Molecular characterization for fragrance of aromatic rice varieties using candidate gene markers
| dc.contributor.advisor | Kumar, Mithilesh | |
| dc.contributor.author | Das, Suparna | |
| dc.date.accessioned | 2020-02-04T07:08:58Z | |
| dc.date.available | 2020-02-04T07:08:58Z | |
| dc.date.issued | 2019 | |
| dc.description.abstract | A study was conducted to examine the genetic diversity in eighteen entries from aromatic rice varieties in order to analyze the nature and extent of genetic variation in relation to fragrance amongst rice varieties using polymorphic and informative primers. To synthesize and utilize fragrance related candidate genes based primers for molecular characterization of some aromatic rice varieties. The materials were grown in petri plates for extraction of genomic DNA from the young seedlings and then targeted amplification of the genomic DNA using a panel of twenty two candidate gene based primer pairs covering two genes namely BADH1 and BADH2. All molecular studies were conducted in the Molecular Biology Laboratory at Pusa. Biochemical analysis for evolution of aroma in different rice varieties used in the study was based on inhalation by different persons and the eighteen genotypes under evaluation were classified into low scented, medium scented and highly scented categories. Using microsatellite identification tool gramene/org/db/markers/ssrtool was used to find out the microsatellite (SSR) sequences within the amplicon screening region of the candidate genes BADH1 and BADH2. Microsatellites within the exons and introns in the gene BADH1 and BADH2 were identified. The statistical methods and parameters used for deriving inference were polymorphism information content, similarity coefficient and numerical taxonomic analysis of divergence. The amplification was successfully achieved with all the candidate gene based primers pairs used in the present study. Appearance of bands at different positions on the gel revealed differential migration of amplified products due to differences in overall size of the products generated from targeted amplification of specific region of genome. The polymorphism among the varieties was recognized on the basis of presence or absence of bands, in addition to variation in respect of number and position of bands. Altogether 66 allelic variants were detected among the eighteen rice entries. The number of alleles per locus ranged from two in the cases of BADH1A7, BADH1A12, BADH1A14, BADH2A7 and BADH2A11 to five in the case of BADH1A3 and BADH1A8. The amplification of genomic DNA using twenty two primer pairs, namely, BADH1A3, BADH1A6, BADH1A7, BADH1A8, BADH1A9, BADH1A10, BADH1A11, BADH1A12, BADH1A13, BADH1A14, BADH1A15, BADH2A3, BADH2A6, BADH2A7, BADH2A8, BADH2A9, BADH2A10, BADH2A11, BADH2A12, BADH2A13, BADH2A14 and BADH2A15 exhibited different levels of polymorphism amongst the eighteen aromatic rice genotypes under consideration in the present study, revealing the existence of differences in molecular size of the candidate genes specific genomic regions flanked by the primer pairs. A total of 38 shared and 28 unique allelic variants were generated in the form of amplified products by polymerase chain reaction using twenty two primer pairs. The number of shared alleles per locus ranged from one in the case of BADH1A7, BADH1A12, BADH1A14, BADH2A3, BADH2A7, BADH2A8 and BADH2A11. Two in the case of BADH1A3, BADH1A6, BADH1A9, BADH1A10, BADH1A11, BADH1A13, BADH1A15, BADH2A6, BADH2A9, BADH2A10, BADH2A12, BADH2A13, BADH2A14 and BADH2A15. Three in the case of BADH1A8. Similarly, the number of unique alleles per locus ranged from one in the case of BADH1A6, BADH1A7, BADH1A9, BADH1A10, BADH1A12, BADH1A13, BADH1A14, BADH1A15, BADH2A6, BADH2A7, BADH2A9, BADH2A10, BADH2A11, BADH2A12, BADH2A13, BADH2A14 and BADH2A15 , two in BADH1A8, BADH1A11, BADH2A3 and BADH2A8, three in BADH1A3. The presence of null allele was inferred due to failure of amplification for a particular repeat locus specific to the unique flanking sequences. Out of twenty two primer pairs two primer pair locus associated with BADH1A3 and BADH2A12 exhibited null alleles ranging from one to five in the entries under evaluation. On the contrary, the remaining twenty primer pairs did not exhibit the presence of null allele(s) in any one of the entries under evaluation during the course of the present investigation. | en_US |
| dc.identifier.uri | http://krishikosh.egranth.ac.in/handle/1/5810142421 | |
| dc.keywords | Plant, Aromatic rice, Breeding Genetics, BADH1, BADH2, BADH1A7, BADH1A12, BADH1A14, BADH2A7 | en_US |
| dc.language.iso | en | en_US |
| dc.publisher | DRPCAU, Pusa, Samastipur | en_US |
| dc.sub | Agricultural Biotechnology | en_US |
| dc.subject | null | en_US |
| dc.theme | Molecular characterization for fragrance of aromatic rice varieties using candidate gene markers | en_US |
| dc.these.type | M.Sc | en_US |
| dc.title | Molecular characterization for fragrance of aromatic rice varieties using candidate gene markers | en_US |
| dc.type | Thesis | en_US |