家鸡SSR和MHC位点的进化关系及群体遗传结构分析
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摘要
DNA分子多态性为鉴定物种的遗传多样性和群体结构提供了重要信息。在研究各种家养动物的群体内遗传多样性和群体间遗传关系和结构中，微卫星DNA标记（SSR）是应用最为广泛的遗传标记之一。迄今为止，有许多研究应用这些中性基因座对来自全世界各大洲和不同生产、管理及历史背景的家鸡群体遗传多样性和群体遗传结构进行了评估和分析，发现群体遗传结构与它们的地理分布基本一致，而遗传多样性水平则与其管理背景相关。鸡主要组织相容性复合物（MHC）位于鸡16号染色体上，是基因组中最高变异区域。MHC区域编码的基因在免疫系统内起到主要作用，许多MHC基因编码的蛋白参与抗原与T细胞呈递过程。所以研究MHC区域的多样性有助于理解病原与宿主间的相互作用。目前，尽管MHC区域的受选择的性质还不清楚，但已有三种假设，如杂合优势、稀有等位基因优势和波动选择，用于解释MHC的高度遗传多样性。本研究旨在比较MHC区域多态性和常染色体微卫星体系所代表的基因组水平遗传多样性和群体结构的异同，探索MHC的进化机制，评价MHC区域的遗传多样性是否适用于研究群体的遗传关系。本研究通过对来自不同大洲、不同背景及培育历史的25个家鸡和野生原鸡群体进行研究，主要结果如下：
1.采用7个MHC微卫星基因座对500份家鸡和原鸡样品进行遗传多样性分析，在25个群体中共发现了94个等位基因，其中在基因座LEI0258、GAB0001和MHC0371上检测到的等位基因数最多，分别为43、12和12个；除了MCW0312、MHC-D和MHC-T的多态信息含量（PIC）较低外，其他各基因座的PIC均大于0.5，呈现较高的多态性；MHC基因座的期望杂合度与群体间的FST呈显著的负相关（R2=-0.9629）。
2.将MHC区域单个基因座和单倍型水平上的NA、HO和HE与29个常染色体微卫星基因座所代表的基因组水平上的遗传多样性进行比较，发现大多数群体MHC区域的遗传多样性要明显高于基因组水平；但是也有个别特殊群体相反，例如按血系B15进行定向培育的实验品系R22。
3.通过估测群体间的遗传分化，表明各大洲地方群体间在MHC区域所表现的变异要小于29个基因座所代表基因组水平上的变异；基因组水平与MHC区域的FST之间无相关性（MHClocus-wise vs29SSR, R2=0.4128; MHC haplotype vs29SSR, R2=0.3145）。
4.在群体遗传结构分析中，25个群体在基因组水平上的变异遵循着地理来源和管理历史的差异；而MHC区域的变异则没有体现出上述特征。
5.为了验证以上试验结果，本研究又开展了相关验证试验，即采用大样本量、大地理距离和管理背景差距的5个群体，深入分析MHC的群体结构特征，进一步印证了上述结果。
Molecular polymorphisms in DNA are an important source of information to characterize andclassify genetic resources. Microsatellites DNA markers have been widely used to assess geneticdiversity within and genetic relationship between populations in all major farm animal species includingchicken in the past20years. Many previous studies used this marker system in a world-wide collectionof chicken breeds originated from various continents and of different management and productionsystems. Using these markers, which are assumed to be neutral to selection, it has been shown that thebreeds cluster according to their geographic location but vary in the degree of genetic diversity independence to their breeding and management histories. The chicken major histocompatibility complex(MHC) is located on the micro-chromosome16and is described as the most variable region in thegenome. The genes of MHC play a central role in the immune system. Particularly, proteins encoded byMHC genes involved in the antigen presentation to T cells. Therefore describing the geneticpolymorphism in this region is crucial in understanding host-pathogen interaction. Although the natureof selection to MHC diversity remains unclear, three major hypotheses have been put forward, such asheterozygote advantage, negative frequency dependence (rare allele advantage) and fluctuating selection.The aim of current study is to quantify different forces that affect the evolution of MHC in chicken byassessing the relationship of MHC diversity in relation to the overall genetic clusters that wereidentified using autosomal microsatellites in chicken. In this study,25populations collected fromdifferent continents, production and management systems were genotyped and the major summary ofresults is as follows:
1. Based on seven MHC microsatellites, the genetic diversity of500individuals from domesticchicken and red Jungle fowl were assessed. Totally,94alleles were identified. The most polymorphicmarkers were LEI0258, GAB0001and MHC0371which had43,12and12observed alleles, respectively.Most of markers carried high polymorphism information content (PIC>0.5) except for MCW0312,MHC-D and MHC-T among25populations, indicating rich genetic variation at these loci. A negativecorrelation (R2=-0.9629) was observed between pairwise genetic differentiation (FST) and expectedheterozygosity (HE) at MHC loci.
2. In comparison with the genome-wide genetic diversity measured using29autosomalmicrosatellites, MHC region, either at single locus and haplotype level, showed relatively high NA, HOand HEamong most of the populations. However, exceptions were present in some unique lines, such asthe R22that was developed following the directional selection for homozygous B15serotype.
