利用微卫星标记评估10个中国地方猪品种的遗传多样性
摘要
本研究采用联合国粮农组织(FAO)和国际动物遗传学会(ISAG)第X次推荐的51对微卫星标记的荧光引物中的20对引物，借助AB1310自动测序仪，检测我国10个地方猪品种(嵊县花猪SX，南阳黑猪NY，嘉兴黑猪JX，淮南黑猪HU，海南猪HN，赣西两头乌GX，监利猪JL，金华猪JH，东山猪DS，沙子岭猪SZ)在DNA水平上的遗传多样性。结果表明，在20个微卫星座位上，10个猪品种具有的等位基因数目和频率均不同程度地呈现出变异，南阳黑猪具有的平均等位基因数目最多(11.55)，金华猪最少(6.25)。其中，一些等位基因如SW1364：158bp等位基因，SW2439：133 bp等位基因，SW938：144bp和146 bp等位基因，SW2509：176bp和190 bp等位基因，SW142：131 bp等位基因，PDYN：137bp和139 bp等位基因，SW1668：186bp，206bp和208 bp等位基因，SW575：147bp和151bp等位基因，S0167：214 bp等位基因，为10个猪品种所共有，推测它们可能是我国猪基因组中最为“原始”的等位基因：一些等位基因如SW1678座位上的129bp，131bp，137 bp等位基因只在淮南黑猪出现。SW1684座位上的117bp，121bp，127 bp等位基因只在南阳黑猪出现。SW2439座位上的113bp，115bp，117 bp等位基因只在嘉兴黑猪出现。SW1364座位上的146bp，202bp，220 bp等位基因只在赣西两头乌出现。SW938座位上的176 bp等位基因只在嵊县花猪上出现。SW1325座位上的108 bp等位基因只在沙子岭猪上出现．而126 bp等位基因只在海南花猪上出现。SW1632座位上的152bp，158bp，190bp，192bp，194bp，202 bp等位基因只在监利猪上出现。SW2509座位上的148 bp等位基因只在东山猪上出现。SW142座位上的103bp和107 bp等位基因只在金华猪上出现。不同品种，不同位点的特定等位基因见表3。通过20个微卫星座位平均多态信息含量和平均遗传杂合度2个指标的比较，10个猪品种内遗传变异程度大小依次为海南猪、嵊县花猪、南阳黑猪、监利猪、沙子岭猪、嘉兴黑猪、淮南黑猪、东山猪、赣西两头乌、金华猪。从平均有效等位基因数的比较来看，10个猪品种内遗传变异程度大小依次为海南猪、嵊县花猪、南阳黑猪、沙子岭猪、嘉兴黑猪、淮南黑猪、监利猪、东山猪、赣西两头乌、金华猪。群体间遗传分化系数(GST)和固定指数
华中月犯月七，悦月卜祠民吐月仑大
(F sT)表明，10个猪品种的遗传变异大部分(约78%)存在于品种内，只有少部分
(约22%)存在于品种间。由Nei(1972)氏标准遗传距离，和DA遗传距离
(Nei 1 983)，以及在此基础上绘制出NJ聚类图和UPGMA聚类图来看，10个地方猪
品种的遗传关系与我国猪种类型划分基本一致，但也略有不同，同属于华中两头乌的
4个品种监利猪、东山猪’、赣西两头乌和沙子岭猪以及浙江金华猪在NJ聚类图和
UPGMA聚类图上，聚成一类，其它5个品种聚成一类，是符合实际情况的，从小的分
枝来看，嵘县花猪和南阳黑猪，淮南猪和海南猪的遗传距离最近，分别聚成一类，似
乎有点让人难以置信，，因此本研究对其分化时间进行推算，发现以上4个猪品种的分
化时间大约在620一630年前，即公元1372一1382年，而中国历史上，这段时期正是明
朝洪武年间，内地民族大迁徙的时期，在明政府的高压下，中原地带(即河南、山
西、河北等地)向沿海大搬迁，因此推测原属猪品种的南阳黑猪、淮南猪分别和原嗓
县、海南猪品种发生了基因交流。但是要提高此推测的可靠性还需其他的旁证相佐，
例如可以把以上地方品种的鸡，狗，鸭，猫或牛同样做亲缘关系的分析，观察上述品
种是否出现一到两个类似的结果。本研究结果提示，仅依据地理分布、生产性能和外
貌特征等分类，并不能完全反映各个品种间的遗传关系和彼此遗传本质的差异。猪品
种的亲缘关系和分化时间在某种程度也反映了人类历史的变迁。
To study the genetic diversity of Chinese indigenous pig breeds, a total of 403 pigs from 10 local populations and 1 exotic Duroc breed were genotyped for 20 microsatellite markers. Heterozygosity and Wright's F-statistics (FIS, FST, and FIT were calculated to determine the genetic variation in those populations. The observed heterozygosities were in the range of 0.31 (Duroc) to 0.66 (Shengxian). The FIS value was in a range of -0.07 to 0.48. The mean FST showed that approximately 78% of the genetic variation was within-population and 22% was across the populations. The 10 Chinese indigenous breeds were classified into two major groups according to the phylogenetic tree, which was based on standard genetic distance. Four pig populations, Jianli, Ganxi Two Ends Black, Shaziling, and Dongshan were grouped into one branch. Before the study, these four populations were all classified as Central China Two-Ends-Black according to coat color, shape of the head, and shape of the ear. The Jinhua pig, which also has t
