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

BMC Genetics

Madhu Sudan Tantia¹  Ashwni Kumar Pandey¹  Avishek Maitra¹  Sonika Ahlawat¹  Manishi Mukesh¹  Amit Kishore¹  Rekha Sharma¹ 

[1] Core lab (Network Project Unit), National Bureau of Animal Genetic Resources, G T Road, Karnal 132001, Haryana, India

关键词: Population structure;    Mitochondrial DNA;    Microsatellite markers;    Indian cattle;    Genetic relationship;    Diversity;    Conservation;   

Others  :  1218921
DOI  :  10.1186/s12863-015-0221-0

 received in 2014-12-30, accepted in 2015-05-22,  发布年份 2015

【 摘 要 】

Background

Indian 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.

Results

The 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.

Conclusions

Nuclear 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.

【 授权许可】

   
2015 Sharma et al.

【 图 表 】

Fig. 1.

Fig. 2.

Fig. 3.

Fig. 4.

【 参考文献 】

• [1]BAHS-basic animal husbandry statistics: Department of Animal Husbandry, Dairying & Fisheries, Ministry of Agriculture, Government of India . Krishi Bhavan, New Delhi; 2012.
• [2]FAO. The state of the world’s animal genetic resources for food and agriculture. In: Rischkowsky B, Pilling D editors. Rome: Commission on Genetic Resources For Food and Agriculture of the Food and Agriculture Organization of the United Nations; 2007
• [3]Barcaccia G, Felicetti M, Galla G, Capomaccio S, Cappelli K, Albertini E et al.. Molecular analysis of genetic diversity, population structure and inbreeding level of the Italian Lipizzan horse. Livest Sci. 2013; 151(2-3):124-33.
• [4]Putman AI, Carbone I. Challenges in analysis and interpretation of microsatellite data for population genetic studies. Ecol Evol. 2014; 4(22):4399-428.
• [5]Loftis DG, Echelle AA, Koike H, Van den Bussche RA, Minckley CO. Genetic structure of wild populations of the endangered desert pupfish complex (Cyprinodontidae: Cyprinodon). Conserv Genet. 2009; 10:453-63.
• [6]Galtier N, Nabholz B, Glémin S, Hurst G. Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Mol Ecol. 2009; 18:4541-50.
• [7]Hoarau G, Piquet AM, Van der Veer HW, Rijnsdorp AD, Stam WT, Olsen JL. Population structure of plaice (Pleuronectesplatessa L.) in northern Europe, a comparison of resolving power between microsatellites and mitochondrial DNA data. J Sea Res. 2004; 51:183-90.
• [8]Sodhi M, Mukesh M, Ahlawat SPS, Sobti RC, Gehlot GC, Mehta SC et al.. Genetic diversity and structure of two prominent Zebu cattle breeds adapted to the arid region of India inferred from microsatellite polymorphism. Biochem Genet. 2008; 46:124-36.
• [9]Sodhi M, Mukesh M, Mishra BP, Ahlawat SPS, Prakash B, Sobti RC. Microsatellite analysis of genetic population structure of Zebu cattle (Bos indicus) breeds from North-Western region of India. Anim Biotech. 2011; 22:16-29.
• [10]Sharma R, Pandey AK, Singh Y, Prakash B, Mishra BP, Kathiravan P et al.. Evaluation of genetic variation and phylogenetic relationship among north Indian cattle breeds. Asian Australs J Anim Sci. 2009; 22:13-9.
• [11]Sharma R, Maitra A, Singh PK, Tantia MS. Genetic diversity and relationship of cattle populations of East India: distinguishing lesser known cattle populations and established breeds based on STR markers. Springer Plus. 2013; 2:359. BioMed Central Full Text
• [12]Sharma R, Maitra A, Pandey AK. Genetic structure and differentiation of four Indian autochthonous cattle populations. Russian J Genet. 2012; 48(6):611-7.
• [13]Sambrook J, Fritsch EF, Maniatis T. Molecular cloning: a laboratory manual. 2nd ed. Cold Spring Harbour Laboratory Press, New York; 1989.
• [14]Molecular genetic characterization of animal genetic resources. FAO Animal Production and Health Guidelines, No. 9. Rome, repost; 2011.
• [15]Peakall R, Smouse PE. A heterogeneity test for fine-scale genetic structure. Mol Ecol Notes. 2008; 17:3389-400.
• [16]Nei M. Molecular evolutionary genetics. Columbia University Press, New York; 1987.
• [17]Page RDM. TreeView: an application to display phylogenetic trees on personal computers. Comp App in Biosci. 1996; 12:357-8.
• [18]Felsenstein J. PHYLIP: phylogeny inference package, version 3.5. Department of Genome Sciences, Washington University, Seattle, Washington; 1993.
• [19]Raymond M, Rousset F. GENEPOP: population genetics software for exact tests and ecumenicism. J Hered. 1995; 86:248-9.
• [20]Pritchard J, Stephensa M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000; 155:945-59.
