金华猪群体遗传结构及其起源和驯化的研究
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摘要
本文利用微卫星标记结合荧光标记检测技术,对金华猪三个品系：金华猪Ⅰ系173头,金华猪Ⅱ系42头,金华猪Ⅲ系56头共271头以及本省猪种嵊县花猪,嘉兴黑猪、外省猪种梅山猪、二花脸猪和外国猪种长白猪共180头的65个微卫星位点进行了检测,根据试验结果对金华猪群体的遗传结构,品系间遗传关系以及金华猪与这几个猪种的遗传分化进行了分析,并结合已公布的相关研究结果计算了金华猪与其它国内外猪种间的遗传距离。
本研究在金华猪3个品系共271个个体的65个卫星座位上共检测到1260个等位基因。平均有效等位基因数是金华猪Ⅰ系最高：Ne=3.49,其次是金华猪Ⅱ系：Ne=2.81和金华猪Ⅲ系：Ne=2.49。金华猪3个品系的平均多态信息含量均高于0.5,其中Ⅱ系最低,为0.5135；最高是Ⅲ系,为0.5862,Ⅰ系居中,为0.5135。金华猪群体各亚群的平均杂合度分别是Ⅰ系为0.3811,Ⅱ系为0.3992,Ⅲ系为0.4415。通过哈迪。温伯格检验,金华猪3个品系趋于哈迪-温伯格平衡的程度不一：金华猪Ⅰ偏离较大,Ⅲ系其次,Ⅱ系偏离相对较小。遗传分化结果显示金华猪Ⅱ系和Ⅲ系群体间遗传分化相对较小(F=0.1883),这两个品系与Ⅰ系间的遗传分化较大F值分别是0.3663和0.3619。金华猪各系与嵊县花猪群体的遗传分化最大,F值分别为0.4499,0.4654和0.4801,与中梅群体遗传分化相对较小,F值分别为0.3581,0.356和0.3572。金华猪与国外猪种(大白除外)遗传距离比较远,其中与金华猪Ⅰ系遗传距离最近的是香猪(Da=1.2106)和大白猪(Da=1.1322)。由以上结果可见金华猪群体中存在着一定的近交积累,品系之间有等位基因丢失的情况,并且群体中可能还受到了遗传漂变的影响。我们还对微卫星位点IGF1与金华猪的生产性能进行了相关性分析,分析结果表明,该微卫星位点可做为标记辅助选择的分子标记,286／286基因型对金华猪初生重有显著影响(P<0.05)；280／286基因型对金华猪开产后出生窝重影响显著(P<0.05),进一步通过等位基因平均替代效应分析发现274 bp和286 bp等位基因有利于提高初生重,280 bp等位基因有利于第二胎出生窝重的提高。同时通过相关性分析发现金华猪开产母猪出生窝重、总产仔数和产活仔数间的相关性极显著(P<0.01),因此出生窝重的增加有利于提高金华猪的产仔性能。另外我们还利用辐射杂种细胞系把一肉质候选基因SIM1定位于猪1号染色体短臂13亚区上的微卫星位点SW781和SW301附近。
本文还利用线粒体DNA的D-loop区序列作为分子标记分析了包括金华猪在内的中国地方品种68个,国外猪种24个共92个猪种单倍型构成,分布和进化关系,从母系的角度研究了中国猪种的起源和进化以探明金华猪的起源与驯化过程。
通过测序获得了68个中国地方猪种的线粒体D-loop区序列。统计分析表明,中国地方猪种线粒体遗传变异性丰富,共检测到66个单倍型。利用Mega,NETWORK等软件通过系统发生树和单倍型网络结构两个角度对中国地方猪种和国外猪种进行了分析。结合来自考古学、微卫星和Y染色体的证据,从母系遗传角度推测：1、中国猪种与欧洲猪种有着同一的母系祖先。2、中国家猪起源南北有别,黄河是中国家猪起源的分界线,北方猪种起源于东北野猪,南方猪种可能起源于浙江野猪。3、长江中下游流域是中国猪种驯化比较集中的区域,并且存在着较大的两个驯化中心,其驯化过程中经历了多个层次。浙江和江西省可能是中国家猪最大的驯化中心和南方猪种的起源地。4、金华猪品系的起源不同,驯化过程也不同,在中国地方品种中金华猪Ⅱ系拥有较为古老的母系血统,金华猪Ⅰ系和Ⅲ系处在一个驯化中心内。5、通过系统发生树和单倍型网络结构结果推测由微卫星结果证明的金华猪品系间等位基因丢失情况实际上是由于金华猪不同的驯化过程导致的。
In this paper, we have detected the genotypes of 65 microsatellite loci by the fluorescent primers in Jinhua subpopulations:LineⅠ,LineⅡ, LineⅢand Jiaxing, Shengxian, Meishan, Erhualian and Landrace.Base on the genotype, we analyzed the genetic structure of Jinhua subpopulation and genetic diversity among Jinhua pig as well as the other breeds.Moreover we calculated the genetic distance among Jinhua and other breeds.
