GENOMIC SIGNATURES OF MEAT TYPE GOAT BREEDS
| dc.contributor.advisor | S.P. DIXIT | |
| dc.contributor.author | RAVINA | |
| dc.date.accessioned | 2023-11-21T12:36:39Z | |
| dc.date.available | 2023-11-21T12:36:39Z | |
| dc.date.issued | 2022 | |
| dc.description.abstract | Natural and artificial selections are known to fix certain genomic regions with reduced heterozygosity, which is a steping stone in the process of breed development. Comprehensive information on genetic variants viz genome-wide single nucleotide polymorphisms (SNPs) and INDELs, offers valuable genomic insights linked to key Kanniadu goat traits, has not yet been investigated. Exploring the genomic signals under positive selection and the overlappng genes in the Kanniadu goat breed is the major goal of the current investigation. High throughput genomic sequence data of Kanniadu (n=10) and Jakhrana (n=10) were generated from whole genome re-sequencing (~10X) using 150 bp paired-end chemistry on the Illumina NOVASEQ 6000 platform, while Saanen samples (n=10) were downloaded. FastQC (version 0.11.9) was utilized to assess the read quality parameters. Fastp (http://opengene.org/fastp/fastp) was employed for adapter trimming and quality filtering. The samples were then aligned to the goat (Capra hircus) genome assembly ARS1 (GCF 001704415.1 ARS1 genomic.fna.gz) from USDA ARS using Burrows Wheeler Aligner (BWA). The picard tool was used to remove duplicate reads and the GATK tool to call variants (SNPs and INDELs). We generated around 202.7 million clean reads which covers an average of 99.5% percent of the reference genome (ARS1), suggesting that high-quality sequences are generated. We identified 22.5 million SNPs and 3.7 million INDELs in the Kanniadu goat. SNPs found in intronic, intergenic, and exonic regions were annotated. Within breed selection signatures of Kanniadu were identified by θπ and CLR methods while regions under divergent selection between Kanniadu vs Jakhrana, Kanniadu vs Saanen and Jakhrana vs Saanen were studied by Fixation Index (FST) analysis. In overlapping regions, two approaches (CLR and θπ) displayed outlier signals (top 1 percent), and these regions were thus regarded as possible selection regions. Within selection signatures of Kanniadu, a total of 262 (θπ) and 1700 (CLR) genes were identified. A total number of 51 overlapping genes between top 1% θπ and CLR signatures were identified. The top signatures were identified on chromosome 16, 25 and 23 harboring important genes like IPO9 (muscle growth formation), LMOD1 (smooth muscle), U6 (carcass marbling), 7SK (carcass traits), SNORA62 (carcass traits), DCN (carcass traits), PTPRR (carcass traits) etc. Consequently, we performed functional annotation, Gene Ontology (GO) and KEGG pathways analysis for the top 1% genes. Overall, the present study highlights the genes under selection in Kanniadu goats, which will be useful in determining the genetic potential of this breed. | |
| dc.identifier.uri | https://krishikosh.egranth.ac.in/handle/1/5810201634 | |
| dc.language.iso | English | |
| dc.pages | 60 p. | |
| dc.publisher | ICAR-NDRI, KARNAL | |
| dc.sub | Animal Genetics and Breeding | |
| dc.theme | ANIMAL GENETICS & BREEDING | |
| dc.these.type | M.V.Sc. | |
| dc.title | GENOMIC SIGNATURES OF MEAT TYPE GOAT BREEDS | |
| dc.type | Thesis |