Abstract
BackgroundIndian agriculture is an economic symbiosis of crop and livestock production with cattle as the foundation. Sadly, the population of indigenous cattle (Bos indicus) is declining (8.94 % in last decade) and needs immediate scientific management. Genetic characterization is the first step in the development of proper management strategies for preserving genetic diversity and preventing undesirable loss of alleles. Thus, in this study we investigated genetic diversity and relationship among eleven Indian cattle breeds using 21 microsatellite markers and mitochondrial D loop sequence.ResultsThe analysis of autosomal DNA was performed on 508 cattle which exhibited sufficient genetic diversity across all the breeds. Estimates of mean allele number and observed heterozygosity across all loci and population were 8.784 ± 0.25 and 0.653 ± 0.014, respectively. Differences among breeds accounted for 13.3 % of total genetic variability. Despite high genetic diversity, significant inbreeding was also observed within eight populations. Genetic distances and cluster analysis showed a close relationship between breeds according to proximity in geographic distribution. The genetic distance, STRUCTURE and Principal Coordinate Analysis concluded that the Southern Indian Ongole cattle are the most distinct among the investigated cattle populations. Sequencing of hypervariable mitochondrial DNA region on a subset of 170 cattle revealed sixty haplotypes with haplotypic diversity of 0.90240, nucleotide diversity of 0.02688 and average number of nucleotide differences as 6.07407. Two major star clusters for haplotypes indicated population expansion for Indian cattle.ConclusionsNuclear and mitochondrial genomes show a similar pattern of genetic variability and genetic differentiation. Various analyses concluded that the Southern breed ‘Ongole’ was distinct from breeds of Northern/ Central India. Overall these results provide basic information about genetic diversity and structure of Indian cattle which should have implications for management and conservation of indicine cattle diversity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0221-0) contains supplementary material, which is available to authorized users.
Highlights
Indian agriculture is an economic symbiosis of crop and livestock production with cattle as the foundation
Direct comparisons between Mitochondrial DNA (mtDNA) and microsatellite loci can be very informative for population diversity and genetic structure, as evolutionary forces affect each class of marker differently [7]
All microsatellite markers used in this study were successfully amplified in five multiplex sets designed with consideration for annealing temperature, product size and specific dye label in all the populations (Table 1)
Summary
Indian agriculture is an economic symbiosis of crop and livestock production with cattle as the foundation. The population of indigenous cattle (Bos indicus) is declining (8.94 % in last decade) and needs immediate scientific management. In this study we investigated genetic diversity and relationship among eleven Indian cattle breeds using 21 microsatellite markers and mitochondrial D loop sequence. Indian zebu cattle (Bos indicus) evolved over centuries under low levels of selection followed in traditional animal husbandry. Employment of microsatellite markers is one of the most powerful means for studying the genetic diversity, calculation of genetic distances, detection of bottlenecks and admixture because of high degree of polymorphism, random distribution across the genome, codominance and neutrality with respect to selection [4]. Direct comparisons between mtDNA and microsatellite loci can be very informative for population diversity and genetic structure, as evolutionary forces affect each class of marker differently [7]
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