Molecular characterization of Indian pathotypes of Puccinia striiformis f. sp. tritici and multigene phylogenetic analysis to establish inter- and intraspecific relationships.

Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is one of the most devastating diseases of wheat (Triticum spp.) worldwide. Indian isolates were characterised based on their phenotypic reaction on differential hosts carrying different Yr genes. Based on virulence/avirulence structure, isolates were characterised into ten different pathotypes viz. 70S0-2, 67S64, 70S4, 66S0, 70S64, 66S64-1, 38S102, 47S102, 46S119, and 78S84. These Indian pathotypes of P. striiformis f. sp. tritici and 38 pathotypes of other rust species (P. graminis tritici and P. triticina) were used in this study to analyze their molecular phylogenetic relationship. The nucleotides of rDNA-ITS, partial ß-tubulin and ketopantoate reductase genes of all the pathotypes were sequenced directly after PCR. Based on sequence data of rDNA-ITS and ß-tubulin, three phylogenetic groups corresponding to three different species of Puccinia were obtained. Asian isolates formed a distinct evolutionary lineage than from those derived from USA. The sequence similarity of Indian pathotypes with other Asian (China and Iran) isolates indicated the same origin of pathotypes. The results will allow rapid identification of Indian P.striiformis f. sp. tritici pathotypes causing stripe rust in wheat, assist in making predictions regarding potential rust pathotypes, and identifying sources of resistance to the disease in advance.

Molecular characterization of Chaetomium species using URP-PCR

Chaetomium spp. are common colonizers of soil and cellulose-containing substrates. Seventeen isolates of Chaetomium spp., which included 15 isolates of C. globosum and one each of C. reflexum and C. perlucidum, were genetically characterized with universal rice primers (URP - primers derived from DNA repeat sequences in the rice genome) using polymerase chain reaction (URP-PCR). Out of the 12 URP's used in the study, nine primers were effective in producing polymorphic fingerprint patterns from DNA of Chaetomium spp. Analysis of the entire fingerprint profile using the unweighted pair-group method with arithmetic averages (UPGMA) clearly differentiated C. globosum isolates from C. perlucidum and C. reflexum. One of the primers, URP-2R, produced a uniform DNA band of 1.9 kb in all the isolates of C. globosum but not in C. perlucidum and C. reflexum, which can be used as molecular marker to differentiate C. globosum from other species. Our results indicate that URP's are sensitive and give reproducible results for assaying the genetic variability in Chaetomium spp.