Research article - Peer-reviewed, 2022
Genome-Wide Association Study (GWAS) and genome prediction of seedling salt tolerance in bread wheat (Triticum aestivum L.)
Javid, Saeideh; Bihamta, Mohammad Reza; Omidi, Mansour; Abbasi, Ali Reza; Alipour, Hadi; Ingvarsson, Paer K.Abstract
Background: Salinity tolerance in wheat is imperative for improving crop genetic capacity in response to the expanding phenomenon of soil salinization. However, little is known about the genetic foundation underlying salinity tolerance at the seedling growth stage of wheat. Herein, a GWAS analysis was carried out by the random-SNP-effect mixed linear model (mrMLM) multi-locus model to uncover candidate genes responsible for salt tolerance at the seedling stage in 298 Iranian bread wheat accessions, including 208 landraces and 90 cultivars.Results: A total of 29 functional marker-trait associations (MTAs) were detected under salinity, 100 mM NaCl (sodium chloride). Of these, seven single nucleotide polymorphisms (SNPs) including rs54146, rs257, rs37983, rs18682, rs55629, rs15183, and rs63185 with R-2 >= 10% were found to be linked with relative water content, root fresh weight, root dry weight, root volume, shoot high, proline, and shoot potassium (K+), respectively. Further, a total of 27 candidate genes were functionally annotated to be involved in response to the saline environment. Most of these genes have key roles in photosynthesis, response to abscisic acid, cell redox homeostasis, sucrose and carbohydrate metabolism, ubiquitination, transmembrane transport, chromatin silencing, and some genes harbored unknown functions that all together may respond to salinity as a complex network. For genomic prediction (GP), the genomic best linear unbiased prediction (GBLUP) model reflected genetic effects better than both bayesian ridge regression (BRR) and ridge regression-best linear unbiased prediction (RRBLUP), suggesting GBLUP as a favorable tool for wheat genomic selection.Conclusion: The SNPs and candidate genes identified in the current work can be used potentially for developing salt-tolerant varieties at the seedling growth stage by marker-assisted selection.Keywords
Association mapping; Abiotic stress; Genomic selection; Genotyping-by-sequencing; Salinity stress; Seedling; Wheat accessionsPublished in
BMC Plant Biology2022, volume: 22, number: 1, article number: 581
Publisher: BMC
Authors' information
Javid, Saeideh
University of Tehran
Bihamta, Mohammad Reza
University of Tehran
Omidi, Mansour
University of Tehran
Abbasi, Ali Reza
University of Tehran
Alipour, Hadi
Urmia University
Swedish University of Agricultural Sciences, Department of Plant Biology
UKÄ Subject classification
Agricultural Science
Publication Identifiers
DOI: https://doi.org/10.1186/s12870-022-03936-8
URI (permanent link to this page)
https://res.slu.se/id/publ/120925