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Genome-wide association study of waterlogging tolerance in barley (Hordeum vulgare L.) under controlled field conditions


Borrego-Benjumea, A and Carter, A and Zhu, M and Tucker, JR and Zhou, M and Badea, A, Genome-wide association study of waterlogging tolerance in barley (Hordeum vulgare L.) under controlled field conditions, Frontiers in Plant Science, 12 Article 711654. ISSN 1664-462X (2021) [Refereed Article]


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Copyright 2021 The Author(s) Licensed under Creative Commons Attribution 4.0 International (CC BY 4.0)

DOI: doi:10.3389/fpls.2021.711654


Waterlogging is one of the main abiotic stresses severely reducing barley grain yield. Barley breeding programs focusing on waterlogging tolerance require an understanding of genetic loci and alleles in the current germplasm. In this study, 247 worldwide spring barley genotypes grown under controlled field conditions were genotyped with 35,926 SNPs with minor allele frequency (MAF) > 0.05. Significant phenotypic variation in each trait, including biomass, spikes per plant, grains per plant, kernel weight per plant, plant height and chlorophyll content, was observed. A genome-wide association study (GWAS) based on linkage disequilibrium (LD) for waterlogging tolerance was conducted. Population structure analysis divided the population into three subgroups. A mixed linkage model using both population structure and kinship matrix (Q+K) was performed. We identified 17 genomic regions containing 51 significant waterlogging-tolerance-associated markers for waterlogging tolerance response, accounting for 5.8-11.5% of the phenotypic variation, with a majority of them localized on chromosomes 1H, 2H, 4H, and 5H. Six novel QTL were identified and eight potential candidate genes mediating responses to abiotic stresses were located at QTL associated with waterlogging tolerance. To our awareness, this is the first GWAS for waterlogging tolerance in a worldwide barley collection under controlled field conditions. The marker-trait associations could be used in the marker-assisted selection of waterlogging tolerance and will facilitate barley breeding.

Item Details

Item Type:Refereed Article
Keywords:barley, waterlogging tolerance, genome-wide associated study, marker-trait association, quantitative trait loci, candidate genes
Research Division:Agricultural, Veterinary and Food Sciences
Research Group:Crop and pasture production
Research Field:Crop and pasture improvement (incl. selection and breeding)
Objective Division:Plant Production and Plant Primary Products
Objective Group:Grains and seeds
Objective Field:Barley
UTAS Author:Zhou, M (Professor Meixue Zhou)
ID Code:151881
Year Published:2021
Web of Science® Times Cited:9
Deposited By:TIA - Research Institute
Deposited On:2022-08-08
Last Modified:2022-09-07
Downloads:8 View Download Statistics

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