid (DH) lines presents an extreme case of inbreeding which results in instantaneous homozygosity genome-wide. Here, we analyzed the effect of DH production on genetic diversity, using genome-wide SNP data from hundreds of individuals of five European landraces and their related DH lines. In contrast to previous findings, we observe a dramatic loss of diversity at both the haplotype level and that of individual SNPs. We identify thousands of SNPs that exhibit allele frequency differences larger than expected under models of neutral genetic drift and document losses of shared haplotypes. We find evidence consistent with selection at functional sites that are potentially involved in the diversity differences between landrace and DH populations. Although we were unable to uncover more details about the mode of selection, we conclude that landrace DH lines may be a valuable tool for the introduction of variation into maize breeding programs but come at the cost of decreased genetic diversity.
</p>
</details>
<p>
</p>
</div>
<div id="section-7" class="section level3">
<h3>2019</h3>
<details>
<summary>
<a href="https://doi.org/10.1101/706739">Single-gene resolution of locally adaptive genetic variation in Mexican maize</a> [<a href="https://doi.org/10.1101/706739">preprint</a>]<br />
<strong>D. J. Gates</strong>, D. Runcie, G. M. Janzen, A. R. Navarro, …[6 authors]…, E. S. Buckler, S. Hearne, M. B. Hufford, <strong>J. Ross-Ibarra<sup>†</sup></strong>
</summary>
<p style="margin-left: 30px">
Abstract Threats to crop production due to climate change are one of the greatest challenges facing plant breeders today. While considerable adaptive variation exists in traditional landraces, natural populations of crop wild relatives, and ex situ germplasm collections, separating adaptive alleles from linked deleterious variants that impact agronomic traits is challenging and has limited the utility of these diverse germplasm resources. Modern genome editing techniques such as CRISPR offer a potential solution by targeting specific alleles for transfer to new backgrounds, but such methods require a higher degree of precision than traditional mapping approaches can achieve. Here we present a high-resolution genome-wide association analysis to identify loci exhibiting adaptive patterns in a large panel of more than 4500 traditional maize landraces representing the breadth of genetic diversity of maize in Mexico. We evaluate associations between genotype and plant performance in 13 common gardens across a range of environments, identifying hundreds of candidate genes underlying genotype by environment interaction. We further identify genetic associations with environment across Mexico and show that such loci are associated with variation in yield and flowering time in our field trials and predict performance in independent drought trials. Our results indicate that the variation necessary to adapt crops to changing climate exists in traditional landraces that have been subject to ongoing environmental adaptation and can be identified by both phenotypic and environmental association.
</p>
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</p>
<details>
<summary>
<a href="https://doi.org/10.1534/genetics.118.301786">Detecting Adaptive Differentiation in Structured Populations with Genomic Data and Common Gardens</a> [<a href="https://doi.org/10.1101/368506">preprint</a>]<br />
<strong>E. B. Josephs<sup>†</sup></strong>, J. J. Berg, <strong>J. Ross-Ibarra</strong>, G. Coop
</summary>
<p style="margin-left: 30px">
Abstract Adaptation in quantitative traits often occurs through subtle shifts in allele frequencies at many loci—a process called polygenic adaptation. While a number of methods have been developed to detect polygenic adaptation in human populations, we lack clear strategies for doing so in many other systems. In particular, there is an opportunity to develop new methods that leverage datasets with genomic data and common garden trait measurements to systematically detect the quantitative traits important for adaptation. Here, we develop methods that do just this, using principal components of the relatedness matrix to detect excess divergence consistent with polygenic adaptation, and using a conditional test to control for confounding effects due to population structure. We apply these methods to inbred maize lines from the United States Department of Agriculture germplasm pool and maize landraces from Europe. Ultimately, these methods can be applied to additional domesticated and wild species to give us a broader picture of the specific traits that contribute to adaptation and the overall importance of polygenic adaptation in shaping quantitative trait variation.
