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Genome-wide SNP identification and annotation from high coverage whole genome sequenced data of Bhadawari buffalo

Indian Agricultural Research Journals

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Title Genome-wide SNP identification and annotation from high coverage whole genome sequenced data of Bhadawari buffalo
 
Creator Ameya Santhosh, Vikas Vohra, Rani Alex and Gopal Gowane
 
Description Eukaryotic genomes are rich in Single Nucloetide Polymorphisms(SNPs) which have gained immense importance as the genetic marker of choice especially for the production traits in livestock species. The high throughput sequencing technologies, which offer the quick and greater coverage genome sequencing data has improved the accuracy of SNP discovery through various bioinformatic pipelines. This is the preliminary study to uncover the SNPs from high coverage (45x) sequenced data of the unique Bhadawari buffalo breed of India. Blood was collected from two pure bred animals from the breeding tract and DNA was sequenced using Illumina Highseq technology. The sequences were aligned to the buffalo reference genome and variant calling was done.The variant count (SNPs, Insertions, and deletions) discoverable at six ascending read depths (2,5,10, 20, 30 and 40) has been analysed. The Transition to Transversion ratio (Ti/Tv ratio) is found to be nearly 2.2. Chromosome wise distribution of SNPs showed that in all read depths maximum number of SNPs were found to be in the 1st chromosome of Bhadawari buffalo genome.
 
Publisher Indian Dairy Association, New Delhi, India
 
Date 2024-02-23
 
Type info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
 
Format application/pdf
 
Identifier https://epubs.icar.org.in/index.php/IJDS/article/view/141688
 
Source Indian Journal of Dairy Science; Vol. 77 No. 1 (2024): Jan Feb 2024
2454-2172
0019-5146
 
Language eng
 
Relation https://epubs.icar.org.in/index.php/IJDS/article/view/141688/54020