he two-ends-black coat color, was also grouped to the same branch but was not traditionally classified into this type. The five populations were located in various provinces in central China. The other five populations, Nanyang Black, Hainan Spotted, Huainan Black, Jiaxing Black, and Shengxian Spotted (black body, white feet), were grouped into another branch. The two groups of pig breeds had the same FsT value (0.14) when calculated separately. This value was similar to that of Iberian pigs (0.13) but smaller than that of the European pigs (0.27) as reported by other researchers.
Our study showed that large genetic differentiation exists in Chinese pig breeds. The grouping of the five two-ends-black populations into one branch of the phylogenetic tree may indicate that the number of conservation farms can be decreased for this type of pig. China has at least a 7,000-yr history of domesticating pigs (Zhang, 1986) Over 100 pig breeds, about a third of the world's pig breeds, exist in China (Li et al., 2000a ). They were classified into six types according to their geographic origin, distribution, body conformation, and coat color: North China, Lower Changjiang Basin, Central China,South China, Southwest, and Plateau (Zhang, 1986). Each type contains a number of breeds. It will be interesting to examine the genetic relationship among local pig breeds by molecular markers such as microsatellites and to compare them to the traditional classification results. Microsatellites have been widely used for genetic variation studies in domestic animals. In the pig, genetic diversity studies of some of the commercial breeds and the Chinese Meishan breed were conducted by genotyping multiple microsatellite loci (Johansson et al., 1992; Fredholm et al., 1993 ; Paszek et al., 1998a ,b ), and the results showed that the Meishan has a significantly higher mean heterozygosity than the Western breeds (Yorkshire, Hampshire, Duroc, Landrace), as observed at several microsatellite loci (Paszek et al., 1998b ). Genetic diversity of some Chinese local breeds investigated by using microsatellites suggested a higher (Li et al., 2000b ) or similar (Fan et al., 2002 ) genetic differentiation among breeds compared with that of Belgian, exotic breeds (British Larger White, Yorkshire, Hampshire), and European breeds (van Zeveren et al., 1995 ; Kacirek et al., 1998 ; Laval et al., 2000 ; Martinez et al.,
2000 ). In this study, we used 20 pairs of microsatellite primers to detect the genetic relationship between 10 local pig populations and to compare two breed-classification methods based on traditional methods or microsatellites.
