Genome-Wide Association Studies for Yield-Related Traits in Soft Red Winter Wheat Grown in Virginia

Authors

Brian P. Ward, North Carolina State University
Gina Brown-Guedira, USDA Agricultural Research Service
Frederic L. Kolb, University of Illinois at Urbana-Champaign
David A. Van Sanford, University of KentuckyFollow
Priyanka Tyagi, North Carolina State University
Clay H. Sneller, The Ohio State University
Carl A. Griffey, Virginia Tech

Abstract

Grain yield is a trait of paramount importance in the breeding of all cereals. In wheat (Triticum aestivum L.), yield has steadily increased since the Green Revolution, though the current rate of increase is not forecasted to keep pace with demand due to growing world population and increasing affluence. While several genome-wide association studies (GWAS) on yield and related component traits have been performed in wheat, the previous lack of a reference genome has made comparisons between studies difficult. In this study, a GWAS for yield and yield-related traits was carried out on a population of 322 soft red winter wheat lines across a total of four rain-fed environments in the state of Virginia using single-nucleotide polymorphism (SNP) marker data generated by a genotyping-by-sequencing (GBS) protocol. Two separate mixed linear models were used to identify significant marker-trait associations (MTAs). The first was a single-locus model utilizing a leave-one-chromosome-out approach to estimating kinship. The second was a sub-setting kinship estimation multi-locus method (FarmCPU). The single-locus model identified nine significant MTAs for various yield-related traits, while the FarmCPU model identified 74 significant MTAs. The availability of the wheat reference genome allowed for the description of MTAs in terms of both genetic and physical positions, and enabled more extensive post-GWAS characterization of significant MTAs. The results indicate a number of promising candidate genes contributing to grain yield, including an ortholog of the rice aberrant panicle organization (APO1) protein and a gibberellin oxidase protein (GA2ox-A1) affecting the trait grains per square meter, an ortholog of the Arabidopsis thaliana mother of flowering time and terminal flowering 1 (MFT) gene affecting the trait seeds per square meter, and a B2 heat stress response protein affecting the trait seeds per head.

Document Type

Article

Publication Date

2-22-2019

Notes/Citation Information

Published in PLOS ONE, v. 14, no. 2, e0208217, p. 1-28.

This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Digital Object Identifier (DOI)

https://doi.org/10.1371/journal.pone.0208217

Funding Information

CHS and GBG received funding from the Agriculture and Food Research Initiative Competitive Grants 2011-68002-30029 (Tritaceae Coordinated Agricultural Project [TCAP]) from the USDA National Institute of Food and Agriculture: https://www.triticeaecap.org/. GBG received funding from the Agriculture and Food Research Initiative Competitive Grant 2017-67007-25939 (Wheat Coordinated Agricultural Project [WheatCAP]) from the USDA National Institute of Food and Agriculture: https://www.triticeaecap.org/. BPW and CAG received funding from Virginia Agricultural Council Grant 617: http://www.vdacs.virginia.gov/boards-virginia-agricultural-council.shtml, and from the Virginia Small Grains Board (no grant number available): http://www.virginiagrains.com/leadership/va-small-grains-board/.

Related Content

All genotypic, phenotypic, and covariate data used in the study may be downloaded from https://doi.org/10.6084/m9.figshare.7700012.

S1 Table. List of germplasm tested in the study. https://doi.org/10.1371/journal.pone.0208217.s001 (XLSX)

S2 Table. Description of traits examined in the study, with trait ontologies as described in http://www.planteome.org/. https://doi.org/10.1371/journal.pone.0208217.s002 (XLSX)

S3 Table. Design of KASP SNP assays for interrogating previously-characterized loci of major effect, and a summary of the allelic effects of these loci. https://doi.org/10.1371/journal.pone.0208217.s003 (XLSX)

S4 Table. List of genes overlapping significant SNPs and haplotype blocks, predicted protein translation effects for all significant SNPs, and list of all wheat genes with annotations in UniProt occurring within 1Mb of significant MTAs. https://doi.org/10.1371/journal.pone.0208217.s004 (XLSX)

S5 Table. Summary information for identified candidate genes. https://doi.org/10.1371/journal.pone.0208217.s005 (XLSX)

S1 Fig. Individual and cumulative portions of variance explained by the first 25 principal components of the imputed genotypic data, prior to LD-based filtering. https://doi.org/10.1371/journal.pone.0208217.s006 (TIFF)

S2 Fig. Number of SNPs per chromosome following the application of all genotypic data filtering steps. https://doi.org/10.1371/journal.pone.0208217.s007 (TIFF)

S1 File. Manhattan and QQ plots for SNP p-values generated by the GCTA leave-one-chromosome-out (LOCO) mixed linear model GWAS. https://doi.org/10.1371/journal.pone.0208217.s008 (PDF)

S2 File. Manhattan and QQ plots for SNP p-values generated by the FarmCPU GWAS. https://doi.org/10.1371/journal.pone.0208217.s009 (PDF)

Repository Citation

Ward, Brian P.; Brown-Guedira, Gina; Kolb, Frederic L.; Van Sanford, David A.; Tyagi, Priyanka; Sneller, Clay H.; and Griffey, Carl A., "Genome-Wide Association Studies for Yield-Related Traits in Soft Red Winter Wheat Grown in Virginia" (2019). Plant and Soil Sciences Faculty Publications. 140.
https://uknowledge.uky.edu/pss_facpub/140