中国部分地方猪种微卫星DNA指纹的群体遗传学研究
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摘要
本研究利用微卫星标记技术对我国的五指山小型猪、滇南小耳猪、贵州小型香猪及其近交系、南宁巴马香猪近交系、荣昌猪、沂蒙黑猪、汉中黑猪、二花脸猪、金华猪等10地方猪品种DNA水平上的遗传多态性进行了研究，探讨了它们之间的亲缘关系、群体内的遗传变异。并首次利用微卫星标记分析估计了8个地方猪品种及2个近交群体的近交系数。结果如下：
1．10个地方猪品种间的遗传变异分析
1．1 本研究所选用的10个微卫星位点，除S0003位点在7个群体中表现为单态，Sw790为中度多态位点外，其它的8个位点均为高度多态位点。在10个微卫星位点上共检测到了153个等位基因，其中Sw769最多为23个，S0003位点最少为5个，平均每个位点的等位基因数为15.3个。IGF-1位点的197bp、Sw769的148bp可作为巴马香猪区别于其它群体的特征性条带；S0005位点的281bp、285bp可作为荣昌猪和滇南小耳猪的特征性条带。
1．2 Hardy-Weinberg检验表明：在Sw781位点上，除巴马香猪表现为单态(x1值等于0)外，其余群体都处于遗传不平衡状态；IGF-1位点上，滇南小耳猪、二花脸猪、金华猪和沂蒙黑猪处于平衡状态，其它均处于遗传不平衡状态。
1．3 10个群体的平均位点杂合度在0.4561～0.6446之间；平均多态信息含量亦较高，在0.4241～0.6184之间，平均有效等位基因数在0.2495～3.7573之间，这表明中国地方猪种的遗传多样性比较高。
1．4 根据Nei氏标准遗传距离绘制了NJ和UPGMA两种聚类图。NJ聚类结果将本研究10个群体分为3个类群：贵州小型香猪及其近交系、滇南小耳猪和五指山小型猪为一个类群；沂蒙黑猪、汉中黑猪和荣昌猪为一个类群；二花脸猪、金华猪和巴马香猪为一个类群。而UPGMA聚类结果则将这10个猪种分为4个类群：贵州小型香猪及其近交系、五指山小型猪、二花脸猪和滇南小耳猪为一类群；汉中黑猪、沂蒙黑猪和荣昌猪为一类群；金华猪和巴马香猪各为一个类群。根据Cavalli—Sforza和Edwards余弦距离所得的NJ聚类结果将这10个群体分为4个类群：贵州小型香猪及其近交系和荣昌猪为一个类群；二花脸猪、金华猪和巴马香猪为一类群；沂蒙黑猪和汉中黑猪为一类群；五指山小型猪与滇南小耳猪为一类群。而UPGMA聚类结果则将这10个猪种进一步划分为5个类群：五指山小型猪、沂蒙黑猪、贵州小型香猪及其
近交系、荣昌猪和二花脸猪为一个大的类群；汉中黑猪、滇南小耳猪、金华猪和巴马
香猪各为一个独立的类群。通过对2种遗传距离所得的4个聚类结果的比较分析发现：
运用Net氏标准遗传距离所得的NJ聚类结果比其它的分类方法更为准确。由Net氏
标准遗传距离而来的NJ聚类结果中，除巴马香猪外，其它的地方猪品种与它们的地
理分布以及根据生产性能、外型特征及血液蛋白所得而来的分类结果基本一致。巴马
香猪的分类结果与地理分布的差异，可能是由于它的近交培育造成的。
2．10个地方猪种的群体近交分析
ZI 随机交配群体的近交系数都比较低，贵州小型香猪的最高，为0．1992，荣昌猪的
最低，为0刀727。小型猪群体内的近交程度较其它5个地方猪种的高，但F检验表明：
各个品种间近交系数的差异不显著卜0刀5人
2，2贵州小型香猪近交系和巴马香猪近交系的近交系数分别为0．5907和0．4761，这表
明两近交系的近交程度较高。
The genetic diversity of the Chinese local pig varieties (ie: Wu zhishan miniature pig, Diannan xiaoer, Guizhou miniature pig and its inbreeding strain, Bama miniature pig of inbreeding strain, Rongchang, Yimenghei, Hanzhonghei, Erhualian and Jinhua) were analyzed by microsatellite marker. The genetic relationship and the inbreeding coefficient on 10 populations (including 8 nature populations and 2 inbreeding populations) were analyzed and evaluated for the first time. The results were showed that:
1. The analysis of the genetic variation on 10 local pig populations
1.1 8 of 10 microsatellite loci were high diversity except that S0003 locus was single in the 7 populations, and Sw790 was medium. It was found that the 10 microsatellite loci had 153 allelic. Sw769 had the great number (23 allelic) among the 10 microsatellite loci, S0003 was the fewest (5 allelic), and the average allelic of each locus was 15.3. 198bp band of IGF-1, 148bp of Sw769 could be seen as the characteristic bands of Bama miniature pig, 281bp and 148bp of S0005 as the characteristic bands of Rongchang and Diannan xiaoer.