</p>
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<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1111/tpj.14489">Transposable elements contribute to dynamic genome content in maize</a> [<a href="https://doi.org/10.1101/547398">preprint</a>]<br />
S. N. Anderson, M. C. Stitzer, A. B. Brohammer, P. Zhou, …[2 authors]…, C. D. Hirsch, J. Ross‐Ibarra, C. N. Hirsch, N. M. Springer
</summary>
<p style="margin-left: 30px">
Summary Transposable elements ( TE s) are ubiquitous components of eukaryotic genomes and can create variation in genome organization and content. Most maize genomes are composed of TE s. We developed an approach to define shared and variable TE insertions across genome assemblies and applied this method to four maize genomes (B73, W22, Mo17 and PH 207) with uniform structural annotations of TE s. Among these genomes we identified approximately 400 000 TE s that are polymorphic, encompassing 1.6 Gb of variable TE sequence. These polymorphic TE s include a combination of recent transposition events as well as deletions of older TE s. There are examples of polymorphic TE s within each of the superfamilies of TE s and they are found distributed across the genome, including in regions of recent shared ancestry among individuals. There are many examples of polymorphic TE s within or near maize genes. In addition, there are 2380 gene annotations in the B73 genome that are located within variable TE s, providing evidence for the role of TE s in contributing to the substantial differences in annotated gene content among these genotypes. TE s are highly variable in our survey of four temperate maize genomes, highlighting the major contribution of TE s in driving variation in genome organization and gene content. Open Research Badges This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at <a href="https://github.com/SNAnderson/maizeTE_variation" class="uri">https://github.com/SNAnderson/maizeTE_variation</a> ; <a href="https://mcstitzer.github.io/maize_TEs" class="uri">https://mcstitzer.github.io/maize_TEs</a> .
</p>
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<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1534/g3.119.400431">Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize</a> [<a href="https://doi.org/10.1101/668558">preprint</a>]<br />
S. N. Anderson<sup>*</sup>, <strong>M. C. Stitzer<sup>*</sup></strong>, P. Zhou, <strong>J. Ross-Ibarra</strong>, C. D. Hirsch, N. M. Springer
</summary>
<p style="margin-left: 30px">
Abstract Transposable Elements (TEs) are mobile elements that contribute the majority of DNA sequences in the maize genome. Due to their repetitive nature, genomic studies of TEs are complicated by the difficulty of properly attributing multi-mapped short reads to specific genomic loci. Here, we utilize a method to attribute RNA-seq reads to TE families rather than particular loci in order to characterize transcript abundance for TE families in the maize genome. We applied this method to assess per-family expression of transposable elements in &amp;gt;800 published RNA-seq libraries representing a range of maize development, genotypes, and hybrids. While a relatively small proportion of TE families are transcribed, expression is highly dynamic with most families exhibiting tissue-specific expression. A large number of TE families were specifically detected in pollen and endosperm, consistent with reproductive dynamics that maintain silencing of TEs in the germ line. We find that B73 transcript abundance is a poor predictor of TE expression in other genotypes and that transcript levels can differ even for shared TEs. Finally, by assessing recombinant inbred line and hybrid transcriptomes, complex patterns of TE transcript abundance across genotypes emerged. Taken together, this study reveals a dynamic contribution of TEs to maize transcriptomes.
