Genetic diversity analysis among Indian goat breeds based on mitochondrial DNA

ANURODH SHARMA; KARAN VEER SINGH; JAYAKUMAR SIVALINGAM; MANIMOHAN P; VINITA SAROHA; D RAVIKUMAR; DINESH KUMAR; S P DIXIT

doi:10.56093/ijans.v90i6.104994

Authors

ANURODH SHARMA ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132 001 India
KARAN VEER SINGH ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132 001 India
JAYAKUMAR SIVALINGAM ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132 001 India
MANIMOHAN P ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132 001 India
VINITA SAROHA ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132 001 India
D RAVIKUMAR ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132 001 India
DINESH KUMAR ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132 001 India
S P DIXIT ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132 001 India

https://doi.org/10.56093/ijans.v90i6.104994

Keywords:

Diversity, Genetic, Goat, Haplotype, mtDNA

Abstract

India ranks second in goat population with 34 genetically recognized and registered breeds. Information on their diversity and origin and ancestry is little known. Hence, the mtDNA based genetic diversity analysis of Indian goats; targeting mitochondrial HVR1 region from 21 Indian breeds belonging to different geographical regions was undertaken. A total of 124 haplotypes were identified and haplotype diversity estimate ranged from 0.67 to 1.0 with an average value of 0.99. The average nucleotide diversity was minimum (0.02) in Kanniadu and maximum in Surti breeds. Analysis of molecular variance revealed 5.16% variation among the breeds and 94.84% within breeds indicating weak phylogeographic structure. Neighbor-joining tree analysis revealed that the maximum number of individuals of Indian goats fall under A and few in B and C lineages. Principal component analyses of the Indian goat breeds revealed that Kanniadu goats clustered distantly from rest of the breeds of the country. Mantel test revealed a significant correlation between F_ST and geographical distance (r=0.29) among the goat breeds. The mismatch distribution analysis of the Indian goat breeds revealed bimodal distribution patterns. The analysis revealed that Kanniadu is highly distinct from the rest of the breeds.

Downloads

Download data is not yet available.

References

Al-Araimi N A, Gaafar O M, Costa V, Neira A L, Al-Atiyat R M, and Beja-Pereira A. 2017. The genetic origin of goat populations in Oman revealed by mitochondrial DNA analysis. PLoS ONE 12(12): 190–235. DOI: https://doi.org/10.1371/journal.pone.0190235

Avise J C. 2000. Phylogeography Harvard University Press. Cambridge, MA. DOI: https://doi.org/10.2307/j.ctv1nzfgj7

Bandelt H, Forster P and Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16(1): 37–48. DOI: https://doi.org/10.1093/oxfordjournals.molbev.a026036

Chen S Y, Su Y H, Wu S F, Sha T and Zhang Y P. 2005. Mitochondrial diversity and phylogeographic structure of Chinese domestic goats. Molecular Phylogenetics and Evolution 37(3): 804–14. DOI: https://doi.org/10.1016/j.ympev.2005.06.014

Clutton_Brock J. 1981. Domestic Animals from Early Times (Heinemann and British Museum of National History, London).

Excoffier L and Lischer H E. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10(3): 564–67. DOI: https://doi.org/10.1111/j.1755-0998.2010.02847.x

Grant W A S and Bowen B W. 1998. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. Journal of Heredity 89(5): 415–26. DOI: https://doi.org/10.1093/jhered/89.5.415

Hoda A, Biçoku Y and Dobi P. 2014. Genetic diversity of Albanian goat breeds revealed by mtDNA sequence variation. Biotechnology and Biotechnological Equipment 28(1): 77–81. DOI: https://doi.org/10.1080/13102818.2014.901672

Joshi M B, Rout P K, Mandal A K, Tyler-Smith C, Singh L and Thangaraj K. 2004. Phylogeography and origin of Indian domestic goats. Molecular Biology and Evolution 21(3): 454– 62. DOI: https://doi.org/10.1093/molbev/msh038

Kamalakkannan R, Jose J, Thomas S, Prabhu V R and Nagarajan M. 2018. Genetic diversity and maternal lineages of south Indian goats. Molecular Biology Reports 45(6): 2741–48. DOI: https://doi.org/10.1007/s11033-018-4322-5

Kibegwa F M, Githui K E, Jung J O, Badamana M S and Nyamu M N. 2016. Mitochondrial DNA variation of indigenous goats Fig. 3. Mean pairwise difference in all Indian goats. in Narok and Isiolo counties of Kenya. Journal of Animal Breeding and Genetics 133(3): 238–47. DOI: https://doi.org/10.1111/jbg.12182