1.2 Hardy-Weinberg equilibrium test showed that: all the breeds were not in genetic equilibrium except for Bama miniature pig in Sw781 locus, and Diannan xiaoer, Erhualian, Jinhua and Yimenghei were in genetic equilibrium in IGF-1 but not others.
1.3 The locus average heterozygosity was between 0.4561 and 0.6184 of the 10 populations, and average polymorphism information content between 0.4241 and 0.6184, and the average effective numbers of allelic between 0.2495 and 3.7573. All these indicated that the genetic diversity of Chinese local pigs was higher.
1.4 The 10 breeds were divided into 3 clusters by NJ phylogenetic from Nei' s genetic distance. The first cluster was Guizhou miniature pig and its inbreeding lines, Diannan xiaoer and Wuzhishan miniature pig. The second Yimenghei, Hanzhonghei and Rongchang. The third Erhualia, Jinhuan and Bama miniature pig. But 4 clusters were divided by UPGMA phylogenetic from Nei's genetic distance. The first was Hanzhonghei and its inbreeding strain, Wuzhishan miniature pig, Erhualian and Diannan xiaoer. The second
Hanzhonghei, Yimenghei and Rongchang. The third Jinhua and the forth Bama miniature pig. And 4 clusters were divided NJ phylogenetic from Cavalli-Sforza and Edwards genetic distance. Firstly, Guizhou miniature pig and its inbreeding line and Rongchang. Secondly, Erhualian, Jinhua and Bama miniature pig. Thirdly, Hanzhonghei and Yimenghei. Fourthly, Wuzhishan miniature pig and Diannan xiaoer. UPGMA phylogenetic from the second distance was that: The first cluster was Wuzhishan miniature pig, Yimenghei, Guizhou miniature pig and its inbreeding strain, Rongchang and Erhualian. Hanzhonghei, Diannan xiaoer, Jinhua and Bama miniature pig belonged to a cluster respectively. The results from 2 different distances were compared that the NJ phylogenetic from Nei's genetic distance was more accurate than any other results. The result was agreed with the before results from productivity, phenotype and blood protein. Bama miniature pig didn't accord with its geography distribution. Perhaps the difference was caused by its inbreeding cultivation.
2. Inbreeding analysis of 10 breeds
2.1 The inbreeding coefficients of the random mating populations were lower. That of Guizhou miniature pig was the highest (0.1992) in the 8 breeds, and Rongchang the lowest (0.0727). The inbreeding degree of miniature pigs was higher than other 5 local pigs. F test showed that the inbreeding coefficient difference was not significant in each breeds.
2.2 The inbreeding coefficient of the Guizhou miniature pig and Bama miniature pig inbreeding lines was 0.5907 and 0.4761 respectively. It indicated that the inbreeding degree of 2 inbreeding lines was higher.
1．10个地方猪品种间的遗传变异分析
1．1 本研究所选用的10个微卫星位点，除S0003位点在7个群体中表现为单态，Sw790为中度多态位点外，其它的8个位点均为高度多态位点。在10个微卫星位点上共检测到了153个等位基因，其中Sw769最多为23个，S0003位点最少为5个，平均每个位点的等位基因数为15.3个。IGF-1位点的197bp、Sw769的148bp可作为巴马香猪区别于其它群体的特征性条带；S0005位点的281bp、285bp可作为荣昌猪和滇南小耳猪的特征性条带。
1．2 Hardy-Weinberg检验表明：在Sw781位点上，除巴马香猪表现为单态(x1值等于0)外，其余群体都处于遗传不平衡状态；IGF-1位点上，滇南小耳猪、二花脸猪、金华猪和沂蒙黑猪处于平衡状态，其它均处于遗传不平衡状态。
1．3 10个群体的平均位点杂合度在0.4561～0.6446之间；平均多态信息含量亦较高，在0.4241～0.6184之间，平均有效等位基因数在0.2495～3.7573之间，这表明中国地方猪种的遗传多样性比较高。
1．4 根据Nei氏标准遗传距离绘制了NJ和UPGMA两种聚类图。NJ聚类结果将本研究10个群体分为3个类群：贵州小型香猪及其近交系、滇南小耳猪和五指山小型猪为一个类群；沂蒙黑猪、汉中黑猪和荣昌猪为一个类群；二花脸猪、金华猪和巴马香猪为一个类群。而UPGMA聚类结果则将这10个猪种分为4个类群：贵州小型香猪及其近交系、五指山小型猪、二花脸猪和滇南小耳猪为一类群；汉中黑猪、沂蒙黑猪和荣昌猪为一类群；金华猪和巴马香猪各为一个类群。根据Cavalli—Sforza和Edwards余弦距离所得的NJ聚类结果将这10个群体分为4个类群：贵州小型香猪及其近交系和荣昌猪为一个类群；二花脸猪、金华猪和巴马香猪为一类群；沂蒙黑猪和汉中黑猪为一类群；五指山小型猪与滇南小耳猪为一类群。而UPGMA聚类结果则将这10个猪种进一步划分为5个类群：五指山小型猪、沂蒙黑猪、贵州小型香猪及其
近交系、荣昌猪和二花脸猪为一个大的类群；汉中黑猪、滇南小耳猪、金华猪和巴马
香猪各为一个独立的类群。通过对2种遗传距离所得的4个聚类结果的比较分析发现：
运用Net氏标准遗传距离所得的NJ聚类结果比其它的分类方法更为准确。由Net氏
标准遗传距离而来的NJ聚类结果中，除巴马香猪外，其它的地方猪品种与它们的地
理分布以及根据生产性能、外型特征及血液蛋白所得而来的分类结果基本一致。巴马
香猪的分类结果与地理分布的差异，可能是由于它的近交培育造成的。
2．10个地方猪种的群体近交分析
ZI 随机交配群体的近交系数都比较低，贵州小型香猪的最高，为0．1992，荣昌猪的
最低，为0刀727。小型猪群体内的近交程度较其它5个地方猪种的高，但F检验表明：
各个品种间近交系数的差异不显著卜0刀5人
