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

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Title Genomic diversity and selection sweeps identified in Indian swamp buffaloes reveals it's uniqueness with riverine buffaloes
Not Available
 
Creator Kumar, D. Ravi
Devadasan, M. Joel
Surya, T.
Vineeth, M. R.
Choudhary, Anjali
Sivalingam, Jayakumar
Kataria, R. S.
Niranjan, S. K.
Tantia, M. S.
Verma, Archana
 
Subject Genomic diversity
ddRAD
Buffalo
SNP
Admixture
 
Description The present work was funded by ICAR-NDRI and the authors thank Directors of ICAR-NDRI and ICAR-NBAGR for the support to carry out this research work. The authors also express their sincere gratitude to Dr Parameswari B, Senior Scientist (Plant Pathology) and Dr Neeraj Kulshreshtha, Principal Scientist (Plant Breeding) and Head, Sugarcane Breeding Institute Regional center, Karnal, Haryana for providing the computational facilities for this work.
The present investigation was focused to study genomic diversity of Indian swamp buffalo populations through reduced representation approach (ddRAD). The heterozygosity (F-ST) 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 (F-IS) 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.
ICAR-NDRI
ICAR-NBAGR
 
Date 2020-08-01T03:50:44Z
2020-08-01T03:50:44Z
2020-05
 
Type Article
 
Identifier Kumar, D. Ravi; Devadasan, M. Joel; Surya, T.; Vineeth, M. R.; Choudhary, Anjali; Sivalingam, Jayakumar; Kataria, R. S.; Niranjan, S. K.; Tantia, M. S.; Verma, Archana. Genomic diversity and selection sweeps identified in Indian swamp buffaloes reveals it's uniqueness with riverine buffaloes, GENOMICS, 112 (3), 2385-2392. doi:10.1016/j.ygeno.2020.01.010
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http://krishi.icar.gov.in/jspui/handle/123456789/38863
 
Language English
 
Relation Not Available
 
Publisher GENOMICS, ACADEMIC PRESS INC ELSEVIER SCIENCE, 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA