Genome wide association analyses for salinity tolerance at seed germination in elite alfalfa germplasm

Genome wide association analyses for salinity tolerance at seed germination in elite alfalfa germplasm

Soil salinity is a major limitation to crop production throughout the world particularly in arid irrigated environments. Selection for resistance to salt tolerance would be greatly facilitated by identification of genes involved in salt tolerance. Genome wide association studies (GWAS) have shown great potential for uncovering genes/loci of interest in plants. The objective to this study was to identify molecular markers associated with salt tolerance for seed germination in alfalfa. An elite population of 265 half-sib families was evaluated by germinating twenty-five seed of each family in 1% sodium chloride (NaCl) solution in a randomized complete block design. Genotyping by sequencing (GBS) approach was used for genotypic characterization of half-sib families, and GWAS was performed with 7280 single nucleotide polymorphisms (SNPs) markers. GWAS identified five and nine SNPs significantly associated with salt tolerance in year 2017 and 2018, respectively. Five markers were repeatedly found significant in both years.  Most significant markers associated with salt tolerance were found on chromosome 1, 5 and 7. The significant markers identified for salt tolerance by GWAS explained 10.9% to 28.6% of phenotypic variation. Two markers identified in this study were also found to be significant in previous reports. Blast search identified a total of nine genes in the vicinity of significant markers. A dehydration responsive element binding protein (DREB) was found to be a potential candidate gene for salt tolerance present on chromosome 1. In addition, a few more significant markers co-localized with genes that have been implicated in the stress tolerance pathways.