Salinity stress tolerance and omics approaches: revisiting the progress and achievements in major cereal crops.

Salinity stress adversely affects plant growth and causes considerable losses in cereal crops. Salinity stress tolerance is a complex phenomenon, imparted by the interaction of compounds involved in various biochemical and physiological processes. Conventional breeding for salt stress tolerance has had limited success. However, the availability of molecular marker-based high-density linkage maps in the last two decades boosted genomics-based quantitative trait loci (QTL) mapping and QTL-seq approaches for fine mapping important major QTL for salinity stress tolerance in rice, wheat, and maize. For example, in rice, 'Saltol' QTL was successfully introgressed for tolerance to salt stress, particularly at the seedling stage. Transcriptomics, proteomics and metabolomics also offer opportunities to decipher and understand the molecular basis of stress tolerance. The use of proteomics and metabolomics-based metabolite markers can serve as an efficient selection tool as a substitute for phenotype-based selection. This review covers the molecular mechanisms for salinity stress tolerance, recent progress in mapping and introgressing major gene/QTL (genomics), transcriptomics, proteomics, and metabolomics in major cereals, viz., rice, wheat and maize.

Genome wide association mapping for heat tolerance in sub-tropical maize.

BACKGROUND: Heat tolerance is becoming increasingly important where maize is grown under spring season in India which coincide with grain filling stage of crop resulting in tassel blast, reduced pollen viability, pollination failure and barren ears that causes devastating yield losses. So, there is need to identify the genomic regions associated with heat tolerance component traits which could be further employed in maize breeding program. RESULTS: An association mapping panel, consisting of 662 doubled haploid (DH) lines, was evaluated for yield contributing traits under normal and natural heat stress conditions. Genome wide association studies (GWAS) carried out using 187,000 SNPs and 130 SNPs significantly associated for grain yield (GY), days to 50% anthesis (AD), days to 50% silking (SD), anthesis-silking interval (ASI), plant height (PH), ear height (EH) and ear position (EPO) were identified under normal conditions. A total of 46 SNPs strongly associated with GY, ASI, EH and EPO were detected under heat stress conditions. Fifteen of the SNPs was found to have common association with more than one trait such as two SNPs viz. S10_1,905,273 and S10_1,905,274 showed colocalization with GY, PH and EH whereas S10_7,132,845 SNP associated with GY, AD and SD under normal conditions. No such colocalization of SNP markers with multiple traits was observed under heat stress conditions. Haplotypes trend regression analysis revealed 122 and 85 haplotype blocks, out of which, 20 and 6 haplotype blocks were associated with more than one trait under normal and heat stress conditions, respectively. Based on SNP association and haplotype mapping, nine and seven candidate genes were identified respectively, which belongs to different gene models having different biological functions in stress biology. CONCLUSIONS: The present study identified significant SNPs and haplotype blocks associated with yield contributing traits that help in selection of donor lines with favorable alleles for multiple traits. These results provided insights of genetics of heat stress tolerance. The genomic regions detected in the present study need further validation before being applied in the breeding pipelines.