Allele mining for phosphorus starvation tolerance gene (pstoli) in wild species of rice
| dc.contributor.advisor | Neelam Kumari | |
| dc.contributor.author | Thakur, Shiwali | |
| dc.date.accessioned | 2018-09-20T05:13:45Z | |
| dc.date.available | 2018-09-20T05:13:45Z | |
| dc.date.issued | 2016 | |
| dc.description.abstract | In present study, 182 accessions of Oryza rufipogon having different countries of origin along with O. sativa cv. PR114, PR121, PR122, PB3 and Vandana (positive control) were screened with flanking, co-dominant and dominant (InDel specific) markers to assess the variability throughout 90 kb insertion region of Kasalath. Previously reported SSRs markers OsPupK-4, OsPupK-05, OsPupK-20, OsPupK-29, K-41, K-42, K-43, K-46, K-48, K-52, and K-59 were applied. Based on analysis, it is inferred that most of the O. rufipogon accessions under study had 90 kb insertion present, whereas O. sativa cv. PR114, PR121, PR122 didn't have amplification with K-46, a diagnostic marker for PSTOL 1. Further, the primers were designed for full length amplification of PSTOL 1 gene (1 kb) and sequencing of 69 representative accessions of O. rufipogon with Vandana were performed. Sequence alignment led to the detection of 74 single nucleotide polymorphism among O. rufipogon accessions when compared to Vandana/ Kasalath. Out of this, 21 turned out to be false positives on manual curation and ultimately fifty three true SNPs were observed in the transcribed region of PSTOL1 gene. Transitions were more common than transversions. There were 39 transitions and 14 transversions observed. The most common SNP was A/G SNP. Based on the nucleotide diversity, a total of 17 haplotypes were formed. Haplotype II forms a major group with 41 accessions of O. rufipogon including Vandana and Kasalath whereas other 16 Haplotype groups had O. rufipogon accessions ranging from 1 to 3. Further, protein sequences were also studied in order to detect if any functional variation is pressent. A total number of 28 conversions for amino acid at different positions with comparison to reference sequence were found. The most common SNP was Lysine/Arginine. Validation of O. rufipogon accessions carrying PSTOL1 gene was done in P-deficient soil along with checks and it was found that O.rufipogon accessions had higher tolerance against P starvation when compared to check Vandna under stress conditions. F1 plants were generated by cross-pollination between cultivars and O. rufipogon accessions in order to transfer the novel alleles of PSTOL1 gene to elite cultivars. Thus, this study found out that allelic variation for locus PSTOL1 is present in Wild germplasm. | en_US |
| dc.identifier.uri | http://krishikosh.egranth.ac.in/handle/1/5810073839 | |
| dc.keywords | Allele mining, Oryza rufipogon | en_US |
| dc.language.iso | en | en_US |
| dc.pages | 62 | en_US |
| dc.publisher | Punjab Agricultural University, Ludhiana | en_US |
| dc.research.problem | Allele mining for phosphorus starvation tolerance gene (pstoli) in wild species of rice | en_US |
| dc.sub | Agricultural Biotechnology | en_US |
| dc.subject | null | en_US |
| dc.theme | Allele mining for phosphorus starvation tolerance gene (pstoli) in wild species of rice | en_US |
| dc.these.type | M.Sc | en_US |
| dc.title | Allele mining for phosphorus starvation tolerance gene (pstoli) in wild species of rice | en_US |
| dc.type | Thesis | en_US |