Kumar S, Stecher G, Li M, Knyaz C and Tamura K. 2018. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution 35(6): 1547–49. DOI: https://doi.org/10.1093/molbev/msy096

Liu R Y, Lei C Z, Liu S H and Yang G S. 2006. Genetic diversity and origin of Chinese domestic goats revealed by complete mtDNA D-loop sequence variation. Asian Australasian Journal of Animal Sciences 20(2): 178–83. DOI: https://doi.org/10.5713/ajas.2007.178

Luikart G, Gielly L, Excoffier L, Vigne J D, Bouvet J and Taberlet P. 2001. Multiple maternal origins and weak phylogeographic structure in domestic goats. Proceedings of the National Academy of Sciences 98(10): 5927–32. DOI: https://doi.org/10.1073/pnas.091591198

MacHugh D E and Bradley D G. 2001. Livestock genetic origins: goats buck the trend. Proceedings of the National Academy of Sciences 98(10): 5382–84. DOI: https://doi.org/10.1073/pnas.111163198

Meadows J R S, Li K, Kantanen J, Tapio M, Sipos W, Pardeshi V and Kijas J W. 2005. The mitochondrial sequence reveals high levels of gene flow between breeds of domestic sheep from Asia and Europe. Journal of Heredity 96(5): 494–501. DOI: https://doi.org/10.1093/jhered/esi100

Naderi S, Rezaei H R, Taberlet P, Zundel S, Rafat S A and Naghash H R. 2007. Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. PLOS ONE 2(10): 10–12. DOI: https://doi.org/10.1371/journal.pone.0001012

Peakall R and Smouse P E. 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28: 2537–39. DOI: https://doi.org/10.1093/bioinformatics/bts460

Porter R. 1996. The Cretan Wild Goat (Capra aegagruscretica) and the Theran Antelopes. Pleistocene and Holocene Fauna of Crete and It’s First Settlers, pp. 295–36.

Pringle H. 1998. Reading the signs of ancient animal domestication. DOI: https://doi.org/10.1126/science.282.5393.1448

Rozas J, Ferrer-Mata A, Sánchez-DelBarrio J C, Guirao-Rico S, Librado P, Ramos-Onsins S E and Sánchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution 34(12): 3299–3302. DOI: https://doi.org/10.1093/molbev/msx248

Sardina M T, Ballester M, Marmi J, Finocchiaro R, Van Kaam J B C H M, Portolano B and Folch J M. 2006. Phylogenetic analysis of Sicilian goats reveals a new mtDNA lineage. Animal Genetics 37(4): 376–78. DOI: https://doi.org/10.1111/j.1365-2052.2006.01451.x

Shackleton D M. 1997. Wild sheep and goats and their relatives. IUCN.

Su L N, Li X C, Meng H Z, Gao X Y, Yin H and Li K. 2015. Population genetic structure and historical demography of the ground beetle Chlaenius costiger in the Tsinling-Dabashan Mountains of central China. Gene tics and Molecular Research 14(2): 3579–89. DOI: https://doi.org/10.4238/2015.April.17.7

Sultana S, Mannen H and Tsuji S. 2003. Mitochondrial DNA diversity of Pakistani goats. Animal Genetics 34(6): 417–421. DOI: https://doi.org/10.1046/j.0268-9146.2003.01040.x

Wu Y P, Guan W J, Zhao Q J, He X H, Pu YB, Huo J H and Ma Y H. 2009. A fine map for maternal lineage analysis by mitochondrial hypervariable region in 12 Chinese goat breeds. Animal Science Journal 80(4): 372–80. DOI: https://doi.org/10.1111/j.1740-0929.2009.00659.x

Wu Y P, Huo J H, Guan W J, Xie J F and Ma Y H. 2012. Sequence analysis of four caprine mitochondria DNA lineages. Italian Journal of Animal Science 11(4): 69. DOI: https://doi.org/10.4081/ijas.2012.e69

Zhao Y, Zhang J, Zhao E, Zhang X, Liu X and Zhang N. 2011. Mitochondrial DNA diversity and origins of domestic goats in Southwest China (excluding Tibet). Small Ruminant Research 95(1): 40–47. DOI: https://doi.org/10.1016/j.smallrumres.2010.09.004

Zhao Y, Zhao R, Zhao Z, Xu H, Zhao E and Zhang J. 2014. Genetic diversity and molecular phylogeography of Chinese domestic goats by large-scale mitochondrial DNA analysis. Molecular Biology Reports 41(6): 3695–3704. DOI: https://doi.org/10.1007/s11033-014-3234-2