3. Pairwise genetic differentiation revealed a lower genetic variation at seven MHC loci than at29genome-wide markers between populations among the continents. There was no correlation betweenthese two sets of FSTestimates (MHC locus-wise vs29SSR, R2=0.4128; MHC haplotype vs29SSR,R2=0.3145).
4. Population genetic structuring patterns suggested a rather different evolutionary process of MHCregion compared with the alignment of geographic origin and management history to the genetic differentiation among these populations unveiled using29autosomal markers.
5. In order to verify the above observations, we chosen five populations with large number ofsamples, well separated geographic locations and unique managemental histories to analyze theirpopulation genetic structure at MHC loci. A similar picture of genetic variation was eventually obtainedto validate the major findings of this study based on various statistical tests.
1.采用7个MHC微卫星基因座对500份家鸡和原鸡样品进行遗传多样性分析，在25个群体中共发现了94个等位基因，其中在基因座LEI0258、GAB0001和MHC0371上检测到的等位基因数最多，分别为43、12和12个；除了MCW0312、MHC-D和MHC-T的多态信息含量（PIC）较低外，其他各基因座的PIC均大于0.5，呈现较高的多态性；MHC基因座的期望杂合度与群体间的FST呈显著的负相关（R2=-0.9629）。
2.将MHC区域单个基因座和单倍型水平上的NA、HO和HE与29个常染色体微卫星基因座所代表的基因组水平上的遗传多样性进行比较，发现大多数群体MHC区域的遗传多样性要明显高于基因组水平；但是也有个别特殊群体相反，例如按血系B15进行定向培育的实验品系R22。
3.通过估测群体间的遗传分化，表明各大洲地方群体间在MHC区域所表现的变异要小于29个基因座所代表基因组水平上的变异；基因组水平与MHC区域的FST之间无相关性（MHClocus-wise vs29SSR, R2=0.4128; MHC haplotype vs29SSR, R2=0.3145）。
4.在群体遗传结构分析中，25个群体在基因组水平上的变异遵循着地理来源和管理历史的差异；而MHC区域的变异则没有体现出上述特征。
5.为了验证以上试验结果，本研究又开展了相关验证试验，即采用大样本量、大地理距离和管理背景差距的5个群体，深入分析MHC的群体结构特征，进一步印证了上述结果。
Molecular polymorphisms in DNA are an important source of information to characterize andclassify genetic resources. Microsatellites DNA markers have been widely used to assess geneticdiversity within and genetic relationship between populations in all major farm animal species includingchicken in the past20years. Many previous studies used this marker system in a world-wide collectionof chicken breeds originated from various continents and of different management and productionsystems. Using these markers, which are assumed to be neutral to selection, it has been shown that thebreeds cluster according to their geographic location but vary in the degree of genetic diversity independence to their breeding and management histories. The chicken major histocompatibility complex(MHC) is located on the micro-chromosome16and is described as the most variable region in thegenome. The genes of MHC play a central role in the immune system. Particularly, proteins encoded byMHC genes involved in the antigen presentation to T cells. Therefore describing the geneticpolymorphism in this region is crucial in understanding host-pathogen interaction. Although the natureof selection to MHC diversity remains unclear, three major hypotheses have been put forward, such asheterozygote advantage, negative frequency dependence (rare allele advantage) and fluctuating selection.The aim of current study is to quantify different forces that affect the evolution of MHC in chicken byassessing the relationship of MHC diversity in relation to the overall genetic clusters that wereidentified using autosomal microsatellites in chicken. In this study,25populations collected fromdifferent continents, production and management systems were genotyped and the major summary ofresults is as follows:
1. Based on seven MHC microsatellites, the genetic diversity of500individuals from domesticchicken and red Jungle fowl were assessed. Totally,94alleles were identified. The most polymorphicmarkers were LEI0258, GAB0001and MHC0371which had43,12and12observed alleles, respectively.Most of markers carried high polymorphism information content (PIC>0.5) except for MCW0312,MHC-D and MHC-T among25populations, indicating rich genetic variation at these loci. A negativecorrelation (R2=-0.9629) was observed between pairwise genetic differentiation (FST) and expectedheterozygosity (HE) at MHC loci.
2. In comparison with the genome-wide genetic diversity measured using29autosomalmicrosatellites, MHC region, either at single locus and haplotype level, showed relatively high NA, HOand HEamong most of the populations. However, exceptions were present in some unique lines, such asthe R22that was developed following the directional selection for homozygous B15serotype.
3. Pairwise genetic differentiation revealed a lower genetic variation at seven MHC loci than at29genome-wide markers between populations among the continents. There was no correlation betweenthese two sets of FSTestimates (MHC locus-wise vs29SSR, R2=0.4128; MHC haplotype vs29SSR,R2=0.3145).
4. Population genetic structuring patterns suggested a rather different evolutionary process of MHCregion compared with the alignment of geographic origin and management history to the genetic differentiation among these populations unveiled using29autosomal markers.
5. In order to verify the above observations, we chosen five populations with large number ofsamples, well separated geographic locations and unique managemental histories to analyze theirpopulation genetic structure at MHC loci. A similar picture of genetic variation was eventually obtainedto validate the major findings of this study based on various statistical tests.
引文
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