There are 1260 alleles on the 65 loci of Jinhua 271 samples of 3 populations.In Jinhua population, Line I has the highest average number of effective allele (Ne=3.49), LineⅡ(Ne-2.81) and LineⅢ(Ne=2.49).The average of polymorphism information content (PIC) in each subpopulation is above 0.5,LineⅢhas the highest value:PIC=0.586, followed by Line I PIC=0.558 and LineⅡPIC=0.514.On the average heterozygosis, LineⅠis 0.3811,LineⅡis 0.3992 and LineⅢis 0.4415.By the Hardy-Weinberg equilibrium test, LineⅠdeviates from it more and behinded is LineⅢ,LineⅡdeviates from it less.The genetic differentiation shows that the differentiation between Jinhua LineⅢand LineⅡis small (F=0.1883),both of them with Jinhua LineⅠhas a big F values (0.3663,0.3619 respectively).The genetic differentiation of all Jinhua subpopulations with Shengxian pig is the highest (F=0.4499,0.4654 and 0.4801 respectively), and with medium Meishan pig is the least (F=0.3581,0.356 and 0.3572 respectively).The genetic distance between Jinhua pig and others show that Jinhua pig far away from abroad breeds except Large white and Jinhua line I has a closed genetic distance with Xiang (Da=1.2106) and Large white breeds (Da=1.1322).Above all,there is some degree of inbred accumulation and many alleles are losted in Jinhua subpopulations, furthermore,all subpopulations were affected by genetic drift. We also analysed the effect of microsatellite IGF1 on growth traits in Jinhua pig. Significant effect was found for microsatellite locus IGF1 genotype on BW (P<0.05),with positive effects associated with the 286/286 genotype, and 280/286 genotype on LWB in second parity (P<0.05). Furthermore, according to analysis of allele average substitution effect, alleles 274bp and 286bp was favourable for BW increase, allele 280bp was favourable for LWB increase in the second parity.By correlation analysis, total number of birth, number of birth alive and LWB of the second parity in jinhua pig had highly significant correlation(P<0.01), therefore increasing LWB of the second parity could improve litter performance of Jinhua pig. Therefore, microsatellite could be a useful MAS molecular marker for Jinhua pig breeding. And we mapping a meat quality candidate gene SIM1 with SW781 and SW301 By IMpRH panel to chromosome 1p13 in porcine.
In addition, mtDNA D-loop sequence was used as molecular marker to analyze the phylogenetic relationship, construction and distribution of haplotypes on 92 breeds that including 68 samples of Chinese domestic pigs, in order to understand the origin and domestication of Chinese pigs from matrilineal and also the evolution of Jinhua pig.
Complete mitochondrial DNA D-loop sequences were determined for 68 Chinese pigs.Comparisons of these sequences revealed 66 haplotypes.We combined the phylogenetic analyses results from software Mega and NETWORK of Chinese domestic breeds with history of archaeology, microsatellite and Y chromosome evidences,from matrilineal we suppose that:1.Chinese pigs and Europwan pigs have a common maternal ancestor.2.It is different on origin between north and south of Chinese breeds,Yellow River is a boundary and north breeds origin from wild boar in northeast China, south breeds origin from Zhejiang wild boar, probably.There is a domestication aggregation area in the Yangtze River mid-downstream drainage basin, and it has two domestication centres, which have mutil-level.Zhejiang and Jiangxi provinces may be the biggest domestication centres of Chinese breeds and the origin of south pigs.4.Jinhua subpopultions have different origin and domestic history, LineⅡhas ancient maternal pedigree moreover LineⅠand LineⅢin the same domestication centra.5.Base on the results of phylogenetic relation and haploid net structure, we believe that the reason of many alleles are losted in Jinhua subpopulations is Jinhua subpopulations have different domestic history.
