黄颡鱼微卫星标记的开发及其遗传连锁图谱的构建
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摘要
黄颡鱼(Pelteobagrus fulvidraco Richardson)属鲶形目(Siluriformes)、鲿科(Bagridae)、黄颡鱼属(Pelteobagrus),广泛分布于我国长江、黄河、珠江及黑龙江各水系。近年来已成为我国一些地区的优质养殖鱼类。针对野生黄颡鱼群体遗传结构、遗传多样性及黄颡鱼遗传连锁图谱等遗传背景的研究对于黄颡鱼种质资源的保护和利用及最终实现黄颡鱼良种的培育具有重要的基础意义。本研究在黄颡鱼微卫星标记开发的基础上,对采集于4个水系的12个野生黄颡鱼群体的遗传结构和遗传多样性进行了分析,并采用AFLP标记和微卫星标记构建了黄颡鱼的第一代遗传连锁图谱。主要研究结果如下：
(1) FIASCO法开发黄颡鱼微卫星引物
物种特异性微卫星标记是对该物种开展各项遗传背景研究的基础。本研究采用FIASCO法对黄颡鱼微卫星引物进行了开发和筛选,实验中共挑取594个阳性克隆,77个克隆送出测序,75个测序成功获得完整序列,其中含有符合要求的微卫星重复序列(二核苷酸重序列复次数大于等于8,三核苷酸序列复次数大于等于6,四核苷酸序列复次数大于等于6)的克隆序列54个,占测序克隆总量的70.13%。
54个含有微卫星的序列共设计出43对引物,有20对引物能够稳定地扩增出预期大小的目的条带,多态性检测显示其中16个位点具有多态性,4个位点在检测群体中呈单态性。16个多态位点中有10个位点符合哈温平衡,其余6个位点经Bonferroni校正后显著偏离哈温平衡(P值为0.0000至0.0059)。16个多态性位点的等位基因数为3-11个,平均等位基因数5.4个；期望杂合度(He)范围为0.6372至0.8772,平均期望杂合度0.7521；观测杂合度为(Ho)范围为0.1250至0.9500,平均观测杂合度0.5990；多态信息含量(PIC)范围为0.3841至0.8809,平均多态信息含量0.6534。
(2)数据库搜索法筛选黄颡鱼微卫星标记
与物种功能基因相对应或本身就是功能基因一部分的Ⅰ型标记在鱼类的遗传学研究尤其是对具有良好经济性状的品种选育种中是非常有效的分子标记,本研究中利用GenBank公共数据库中搜索到的6条含有微卫星序列的黄颡鱼功能基因序列设计出9对引物,有5对引物可以扩增出稳定的目的条带。多态性检测结果显示,有3个位点具有多态性,位点EST01和EST07在检测群体呈单态性。3个微卫星位点的等位基因数为2-4个,观测杂合度为0.5750-0.9750,期望杂合度范围为0.4949-0.7516,多态信息含量在0.3693-0.6940之间,除位点EST06符合哈温平衡外,其余2个位点经Bonferroni校正后均显著偏离哈温平衡(P值分别为0.0000和0.0062)。3个多态性微卫星标记均为Ⅰ型微卫星标记。
(3)黄颡鱼野生群体遗传多样性和遗传结构的微卫星分析
遗传多样性和遗传结构是一个物种的重要特征,反映一个物种适应环境的能力和对环境变迁持续进化的潜力,同时也反映了生态适应进化、环境变迁与自然选择的效应。本研究利用8个微卫星标记对采自4个水系的12个野生黄颡鱼群体(共460个样本)进行了群体遗传多样性和遗传结构分析,12个黄颡鱼野生群体的期望杂合度(He)在0.6222-0.6940之间,观测杂合度(Ho)在0.4489-0.9611之间,等位基因丰度AR在3.2794-4.1543之间,有效等位基因数在3.1-4.4之间,多态信息含量PIC为0.4968-0.6378。12个黄颡鱼遗传多样性普遍处于较高水平,但采自珠江水系的西江群体XJR的遗传多样性最低,并在位点Pf428显示出单态性。
NJ聚类和UPGMA聚类结果均显示12个群体被分为3支：西江群体为独立的一支,巢湖群体CHL、黑龙江干流群体HLJR和洪泽湖群体HZL构成第二支,其余8个位于长江中下游的黄颡鱼群体组成了第三支,三个分支的划分恰好与各群体所处水系的位置相同。基于遗传距离DA构建的带有自展值的UPGMA聚类树也显示出相同的聚类结果。分子方差分析显示总变异的11.69%来自于三个黄颡鱼地理分支间的变异,6.02%来自于地理组群内群体间变异,而群体内变异占总变异的82.29%,黄颡鱼三个地理分支间的遗传分化系数为0.1771(P<0.001),遗传分化程度为中度。
群体间遗传距离与地理直线距离的Mantel检测结果显示,12个黄颡鱼群体间的遗传距离(Nei氏无偏距离)与地理直线距离的对数之间无显著相关性(r=0.3937,R2=0.155,P=0.9200),黄颡鱼群体间的遗传距离不符合地理隔离模式。
(4)黄颡鱼遗传连锁图谱的构建
遗传连锁图谱的构建是黄颡鱼遗传学研究的一个重要方向,为进一步了解黄颡鱼基因组成、基因克隆及重要经济性状定位奠定基础,实现对黄颡鱼遗传改良和新品种培育提供资料。本研究利用81对AFLP引物组合产生的411个多态性位点和15个微卫星标记,以黄颡鱼单对亲本及其杂交F1代为作图群体,运用拟测交策略分别构建了黄颡鱼雌雄遗传连锁图谱。
在黄颡鱼雄性连锁图谱中,100个AFLP标记组成了13个连锁群(遗传标记数量大于4)、6个三联体和7个连锁对,总图距为1142.2 cM。其中框架图总长度为813.2 cM,连锁群长度为17.1 cM至194.2 cM,标记间平均间隔距离为15.6 cM。雌性连锁图谱中,由75个标记组成的6个连锁群,7个三联体,13个连锁对,总图距为1115.8 cM。其中框架图长度为612.2 cM,连锁群长度介于60.3 cM至160.0 cM之间,标记间平均间隔距离为22.3 cM。由雄性和雄性连锁图谱估算的黄颡鱼基因组长度分别为1951.7 cM和2180.4 cM。所构建的雄性和雌性黄颡鱼框架图谱覆盖率分别为41.67%和28.08%。如果将三联体和连锁对也考虑进去,雄性和雌性黄颡鱼图谱总覆盖率则分别为58.53%和51.18%。
Yellow catfish(Pelteobagrus fulvidraco Richardson), a member of the family Bagridae of order Siluriformes, is widely distributed in most of water systems in China. Due to its high-quality meat, yellow catfish has become increasing important as a high-value species in aquaculture. Basic knowledge on the genetic diversity, population structure and linkage map of yellow catfish is essential to the effective conservation of wild germ plasm resource, further studies of genetics and marker-assisted breeding in this species. Here, we developed microsatellite loci from yellow catfish, and estimated the genetic diversity and population structure of the yellow catfish for 12 wild populations (N = 460 individuals from ten lakes and two rivers) based on eight polymorphic microsatellite markers. Meanwhile, a primary genetic linkage map of yellow catfish was also constructed. The main contents include:
(1) Isolation of microsatellite loci from yellow catfish by FIASCO protocol
