Abstract:The present study aims to understand the existing genetic diversity and structure of six native cattle breeds (Rathi, Tharparkar, Nagori, Mewati, Gir, and Kankrej) adapted to the north-western arid and semi-arid region of India based on microsatellite loci. Various diversity estimates, mean number of alleles (12.84); effective number of alleles (5.02); gene diversity (0.769), and observed heterozygosity (0.667) reflected the existence of substantial within-breed diversity in all the investigated cattle breeds.… Show more
“…All loci contributed to the differentiation with the highest values found for ILSTS11 (23.8%). Much higher F ST value have been reported in some other indigenous cattle; Tharparkar and Rathi F ST = 0.065 ± 0.017 [21] and six cattle breeds F ST = 0.078 ± 0.014 [23]. While, North European breeds F ST = 0.107 [24], seven Euro pean cattle breeds F ST = 0.112 [25] and Swiss cattle F ST = 0.090 [26] also depicted higher genetic differen tiation than present populations.…”
Cattle are the most important livestock in India and play a pivotal role in agrarian economy. There are 34 recognized breeds of cattle and number of unexplored lesser known populations. The present study is a contribution towards determining genetic Variation and understanding the relationship among four lesser known populations. A total of 194 unrelated DNA samples from three cattle populations of Orissa (Binjhar puri, Ghumsuri, Motu) and Hill cattle of Kumaun (Kumauni) were collected from respective breeding tracts. Genotyping was done with 23 bovine microsatellite markers as suggested by International Society for Animal Genetics (ISAG) and FAO (DAD IS) on automated sequencer. The average observed heterozygosity in the four populations lie within the narrow range of 0.623 ± 0.04 in Binjharpuri to 0.664 ± 0.03 in Kumauni. Mean estimates of observed and expected heterozygosity over all loci and breeds were 0.651 ± 0.02 and 0.720 ± 0.01, respectively. In the overall population, the homozygote excess (F IT ) of 0.132 ± 0.03, was partly due to the genetic differentiation among breeds (F ST = 0.044 ± 0.01) and, to a larger extent, to a significant homozygote excess within breeds (F IS = 0.094 ± 0.03). The phylogenetic reconstruction from a UPGMA clustering based on Nei's Standard genetic distance yielded a tree with Binjharpuri and Ghumsuri on a single node and Motu and Kumauni on separate nodes. The most probable clustering detected by STRUCTURE in population was three. Binjharpuri and Ghumsuri animals were assigned to one cluster with high proportion of membership.
“…All loci contributed to the differentiation with the highest values found for ILSTS11 (23.8%). Much higher F ST value have been reported in some other indigenous cattle; Tharparkar and Rathi F ST = 0.065 ± 0.017 [21] and six cattle breeds F ST = 0.078 ± 0.014 [23]. While, North European breeds F ST = 0.107 [24], seven Euro pean cattle breeds F ST = 0.112 [25] and Swiss cattle F ST = 0.090 [26] also depicted higher genetic differen tiation than present populations.…”
Cattle are the most important livestock in India and play a pivotal role in agrarian economy. There are 34 recognized breeds of cattle and number of unexplored lesser known populations. The present study is a contribution towards determining genetic Variation and understanding the relationship among four lesser known populations. A total of 194 unrelated DNA samples from three cattle populations of Orissa (Binjhar puri, Ghumsuri, Motu) and Hill cattle of Kumaun (Kumauni) were collected from respective breeding tracts. Genotyping was done with 23 bovine microsatellite markers as suggested by International Society for Animal Genetics (ISAG) and FAO (DAD IS) on automated sequencer. The average observed heterozygosity in the four populations lie within the narrow range of 0.623 ± 0.04 in Binjharpuri to 0.664 ± 0.03 in Kumauni. Mean estimates of observed and expected heterozygosity over all loci and breeds were 0.651 ± 0.02 and 0.720 ± 0.01, respectively. In the overall population, the homozygote excess (F IT ) of 0.132 ± 0.03, was partly due to the genetic differentiation among breeds (F ST = 0.044 ± 0.01) and, to a larger extent, to a significant homozygote excess within breeds (F IS = 0.094 ± 0.03). The phylogenetic reconstruction from a UPGMA clustering based on Nei's Standard genetic distance yielded a tree with Binjharpuri and Ghumsuri on a single node and Motu and Kumauni on separate nodes. The most probable clustering detected by STRUCTURE in population was three. Binjharpuri and Ghumsuri animals were assigned to one cluster with high proportion of membership.
“…These results reflect that within-breed genetic variation is more (86.7 %) than between-breed (13.3 %) and this variation could be a valuable tool for genetic improvement and conservation of cattle populations of India. Genetic differentiation of similar magnitude has been reported in some other indigenous cattle [9]. However, much lower F ST value has been reported among cattle breeds of Orissa and hill cattle of Kumaun (0.044) from India [12], as well as zebu cattle of Bangladesh [41].…”
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.
“…Genetic differentiation of similar magnitude has been reported among cattle breeds of Orissa and hill cattle of Kumaun (0.044) from India (Sharma et al 2012a). Much higher F ST value have been reported in other indigenous cattle (Sodhi et al 2011). While, several reports on exotic cattle viz.…”
Section: Resultsmentioning
confidence: 59%
“…Considering the importance of cattle in Indian agriculture, efforts have been made to evaluate the genetic diversity and relationship in Indian cattle using microsatellite markers. These included native cattle breeds adapted to the north-western arid and semi-arid region of India (Sodhi et al 2008; 2011), north Indian cattle breeds (Sharma et al 2009), South Indian breeds (Metta et al 2004) and cattle of Orissa state and hill cattle of Kumaun (Sharma et al 2012a). However, the genetic relationship between native cattle breeds of eastern India is unknown.Figure 1 Distribution of cattle populations.…”
India has 34 recognized breeds of cattle in addition to many more not characterized and accredited so far. It is imperative to characterize all the cattle germplasm of the country so as to have better breeding and conservation options. Thus, present study was planned for assessing genetic diversity and relationship between three local cattle populations (Gangatiri, Shahabadi and Purnea) and two established cattle breeds (Bachaur and Siri) of eastern India by using 21 FAO and ISAG recommended microsatellite markers. A total of 243 unrelated DNA samples of five cattle populations were collected from respective habitats. A total of 304 microsatellite alleles were identified with number of alleles at one locus ranging from 5 to 29. The average observed heterozygosity lie within the narrow range of 0.681 ± 0.04 in Purnea to 0.721 ± 0.03 in Siri. Mean estimates of observed and expected heterozygosity over all loci and breeds were 0.704 ± 0.02 and 0.720 ± 0.01, respectively. In the overall population, the homozygote excess (FIT) of 0.073 ± 0.02, was partly due to the homozygote excess within breeds (FIS = 0.026 ± 0.02) and to a larger extent due to genetic differentiation among breeds (FST = 0.048 ± 0.01). The genetic distance, STRUCTURE and Principal Component Analyses concluded that the Siri cattle are most distinct among the investigated cattle populations. Furthermore the analysis of genetic structure indicated that the most probable number of clusters is four. All analysis showed that a significant amount of genetic variation is maintained in local cattle populations of which Shahabadi and Purnea are distinct from the recognized breeds of the area and needs recognition as breeds.
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