|
|
|
| The Genetic Diversity of mtDNA D-loop and the Differentiation of Goats (Capra hircus) in South and Northwest of China |
|
|
|
|
Abstract Abstract Domestic goats (Capra hircus) are evolved from wild goats, and there are good adaptability, wide distribution and abundant breed resource for goats in China. Natural and artificial selection for long time may lead to differences in polymorphism and differentiation between goats of South and North of China. To study genetic diversity and origin as well as differentiation of goats in South and Northwest of China, D-loop region of 69 individuals belonging to 5 goat breeds distributing in South-China were sequenced and analyzed combing with 33 sequences from 3 goat breeds distributing in Northwest of China. The results showed that content of A+T and G+C in South and Northwest were 60.1%, 39.9% and 60.0%, 40.0%, respectively, indicating no apparent difference in base composition between the 2 areas. The average haplotype diversity (Hd) and nucleotide diversity (π) of goats in South China were 0.954±0.005 and 0.019 57±0.002 10, respectively, while they were 0.919±0.106 and 0.019 08±0.001 15 for goats in Northwest; Fs of all data sets were large negative value (P＜0.05) while values of sum of squared deviation (SSD) and raggedness had no significant difference (P＞0.05), which indicated nucleotide mismatch distribution had not deviated from population expansion model, and at 13th、37th、61st nucleotide, there was a peak for each site; NJ (neighbor-joining) tree showed 2 lineages: A and B, and all goats of South and Northwest distributed in the 2 lineages. Furthermore, lineage B divided into 2 sub-clade, B1 and B2, implying persistently differentiation. Media-joining network showed the same result to the NJ tree, and further pointed out H1 was the highest frequency haplotype appearing. When it comes to genetic distance, it was 0.022 and 0.019 within population for goats of South and Northwest. These results suggested that genetic diversity of goats in South area was slightly higher than in Northwest, although a little lower than that in past several years; events of population expansion had arisen for the whole haplotype group as well as A and B lineages; C. aegagrus was the wild ancestor for domestic goats of South and Northwest of China referred in this study. This research offers theoretical support for further understanding origin, differentiation and genetic diversity of goats which distributed in South and Northwest of China, and provide theoretical basis for protecting native breeds.
|
|
Received: 18 September 2016
Published: 13 January 2017
|
|
|
|
| [1]郝荣超, 昝林森, 刘丑生.等.中国部分家养山羊线粒体 环区遗传多样性与起源遗传[J].Hereditas, 2008, 30(9):1187-1194[2]潘建飞, 史兆国, 成述儒, 等.甘肃主要马群体遗传多样性及系统发育研究农业生物技术学报[J].Journal of agricultural biotechnology, 2014, 22(2):210-218[3]武建亮, 肖宇航, 刘文忠.山羊线粒体 - 区遗传多样性研究, 中国畜牧兽医[J].China animal husbandry and veterinary medicine, 2009, 36(5):120-122[4]Chen S Y, Su Y H, Wu S F, et al.Mitochondrial diversity and phylogeographic structure of Chinese domestic goats[J].Mol phylogenet evol, 2005, 37(3):804-814[5]Fu Y X.1997.Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection [J]. Genetics, 147(2): 915-925[6]Harpending H C.Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution[J].Hum Biol, 1994, 66(4):591-600[7]Kang J F, Li X L, Zhou R Y, et al.Genetic diversity and differentiation of four goat lineages based on analysis of complete mtDNA d-loop[J].Frontiers of Agriculture in China, 2011, 5(1):87-93[8]Larkin M A, Blackshields G, Brown NP, et al.Clustal W and clustal X version 20[J].Bioinformatics, 2007, 23(21):2947-2948[9]Librado P, Rozas J.DnaSP v5: a software for comprehensive analysis of DNA polymorphism data[J]. Bioinformatics, 2009, 25(11), 1451–1452.[10]Lin B Z, Odahara S, Ishida M, et al., Molecular phylogeography and genetic diversity of East Asian goats[J]. Animal genetics, 2013, 44, 79–85.[11]Liu R Y, Yang G S, Lei C Z.The genetic diversity of mtDNA D-loop and the origin of chinese goats[J]. Acta Genetica Sinica, 2006, 33(5), 420-428.[12]Liu R Y, Lei C Z, Liu S H, et al.Genetic diversity and origin of Chinese domestic goats revealed by complete mtDNA D-loop sequence variation[J].Asian Austral J Anim, 2007, 20(2):178-183[13]Luikart G, Gielly L, Excoffier L, et al.Multiple maternal origins and weak phylogeographic structure in domestic goats[J].P Natl Acad Sci USA, 2001, 98(10):5927-5932[14]Naderi S, Rezaei H R, Pompanon F, et al.The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals[J].Proc Natl Acad Sci USA, 2008, 105(46):17659-17664[15]Naderi S, Rezaei H R, Taberlet P, et al.Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity[J].Plos One, 2007, 2(10):e1012-e1012[16]Peng M S, Fan L, Shi N N, et al., DomeTree: a canonical toolkit for mitochondrial DNA[J].Molecular ecology resources, 2015, 15(5):1238-1242[17]Porter V.Goats of the World[J].Farming Press, 1996, :-[18]Porter V.Goats of the World [M].Farming Press, Ipswich, U.K, 1996[19]Tu Y R.Sheep and goat breeds in China [M]. Shanghai: Shanghai Scientific & Technical Puplishers, 1989, 3-4 (in Chinese).[20]Sultana S, Mannen H, Tsuji S.Mitochondrial DNA diversity of Pakistani goats[J].Anim Genet, 2003, 34(6):417-21[21]Zeder, M A, Hesse B.The initial domestication of goats (Capra hircus) in the Zagros[22]mountains 10, 000 years ago[J].Science, 2000, 287: 2254–2257. |
|
|
|
