title: Genetic diversity and relationship of Indian cattle inferred from microsatellite and mitochondrial DNA markers.
abstract: 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.
authors.affiliation: Core lab (Network Project Unit), National Bureau of Animal Genetic Resources, G T Road, Karnal, 132001, Haryana, India. rekvik@gmail.com.
authors.forename: Rekha
authors.initials: R
authors.lastname: Sharma
authors.affiliation: Core lab (Network Project Unit), National Bureau of Animal Genetic Resources, G T Road, Karnal, 132001, Haryana, India. amitkishore.bio@gmail.com.
authors.forename: Amit
authors.initials: A
authors.lastname: Kishore
authors.affiliation: Core lab (Network Project Unit), National Bureau of Animal Genetic Resources, G T Road, Karnal, 132001, Haryana, India. mmukesh_26@hotmail.com.
authors.forename: Manishi
authors.initials: M
authors.lastname: Mukesh
authors.affiliation: Core lab (Network Project Unit), National Bureau of Animal Genetic Resources, G T Road, Karnal, 132001, Haryana, India. sonika.ahlawat@gmail.com.
authors.forename: Sonika
authors.initials: S
authors.lastname: Ahlawat
authors.affiliation: Core lab (Network Project Unit), National Bureau of Animal Genetic Resources, G T Road, Karnal, 132001, Haryana, India. maitra.avishek@gmail.com.
authors.forename: Avishek
authors.initials: A
authors.lastname: Maitra
authors.affiliation: Core lab (Network Project Unit), National Bureau of Animal Genetic Resources, G T Road, Karnal, 132001, Haryana, India. ashwni.pandey@gmail.com.
authors.forename: Ashwni Kumar
authors.initials: AK
authors.lastname: Pandey
authors.affiliation: Core lab (Network Project Unit), National Bureau of Animal Genetic Resources, G T Road, Karnal, 132001, Haryana, India. tantiams@gmail.com.
authors.forename: Madhu Sudan
authors.initials: MS
authors.lastname: Tantia
mesh_terms: D000818:Animals; D002417:Cattle; D016000:Cluster Analysis; D004272:DNA, Mitochondrial / Q000235:genetics*; D005787:Gene Frequency; D005819:Genetic Markers; D014644:Genetic Variation; D005828:Genetics, Population; D005843:Geography; D006239:Haplotypes; D007194:India; D018895:Microsatellite Repeats / Q000235:genetics*; D011110:Polymorphism, Genetic
chemical_list: D004272:DNA, Mitochondrial; D005819:Genetic Markers