Genomic diversity and selection sweeps identified in Indian swamp buffaloes reveals it's uniqueness with riverine buffaloes

• Published in: Genomics (San Diego, Calif.) Vol. 112; no. 3; pp. 2385 - 2392
• Main Authors: Ravi Kumar, D., Joel Devadasan, M., Surya, T., Vineeth, M.R., Choudhary, Anjali, Sivalingam, Jayakumar, Kataria, R.S., Niranjan, S.K., Tantia, M.S., Verma, Archana
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-05-2020
• Subjects: Admixture; Animals; Buffalo; Buffaloes - classification; Buffaloes - genetics; ddRAD; Genetic Variation; Genomic diversity; Genomics - standards; Genotyping Techniques; India; Microsatellite Repeats; Molecular Sequence Annotation; Phylogeny; Polymorphism, Single Nucleotide; SNP; India; ddRAD; SNP; Genomic diversity; Admixture; Buffalo
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2020.01.010

The present investigation was focused to study genomic diversity of Indian swamp buffalo populations through reduced representation approach (ddRAD). The heterozygosity (FST) among the swamp buffaloes was 0.11 between Assam and Manipuri; 0.20 between swamp (Manipuri) and riverine buffaloes; 0.30 between swamp (Manipuri) and cattle. The average observed and expected heterozygosity in swamp buffalo populations was 0.254 and 0.221 respectively. The Inbreeding coefficient (FIS) value was 0.02 among the swamp buffaloes. PCA and structure analysis revealed Manipuri swamp buffalo was genetically distinct and closely related to Nagaland swamp buffalo and least to Assam swamp buffalo. Identification of selective sweeps revealed 1087 regions to have undergone selection related to immune response, adaptation and nervous system. A total of 3451 SSRs were identified in the genome of swamp buffaloes. The study evidenced the genomic diversity in the swamp buffalo populations and its uniqueness in comparison with riverine buffalo and cattle.
•Manipur swamp buffalo was found to be genetically distinct and closely related to Nagaland; least to Assam swamp buffalo.•A total of 1087 regions were found to have undergone selection related to immune response, adaptation and nervous system.•A total of 3451 SSRs were identified in the genome of swamp buffaloes.•The study evidenced genomic diversity in the swamp buffalo and its uniqueness in comparison with riverine buffalo and cattle.