Edward Buckler

• Doctor of Philosophy
• Cornell University

Objectives This release note describes the Maize GxE project datasets within the Genomes to Fields (G2F) Initiative. The Maize GxE project aims to understand genotype by environment (GxE) interactions and use the information collected to improve resource allocation efficiency and increase genotype predictability and stability, particularly in scena...

Objectives The Genomes to Fields (G2F) 2022 Maize Genotype by Environment (GxE) Prediction Competition aimed to develop models for predicting grain yield for the 2022 Maize GxE project field trials, leveraging the datasets previously generated by this project and other publicly available data. Data description This resource used data from the Maiz...

Objectives This report provides information about the public release of the 2018–2019 Maize G X E project of the Genomes to Fields (G2F) Initiative datasets. G2F is an umbrella initiative that evaluates maize hybrids and inbred lines across multiple environments and makes available phenotypic, genotypic, environmental, and metadata information. The...

Objectives: The Genomes to Fields (G2F) 2022 Maize Genotype by Environment (G x E) Prediction Competition aimed to develop models for predicting grain yield for the 2022 Maize G x E project field trials, leveraging the datasets previously generated by this project and other publicly available data. Data description: This resource used data from the...

Objectives: This release note describes the Maize G x E project datasets within the Genomes to Fields (G2F) Initiative. The Maize G x E project aims to understand genotype by environment (G × E) interactions and use the information collected to improve resource allocation efficiency and increase genotype predictability and stability, particularly i...

Stomata allow CO2 uptake by leaves for photosynthetic assimilation at the cost of water vapor loss to the atmosphere. The opening and closing of stomata in response to fluctuations in light intensity regulate CO2 and water fluxes and are essential for maintaining water-use efficiency (WUE). However, little is known about the genetic basis for natur...

Genomic applications such as genomic selection and genome-wide association have become increasingly common since the advent of genome sequencing. The cost of sequencing has decreased in the past two decades, however genotyping costs are still prohibitive to gathering large datasets for these genomic applications, especially in non-model species whe...

Sweet corn (Zea mays L.), a highly consumed fresh vegetable in the United States, varies for tocochromanol (tocopherol and tocotrienol) levels but makes only a limited contribution to daily intake of vitamin E and antioxidants. We performed a genome‐wide association study of six tocochromanol compounds and 14 derivative traits across a sweet corn i...

Sorghum (Sorghum bicolor L.) is a major food cereal for millions of people worldwide. The sorghum genome, like other species, accumulates deleterious mutations, likely impacting its fitness. The lack of recombination, drift, and the coupling with favorable loci impede the removal of deleterious mutations from the genome by selection. To study how d...

Objectives: Crop improvement relies on analysis of phenotypic, genotypic, and environmental data. Given large, well-integrated, multi-year datasets, diverse queries can be made: Which lines perform best in hot, dry environments? Which alleles of specific genes are required for optimal performance in each environment? Such datasets also can be leve...

Understanding the quantitative genetics of crops has been and will continue to be central to maintaining and improving global food security. We outline four stages that plant breeding either has already achieved or will probably soon achieve. Top-of-the-line breeding programs are currently in Breeding 3.0, where inexpensive, genome-wide data couple...

Plant genomes reduce in size following a wholegenome duplication event, and one gene in a duplicate gene pair can lose function in absence of selective pressure to maintain duplicate gene copies. Maize (Zea mays L.) and its sister genus, Tripsacum, share a genome duplication event that occurred 5 to 26 million years ago. Because few genomic resourc...

One Sentence Summary HPLC-MS metabolite profiling of maize seedlings, in combination with genome-wide association studies, identifies numerous quantitative trait loci that influence the accumulation of foliar metabolites. Abstract Cultivated maize ( Zea mays ) retains much of the genetic and metabolic diversity of its wild ancestors. Non-targeted...

The production and regulation of defensive specialized metabolites play a central role in pathogen resistance in maize (Zea mays) and other plants. Therefore, identification of genes involved in plant specialized metabolism can contribute to improved disease resistance. We used comparative metabolomics to identify previously unknown antifungal meta...

Maize is an important crop with a high level of genome diversity and heterosis. The genome sequence of a typical female line, B73, was previously released. Here, we report a de novo genome assembly of a corresponding male representative line, Mo17. More than 96.4% of the 2,183 Mb assembled genome can be accounted for by 362 scaffolds in ten pseudoc...

The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a W22 reference genome using short-read sequencing technologies. We show that significant structural heterogeneity exists in comparison to the B73 reference genome at multiple...

Ribosomal repeats occupy 5% of a plant genome, yet there has been little study of their diversity in the modern age of genomics. Ribosomal copy number and expression variations present an opportunity to tap a novel source of diversity. In the present study, we estimated the ribosomal DNA copy (rDNA) number and ribosomal RNA (rRNA) expression for a...

The degree to which the genotype of an organism can affect the composition of its associated microbial communities (“microbiome”) varies by organism and habitat, and in many cases is unknown. We analyzed the metabolically active bacteria of maize leaves across 300 diverse maize lines growing in a common environment. We performed comprehensive herit...

