Genome-wide association and transcriptome analysis reveals candidate genes for potassium transport under salinity stress in wheat

Abstract

Soil salinity is one of the main challenges limiting the global production of crops. It primarily affects potassium (K + ) and sodium (Na + ) accumulation, which is crucial for plant growth. Exploitation of the molecular mechanisms of K + and Na + accumulation is essential for developing salt-tolerant cultivars. We integrated a genome-wide association study (GWAS) with a transcriptome sequencing to investigate the genetic basis of K + and Na + concentration and salinity tolerance in wheat. Twenty-seven quantitative trait locus (QTLs) significantly associated with leaf Na + and K + concentrations by the GWAS. These significant SNPs were distributed on 12 chromosomes, and 86 genes were identified around these SNPs. Among them, novel association signals were identified, involves 23 genes on chromosome 5A, 6B and 7A. RNA-seq analysis identified 323 differentially expressed genes (DEGs), most of which were associated with metabolism, transportation, signal transduction and transcriptional regulation. By combining the GWAS and RNA-seq analyses, we identified 31 candidate genes associated with Na + concentration, K + concentration and the Na + /K + ratio, from which a HAK family ion transporter TaHAK25 was screened. TaHAK25 is highly expressed in leaves. Heterologous overexpression of TaHAK25 in rice induced significant reduction in shoot and root dry weight, and root K + concentration, and increase shoot Na + concentration. These results provide valuable insights into the genetic basis of Na + and K + transport and salinity tolerance in wheat and provide candidate genes to accelerate the breeding of salt-tolerant wheat. • Three new QTLs responsible for K+ content were found on chromosomes 5 A, 6B and 7 A. • The combination of GWAS and RNA-seq identified key genes for salinity tolerance. • TaHAK25 negatively regulated salinity tolerance.