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Genome-wide association study reveals marker trait associations (MTA) for waterlogging-triggered adventitious roots and aerenchyma formation in barley


Nuruzzaman Manik, SM and Quamruzzaman, MD and Zhao, C and Johnson, P and Hunt, I and Shabala, SN and Zhou, M, Genome-wide association study reveals marker trait associations (MTA) for waterlogging-triggered adventitious roots and aerenchyma formation in barley, International Journal of Molecular Sciences, 23, (6) Article 3341. ISSN 1422-0067 (2022) [Refereed Article]


Copyright Statement

Copyright 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://

DOI: doi:10.3390/ijms23063341


Waterlogging is an environmental stress, which severely affects barley growth and development. Limited availability of oxygen in the root zone negatively affects the metabolism of the whole plant. Adventitious roots (AR) and root cortical aerenchyma (RCA) formation are the most important adaptive traits that contribute to a plant's ability to survive in waterlogged soil conditions. This study used a genome-wide association (GWAS) approach using 18,132 single nucleotide polymorphisms (SNPs) in a panel of 697 barley genotypes to reveal marker trait associations (MTA) conferring the above adaptive traits. Experiments were conducted over two consecutive years in tanks filled with soil and then validated in field experiments. GWAS analysis was conducted using general linear models (GLM), mixed linear models (MLM), and fixed and random model circulating probability unification models (FarmCPU model), with the FarmCPU showing to be the best suited model. Six and five significant (approximately -log10 (p) ≥ 5.5) MTA were identified for AR and RCA formation under waterlogged conditions, respectively. The highest -log10 (p) MTA for adventitious root and aerenchyma formation were approximately 9 and 8 on chromosome 2H and 4H, respectively. The combination of different MTA showed to be more effective in forming RCA and producing more AR under waterlogging stress. Genes from major facilitator superfamily (MFS) transporter and leucine-rich repeat (LRR) families for AR formation, and ethylene responsive factor (ERF) family genes and potassium transporter family genes for RCA formation were the potential candidate genes involved under waterlogging conditions. Several genotypes, which performed consistently well under different conditions, can be used in breeding programs to develop waterlogging-tolerant varieties.

Item Details

Item Type:Refereed Article
Keywords:barley waterlogging, Hordeum vulgare, adventitious roots, aerenchyma formation, hypoxia, stress
Research Division:Agricultural, Veterinary and Food Sciences
Research Group:Crop and pasture production
Research Field:Agrochemicals and biocides (incl. application)
Objective Division:Plant Production and Plant Primary Products
Objective Group:Grains and seeds
Objective Field:Barley
UTAS Author:Nuruzzaman Manik, SM (Mr S M Nuruzzaman Manik)
UTAS Author:Quamruzzaman, MD (Dr Md Quamruzzaman)
UTAS Author:Zhao, C (Dr Chenchen Zhao)
UTAS Author:Johnson, P (Dr Peter Johnson)
UTAS Author:Hunt, I (Dr Ian Hunt)
UTAS Author:Shabala, SN (Professor Sergey Shabala)
UTAS Author:Zhou, M (Professor Meixue Zhou)
ID Code:153051
Year Published:2022
Web of Science® Times Cited:1
Deposited By:TIA - Research Institute
Deposited On:2022-09-02
Last Modified:2022-11-18
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