Integrated GWAS and transcriptomic analysis reveal the candidate salt-responding genes regulating Na+/K+ balance in barley (Hordeum vulgare L.)

Abstract

Salt stress is one of the main abiotic stresses affecting crop yield and quality. Barley has strong salt tolerance, however, the underlying genetic basis is not fully clear, especially in the seedling stage. This study examined the ionic changes in barley core germplasms under the control and salt conditions. Genome-wide association study (GWAS) analysis revealed 54 significant SNPs from a pool of 25,342 SNPs distributed in 7 chromosomes (Chr) of the Illumina Barley 50K SNP array. These SNPs are associated with ion homeostasis traits, sodium (Na+) and potassium (K+) content, and Na+/K+ ratio representing five genomic regions on Chr 2, 4, 5, 6, and 7 in the leaves of worldwide barley accessions. And there are 3 SNP peaks located on the Chr 4, 6, and 7, which could be the “hot spots” regions for mining and identifying candidate genes for salt tolerance. Furthermore, 616 unique candidate genes were screened surrounding the significant SNPs, which are associated with transport proteins, protein kinases, binding proteins, and other proteins of unknown function. Meanwhile, transcriptomic analysis (RNA-Seq) was carried out to compare the salt-tolerant (CM72) and salt-sensitive (Gairdner) genotypes subjected to salt stress. And there was a greater accumulation of differentially expressed genes(DEGs) in Gairdner compared to CM72, mainly enriched in metabolic pathway, biosynthesis of secondary metabolites, photosynthesis, signal transduction,emphasizing the different transcriptional response in both genotypes following salt exposure. Combined GWAS and RNA-Seq analysis revealed 5 promising salt-responding genes (PGK2, BASS3, SINAT2, AQP, and SYT3) from the hot spot regions, which were verified between the salt-tolerant and salt-sensitive varieties by qRT-PCR. In all, these results provide candidate SNPs and genes responsible for salinity responding in barley, and a new idea for studying such genetic basis in similar crops.

Transcriptome-Based WGCNA Analysis Reveals the Mechanism of Drought Resistance Differences in Sweetpotato (Ipomoea batatas (L.) Lam.)

“…CIPK3 is a calcium sensor-associated protein kinase, which can regulate ABA and cold signal transduction in Arabidopsis [ 28 ]. Based on comprehensive GWAS and transcriptomics analysis, SYT3 and the other four most promising salt responsive genes were screened [ 41 ]. ABI5 is a key regulator of ABA signaling and stress response, and ABF2 can interact with ABI5 to enhance plant resistance to abiotic stress [ 31 ].…”

Characterization and Comprehensive Evaluation of Phenotypic and Yield Traits in Salt-Stress-Tolerant Peanut Germplasm for Conservation and Breeding

“…Various cultivars exhibit varying degrees of sensitivity to environmental conditions, making the selection or enhancement of local cultivars more appropriate for natural cultivation conditions in a given area than introducing foreign cultivars [29]. This can fundamentally solve the problem of saline-alkali soil and improve crop yield and quality [30]. Moreover, crops phenotypes are always critical to consider in domestication and breeding [31].…”