Genetic Diversity and Structure of Two Prominent Zebu Cattle Breeds Adapted to the Arid Region of India Inferred from Microsatellite Polymorphism

Sodhi, Monika; Mukesh, Manishi; Ahlawat, Sonika; Sobti, Ranbir Chander; Gahlot, G. C.; Mehta, S. L.; Prakash, B.; Mishra, Bina

doi:10.1007/s10528-007-9135-5

Cited by 13 publications

(20 citation statements)

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“…Lower allelic diversity than currently studied populations have also been reported in exotic cattle-Burlina 6.7 [18], Brown Swiss 5.4 [19], Creole cattle 7.2 [20]. Allelic diversity of similar magnitude has been reported in Tharparkar 9 and Rathi 9.6 [21] cattle breeds of India. However, higher allelic diversity has been reported in Chinese cattle 29.33 [22].…”

Section: Resultssupporting

confidence: 56%

“…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.…”

Section: Resultssupporting

confidence: 42%

“…Most of the indigenous breeds including Kheri garh 0.57 [12], Kenkatha 0.54 [13], Sahiwal 0.43 [14], Gangatiri 0.46 [15], Bachaur 0.53 [16] and Deoni 0.59 [17] showed lower estimates of observed heterozygosity than Orissa and Kumauni populations. Overall heterozygosity estimates are comparable with Tharparkar cattle (0.64) of India [21], Chinese cattle (0.62) [22] and Creole cattle 0.61 [20]. Binjharpuri cattle represented the lowest observed and effective number of alleles as well as observed and expected het erozygosity.…”

Section: Resultsmentioning

confidence: 53%

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Differentiation of four indian aboriginal cattle populations revealed by SIR markers

et al. 2012

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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.

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Section: Resultssupporting

confidence: 56%

Section: Resultssupporting

confidence: 42%

Section: Resultsmentioning

confidence: 53%

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Differentiation of four indian aboriginal cattle populations revealed by SIR markers

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“…Considering the importance of cattle in Indian agriculture, few efforts have been made to evaluate the genetic diversity and relationship in Indian cattle using microsatellite markers [8–12]. However, ecomprehensive knowledge of the breed characteristics, including within-and between-breed genetic diversity which will result in complete representation possible of biological diversity is required to facilitate effective management.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and relationship of Indian cattle inferred from microsatellite and mitochondrial DNA markers

et al. 2015

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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.

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“…These markers display higher levels of variations and have been extensively used for diversity analysis in different farm animal species like cattle (Metta et al 2004;Sodhi et al 2008), sheep (Mukesh et al 2006;Bhatia and Arora 2007) and goat (Rout et al 2008). In case of riverine buffaloes, although the genetic relationship/differentiation between different Indian breeds had been evaluated by various workers (Kumar et al 2006;Mishra et al 2008;Vijh et al 2008a,b) Banni, the important buffalo population from Western India was not included.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of genetic variability and mutation drift equilibrium of Banni buffalo using multi locus microsatellite markers

Mishra

Kataria

Kathiravan

et al. 2009

Trop Anim Health Prod

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The present study was conducted to evaluate genetic diversity of Banni buffalo and its relationship/differentiation with Murrah using genotypic data on 24 heterologus bovine specific microsatellite marker loci. A total of 138 alleles were observed with a mean of 5.75 alleles/locus across two populations. The mean observed and expected heterozygosities were found to be 0.441 and 0.572 respectively in Banni buffaloes while it was 0.464 and 0.610 respectively in Murrah buffaloes. The average heterozygosity deficit was significantly positive with substantially higher values observed in Banni (22.3%) and Murrah (24%) buffalo populations. Banni buffalo population, when evaluated for mutation drift equilibrium revealed significant heterozygosity excess under IAM while no such excess was observed under SMM and TPM. The qualitative graphical test revealed a normal L-shaped distribution of allele frequencies indicating the absence of genetic bottleneck in Banni buffaloes. The mean estimates of F-statistics over all the loci were 0.376 for F(IT), 0.187 for F(ST) and 0.232 for F(IS) respectively. Analysis of molecular variance (AMOVA) revealed 18.95% of the total variation being explained by between breed differences while 14.36% of the variation explained differences between individuals within each breed. Genotype assignment test revealed distinct clustering of Banni and Murrah buffaloes. Genetic distance was estimated using three different methods, the results of which revealed considerable genetic differentiation between these two buffalo populations. The divergence time between Banni and Murrah buffaloes was estimated to be around 7286 years. The results of the present study may be helpful in decision making for conservation programs as Banni buffalo population is on decline.

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Genetic Diversity and Structure of Two Prominent Zebu Cattle Breeds Adapted to the Arid Region of India Inferred from Microsatellite Polymorphism

Cited by 13 publications

References 31 publications

Differentiation of four indian aboriginal cattle populations revealed by SIR markers

Differentiation of four indian aboriginal cattle populations revealed by SIR markers

Genetic diversity and relationship of Indian cattle inferred from microsatellite and mitochondrial DNA markers

Evaluation of genetic variability and mutation drift equilibrium of Banni buffalo using multi locus microsatellite markers

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