Genetic structure of Jinhua pig and genetic differentiation of Jinhua pig and Taihu pig breeds based on microsatellite DNA markers

doi:10.3724/SP.J.1003.2008.07399

Abstract

Abstract:

The genotypes of Jinhua (lines I, II, and III), Shengxianhua, and four Taihu pigs (Jiaxing Black, Middle Meishan, Small Meishan, Erhualian) were investigated using 65 microsatellite DNA markers through fluorescence PCR. Our objectives were to investigate the genetic structure within Jinhua pigs as well as genetic differentiation of Jinhua pigs from the other five breeds. We found a large range of genetic variation in Jinhua pigs. LineIhad the highest average number of effective alleles (N_e = 3.5), followed by LineII (N_e = 2.8), and Line III (N_e = 2.5). The average polymorphism information content (PIC) in each line was above 0.5, with an average observed heterozygosity of 0.381, 0.399, and 0.442, in lines I, II, and III, respectively. Furthermore, a decreasing number of microsatellite loci that deviated from Hardy-Weinberg equilibrium were found in lines I, III, and II, respectively. Inbreeding has occurred to some extent in each of the Jinhua lines. Analyses showed that differentiation between Jinhua lines III and II was relatively small (F_ST= 0.1883). However, greater differentiation was found between lineIand lines II and III (F_ST-value 0.3663 and 0.3619, respectively). Moreover, the genetic relationship between Jinhua pigs and Taihu pigs were close. The Taihu pig breed with the smallest differentiation from Jinhua pigs was Middle Meishan, but a high degree of genetic differentiation existed in Shengxianhua pig and each Jinhua line. In conclusion, Jinhua pig has a unique evolution process in terms of the origin and domestication history, which is different from other Zhejiang native breeds.

Key words: Jinhua pig, microsatellite, polymorphism information content, heterozygosity, genetic differentiation

Zhao Xiaofeng, Wu Junhong, Xu Ningying, Hu Xiaoxiang, Li Ning. Genetic structure of Jinhua pig and genetic differentiation of Jinhua pig and Taihu pig breeds based on microsatellite DNA markers[J]. Biodiv Sci, 2008, 16(4): 339-345.

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URL: https://www.biodiversity-science.net/EN/10.3724/SP.J.1003.2008.07399