Promoter-proximal pausing and divergent transcription at promoters and enhancers, which are prominent features in animals, have been reported to be absent in plants based on a study of Arabidopsis thaliana. Here, our PRO-Seq analysis in cassava (Manihot esculenta) identified peaks of transcriptionally-engaged RNA polymerase II (Pol2) at both 5' and...

Deep learning methodologies have revolutionized prediction in many fields, and show potential to do the same in molecular biology and genetics. However, applying these methods in their current forms ignores evolutionary dependencies within biological systems and can result in false positives and spurious conclusions. We developed two novel approach...

Modern improvement of complex traits in agricultural species relies on successful associations of heritable molecular variation with observable phenotypes. Historically, this pursuit has primarily been based on easily measurable genetic markers. The recent advent of new technologies allows assaying and quantifying biological intermediates (hereafte...

Sorghum (Sorghum bicolor (L.) Moench) is a major staple food cereal for millions of people worldwide. The sorghum genome, like other species, accumulates deleterious mutations, likely impacting its fitness. Though selection keeps deleterious mutations rare, their complete removal from the genome is impeded due to lack of recombination, drift, and t...

Significance In this very large-scale longitudinal field study of the maize rhizosphere microbiome, we identify heritable taxa. These taxa display variance in their relative abundances that can be partially explained by genetic differences between the maize lines, above and beyond the strong influences of field, plant age, and weather on the divers...

The production and regulation of defensive specialized metabolites plays a central role in pathogen resistance in maize ( Zea mays ) and other plants. Therefore, identification of genes involved in plant specialized metabolism can contribute to improved disease resistance. We used comparative metabolomics to identify previously unknown antifungal m...

Southern leaf blight (SLB) and northern leaf blight (NLB) are the two major foliar diseases limiting maize production worldwide. Upon previous study with the nested association mapping (NAM) population, which consist of 5,000 recombinant inbred lines from 25 parents crossed with B73, we expanded the phenotyping environments from the United States (...

Improvement of statistical methods is crucial for realizing the potential of increasingly dense genetic markers. Bayesian methods treat all markers as random effects, exhibit an advantage on dense markers, and offer the flexibility of using different priors. In contrast, genomic best linear unbiased prediction (gBLUP) is superior in computing speed...

Nat. Biotechnol. 35, 969–976 (2017); published online 18 September 2017; corrected after print 28 February 2018 In the version of this article initially published, in the HTML, the wrong Creative Commons Attribution license (cc-by-nc rather than cc-by) was inserted. The error has been corrected in the HTML version of the article.

Here we report a multi-tissue gene expression resource that represents the genotypic and phenotypic diversity of modern inbred maize, and includes transcriptomes in an average of 255 lines in seven tissues. We mapped expression quantitative trait loci and characterized the contribution of rare genetic variants to extremes in gene expression. Some o...

Background Characterization of genetic variations in maize has been challenging, mainly due to deterioration of collinearity between individual genomes in the species. An international consortium of maize research groups combined resources to develop the maize haplotype version 3 (HapMap 3), built from whole genome sequencing data from 1,218 maize...

The recent rapid emergence of maize lethal necrosis (MLN), caused by coinfection of maize with maize chlorotic mottle virus (MCMV) and a second virus usually from the family Potyviridae, is causing extensive losses for farmers in East Africa, Southeast Asia and South America. Although the genetic basis of resistance to potyviruses is well understoo...

Remarkable productivity has been achieved in crop species through artificial selection and adaptation to modern agronomic practices. Whether intensive selection has changed the ability of improved cultivars to maintain high productivity across variable environments is unknown. Understanding the genetic control of phenotypic plasticity and genotype...

Hop (Humulus lupulus L.) breeding programs seek to exploit genetic resources for bitter flavor, aroma, and disease resistance. However, these efforts have been thwarted by segregation distortion including female-biased sex ratios. To better understand the transmission genetics of hop, we genotyped 4512 worldwide accessions of hop, including cultiva...

Significance Meiotic recombination is a process in plants, animals, and fungi during which chromosomes exchange their parts. It generates new genetic variation in the progeny and is one of the reasons why progeny are both similar to and different from their parents. Recombination is initiated by formation of breaks in chromosomal DNA. We generated...

Tocopherols, tocotrienols and plastochromanols (collectively termed tocochromanols) are lipid-soluble antioxidants synthesized by all plants. Their dietary intake, primarily from seed oils, provides vitamin E and other health benefits. Tocochromanol biosynthesis has been dissected in the dicot Arabidopsis thaliana, which has green, photosynthetic s...

Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ~1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for...

Deleterious alleles have long been proposed to play an important role in patterning phenotypic variation and are central to commonly held ideas explaining the hybrid vigor observed in the offspring of a cross between two inbred parents. We test these ideas using evolutionary measures of sequence conservation to ask whether incorporating information...

Linear regressions of GERP-SNPs’ additive variance, dominance variance and total variance of seven traits per se against their GERP scores. Solid and dashed lines represent significant and non-significant linear regressions, with grey bands representing 95% confidence intervals. Data are only shown for SNPs which explain more phenotypic variance th...

