Genomewide identification and annotation of SNPs in Bubalus bubalis

• Published in: Genomics (San Diego, Calif.) Vol. 111; no. 6; pp. 1695 - 1698
• Main Authors: Surya, T., Vineeth, M.R., Sivalingam, Jayakumar, Tantia, M.S., Dixit, S.P., Niranjan, S.K., Gupta, I.D.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.12.2019
• Subjects: Animals; Buffalo; Buffaloes - genetics; ddRAD; Genome; Genome-Wide Association Study; Molecular Sequence Annotation; NGS; Polymorphism, Single Nucleotide; Quantitative Trait, Heritable; SNP; ddRAD; NGS; SNP; Buffalo
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2018.11.021

The present study was carried out to identify and annotate the genome wide SNPs in Murrah buffalo genome. A total of 21.2 million raw reads from 4 pooled female Murrah buffalo samples were obtained using restriction enzyme digestion followed by sequencing with Illumina Hiseq 2000. After quality filtration, the reads were aligned to Murrah buffalo genome (ICAR-NBAGR) and Water buffalo genome (UMD_CASPUR_WB_2.0) which resulted in 99.37% and 99.67% of the reads aligning, respectively. A total of 130,688 high quality SNPs along with 35,110 indels were identified versus the Murrah bufffalo genome. Similarly 219,856 high quality SNPs along with 15,201 indels were identified versus the Water buffalo genome. We report 483 SNPs in 66 genes affecting Milk Production, 436 SNPs in 38 genes affecting fertility and 559 SNPs in 72 genes affecting other major traits. The average genome coverage was 13.4% and 14.8% versus the Murrah and Water buffalo genomes, respectively. •Genome wide identification and annotation of SNPs was carried out in Murrah buffalo.•A total of 130,688 and 219,856 high quality SNPs were identified versus the Murrah and Water buffalo genomes respectively.•A total of 483, 436 and 559 SNPs affecting milk production, fertility and other major traits respectively were identified.•The average genome coverage was found to be 13.4% and 14.8% versus the Murrah and Water buffalo genomes, respectively.