Development and validation of heat-responsive candidate gene and miRNA gene based SSR markers to analysis genetic diversity in wheat for heat tolerance breeding.

Being a major staple food crop of the world, wheat provides nutritional food security to the global populations. Heat stress is a major abiotic stress that adversely affects wheat production throughout the world including Indo-Gangatic Plains (IGP) where four wheat growing countries viz., India, Bangladesh, Nepal and Pakistan produce 42% of the total wheat production. Therefore, identification of heat stress responsive molecular markers is imperative to marker assisted breeding programs. Information about trait specific gene based SSRs is available but there is lack of information on SSRs from non-coding regions. In the present study, we developed 177 heat-responsive gene-based SSRs (cg-SSR) and MIR gene-based SSR (miRNA-SSR) markers from wheat genome for assessing genetic diversity analysis of thirty- six contrasting wheat genotypes for heat tolerance. Of the 177 SSR loci, 144 yielded unambiguous and repeatable amplicons, however, thirty-seven were found polymorphic among the 36 wheat genotypes. The polymorphism information content (PIC) of primers used in this study ranged from 0.03-0.73, with a mean of 0.35. Number of alleles produced per primer varied from 2 to 6, with a mean of 2.58. The UPGMA dendrogram analysis grouped all wheat genotypes into four clusters. The markers developed in this study has potential application in the MAS based breeding programs for developing heat tolerant wheat cultivars and genetic diversity analysis of wheat germplasm. Identification of noncoding region based SSRs will be fruitful for identification of trait specific wheat germplasm.