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ThesisItem Open Access Use of molecular markers for varietal identification and assessing phylogenetic status of Basmati rice in genus Oryza sativa L.(CCSHAU, 2011) Jyoti; Jain, SunitaMolecular markers provide novel tools for varietal identification, diversity analysis and assessing phylogenetic relationships among various rice groups in genus Oryza. A set of 50 rice genotypes comprising of seven japonica rice varieties, six traditional Basmati, thirteen cross-bred Basmati and 24 indica rice varieties was investigated using 54 markers (28 on chromosome 8 and 26 on rest of the chromosomes); data obtained has been used to assess the phylogenetic status of Basmati rice in genus Oryza sativa L. A total of 217 alleles were detected, with an average of 4.01 alleles per locus. Number of alleles per locus (3.5 alleles) for markers on chromosome 8 was less than the mean value (4.58 alleles) based on 26 SSR markers on rest of eleven chromosomes of rice. Eleven of these alleles were unique, present in only one genotype. Null allele was observed at only one locus (RM408) in Super Basmati. The number and size of alleles and Polymorphism Information Content (PIC) values ranged between 2-7, 83-381 bp and 0.074-0.810, respectively. An average PIC of 0.55 per locus was obtained, which confirms that markers used in this study were highly informative. Genetic relationships generated using the whole genome marker data as well as allelic profile on chromosome 8 and rest of eleven chromosomes separately placed 50 rice genotypes in three distinct clusters. Seventeen of the nineteen Basmati rice varieties (except two cross-bred Basmati rice varieties, Sabarmati and Improved Sabarmati) formed a separate cluster quite distinct from the indica and japonica rice clusters. Interestingly, mean similarity indices obtained from chromosome 8 dataset placed Basmati rice cluster at equal distance from japonica and indica rice types. However, whole genome as well as rest of the genome marker datasets placed Basmati group closer to indica rice varieties than japonica. Chromosome 8 dataset showed a positive correlation (Mantel test, r = 0.631) with the rest of the genome dataset, indicating a higher level of similarity between the two. All the traditional and crossbred Basmati rice varieties and two aromatic japonica varieties shared the same BAD2 alleles at the aroma locus, indicated the distinctness of the aroma locus. While the present study gives support to the hypothesis that japonica genotypes may have contributed towards the evolution of chromosome 8 or a part of chromosome 8 in Basmati rice, it also indicate the active flow of genes from indica rices during the course of parallel evolution in northern Indian sub-continent. The study also demonstrates the distinctness of TB from other rice types (indica and japonica) and also provides a number of novel SSR markers which can be used to differentiate within/among the various rice groups at commercial level. It was observed that the amplified products differing in ≥12bp can be separated on 3% agarose gels for varietal identification in Basmati rice, which is faster, much cheaper and relatively simple method compared to the advanced molecular methods already available for the purpose.ThesisItem Open Access Use Of Molecular Markers For Warietal Identification And Assessing Phylogenetic Status Of Basmati Rice In Genus Oryza Sativa L.(Department Of Biochemistry College Of Basic Sciences And Humanities CCS Haryana Agricultural University : Hisar, 2010) Jyoti; Jain,Sunita.