Puccinia triticina is one of the most virulant pathogen of common wheat (Triticum aestivum L.) that causes leaf rust. Depending on leaf rust resistance genes (Lr genes) deployed and leaf rust isolates composition of the virulence in the region different yield losses could be caused. Developing resistant cultivars is the most effective and safest way to reduce the damage. DNA based molecular markers such as single nucleotide polymorphism (SNP) can be used for marker assisted selection of resistant varieties. SNP is an individual nucleotide base difference between two DNA sequences. SNPs being abundant, ubiquitous and amenable to high-throughput automation have rapidly gained center stage in plant molecular genetics. Whereas SNP discovery in simple genomes is relatively straightforward, complex genomes such as bread wheat with no completed genome sequence, pose serious obstacles for SNP discovery. There is very little knowledge about SNPs in wheat because of the difficulty in discerning truly polymorphic loci from differences between homoeologous loci (homoeologous SNPs) or from paralogous loci in duplicated regions.
To identify SNPs that could help studies on leaf rust resistance and enable molecular breeding for leaf rust resistance we have identified 83 SNPs from data obtained through the Next Generation Sequencing platform Sequencing by Oligonucleotide Ligation and Detection (SOLiD), performed on four (Serial Analysis of Gene Expression) SAGE libraries from mock and leaf rust pathogen-infected near isogenic line pair HD2329 and HD2329+Lr28. Two softwares CLC Genomics Workbench and Freebayes were used for computational prediction of the SNPs. SNPs found common by both the softwares were validated using a panel of 47 wheat germplasm accessions through SNP genotyping using the KASP service provided by LGC Genomics, UK. The SNPs discovered in the present study can be used in association mapping and molecular breeding for sustainable development of wheat for leaf rust resistance besides increasing the SNP repertoire for wheat.