https://www.biodiversity-science.net/EN/Y2008/V16/I4/339

Figures/Tables 7

References 16

[1]	Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32,314-331. URL PMID
[2]	Chen HJ (陈红菊), Yue YS (岳永生), Fan XZ (樊新忠), Zhang CS (张传生), Du LX (杜立新) (2004) A comparative study of genetic distance and clustering analysis among Shandong indigenous chicken breeds. Acta Veterinaria et Zootechnica Sinica (畜牧兽医学报), 35,33-36. (in Chinese with English abstract)
[3]	Huang SH (黄胜海), Li HF (李慧芳), Chen KW (陈宽维), Tang QP (汤青萍), Tu YJ (屠云洁), Yang N (杨宁) (2006) Study on genetic structure and evolution of five domestic white goose breeds. Animal Husbandry and Veterinary Medicine (畜牧与兽医), 38,20-22. (in Chinese with English abstract)
[4]	Li N (李宁) (2002) Animal Genetics(动物遗传学),2nd edn. Chinese Agricultural Press,Beijing. (in Chinese)
[5]	Marshall TC, Slate J, Kruuk LEB, Pemberton JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology, 7,639-655. DOI URL PMID
[6]	Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 8,583-590.
[7]	Raymond M, Rousset F (1995) GENEPOP version 3.2: population genetics software for exact tests and ecumenicism. Journal of Heredity, 86,248-249. DOI URL
[8]	Simianer H, Meyer JN (2003) Past and future activities to harmonize farm animal biodiversity studies on a global scale. Archivos de Zootecnia, 52,1-5.
[9]	Wang JM (王建民), Yue WB (岳文斌) (2008) Genetic relationships of domestic sheep and goats in the lower reaches of the Yellow River based on microsatellite analysis. Biodiversity Science(生物多样性), 16,53-62. (in Chinese with English abstract) DOI URL
[10]	Wang X (王昕), Chen H (陈宏), Cao HH (曹红鹤) (2005) Phylogenesis analysis of 10 Chinese indigenous pig populations. Hereditas(Beijing)(遗传), 27,715-718. (in Chinese with English abstract) URL PMID
[11]	Zerger KR, Richarderson BJ (2003) A rapid population expansion retains genetic diversity within European rabbit in Australia. Molecular Ecology, 12,789-794. DOI URL PMID
[12]	Zhang DJ (张冬杰), Yang GW (杨国伟), Liu D (刘娣) (2005) Origin and domestication of northeast wild boar. Jiangsu Agricultural Science(江苏农业科学), 5,92-94. (in Chinese with English abstract)
[13]	Zhang GX (张桂香), Wang ZG (王志刚), Sun FZ (孙飞舟), Chen WS (陈伟生), Yang GY (杨国义), Guo SJ (郭式健), Li YJ (李拥军), Zhao XL (赵小丽), Zhang Y (张沅), Sun J (孙军), Fan B (樊斌), Yang SL (杨述林), Li K (李奎) (2003) The genetic diversity of microsatellite loci in 56 Chinese native pig breeds. Acta Genetica Sinica (遗传学报), 30,225-233. (in Chinese with English abstract)
[14]	Zhang ZG (张仲葛) (1986) Pig Breeds in China (中国猪品种志). Shanghai Scientificand Technical Publishers, Shanghai .
[15]	Zhao XF (赵晓枫), Xu NY (徐宁迎), Hu XX (胡晓湘), Li N (李宁) (2007) Effects of microsatellite in the regulatory region of IGF1 on growth traits in Jinhua swine. Hereditas (Beijing)(遗传), 29,206-210. (in Chinese with English abstract) DOI URL PMID
[16]	Zhao LL (赵丽莉), Nie GJ (聂光军), Guo XL (郭晓令), Xu NY (徐宁迎) (2006) Polymorphism of growth hormone gene and its effect on economic traits in Jinhua pigs. Chinese Journal of Animal Science (中国畜牧杂志), 42(5),8-11. (in Chinese with English abstract)

位点 Locus	荧光标记 Fluorescent dye	退火温度 Annealing temperature (℃)	所在染色体 Chromosome	位点 Locus	荧光标记 Fluorescent dye	退火温度 Annealing temperature (℃)	所在染色体 Chromosome
S0155	Fam	55	01	SW951	Hex	58	10
SW1828	Fam	60	01	SWR67	Hex	60	10
SWR2516	Hex	60	02	S0392	Fam	58	11
SW1564	Fam	58	02	SW2008	Hex	60	11
S0226	Fam	55	02	SW1377	Tet	60	11
SW72	Fam	58	03	SW66	Fam	62	11
SW902	Fam	55	03	SW168	Hex	62	12
SW717	Tet	58	03	S0090	Fam	55	12
S0227	Hex	55	04	SW452	Hex	60	13
S0301	Fam	55	04	SW1030	Tet	58	13
SW969	Fam	60	04	SW769	Fam	55	13
S0217	Tet	62	04	S0215	Hex	55	13
SW332	Hex	58	05	SW295	Tet	55	14
S0005	Tet	58	05	SW886	Tet	58	14
SW1987	Fam	58	05	SW55	Fam	58	14
IGF1	Fam	58	05	SW1111	Tet	55	15
SW1302	Tet	58	06	SW1945	Tet	58	15
S0228	Tet	55	06	SW936	Fam	58	15
SW2155	Fam	65	07	SW1510	Hex	60	15
SW175	Hex	55	07	SW742	Hex	60	16
SW632	Tet	58	07	SW1897	Fam	62	16
S0101	Hex	60	07	SWR1004	Fam	60	17
SW1816	Tet	60	07	SW24	Tet	58	17
SW1843	Hex	62	08	SWR1120	Fam	62	17
SW790	Hex	62	08	SW2142	Tet	60	17
S0178	Tet	58	08	SW1023	Fam	55	18
SW911	Fam	55	09	SW787	Fam	55	18
SW174	Tet	55	09	SW1682	Tet	58	18
SW1349	Fam	58	09	S0177	Tet	50	18
SW830	Fam	55	10	SW2476	Hex	62	X
SWR136	Tet	58	10	SW1943	Tet	62	X
S0351	Hex	55	10	S0218	Tet	55	X
S0070	Hex	55	10