华中月犯月七，悦月卜祠民吐月仑大
(F sT)表明，10个猪品种的遗传变异大部分(约78%)存在于品种内，只有少部分
(约22%)存在于品种间。由Nei(1972)氏标准遗传距离，和DA遗传距离
(Nei 1 983)，以及在此基础上绘制出NJ聚类图和UPGMA聚类图来看，10个地方猪
品种的遗传关系与我国猪种类型划分基本一致，但也略有不同，同属于华中两头乌的
4个品种监利猪、东山猪’、赣西两头乌和沙子岭猪以及浙江金华猪在NJ聚类图和
UPGMA聚类图上，聚成一类，其它5个品种聚成一类，是符合实际情况的，从小的分
枝来看，嵘县花猪和南阳黑猪，淮南猪和海南猪的遗传距离最近，分别聚成一类，似
乎有点让人难以置信，，因此本研究对其分化时间进行推算，发现以上4个猪品种的分
化时间大约在620一630年前，即公元1372一1382年，而中国历史上，这段时期正是明
朝洪武年间，内地民族大迁徙的时期，在明政府的高压下，中原地带(即河南、山
西、河北等地)向沿海大搬迁，因此推测原属猪品种的南阳黑猪、淮南猪分别和原嗓
县、海南猪品种发生了基因交流。但是要提高此推测的可靠性还需其他的旁证相佐，
例如可以把以上地方品种的鸡，狗，鸭，猫或牛同样做亲缘关系的分析，观察上述品
种是否出现一到两个类似的结果。本研究结果提示，仅依据地理分布、生产性能和外
貌特征等分类，并不能完全反映各个品种间的遗传关系和彼此遗传本质的差异。猪品
种的亲缘关系和分化时间在某种程度也反映了人类历史的变迁。
To study the genetic diversity of Chinese indigenous pig breeds, a total of 403 pigs from 10 local populations and 1 exotic Duroc breed were genotyped for 20 microsatellite markers. Heterozygosity and Wright's F-statistics (FIS, FST, and FIT were calculated to determine the genetic variation in those populations. The observed heterozygosities were in the range of 0.31 (Duroc) to 0.66 (Shengxian). The FIS value was in a range of -0.07 to 0.48. The mean FST showed that approximately 78% of the genetic variation was within-population and 22% was across the populations. The 10 Chinese indigenous breeds were classified into two major groups according to the phylogenetic tree, which was based on standard genetic distance. Four pig populations, Jianli, Ganxi Two Ends Black, Shaziling, and Dongshan were grouped into one branch. Before the study, these four populations were all classified as Central China Two-Ends-Black according to coat color, shape of the head, and shape of the ear. The Jinhua pig, which also has t
he two-ends-black coat color, was also grouped to the same branch but was not traditionally classified into this type. The five populations were located in various provinces in central China. The other five populations, Nanyang Black, Hainan Spotted, Huainan Black, Jiaxing Black, and Shengxian Spotted (black body, white feet), were grouped into another branch. The two groups of pig breeds had the same FsT value (0.14) when calculated separately. This value was similar to that of Iberian pigs (0.13) but smaller than that of the European pigs (0.27) as reported by other researchers.
Our study showed that large genetic differentiation exists in Chinese pig breeds. The grouping of the five two-ends-black populations into one branch of the phylogenetic tree may indicate that the number of conservation farms can be decreased for this type of pig. China has at least a 7,000-yr history of domesticating pigs (Zhang, 1986) Over 100 pig breeds, about a third of the world's pig breeds, exist in China (Li et al., 2000a ). They were classified into six types according to their geographic origin, distribution, body conformation, and coat color: North China, Lower Changjiang Basin, Central China,South China, Southwest, and Plateau (Zhang, 1986). Each type contains a number of breeds. It will be interesting to examine the genetic relationship among local pig breeds by molecular markers such as microsatellites and to compare them to the traditional classification results. Microsatellites have been widely used for genetic variation studies in domestic animals. In the pig, genetic diversity studies of some of the commercial breeds and the Chinese Meishan breed were conducted by genotyping multiple microsatellite loci (Johansson et al., 1992; Fredholm et al., 1993 ; Paszek et al., 1998a ,b ), and the results showed that the Meishan has a significantly higher mean heterozygosity than the Western breeds (Yorkshire, Hampshire, Duroc, Landrace), as observed at several microsatellite loci (Paszek et al., 1998b ). Genetic diversity of some Chinese local breeds investigated by using microsatellites suggested a higher (Li et al., 2000b ) or similar (Fan et al., 2002 ) genetic differentiation among breeds compared with that of Belgian, exotic breeds (British Larger White, Yorkshire, Hampshire), and European breeds (van Zeveren et al., 1995 ; Kacirek et al., 1998 ; Laval et al., 2000 ; Martinez et al.,
2000 ). In this study, we used 20 pairs of microsatellite primers to detect the genetic relationship between 10 local pig populations and to compare two breed-classification methods based on traditional methods or microsatellites.