本研究在金华猪3个品系共271个个体的65个卫星座位上共检测到1260个等位基因。平均有效等位基因数是金华猪Ⅰ系最高：Ne=3.49,其次是金华猪Ⅱ系：Ne=2.81和金华猪Ⅲ系：Ne=2.49。金华猪3个品系的平均多态信息含量均高于0.5,其中Ⅱ系最低,为0.5135；最高是Ⅲ系,为0.5862,Ⅰ系居中,为0.5135。金华猪群体各亚群的平均杂合度分别是Ⅰ系为0.3811,Ⅱ系为0.3992,Ⅲ系为0.4415。通过哈迪。温伯格检验,金华猪3个品系趋于哈迪-温伯格平衡的程度不一：金华猪Ⅰ偏离较大,Ⅲ系其次,Ⅱ系偏离相对较小。遗传分化结果显示金华猪Ⅱ系和Ⅲ系群体间遗传分化相对较小(F=0.1883),这两个品系与Ⅰ系间的遗传分化较大F值分别是0.3663和0.3619。金华猪各系与嵊县花猪群体的遗传分化最大,F值分别为0.4499,0.4654和0.4801,与中梅群体遗传分化相对较小,F值分别为0.3581,0.356和0.3572。金华猪与国外猪种(大白除外)遗传距离比较远,其中与金华猪Ⅰ系遗传距离最近的是香猪(Da=1.2106)和大白猪(Da=1.1322)。由以上结果可见金华猪群体中存在着一定的近交积累,品系之间有等位基因丢失的情况,并且群体中可能还受到了遗传漂变的影响。我们还对微卫星位点IGF1与金华猪的生产性能进行了相关性分析,分析结果表明,该微卫星位点可做为标记辅助选择的分子标记,286／286基因型对金华猪初生重有显著影响(P<0.05)；280／286基因型对金华猪开产后出生窝重影响显著(P<0.05),进一步通过等位基因平均替代效应分析发现274 bp和286 bp等位基因有利于提高初生重,280 bp等位基因有利于第二胎出生窝重的提高。同时通过相关性分析发现金华猪开产母猪出生窝重、总产仔数和产活仔数间的相关性极显著(P<0.01),因此出生窝重的增加有利于提高金华猪的产仔性能。另外我们还利用辐射杂种细胞系把一肉质候选基因SIM1定位于猪1号染色体短臂13亚区上的微卫星位点SW781和SW301附近。
本文还利用线粒体DNA的D-loop区序列作为分子标记分析了包括金华猪在内的中国地方品种68个,国外猪种24个共92个猪种单倍型构成,分布和进化关系,从母系的角度研究了中国猪种的起源和进化以探明金华猪的起源与驯化过程。
通过测序获得了68个中国地方猪种的线粒体D-loop区序列。统计分析表明,中国地方猪种线粒体遗传变异性丰富,共检测到66个单倍型。利用Mega,NETWORK等软件通过系统发生树和单倍型网络结构两个角度对中国地方猪种和国外猪种进行了分析。结合来自考古学、微卫星和Y染色体的证据,从母系遗传角度推测：1、中国猪种与欧洲猪种有着同一的母系祖先。2、中国家猪起源南北有别,黄河是中国家猪起源的分界线,北方猪种起源于东北野猪,南方猪种可能起源于浙江野猪。3、长江中下游流域是中国猪种驯化比较集中的区域,并且存在着较大的两个驯化中心,其驯化过程中经历了多个层次。浙江和江西省可能是中国家猪最大的驯化中心和南方猪种的起源地。4、金华猪品系的起源不同,驯化过程也不同,在中国地方品种中金华猪Ⅱ系拥有较为古老的母系血统,金华猪Ⅰ系和Ⅲ系处在一个驯化中心内。5、通过系统发生树和单倍型网络结构结果推测由微卫星结果证明的金华猪品系间等位基因丢失情况实际上是由于金华猪不同的驯化过程导致的。
In this paper, we have detected the genotypes of 65 microsatellite loci by the fluorescent primers in Jinhua subpopulations:LineⅠ,LineⅡ, LineⅢand Jiaxing, Shengxian, Meishan, Erhualian and Landrace.Base on the genotype, we analyzed the genetic structure of Jinhua subpopulation and genetic diversity among Jinhua pig as well as the other breeds.Moreover we calculated the genetic distance among Jinhua and other breeds.
