EXOME WIDE DNA CAPTURE AND NEXT GENERATION SEQUENCING IN VECHUR CATTLE OF KERALA
| dc.contributor.advisor | Aravindakshan, T. V | |
| dc.contributor.author | Reshma R S | |
| dc.date.accessioned | 2019-07-01T07:16:06Z | |
| dc.date.available | 2019-07-01T07:16:06Z | |
| dc.date.issued | 2016-07-05 | |
| dc.description.abstract | Genome wide searches have to be carried out to identify genetic markers associated with economically important traits of native cattle like adaptability to hot and humid environmental conditions and resistance to various diseases. The present study was undertaken to assess the genetic variants present in the exonic regions of Vechur cattle by exome wide DNA capture and Next Generation Sequencing technology. Blood sample taken from Vechur cow belonging to Vechur Cattle Conservation Unit attached to Kerala Veterinary and Animal Sciences University was used for exome capture and next generation sequencing. When the sequenced reads were mapped to the Bos taurus reference genome downloaded from Ensembl (ftp://ftp.ensembl.org/pub/release-81/gtf/bos_taurus/ Bos_taurus.UMD3.1.81.gtf.gz) 17, 16,847 variants (15, 78,749 SNPs and 1, 38,098 indels) were identified. Comparing these variants with dbSNP database revealed 3, 59,034 novel variants in Vechur cattle. The annotation of the 1,11,500 variants identified in the exonic regions, confirmed that 93,294 variants were located in the coding region, 2,558 variants in non-coding gene, 495 variants in ncRNA and 15,153 variants in the un-translated regions. The functional annotation of the variants in the exonic regions identified 62,693 silent, 37,564 non-synonymous, 1,345 frame shift, 799 inframe, 322 nonsense, 67 start loss and a single stop loss variants. In order to validate the NGS data, three missense novel SNPs identified in two innate immune genes were selected for genotyping 50 Vechur animals by PCR-RFLP technique. The SNP (A T transversion) located at 15241430th position of chromosome 27, which is 1348th position of exon 4 of Toll like receptor 3 gene, was found to be polymorphic with two genotypes AA and AT. The SNP (G A transition) identified at 35815099th position of chromosome 28, that is 21st position of exon 1 of surfactant protein D gene was polymorphic with two genotypes GG and GA. The SNP (A C transversion) at 35824058th position of chromosome 28, that is 52nd position of exon 7 of surfactant protein D gene, was found to be polymorphic with three genotypes AA, AC and CC. | en_US |
| dc.identifier.citation | KVASU REFERANCE CITATION | en_US |
| dc.identifier.uri | http://krishikosh.egranth.ac.in/handle/1/5810111086 | |
| dc.language.iso | en | en_US |
| dc.publisher | COLLEGE OF VETERINARY AND ANIMAL SCIENCE-MANNUTHY,THRISSUR | en_US |
| dc.research.problem | EXOME WIDE DNA CAPTURE AND NEXT GENERATION SEQUENCING IN VECHUR CATTLE OF KERALA | en_US |
| dc.sub | Animal Biotechnology | en_US |
| dc.subject | null | en_US |
| dc.theme | Animal Biotechnology | en_US |
| dc.these.type | M.V.Sc. | en_US |
| dc.title | EXOME WIDE DNA CAPTURE AND NEXT GENERATION SEQUENCING IN VECHUR CATTLE OF KERALA | en_US |
| dc.type | Thesis | en_US |