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Mandal A.K.,Indian Agricultural Research Institute | Mandal A.K.,Directorate of Seed Research | Dubey S.C.,Indian Agricultural Research Institute
World Journal of Microbiology and Biotechnology

Sclerotinia sclerotiorum is one of the most devastating soil-inhabiting fungal plant pathogens infecting various crop plants including chickpea. Genetic diversity of 24 isolates of S. sclerotiorum representing 10 different states of India was determined by different molecular markers and mycelial compatibility grouping (MCG). The majority of the isolates showed more than 90% genetic similarity. Unweighted paired group method with arithmetic average cluster analysis of DNA profiles generated by 21 RAPD primers grouped the isolates into seven categories showing high magnitude of genetic homogeneity and showed partial correlation with geographical origin of the isolates. Identical ITS-RFLP profiles were generated in all the isolates. Limited variability was observed among the nucleotide sequences of ITS region of the isolates. The phylogenetic tree generated from bootstrap neighbor-joining analysis indicated that 50% of Indian populations were distinct and grouped separately. The isolates were variable in mycelial compatibility and they were grouped into seven MCGs, namely, MCG A, MCG B, MCG C, MCG D, MCG E, MCG F and MCG G. © 2011 Springer Science+Business Media B.V. Source

Tanveer H.,Krishi Vigyan Kendra | Ray Choudhury P.,Directorate of Seed Research | Dixi G.P.,Indian Institute of Pulses Research | Jha G.K.,Indian Agricultural Research Institute
Indian Journal of Genetics and Plant Breeding

Studied the molecular divergence and develop DNA fingerprints in selected popular fieldpea cultivars from India. Those RAPD primers from the four sets (viz. OPP, OPBA, OPAQ and OPH) which showed at least 75 percent band polymorphism were selected for molecular diversity analysis. Twenty four primers generated a total of 256 amplified fragments out of which 228 (89.06%) were polymorphic. On an average, 10.67 bands were amplified per primer. Cluster analysis based upon DNA amplification polymorphism using Jaccard's similarity coefficient and UPGMA could unveil substantial amount of polymorphism among the cultivars. Genotype specific bands were represented in a diagrammatic form and can be used as a reference fingerprint. The arithmetic mean heterozygosity (Hav) value and marker index (MI) was found to be 0.592 and 6.317, respectively, indicating the efficiency and usefulness of RAPD as a marker system. Source

Naik B.K.,Indian Agricultural Research Institute | Naik B.K.,Directorate of Seed Research | Vinod,Indian Agricultural Research Institute | Sharma J.B.,Indian Agricultural Research Institute | And 4 more authors.
Molecular Breeding

The mode of inheritance of wheat leaf rust resistance gene Lr45 was studied at seedling stage under greenhouse conditions against leaf rust race 77-5 in two F2 populations derived from the crosses between Thatcher (Tc)+Lr45 and two susceptible cultivars Agra Local and NI5439. The genetic analysis in F2:3 progeny validated the F2 results which unambiguously showed segregation for a single dominant gene. Genetic analysis in F2 and BC1F1 generations against five other leaf rust races confirmed the single dominant gene inheritance of Lr45. Mapping was carried out with 92 microsatellite markers specific to chromosome 2A on the F2 population of the cross Agra Local × Tc+Lr45. Out of seven markers linked to the gene, four (gwm372, gwm275, gpw3167 and gwm122) were co-dominant and the other three (cfd168, cfd6 and gwm249) showed dominance, amplifying the allele only in the susceptible parent. The genetic map of 13.1 cM was constructed based on the results in 140 homozygous resistant and homozygous susceptible plants. cfd168 was the closest marker linked to Lr45, followed by gwm372. These markers were validated on the NI5439 × Tc+Lr45 F2 population, 12 different backcross lines carrying Lr45 and near-isogenic lines, mostly in Tc background isogenic for 46 different Lr genes belonging to both native and alien species. The marker gwm122 was found to be monomorphic. The closest co-dominant marker gwm372 showed reduced polymorphism. Two sequence-based primer pairs, G37294 and G372185, were designed and validated. Hence, the markers G37294 and G372185 closely linked to the gene can serve as robust co-dominant markers for utilization of Lr45 in wheat improvement. © 2015, Springer Science+Business Media Dordrecht. Source

Vetriventhan M.,Indian International Crops Research Institute for the Semi Arid Tropics | Vetriventhan M.,Directorate of Seed Research | Upadhyaya H.D.,Indian International Crops Research Institute for the Semi Arid Tropics | Anandakumar C.R.,Tamil Nadu Agricultural University | And 7 more authors.
Plant Genetic Resources: Characterisation and Utilisation

Foxtail millet (Setaria italica (L.) P. Beauv.) is an ideal crop for changing climate and food habits of peoples due to its short duration, high photosynthetic efficiency, nutritional richness and fair resistance to pest and diseases. However, foxtail millet yields are low mainly due to the lack of effort for its improvement and the lack of proper utilization of existing genetic variability. To enhance the use of diverse germplasm in breeding programmes, a core collection in foxtail millet consisting of 155 accessions was established. Core collection accessions were fingerprinted using 84 markers (81 simple sequence repeats (SSRs) and three Expressed Sequence Tag (EST)-SSRs). Our results showed the presence of greater molecular diversity in the foxtail millet core collection. The 84 markers detected a total of 1356 alleles with an average of 16.14 alleles (4-35) per locus. Of these, 368 were rare alleles, 906 common alleles and 82 the most frequent alleles. Sixty-one unique alleles that were specific to a particular accession and useful for germplasm identification were also detected. In this study, the genetic diversity of foxtail millet was fairly correlated well with racial classification, and the race Indica showed a greater genetic distance from the races Maxima and Moharia. The pairwise estimate of dissimilarity was >0.50 except in 123 out of 11,935 pairs which indicated a greater genetic variability. Two hundred and fifty pairs of genetically most diverse accessions were identified. This large molecular variation observed in the core collection could be utilized effectively by breeders or researchers for the selection of diverse parents for breeding cultivars and the development of mapping populations. © NIAB 2012. Source

Kumar M.B.A.,Directorate of Seed Research | Kumar M.B.A.,Oregon State University | Martin R.C.,U.S. Department of Agriculture | Nonogaki H.,Oregon State University
Methods in Molecular Biology

MicroRNAs (miRNAs) play an important role in gene regulation in many plant tissues and organs during various developmental stages. Previous studies have suggested the importance of gene regulation by miRNA in seeds. Characterizing the expression of miRNAs and their target genes in dormant and germinating seeds helps to gain a better understanding of the regulatory role of miRNAs during seed dormancy and germination. This can be achieved by implementing a simple miRNA extraction method using fractionation with isopropanol and Northern blot analysis using nonradioactive miRNA probes. Functional analysis of miRNA target genes potentially associated with seed dormancy and germination can be examined using mutant seeds in which specific miRNAs are deregulated by introducing silent mutations in the miRNA target sites of these genes. © 2011 Springer Science+Business Media, LLC. Source

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