There are 1260 alleles on the 65 loci of Jinhua 271 samples of 3 populations.In Jinhua population, Line I has the highest average number of effective allele (Ne=3.49), LineⅡ(Ne-2.81) and LineⅢ(Ne=2.49).The average of polymorphism information content (PIC) in each subpopulation is above 0.5,LineⅢhas the highest value:PIC=0.586, followed by Line I PIC=0.558 and LineⅡPIC=0.514.On the average heterozygosis, LineⅠis 0.3811,LineⅡis 0.3992 and LineⅢis 0.4415.By the Hardy-Weinberg equilibrium test, LineⅠdeviates from it more and behinded is LineⅢ,LineⅡdeviates from it less.The genetic differentiation shows that the differentiation between Jinhua LineⅢand LineⅡis small (F=0.1883),both of them with Jinhua LineⅠhas a big F values (0.3663,0.3619 respectively).The genetic differentiation of all Jinhua subpopulations with Shengxian pig is the highest (F=0.4499,0.4654 and 0.4801 respectively), and with medium Meishan pig is the least (F=0.3581,0.356 and 0.3572 respectively).The genetic distance between Jinhua pig and others show that Jinhua pig far away from abroad breeds except Large white and Jinhua line I has a closed genetic distance with Xiang (Da=1.2106) and Large white breeds (Da=1.1322).Above all,there is some degree of inbred accumulation and many alleles are losted in Jinhua subpopulations, furthermore,all subpopulations were affected by genetic drift. We also analysed the effect of microsatellite IGF1 on growth traits in Jinhua pig. Significant effect was found for microsatellite locus IGF1 genotype on BW (P<0.05),with positive effects associated with the 286/286 genotype, and 280/286 genotype on LWB in second parity (P<0.05). Furthermore, according to analysis of allele average substitution effect, alleles 274bp and 286bp was favourable for BW increase, allele 280bp was favourable for LWB increase in the second parity.By correlation analysis, total number of birth, number of birth alive and LWB of the second parity in jinhua pig had highly significant correlation(P<0.01), therefore increasing LWB of the second parity could improve litter performance of Jinhua pig. Therefore, microsatellite could be a useful MAS molecular marker for Jinhua pig breeding. And we mapping a meat quality candidate gene SIM1 with SW781 and SW301 By IMpRH panel to chromosome 1p13 in porcine.
In addition, mtDNA D-loop sequence was used as molecular marker to analyze the phylogenetic relationship, construction and distribution of haplotypes on 92 breeds that including 68 samples of Chinese domestic pigs, in order to understand the origin and domestication of Chinese pigs from matrilineal and also the evolution of Jinhua pig.
Complete mitochondrial DNA D-loop sequences were determined for 68 Chinese pigs.Comparisons of these sequences revealed 66 haplotypes.We combined the phylogenetic analyses results from software Mega and NETWORK of Chinese domestic breeds with history of archaeology, microsatellite and Y chromosome evidences,from matrilineal we suppose that:1.Chinese pigs and Europwan pigs have a common maternal ancestor.2.It is different on origin between north and south of Chinese breeds,Yellow River is a boundary and north breeds origin from wild boar in northeast China, south breeds origin from Zhejiang wild boar, probably.There is a domestication aggregation area in the Yangtze River mid-downstream drainage basin, and it has two domestication centres, which have mutil-level.Zhejiang and Jiangxi provinces may be the biggest domestication centres of Chinese breeds and the origin of south pigs.4.Jinhua subpopultions have different origin and domestic history, LineⅡhas ancient maternal pedigree moreover LineⅠand LineⅢin the same domestication centra.5.Base on the results of phylogenetic relation and haploid net structure, we believe that the reason of many alleles are losted in Jinhua subpopulations is Jinhua subpopulations have different domestic history.
引文
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