Jeffrey Ross‐Ibarra

The paper quantifies anthropogenic effects on maize genetic diversity in the Americas using genotyping, human genomic data, and linguistic maps, finding weak genome-wide effects but localized language-associated loci.

This study identifies cellular and genetic changes in maize and teosinte ears, showing how cytokinin signaling and transcription factor expression differences drive cob thickening and increased kernel number during domestication.

The paper quantifies bias in genetic diversity and neutrality tests caused by neutral polymorphic structural variants and proposes corrected estimators.

The paper uses a MAGIC population to study genetic architecture of clinal traits in Mexican maize, finding one major QTL for tassel branching and multiple QTL for flowering time with complex environmental associations.

This study investigates the origins and adaptive consequences of polyploidy in the prairie grass Andropogon gerardi, finding that whole genome duplication is common and provides fitness advantages in xeric climates.

The paper investigates how trans-eQTL hotspots contribute to phenotypic heterosis in maize by regulating non-additive gene expression through transcription factors.

This study uses long-read genome assemblies from maize to develop a new method for detecting selection on transposable elements, identifying factors like gene distance and DNA methylation levels that influence TE selection.

This paper estimates heritability and identifies QTL for aerial root traits and yield components in maize, finding genetic overlap with introgression from wild mexicana.

The paper identifies genetic variants at transcription factor binding sites that explain a large portion of phenotypic heritability in maize under different water conditions.

This study shows the tga1 allele in maize originated 41,000-49,000 years ago, predating domestication, and suggests standing genetic variation, not de novo mutation, drove maize domestication.

This study evaluates the use of environmental and genomic data to identify climate-adaptive maize varieties, finding that genomic data better predict yield traits than environmental data alone.

The paper investigates the molecular evolution of three reproductive barrier loci in maize and related species, identifying gene duplication, selection, and epigenetic silencing mechanisms.

The paper examines genome evolution in maize and related grasses, revealing variable outcomes of polyploidy across species.

The paper provides a unified VCF dataset from 1,498 maize accessions to explore genomic diversity using a standardized variant-calling pipeline.

The paper characterizes genomic variation across 744 Zea genomes, identifies adaptive variants, and highlights their potential for breeding applications.

This paper introduces an age-adjusted site frequency spectrum to better assess selective constraints on transposable elements by accounting for transposition bursts and demographic changes.

A multi-genome analysis of maize reveals previously unknown variation in gene content, genome structure, and methylation.

The paper analyzes gene body methylation in Arabidopsis thaliana to show it is under selection, with some genes being selected to remain methylated and others to be unmethylated, and finds a link between methylation and gene expression.

This study compares deleterious mutation patterns between sorghum and maize, finding sorghum diverges from the domestication cost hypothesis and develops a gene deleterious index with accuracy over 0.5.

This study characterizes TE family transcript abundance in maize using RNA-seq data from over 800 libraries, revealing dynamic and tissue-specific expression patterns.

The paper identifies variable transposable element (TE) insertions across four maize genomes, showing their role in genome organization and gene content variation.

The paper describes a transgenerational epigenetic decline in vigor and viability in maize-teosinte backcross populations, termed 'hybrid decay', characterized by genomic instability and altered gene expression.

The paper constructs the third generation Zea mays haplotype map using whole genome sequencing data from 1,218 maize lines, identifying 83 million variant sites.

The paper investigates the role of deleterious alleles in trait variation and heterosis in maize by integrating sequence conservation and genomic prediction models.

The paper examines gene expression changes in maize and teosinte under past and present environmental conditions to explore the role of genetic assimilation in maize domestication.

The paper improves the maize reference genome using single molecule technologies, resulting in longer contigs and better annotation of repetitive elements and genes.

The paper shows that gene expression levels and subgenome fractionation influence phenotypic variation in maize.

The paper examines convergent adaptation in maize to highland climates, finding limited nucleotide-level convergence but evidence of selection on standing variation and introgression from wild teosinte.

This study uses ancient population genomic techniques to trace the origin and evolution of maize in the American Southwest, identifying two diffusion routes and genetic adaptations to local environments.

The paper investigates the prevalence and role of the Hopscotch transposable element at the tb1 locus in teosinte, finding it present in multiple populations but not strongly linked to tillering.