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Research Article | Open Access

Fine-mapping and characterisation of genes on barley (Hordeum vulgare) chromosome 2H for salinity stress tolerance during germination

Edward Mwandoa,b,c, Yong Hana,b,c, Tefera Angessaa,b,c, Xiao-Qi Zhanga,b, Chengdao Lia,b,c( )
Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia
Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA 6150, Australia
Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA 6151, Australia
Show Author Information

Abstract

Salinity causes a detrimental impact on plant growth, particularly when the stress occurs during germination and early development stages. Barley is one of the most salt-tolerant crops; previously we mapped two quantitative trait loci (QTL) for salinity tolerance during germination on the short arm of chromosome 2H using a CM72/Gairdner doubled haploid (DH) population. Here, we narrowed down the major QTL to a region of 0.341 or 0.439 Mb containing 9 or 24 candidate genes belonging to 6 or 20 functional gene families according to barley reference genomes v1 and v3 respectively, using two DH populations of CM72/Gairdner and Skiff/CM72, F2 and F3 generations of CM72/Gairdner/*Spartacus CL. Two Receptor-like kinase 4 (RLPK4) v1 or Receptor-like kinase (RLK) v3 could be the candidates for enhanced germination under salinity stress because of their upregulated expression in salt-tolerant variety CM72. Besides, several insertion/deletion polymorphisms were identified within the 3rd exon of the genes between CM72 and Gairdner. The sequence variations resulted in shifted functional protein domains, which may be associated with differences in salinity tolerance. Two molecular markers were designed for selecting the locus with receptor-like protein kinase 4, and one was inside HORVU2Hr1G111760.1 or HORVU.MOREX.r3.2HG0202810.1. The diagnostic markers will allow for pyramiding of 2H locus in barley varieties and facilitate genetic improvement for saline soils. Further, validation of the genes to elucidate the mechanisms involved in enhancing salinity tolerance at germination and designing RLPK4 specific markers is proposed. For this publication, all the analysis was based on barley reference genome of 2017 (v1), and it was used throughout for consistence. However, the positions of the markers and genes identified were updated according to new genome (v3) for reference.

Keywords

BarleyGerminationSalinity toleranceDiagnostic markersReceptor-like protein kinase 4Gene expressionSequence analysis

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The Crop Journal
Volume 10 Issue 3,
June 2022
Pages 754-766
DOI: 10.1016/j.cj.2021.10.008
Cite this article:
Mwando E, Han Y, Angessa T, et al. Fine-mapping and characterisation of genes on barley (Hordeum vulgare) chromosome 2H for salinity stress tolerance during germination. The Crop Journal, 2022, 10(3): 754-766. https://doi.org/10.1016/j.cj.2021.10.008

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Received: 07 May 2021
Revised: 12 October 2021
Accepted: 13 October 2021
Published: 06 December 2021
© 2021 Crop Science Society of China and Institute of Crop Science, CAAS.

This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
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