Nucleotide diversity of leaf rust resistance genes in resistant and susceptible bread wheat genotypes

Leaf rust caused by Puccinia triticina, is one of the most important diseases of wheat worldwide. Epidemics of this disease can lead to severe loss of grain yield and nutritional quality. In this study, structural changes and nucleotide diversity in some of the leaf rust resistance genes was investigated in seven bread wheat genotypes. Leaf rust resistance genes or regions linked to the genes were amplified using gene specific primers designed based on the sequences available on GenBank. The amplified fragments were cloned in E. coli and sequenced. Based on the blast results, isolated gene sequences revealed high similarity with resistance gene sequences such as NBS-LRR genes and RGAs. Alignment of the resistant gene sequences with the sequences available in NCBI revealed the similarity of Lr51 with agp2 gene. Lr39 showed 88% similarity with VRN-1 gene a vernilization gene in winter wheat. The result of sequence alignment and grouping revealed structural changes and nucleotide diversity of these genes in the studied wheat genotypes. Synonymous /non synonymous substitution rate (Ka/Ks) in Lr1 gene fragments amplified using Lr1-2, Lr1-3, Lr1-4, Lr21 primer pairs and Lr39 gene was smaller than one indicating negative selection for substitution of amino acid residue in this area of Lr1 and Lr39 genes. In the amplified fragments of Lr1 gene amplified using Lr1-5 primer pair, Ka/Ks was greater than one indicating positive selection for generating diversity in order to replacing an amino acid residue. The studied genotypes had few nucleotides differences for L1, Lr21, Lr39 and Lr51 genes sequences which could use for development of SNP specific primers for identification of resistant and susceptible genotypes.