位点 Locus	荧光标记 Fluorescent dye	退火温度 Annealing temperature (℃)	所在染色体 Chromosome	位点 Locus	荧光标记 Fluorescent dye	退火温度 Annealing temperature (℃)	所在染色体 Chromosome
S0155	Fam	55	01	SW951	Hex	58	10
SW1828	Fam	60	01	SWR67	Hex	60	10
SWR2516	Hex	60	02	S0392	Fam	58	11
SW1564	Fam	58	02	SW2008	Hex	60	11
S0226	Fam	55	02	SW1377	Tet	60	11
SW72	Fam	58	03	SW66	Fam	62	11
SW902	Fam	55	03	SW168	Hex	62	12
SW717	Tet	58	03	S0090	Fam	55	12
S0227	Hex	55	04	SW452	Hex	60	13
S0301	Fam	55	04	SW1030	Tet	58	13
SW969	Fam	60	04	SW769	Fam	55	13
S0217	Tet	62	04	S0215	Hex	55	13
SW332	Hex	58	05	SW295	Tet	55	14
S0005	Tet	58	05	SW886	Tet	58	14
SW1987	Fam	58	05	SW55	Fam	58	14
IGF1	Fam	58	05	SW1111	Tet	55	15
SW1302	Tet	58	06	SW1945	Tet	58	15
S0228	Tet	55	06	SW936	Fam	58	15
SW2155	Fam	65	07	SW1510	Hex	60	15
SW175	Hex	55	07	SW742	Hex	60	16
SW632	Tet	58	07	SW1897	Fam	62	16
S0101	Hex	60	07	SWR1004	Fam	60	17
SW1816	Tet	60	07	SW24	Tet	58	17
SW1843	Hex	62	08	SWR1120	Fam	62	17
SW790	Hex	62	08	SW2142	Tet	60	17
S0178	Tet	58	08	SW1023	Fam	55	18
SW911	Fam	55	09	SW787	Fam	55	18
SW174	Tet	55	09	SW1682	Tet	58	18
SW1349	Fam	58	09	S0177	Tet	50	18
SW830	Fam	55	10	SW2476	Hex	62	X
SWR136	Tet	58	10	SW1943	Tet	62	X
S0351	Hex	55	10	S0218	Tet	55	X
S0070	Hex	55	10

品系 Breed	等位基因数 N_A	有效等位基因数 N_e	期望杂合度 H_e	观察杂合度 H_o	多态信息含量 PIC
金华猪I系 Jinhua line I	8.9	3.5	0.591	0.381	0.558
金华猪II系 Jinhua line II	10.0	2.8	0.549	0.399	0.514
金华猪III系 Jinhua line III	9.7	2.5	0.626	0.442	0.586

品系 Breed	等位基因数 N_A	有效等位基因数 N_e	期望杂合度 H_e	观察杂合度 H_o	多态信息含量 PIC
金华猪I系 Jinhua line I	8.9	3.5	0.591	0.381	0.558
金华猪II系 Jinhua line II	10.0	2.8	0.549	0.399	0.514
金华猪III系 Jinhua line III	9.7	2.5	0.626	0.442	0.586

	金华猪I系 Jinhua I	金华猪II系 Jinhua II	金华猪III系 Jinhua III	二花脸 Erhualian	嘉兴黑 Jiaxing Black	小梅山 Small Meishan	中梅山 Middle Meishan	嵊县花 Shengxianhua
金华猪I系 Jinhua I		0.4325	0.4408	0.3855	0.3410	0.3799	0.4481	0.3057
金华猪II系 Jinhua II	0.3663		1.0777	0.3910	0.3272	0.3722	0.4522	0.2872
金华猪III系 Jinhua III	0.3619	0.1883		0.3656	0.3205	0.3734	0.4499	0.2707
二花脸 Erhualian	0.3934	0.3900	0.4061		0.8075	1.1664	1.4133	0.5166
嘉兴黑 Jiaxing Black	0.4230	0.4331	0.4382	0.2364		0.6684	0.7809	0.3666
小梅山 Small Meishan	0.3969	0.4018	0.4010	0.1765	0.2722		2.1819	0.3388
中梅山 Middle Meishan	0.3581	0.3560	0.3572	0.1503	0.2425	0.1028		0.3076
嵊县花 Shengxianhua	0.4499	0.4654	0.4801	0.3261	0.4319	0.4879	0.5627