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Mo D.L,B.Liu,Z.G.Wang,S.H.Zhao,M.Yu,B,Fan, M.H.Li,S.L.Yang, G.X.Zhang,T.A.Xiong and K.Li*.Genetic variation and relationship of seventeen Chinese indigenous pig breeds using ten serum protein loci. Asian-Australasian Journal of Animal Sciences, 2003,17(1):939-944.
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YANG J., J. WANG, J. KIJAS, B. LIU, H. HAN, M. YU, H. YANG, S. ZHAO, AND K. LI*, Genetic Diversity Present Within the Near-Complete mtDNA Genome of 17 Breeds of Indigenous Chinese Pigs, Journal of Heredity, 2003:94(5):381-385
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Mo D.L,B.Liu,Z.G.Wang,S.H.Zhao,M.Yu,B,Fan, M.H.Li,S.L.Yang, G.X.Zhang,T.A.Xiong and K.Li*.Genetic variation and relationship of seventeen Chinese indigenous pig breeds using ten serum protein loci. Asian-Australasian Journal of Animal Sciences, 2003,17(1):939-944.
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Schook. Evaluating evolutionary divergence with microsatellites. J Mol Evol, 1998a,46(1):121-126.
Paszek, A. A., G. H. Flickinger, L. Fontanesi, G. A. Rohrer, L. Alexander, C. W. Beattie, and L. B.
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Raymond, M., and F. Rousset. GENEPOP (Version 3.3):Population genetics software for exact tests and ecumenicism. J.Hered,1995,86(1):248-249.
Rohrer, G. A., L. A. Alexander, J. W. Keele, T. P. Smith, and C. G. Beattie. A microsatellite linkage map of the porcine genome. Genetics, 1994,136(1):231-245.
Rohrer, G. A., L. J. Alexander, Z. Hu, T. P. L. Smith, J. W. Keele, and C. W. Beattie. A
comprehensive map of the porcince genome. Genome Res, 1996, 6(1):371-391.
Rohrer, G. A., and C. W. Beattie. Cloning and Characterization of 414 polymorphic porcine microsatellites. Anita Genet, 1996,27(1):137-147.
Ruyter, D., A. J. Mverstage, J. J. van der Peel, and M. A. M. Groenen. Five porcine polymorphic microsatellite markers. Anita Genet, 1994, 25(1):53-54.
Takezaki, N., and M. Nei. Genetic distances and reconstruction of phylogenetic tree from microsatellite DNA. Genetics, 1996,144(1):389-399.
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Wintero, A. K., B. Chowdhary, and M. Fredholm. A porcine polymorhic microsatelite locus (S0076) at chromosome 13q12. Anim Genet, 1994,25(1):430-431.
Van Zeveren, A., L. Peelman, A. Van de Weghe, and Y. Bouquet. A genetic study of four Belgian pig populations by means of seven microsatellite loci. J Anita Breed Genet, 1995, 112(1): 191-204.
Wang Y. F., M. Yu, M. Yerle, B. Liu, S. H. Zhao,T. A. Xiong, B. Fan and K. Li*. Mapping of genes encoding four ATPase and three non-ATPase components of the pig 26S proteasome. Animal Genetics, 2003, 34(1): 393-395
YANG J., J. WANG, J. KIJAS, B. LIU, H. HAN, M. YU, H. YANG, S. ZHAO, AND K. LI*, Genetic Diversity Present Within the Near-Complete mtDNA Genome of 17 Breeds of Indigenous Chinese Pigs, Journal of Heredity, 2003:94(5):381-385
YANG Shu-Lin, Zhi-Gang WANG, Bang LIU, Gui-Xiang ZHANG, Shu-Hong ZHAO, Mei YU, Bin FAN, Meng-Hua LI, Tong-An XIONG, Kui LI*. Genetic variation and relationships of eighteen Chinese indigenous pig breeds.Genet Sel Evol, 2003, 35(1): 657-671
Yu M., B. Liu, M. Yerle, M. Zhu, P. Pan, B. Fan and K. Li*. Physical mapping of the rod cGMP-phosphodiesterase-subunit (PDE6G) gene to pig chromosome 12. Animal Genetics, 2003, 34(1): 76-77
Yu M., S.Zhao, M.Yerle, B.Liu, T.Xiong and K.Li*. Isolation, physical mapping and polymorphism of the porcine ferredoxin reductase (FDXR) gene. Animal Genetics, 2002,33(1): 394-395.