Genetic and genomic architecture of salt tolerance in bread wheat

Official URL: http://risc01.sabanciuniv.edu/record=b1817258 (Table of Contents)

Soil salinization is the consequence of climate change and soil salinity significantly reduces wheat yield. Therefore, development of salt tolerant wheat is a feasible option for 1 billion hectares of salt affected land and wheat breeding for this trait could be enhanced by marker assisted selection (MAS) and identification of major genes for salt tolerance. The Axiom Wheat Breeder's Genotyping Array was used to genotype 154 F2 wheat lines developed from parents with contrasting salt tolerance. A high-density genetic linkage map consisting of 988 single nucleotide polymorphisms (SNPs) markers was constructed and 49 quantitative trait loci (QTL) were mapped for salt tolerance related traits and mineral nutrients concentrations under salt stress. Two Na+ exclusion (NAX) QTLs located on chromosome 2A coincided with a major reported QTL (Nax1 or HKT1;4) while two major NAX QTLs mapped on 7A contributed 18.79 and 11.23 % to salt tolerance. Another 13 QTLs including major QTLs were mapped for K+, Ca+2 and Mg+2 concentrations while 27 novel QTLs were identified for tissue Boron, Copper, Iron, Manganese Phosphorus, Sulphur and Zinc concentrations under salinity. Several of these QTLs were validated in two mapping populations. The segregating markers were annotated/located on 1257 genes for various ion channels, transcription factors (TFs), signaling pathways, genetic and epigenetic factors, tolerance mechanisms, metabolic pathways etc. The in-silico transcriptomics analysis found 258 of these genes to be differentially expressed under salinity, another 74 genes were found to be vital for plants under both normal and saline conditions. Another 156 genes showed the expression only under salt stress while 54 of them had significant number of alignments with salt-expressed transcriptome. The transcriptomics analysis for 478 NAC, WRKY, MADS-box, AP2-containing, MYB and MYB-related TF families revealed that 181 TFs were differentially expressed under salinity in wheat. Taken together, the SNPs, QTLs, genes, transcripts and TFs identified in this study will be a valuable source for wheat breeding for salt tolerance.