Genetic characterization and population structure of different coat colour variants of Badri cattle
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ORIGINAL ARTICLE
Genetic characterization and population structure of different coat colour variants of Badri cattle Aashaq Hussain Dar1 · Sanjay Kumar1 · Manishi Mukesh2 · Sheikh Firdous Ahmad3,4 · Dev Vrat Singh1 · Rabendra Kumar Sharma1 · Ashis Kumar Ghosh1 · Balwinder Singh1 · Javid Ur Rahman1 · Monika Sodhi2 Received: 13 April 2020 / Accepted: 3 October 2020 © Springer Nature B.V. 2020
Abstract The present study aimed to genetically characterize the Badri cattle and its three colour variants and assess their population structure using 24 microsatellite markers. Out of 96 animals analyzed, 32 each were collected from grey (GVBC), brown (BrVBC) and black (BVBC) colour variants of Badri cattle (BC). The genetic diversity parameters including allele frequencies, observed and effective number of alleles, observed and expected heterozygosity, PIC, Shannon’s indices and F-statistics were estimated using POPGENE software. Bottleneck analysis was performed using both qualitative and quantitative approaches. A total of 274 alleles (50 private and 224 shared) were scored for BC, GVBC, BrVBC and BVBC with mean number of 11.417, 9.083, 9.125 and 9.083 alleles, respectively. All populations exhibited average heterozygosity estimate > 0.5 indicating existence of substantial genetic variability, concurrent with revelations from Shannon’s indices. Observed mean PIC estimates (> 0.74) were indicative of optimum informativeness of used microsatellite markers. The mean inbreeding estimates (F) in GVBC, BrVBC and BVBC were 0.041, − 0.024 and 0.016, respectively. The pair wise genetic (> 0.91) pointed towards similarity between different colour variant populations. STRUCTURE analysis also revealed clear admixture for the three Badri colour variants indicating absence of genetic differentiation. The present study revealed firsthand information that populations of Badri cattle with different phenotypes with respect to coat colour are genetically related and can be considered as a single breed. The comprehensive knowledge generated for Badri cattle will help in designing breeding plan for its genetic improvement and deciding the conservation priorities. Keywords Genetic diversity · Bottleneck · Inbreeding · Indigenous · Microsatellite markers
Introduction
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11033-020-05890-w) contains supplementary material, which is available to authorized users. * Monika Sodhi [email protected] 1
Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145, India
2
ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal 132001, India
3
ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh 243122, India
4
ICAR-National Research Centre on Pig, Rani, Guwahati, Assam 781131, India
Livestock sector contributes about 25.6% of total output in Agriculture, Fishing & Forestry sector and about 4.11% of total gross domestic product (GDP) in India [1]. Indigenous ca
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