Genome-wide association study of agronomy and morphology and morphology traits in elite spring wheat Germplasm evaluated under salt stress conditions in Egypt

Abstract

Soil salinity is a long-term issue that needs addressing by developing tolerant cultivars. Today, genome-wide association studies (GWAS) is a preferred tool for quantitative trail loci detection for different traits. Ten salinity-related attributes in a broad panel of bread wheat were evaluated in saline field (10 dSm-1 NaCl), at El-Arish, North Sinai, Egypt. We detected genomic loci associated with salt tolerance using over, 24145 single nucleotide polymorphism. One experiment was conducted in two seasons; under saline soil conditions of El-Arish, Sinai, where soil ECe was 8.68 and 9.31 dSm-1 in the first and second season, respectively. Ten trait-marker associations were detected on the 1D, 3A, and 6B chromosomes of bread wheat. For spikes/plant and tillers/plant, seven common SNPs (SNP- BobWhite_c8340_511, SNP- BobWhite_rep_c49102_169, SNPBS00068520_51, SNP- IAAV3900, SNP- Kukri_c34195_357, SNP- Kukri_c80104_809 and SNPwsnp_RFL_Contig429_4978628) were identified on chromosome 3A. For plant height, SNPExcalibur_c91980_139 was identified on chromosome 6B in the two seasons and for spike length, SNP- D_GA8KES401EYUM8_190 was identified on chromsome 1D. SNP BobWhite_rep_c49102_169 was previously reported to be linked to germination under salt stress. BS00068520_51 was found to be associated to thousand kernel weight while the SNPs Kukri_c34195_357 and Kukri_c80104_809 were associated with flour colour related traits, under non saline conditions. These SNPs were associated with spikes and tillers/plant in the present study. The other six SNPs are novel to be found to salinity tolerance related traits.