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Soil salinity is a serious threat to wheat yield affecting sustainable agriculture. Although salt tolerance is important for plant establishment at seedling stage, its genetic architecture remains unclear. In the present study, we have evaluated eight salt tolerance–related traits at seedling stage and identified the loci for salt tolerance by genome-wide association study (GWAS). This GWAS panel comprised 317 accessions and was genotyped with the wheat 90 K single-nucleotide polymorphism (SNP) chip. In total, 37 SNPs located at 16 unique loci were identified, and each explained 6.3 to 18.6% of the phenotypic variations. Among these, six loci were overlapped with previously reported genes or quantitative trait loci, whereas the other 10 were novel. Besides, nine loci were detected for two or more traits, indicating that the salt-tolerance genetic architecture is complex. Furthermore, five candidate genes were identified for salt tolerance–related traits, including kinase family protein, E3 ubiquitin-protein ligase-like protein, and transmembrane protein. SNPs identified in this study and the accessions with more favorable alleles could further enhance salt tolerance in wheat breeding. Our results are useful for uncovering the genetic mechanism of salt tolerance in wheat at seeding stage.

Salinity is one of the limiting factors of wheat production worldwide. A total of 334 internationally derived wheat genotypes were employed to identify new germplasm resources for salt tolerance breeding. Salt stress caused 39, 49, 58, 55, 21 and 39% reductions in shoot dry weight (SDW), root dry weight (RDW), shoot fresh weight (SFW), root fresh weight (RFW), shoot height (SH) and root length (RL) of wheat, respectively, compared with the control condition at the seedling stage. The wheat genotypes showed a wide genetic and tissue diversity for the determined characteristics in response to salt stress. Finally, 12 wheat genotypes were identified as salt-tolerant through a combination of one-factor (more emphasis on the biomass yield) and multifactor analysis. In general, greater accumulation of osmotic substances, efficient use of soluble sugars, lower Na+/K+ and a higher-efficiency antioxidative system contribute to better growth in the tolerant genotypes under salt stress. In other words, the tolerant genotypes are capable of maintaining stable osmotic potential and ion and redox homeostasis and providing more energy and materials for root growth. The identified genotypes with higher salt tolerance could be useful for developing new salt-tolerant wheat cultivars as well as in further studies to underline the genetic mechanisms of salt tolerance in wheat.

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