</p>
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<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1111/evo.13818">Adaptive phenotypic divergence in an annual grass differs across biotic contexts*</a> [<a href="https://doi.org/10.1101/382770">preprint</a>]<br />
<strong>A. M. O’Brien<sup>†</sup></strong>, R. J. Sawers, S. Y. Strauss, J. Ross‐Ibarra
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p>
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<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1534/genetics.119.302378">Hybrid Decay: A Transgenerational Epigenetic Decline in Vigor and Viability Triggered in Backcross Populations of Teosinte with Maize</a> [<a href="https://doi.org/10.1101/588715">preprint</a>]<br />
W. Xue, S. N. Anderson, X. Wang, L. Yang, …[8 authors including <strong>P. Bilinski</strong>, <strong>M. C. Stitzer</strong>, <strong>J. Ross-Ibarra</strong>]…, S. Flint-Garcia, X. Chen, N. M. Springer, J. F. Doebley
</summary>
<p style="margin-left: 30px">
Abstract Xue et al. describe a phenomenon in maize and its nearest wild relative, teosinte, by which backcross progeny of a specific teosinte and maize exhibit a sickly whole-plant phenotype involving changes in morphology, vigor, and viability… In the course of generating populations of maize with teosinte chromosomal introgressions, an unusual sickly plant phenotype was noted in individuals from crosses with two teosinte accessions collected near Valle de Bravo, Mexico. The plants of these Bravo teosinte accessions appear phenotypically normal themselves and the F1 plants appear similar to typical maize × teosinte F1s. However, upon backcrossing to maize, the BC1 and subsequent generations display a number of detrimental characteristics including shorter stature, reduced seed set, and abnormal floral structures. This phenomenon is observed in all BC individuals and there is no chromosomal segment linked to the sickly plant phenotype in advanced backcross generations. Once the sickly phenotype appears in a lineage, normal plants are never again recovered by continued backcrossing to the normal maize parent. Whole-genome shotgun sequencing reveals a small number of genomic sequences, some with homology to transposable elements, that have increased in copy number in the backcross populations. Transcriptome analysis of seedlings, which do not have striking phenotypic abnormalities, identified segments of 18 maize genes that exhibit increased expression in sickly plants. A de novo assembly of transcripts present in plants exhibiting the sickly phenotype identified a set of 59 upregulated novel transcripts. These transcripts include some examples with sequence similarity to transposable elements and other sequences present in the recurrent maize parent (W22) genome as well as novel sequences not present in the W22 genome. Genome-wide profiles of gene expression, DNA methylation, and small RNAs are similar between sickly plants and normal controls, although a few upregulated transcripts and transposable elements are associated with altered small RNA or methylation profiles. This study documents hybrid incompatibility and genome instability triggered by the backcrossing of Bravo teosinte with maize. We name this phenomenon “hybrid decay” and present ideas on the mechanism that may underlie it.
</p>
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<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.7717/peerj.6815">Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize</a><br />
E. Gonzalez-Segovia, S. Pérez-Limon, G. C. Cíntora-Martínez, A. Guerrero-Zavala, G. M. Janzen, M. B. Hufford, <strong>J. Ross-Ibarra</strong>, R. J. H. Sawers
</summary>
<p style="margin-left: 30px">
Background The spread of maize cultivation to the highlands of central Mexico was accompanied by substantial introgression from the endemic wild teosinte Zea mays ssp. mexicana , prompting the hypothesis that the transfer of beneficial variation facilitated local adaptation. Methods We used whole-genome sequence data to map regions of Zea mays ssp. mexicana introgression in three Mexican highland maize individuals. We generated a genetic linkage map and performed Quantitative Trait Locus mapping in an F 2 population derived from a cross between lowland and highland maize individuals. Results Introgression regions ranged in size from several hundred base pairs to Megabase-scale events. Gene density within introgression regions was comparable to the genome as a whole, and over 1,000 annotated genes were located within introgression events. Quantitative Trait Locus mapping identified a small number of loci linked to traits characteristic of Mexican highland maize. Discussion Although there was no strong evidence to associate quantitative trait loci with regions of introgression, we nonetheless identified many Mexican highland alleles of introgressed origin that carry potentially functional sequence variants. The impact of introgression on stress tolerance and yield in the highland environment remains to be fully characterized.
