Genetic Diversity Assessment In Relation To Submergence Tolerance In Rice Using Microsatellite Markers

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dc.contributor.advisorKumar, Mithilesh
dc.contributor.authorPrakash, Nilmani
dc.date.accessioned2017-09-04T06:37:57Z
dc.date.available2017-09-04T06:37:57Z
dc.date.issued2016
dc.description.abstractA study was undertaken to initially characterize and evaluate 184 submergence tolerance related varieties of rice, but 38 were taken for further analysis in the present study for five submergence related characters. To investigate the SSR marker based polymorphism for characterization and differentiation, nineteen rice varieties were selected on the basis of maximum plant percent survival to estimate the extent of genetic diversity among these rice varieties using morphological characters and SSR markers. The experimental materials were evaluated in randomized complete block design with four replications at the research farm of Dr. Rajendra Prasad Central Agricultural University, Pusa during Kharif, 2014-15. Using standard formula for calculation of different submergence related traits in rice observations were recorded. The materials were also grown in pots for extraction of genomic DNA from the young seedlings and then targeted amplification of the genomic DNA using a panel of thirty four SSR primer pairs covering especially the chromosome 9 of rice. All molecular studies were conducted in the Rice Molecular Breeding Laboratory, Deptt. of PBG at Pusa. The statistical methods and parameters used for deriving inference were analysis of variance, range, mean values, coefficient of variation, taxonomic distance and similarity coefficient based dendrogram and numerical taxonomic analysis of divergence. High heritability values were observed for all the five submergence related characters percent plant survival, tolerance score, leaf senescence, total shoot elongation and relative shoot elongation. Considerable extent of variability existed for the values of genetic advance expressed as per cent of mean was observed to be high for all five characters relative shoot elongation, per cent plant survival, total shoot elongation, leaf senescence and tolerance score. By considering mean performance in conjunction with clustering pattern of entries based on quantitative attributes, hybridization involving CR 1009 with AnhHsungSeln (CI 1), Karnal Local and Suraha with Swarna, Jadhan and HsungTeing with Moroberekan, FR 13B and S-150 with Paiam, Zobgui and Rom Runtik with IR-36, Kala Bunde with AI Chih AI K Who 2, Swarna Sub-1 with Lunishreeappeared as superior combinations for their further utilization in genetic enhancement programme. A panel of thirty four primers generated 410 allelic variants ranging from four in the cases of RM 23843 to twenty seven in the cases of RM 23662. Altogether 410 allelic variants were detected at 42 SSR loci with an average of 9.76 alleles per locus. Out of 410 alleles, 177 were shared and 233 were unique alleles. The primer pairs RM 8300, RM 23901, RM 23958, RM 215, RM 257, RM 316 and RM 23662 generated amplified products due to amplification of more than one locus. In general, the SSR loci with di-nucleotide repeat motifs tended to detect greater number of alleles than the locus with tri-nucleotide, tetra-nucleotide or penta-nucleotide repeat sequence. The marker with a GA or AG repeat motif showed greater variability than marker with a CT or TG or TA repeat motif among the loci with perfect di-nucleotide repeat motifs. The number of unique allelic variants per primer ranged from 0 out of 5 amplified products in the case of SC 3 to 13 out of 15 amplified products in the case of RM 23901. The primer pairs RM 23901, RM 910, RM 23770, RM 23928, RM 23958, RM 24103 RM 23662, RM 23915 and RM 24005 generated considerably greater percentage of unique alleles. Considering the number of alleles in conjunction with the level of polymorphism detected, the primers RM 23662, RM 23958, RM 257, RM 23901, RM 8300, RM 215, RM 23928, RM 23915, RM 24005, RM 23902, RM 23679, RM 8303, RM 23770 and RM 23788 appeared to be more informative primers. Occurrence of null alleles for a particular repeat locus was noticed with primer pairs RM 23843, RM 23902, RM 23922, RM 24103, and RM 23865 in some of the varieties. The total repeat count of the di-nucleotide SSR loci seemed to be associated with the number of alleles, revealing that the larger the repeat number involved in the SSR locus, the larger was the number of identified alleles. Presence of stutter bands was detected generally for di-nucleotide SSR motif amplified by primer pairs RM 8303, RM 23770, RM 23805, RM 23831, RM 8300, RM 23901, RM 23915, RM 23917, RM 23922, RM 23928, RM 23958, RM 23996, RM 24103, RM 105, RM 215, RM 316, RM 23662, RM 24013, RM 910, RM 7175, ART 5, SC3, Sub 1BC2 and RM 23865 with generation of minor products. Among the rice varieties evaluated in the present study, AnhHsung Seln (CI 1) and HsungTeing exhibited maximum similarity in the divergence analysis using quantitative characters as well as SSR markers. Analysis of divergence pattern based on SSR markers allowed differentiation and classification of rice varieties into eight clusters. Use of SSR markers appeared more efficient in achieving unique and unambiguous characterization and differentiation of varieties used in the present study.The SSR analysis also revealed unique or variety specific allele, which could be useful as DNA fingerprints in the identification and preservation of rice varieties.en_US
dc.identifier.urihttp://krishikosh.egranth.ac.in/handle/1/5810030277
dc.keywordsRice, Genetic diversity, Microsatellite markers, Submerge toleranceen_US
dc.language.isoenen_US
dc.pages156+xvien_US
dc.publisherDR. Rajendra Prasad Central Agricultural University, Pusa (Samastipur)en_US
dc.subAgricultural Biotechnologyen_US
dc.subjectnullen_US
dc.themeTo characterize and evaluate 184 submergence tolerance related varieties of riceen_US
dc.these.typePh.Den_US
dc.titleGenetic Diversity Assessment In Relation To Submergence Tolerance In Rice Using Microsatellite Markersen_US
dc.typeThesisen_US
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