A half-diallel population and distributions of phenotypes. (a) Twelve maize inbred lines were selected and crossed in a half-diallel fashion. Each inbred lines was used as both male and female and the resulting F1 seed was bulked. (b) Density plots of normalized BLUE values for the seven phenotypic traits. We used the “scale” function in R to norma...

Cross-validation prediction accuracy for trait per se and heterosis. Beanplots represent prediction accuracy estimated from cross-validation experiments for traits per se (a, b) and heterosis (c, d) under additive (a, c) and dominance (b, d) models. Prediction accuracy using real data is shown on the left (red) and permutation results on the right...

Breeding values of grain yield for diploid and simulated triploid hybrids. Each line represents the posterior breeding values of a diploid hybrid (red circle), its best parent (black diamond), and predicted breeding values of simulated AAB triploid (blue square) and ABB triploid (green triangle) plants based on estimated effect sizes and dominance...

General combining ability and specific combining ability of the seven phenotypic traits. (CSV)

SNP missing rate in our diallel parental lines. (CSV)

Summary statistics of SNP annotation results. (XLSX)

The correlation between the number of homozygote GERP-SNPs and the hybrid phenotypes. (CSV)

Pairwise correlation plots of seven phenotypic traits. The upper right panels show the scatter plots of all possible pairwise comparisons of two traits. The red line is a fitted loess curve. In the lower left panels, the numbers are the Spearman correlation coefficients (r) and the asterisks (*) indicate the correlation coefficients are statistical...

The minor allele frequency estimated from 12 parental lines in bins of 0.01 GERP score. Red solid and grey dashed lines define the best-fit regression line and its 95% confidence interval. (PDF)

Segregating genetic load across ten maize chromosomes. ots indicate mean GERP scores of putatively deleterious SNPs (GERP scores > 0) carried by the 12 parental maize lines (bin size = 1 cM). Vertical red lines indicate centromeres. (PDF)

Cumulative variance explained by GERP-SNPs. Additive and dominance effects are indicated by red and blue colors respectively. (PDF)

Linear regressions after filtering out GERP-SNPs located in regions in the lowest quartiles of recombination. Solid and dashed lines represent significant and non-significant linear regressions, with grey bands representing 95% confidence intervals. Data are only shown for GERP-SNPs which explain more variance than the genome-wide mean and found in...

Best Linear Unbiased Estimator (BLUE) values and levels of heterosis of the seven phenotypic traits for the 66 hybrids. Abbreviations for phenotypic traits are plant height (PHT, in cm), height of primary ear (EHT, in cm), days to 50% pollen shed (DTP), days to 50% silking (DTS), anthesis-silking interval (ASI, in days), grain yield adjusted to 15....

Number of complementation and homozygote deleterious load for GERP-SNPs in hybrids. (CSV)

Haplotype block identification using an IBD approach. In the upper panel, regions in red are IBD blocks identified by pairwise comparison of the two parental lines of a hybrid. The vertical dashed lines define haplotype blocks. In the lower panel, hybrid genotypes in each block are coded as heterozygotes (0) or homozygotes (1). (PDF)

Phenotypic variance explained for observed data and for randomly shuffled data using the genomic selection model. Histograms show the results for the randomly shuffled (10 times) degrees of dominance (k) in each trait. Red lines show the phenotypic variance explained using the observed k. (PDF)

Phenotypic variance explained for grain yield and degree of dominance (k) of GERP-SNPs after removing 11 hybrids that B73 as one parent. (a) Total per-SNP variance explained for grain yield per se by deleterious (red lines) and randomly sampled SNPs (grey beanplots). (b) Density plots of the degree of dominance (k). Extreme values of k were truncat...

Regression of degree of dominance (k) on GERP scores for simulated data. The solid blue line indicates the regression line fitted to data simulated under mutation-selection balance (see Methods for details). (PNG)

Number of deleterious SNPs carried per line. (CSV)

Model comparisons P values and AICs. (CSV)

Cross-validation accuracy using GERP-SNPs in genic regions. Beanplots represent prediction accuracy estimated from cross-validation experiments for traits per se (a, b, c) and heterosis (d, e, f) under additive (a, d), dominance (b, e), and incomplete dominance (c, f) models. Prediction accuracy using real data is shown on the left (green) and perm...

Estimating temperate adaptation in ancient maize Maize as a staple food crop in temperate North America required adaptation to a shorter growing season. On its first introduction in the southwestern United States ∼4000 years ago, maize was extensively grown in the lowlands. Cultivation in the temperate uplands did not occur for another 2000 years....

Grapes are one of the most economically and culturally important crops worldwide, and they have been bred for both winemaking and fresh consumption. Here we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world’s largest grape gene banks, the grap...

Leaf architecture directly influences canopy structure, consequentially affecting yield. We discovered a maize (Zea mays) mutant with aberrant leaf architecture, which we named drooping leaf1 (drl1). Pleiotropic mutations in drl1 affect leaf length and width, leaf angle, and internode length and diameter. These phenotypes are enhanced by natural va...