• [21]Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol. 2005; 14:2611-20.
• [22]Earl DA, vonHoldt BM. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour. 2012; 4(2):359-61.
• [23]Suzuki R, Kemp SJ, Teale AJ. Polymerase chain reaction analysis of mitochondrial DNA polymorphism in Ndama and Zebu catle. Anim Genet. 1993; 24:39-343.
• [24]Excoffier L, Laval G, Schneider S. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform. 2005; 1:47-50.
• [25]Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mole Biol Evol. 2013; 30:2725-9.
• [26]Bandelt HJ, Forster P, Rohl A. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 1999; 16:37-48.
• [27]Buchanan FC, Adams LJ, Littlejohn RP, Maddox JF, Crawford AM. Determination of evolutionary relationships among sheep breeds using microsatellites. Genomics. 1994; 22:397-403.
• [28]Mukesh M, Sodhi M, Bhatia S, Mishra BP. Genetic diversity of Indian native cattle breeds as analyzed with 20 microsatellite loci. J Anim Breed Genet. 2004; 121:416-24.
• [29]Pandey AK, Sharma R, Singh Y, Prakash B. Genetic diversity studies of Kherigarh cattle based on microsatellite markers. J Genet. 2006; 85:117-22.
• [30]Pandey AK, Sharma R, Singh Y, Prakash B, Ahlawat SPS. Evaluation of genetic variation in Kenkatha cattle by microsatellite markers. Asian Australs J Anim Sci. 2006; 19:1685-90.
• [31]Dalvit C, De Marchi M, Dal ZR, Zanetti E, Meuwissen T, Cassandro M. Genetic characterization of Burlina cattle breed using microsatellite markers. J Anim Breed Genet. 2008; 125:137-44.
• [32]Schmid M, Saipveaova N, Gaillard C, Dolf G. Genetic diversity in Swiss cattle breeds. J Anim Breed Genet. 1999; 116:1-8.
• [33]Egito AA, Paiva SR, Albuquerque MM, Mariante AS, Almeida LD, Castro SR et al.. Microsatellite based genetic diversity and relationships among ten Creole and commercial cattle breeds raised in Brazil. BMC Genet. 2007; 8:83-97. BioMed Central Full Text
• [34]Joshi BK, Sodhi M, Mukesh M, Mishra BP. Genetic characterization of farm animal genetic resources of India: a review. Indian J of Anim Sci. 2012; 82(3):1259-75.
• [35]Bataillon TM, David JL, Schoen DJ. Neutral genetic markers and conservation genetics: simulated germplasm collections. Genetics. 1996; 144:409-17.
• [36]Petit RJ, EI Mousadik A, Pons O. Identifying populations for conservation on the basis of genetic markers. Conserv Biol. 1998; 12:844-55.
• [37]Sun W, Chen H, Lei C. Genetic variation in eight Chinese cattle breeds based on the analysis of microsatellite markers. Genet Sel Evol. 2008; 40:681-92. BioMed Central Full Text
• [38]Baig M, Beja-Pereira A, Mohammad R, Kulkarni K, Farah S, Luikart G. Phylogeography and origin of Indian domestic cattle. Curr Sci. 2005; 89:38-40.
• [39]Bhuiyan MSA, Bhuiyan AKFH, Yoon DH, Jeon JT, Park CS, Lee JH. Mitochondrial DNA diversity and origin of Red Chittagong cattle. Asian Australas J Anim Sci. 2007; 20:1478-84.
• [40]Decker JE, McKay SD, Rolf MM, Kim JW, Alcalá AM, Sonstegard TS et al.. Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. PLoS Genet. 2014; 10:E1004254.44.
• [41]Uzzaman MR, Edea Z, Bhuiyan MSA, Walker J, Bhuiyan AKFH, Kim K. Genome-wide single nucleotide polymorphism analyses reveal genetic diversity and structure of wild and domestic cattle in Bangladesh. Asian Australas J Anim Sci. 2014; 27(10):1381-6.
• [42]McHugh DE, Loftus RT, Cunningham P, Bradley DG. Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers. Anim Genet. 1998; 28:333-40.
• [43]Kantanen J, Edwards CJ, Bradley DG, Viinalass H, Thessler S, Ivanova Z et al.. Maternal and paternal genealogy of Eurasian taurine cattle (Bostaurus). Heredity. 2009; 103:404-15.
• [44]Zeder MA. Archaeozoology in Southwest Asia: a status report based on the eighth meeting of the Archaeozoology of Southwest Asia and Adjacent Areas Working Group. Pale’orient. 2006; 32:137-47.
• [45]Chen S, Lin BZ, Baig M, Mitra B, Lopes RJ, Santos AM et al.. Zebu cattle are an exclusive legacy of the South Asia Neolithic. Mol Biol Evol. 2010; 27:1-6.
• [46]Fuller DQ. Agricultural origins and frontiers in South Asia: a working synthesis. Journal of World Prehistory. 2006; 20:1-86.
• [47]Korisettar R, Venkatasubbaiah PC, Fuller DQ. Brahmagiri and beyond: the archaeology of the Southern Neolithic. In: Indian archaeology in retrospect. Settar S, Korisettar R, editors. Manohar Press, New Delhi (India); 2001: p.151-237.