Genome-wide identification of microsatellites for mapping, genetic diversity and cross-transferability in wheat...

Wheat (Triticum aestivum L.) is a crucial global staple crop, and is consistently being improved to enhance yield, disease resistance, and quality traits. However, the development of molecular markers is a challenging task due to its hexaploid genome. Molecular marker system such as simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) are helpful for breeding, but SNP has limitations due to its development cost and its conversion to breeder markers. The study proposed an in-silico approach, by utilizing the low-cost transcriptome sequencing of two parental lines, 'TAC 75' and 'WH 1105', to identify polymorphic SSRs for mapping in a recombinant inbred line (RIL) population. This study introduces a new approach to bridge wheat genetics intricacies and next-generation sequencing potential. It presents a comprehensive genome-wide SSR distribution using IWGSC CS RefSeq v2.1 genome assembly and to identify 189 polymorphic loci through in-silico strategy. Of these, 54.76% showed polymorphism between parents, surpassing the traditional low polymorphic success rate. A RIL population screening validated these markers, demonstrating the fitness of identified markers through chi-square tests. The designed SSRs were also validated for genetic diversity analysis in a subset of 37 Indian wheat genotypes and cross-transferability in the wild/relative wheat species. In diversity analysis, a subset of 38 markers revealed 95 alleles (2.5 allele/locus), indicating substantial genetic variation. Population structure analysis unveiled three distinct groups, supported by phylogenetic and PCoA analyses. Further the polymorphic SSRs were also analyzed for SSR-gene association using gene ontology analysis. By utilizing the developing seed transcriptome data within parental lines, the study has enhanced the polymorphic SSR identification precision and facilitated in the RIL population. The undertaken study pioneers the use of transcriptome sequencing and genetic mapping to overcome challenges posed by the intricate wheat genome. This approach offers a cost-effective, less labour-intensive alternative to conventional methods, providing a platform for advancing wheat breeding research.