</p>
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<p>
</p>
</div>
<div id="section-8" class="section level3">
<h3>2018</h3>
<details>
<summary>
<a href="https://doi.org/10.1007/978-3-319-97427-9_19">Evolution and Adaptation in the Maize Genome</a><br />
N. Manchanda, S. J. Snodgrass, <strong>J. Ross-Ibarra</strong>, M. B. Hufford
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1016/j.envsci.2018.01.001">Harnessing cross-border resources to confront climate change</a><br />
O. Aburto-Oropeza, A. F. Johnson, M. Agha, E. B. Allen, …[85 authors including <strong>J. Ross-Ibarra</strong>]…, G. Woolrich-Piña, A. Yunez-Naude, J. A. Zertuche-González, J. E. Taylor
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1111/nph.15350">Maize domestication and gene interaction</a><br />
M. C. Stitzer, J. Ross‐Ibarra
</summary>
<p style="margin-left: 30px">
Contents Summary 395 I. Introduction 395 II. The genetic basis of maize domestication 396 III. The tempo of maize domestication 401 IV. Genetic interactions and selection during maize domestication 401 V. Gene networks of maize domestication alleles 404 VI. Implications of gene interactions on evolution and selection 404 VII. Conclusions 405 Acknowledgements 405 References 405 Summary Domestication is a tractable system for following evolutionary change. Under domestication, wild populations respond to shifting selective pressures, resulting in adaptation to the new ecological niche of cultivation. Owing to the important role of domesticated crops in human nutrition and agriculture, the ancestry and selection pressures transforming a wild plant into a domesticate have been extensively studied. In Zea mays , morphological, genetic and genomic studies have elucidated how a wild plant, the teosinte Z. mays subsp. parviglumis , was transformed into the domesticate Z. mays subsp. mays . Five major morphological differences distinguish these two subspecies, and careful genetic dissection has pinpointed the molecular changes responsible for several of these traits. But maize domestication was a consequence of more than just five genes, and regions throughout the genome contribute. The impacts of these additional regions are contingent on genetic background, both the interactions between alleles of a single gene and among alleles of the multiple genes that modulate phenotypes. Key genetic interactions include dominance relationships, epistatic interactions and pleiotropic constraint, including how these variants are connected in gene networks. Here, we review the role of gene interactions in generating the dramatic phenotypic evolution seen in the transition from teosinte to maize.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1002/ajb2.1002">Adaptation in plant genomes: Bigger is different</a> [<a href="https://doi.org/10.1101/196501">preprint</a>]<br />
<strong>W. Mei</strong>, M. G. Stetter, D. J. Gates, M. C. Stitzer, J. Ross‐Ibarra
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1016/j.cell.2018.03.009">A Kinesin-14 Motor Activates Neocentromeres to Promote Meiotic Drive in Maize</a><br />
R. K. Dawe, E. G. Lowry, J. I. Gent, <strong>M. C. Stitzer</strong>, …[10 authors including <strong>J. Ross-Ibarra</strong>]…, J. A. Birchler, A. E. Harkess, A. L. Hodges, E. N. Hiatt
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1371/journal.pgen.1007794">Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima</a> [<a href="https://doi.org/10.1101/313247">preprint</a>]<br />
<strong>M. G. Stetter<sup>†</sup></strong>, K. Thornton, <strong>J. Ross-Ibarra<sup>†</sup></strong>
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1371/journal.pgen.1007162">Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays</a> [<a href="https://doi.org/10.1101/134528">preprint</a>]<br />
<strong>P. Bilinski</strong>, P. S. Albert, J. J. Berg, J. A. Birchler, …[2 authors including <strong>A. Lorant</strong>]…, <strong>J. Quezada</strong>, K. Swarts, <strong>J. Yang</strong>, <strong>J. Ross-Ibarra<sup>†</sup></strong>
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p>
</details>
<p>
</p>
<details>
<summary>
<a href="https://doi.org/10.1086/700118">Evolutionary Responses to Conditionality in Species Interactions across Environmental Gradients</a> [<a href="https://doi.org/10.1101/031195">preprint</a>]<br />
A. M. O’Brien, R. J. H. Sawers, <strong>J. Ross-Ibarra</strong>, S. Y. Strauss
</summary>
<p style="margin-left: 30px">
Abstract unavailable.
</p>
</details>
<p>
</p>
</div>
<div id="section-9" class="section level3">
<h3>2017</h3>
<details>