2，2贵州小型香猪近交系和巴马香猪近交系的近交系数分别为0．5907和0．4761，这表
明两近交系的近交程度较高。
The genetic diversity of the Chinese local pig varieties (ie: Wu zhishan miniature pig, Diannan xiaoer, Guizhou miniature pig and its inbreeding strain, Bama miniature pig of inbreeding strain, Rongchang, Yimenghei, Hanzhonghei, Erhualian and Jinhua) were analyzed by microsatellite marker. The genetic relationship and the inbreeding coefficient on 10 populations (including 8 nature populations and 2 inbreeding populations) were analyzed and evaluated for the first time. The results were showed that:
1. The analysis of the genetic variation on 10 local pig populations
1.1 8 of 10 microsatellite loci were high diversity except that S0003 locus was single in the 7 populations, and Sw790 was medium. It was found that the 10 microsatellite loci had 153 allelic. Sw769 had the great number (23 allelic) among the 10 microsatellite loci, S0003 was the fewest (5 allelic), and the average allelic of each locus was 15.3. 198bp band of IGF-1, 148bp of Sw769 could be seen as the characteristic bands of Bama miniature pig, 281bp and 148bp of S0005 as the characteristic bands of Rongchang and Diannan xiaoer.
1.2 Hardy-Weinberg equilibrium test showed that: all the breeds were not in genetic equilibrium except for Bama miniature pig in Sw781 locus, and Diannan xiaoer, Erhualian, Jinhua and Yimenghei were in genetic equilibrium in IGF-1 but not others.
1.3 The locus average heterozygosity was between 0.4561 and 0.6184 of the 10 populations, and average polymorphism information content between 0.4241 and 0.6184, and the average effective numbers of allelic between 0.2495 and 3.7573. All these indicated that the genetic diversity of Chinese local pigs was higher.
1.4 The 10 breeds were divided into 3 clusters by NJ phylogenetic from Nei' s genetic distance. The first cluster was Guizhou miniature pig and its inbreeding lines, Diannan xiaoer and Wuzhishan miniature pig. The second Yimenghei, Hanzhonghei and Rongchang. The third Erhualia, Jinhuan and Bama miniature pig. But 4 clusters were divided by UPGMA phylogenetic from Nei's genetic distance. The first was Hanzhonghei and its inbreeding strain, Wuzhishan miniature pig, Erhualian and Diannan xiaoer. The second
Hanzhonghei, Yimenghei and Rongchang. The third Jinhua and the forth Bama miniature pig. And 4 clusters were divided NJ phylogenetic from Cavalli-Sforza and Edwards genetic distance. Firstly, Guizhou miniature pig and its inbreeding line and Rongchang. Secondly, Erhualian, Jinhua and Bama miniature pig. Thirdly, Hanzhonghei and Yimenghei. Fourthly, Wuzhishan miniature pig and Diannan xiaoer. UPGMA phylogenetic from the second distance was that: The first cluster was Wuzhishan miniature pig, Yimenghei, Guizhou miniature pig and its inbreeding strain, Rongchang and Erhualian. Hanzhonghei, Diannan xiaoer, Jinhua and Bama miniature pig belonged to a cluster respectively. The results from 2 different distances were compared that the NJ phylogenetic from Nei's genetic distance was more accurate than any other results. The result was agreed with the before results from productivity, phenotype and blood protein. Bama miniature pig didn't accord with its geography distribution. Perhaps the difference was caused by its inbreeding cultivation.
2. Inbreeding analysis of 10 breeds
2.1 The inbreeding coefficients of the random mating populations were lower. That of Guizhou miniature pig was the highest (0.1992) in the 8 breeds, and Rongchang the lowest (0.0727). The inbreeding degree of miniature pigs was higher than other 5 local pigs. F test showed that the inbreeding coefficient difference was not significant in each breeds.
2.2 The inbreeding coefficient of the Guizhou miniature pig and Bama miniature pig inbreeding lines was 0.5907 and 0.4761 respectively. It indicated that the inbreeding degree of 2 inbreeding lines was higher.
引文
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