Twenty microsatellite loci from yellow catfish(Pelteobagrus fulvidraco Richardson) have been isolated using the fast isolation by AFLP of sequences containing repeats (FIASCO) protocol, sixteen loci were polymorphic and four ones were monomorphic. Those polymorphic loci were characterized by genotyping 40 individuals. The observed number of alleles ranged from 3 to 11 with an average of 5.4 of each locus. The expected and observed heterozygosities ranged from 0.6372 to 0.8770 with a mean value of 0.7521 and from 0.1250 to 0.9500 with a mean value of 0.5990, respectively. And the polymorphic information content indexes were varied from 0.3841 to 0.8809 with an average of 0.6534. Among these polymorphic microsatellite loci, ten ones conformed to Hardy-Weinberg Equilibrium. These microsatellite markers would be useful for investigating the genetic diversity and population structure of yellow catfish.
(2) Development of type I makers of yellow catfish based on Public Data Base
Five microsatellite loci were obtained based on sequences of six microsatellite-containing genes by searching Genbank. Among these loci, three ones were polymorphic. The observed number of alleles ranged from 2 to 4. The expected and observed heterozygosities ranged from 0.4949 to 0.7516 and from 0.5750 to 0.9750, respectively. And the polymorphic information content indexes were varied from 0.3693 to 0.6940. Only one polymorphic loci conformed to Hardy-Weinberg Equilibrium. These typeⅠmarkers would play an important role in map construction, QTL analysis, gene mapping and marker-assisted selection of yellow catfish.
(3) Population structure and genetic diversity of the yellow catfish inferred from microsatellite markers
We estimated the genetic diversity and population structure of the yellow catfish for 12 wild populations (N=460 individuals from ten lakes and two rivers) based on eight polymorphic microsatellite markers. The expected and observed heterozygosities of these populations ranged from 0.6222 to 0.6940 and from 0.4489 to 0.9611, respectively. The mean number of alleles and the number of effective alleles were varied from 3.2794 to 4.1543 and from3.1 to 4.4, respectively. These genetic indices indicated the genetic diversity of wild yellow catfish populations was at a high level. However, the population XJR sampled from Xijiang River of Guangdong Province showed lowest level of genetic diversity and monomorphism at locus Pf428 was detected while other populations showing polymorphism at the locus.
Cluster analysis revealed three clusters that reflected geographical separation and isolation, for each cluster represented one geographic group. Population XJR being located in Xijiang River in southern China formed a separate cluster. The large cluster included almost all populations in the middle and lower reaches of Yangtze River Basin with only one exception (the population CHL). Population CHL and the other two populations (HLJR and HZL) whose sits belong to northern river system of China formed the third cluster. AMOVA showed that a major portion (82.29%) of the total genetic variation resulted from the within-populations component, while among geographic groups variation and the variance among population within groups accounted for 11.69% and 6.02% of the total genetic variation, respectively. The differenciation among three geographic groups were highly significant (FST=0.1771, P<0.001). However, when we further analyzed correlation between genetic and geographical distances with the Mantel test, the result showed no significant correlation between genetic and geographical distances (r=0.3937, R2=0.155, P=0.9200).
(4) A primary linkage map of yellow catfish based on AFLP and microsatellite markers
Genetic linkage map is useful for genetic improvement and selective breeding of yellow catfish. Linkage maps were constructed using an intraspecific F1cross and amplified fragment length polymorphism (AFLP) markers.411 AFLP markers produced from eighty-one selected AFLP primer combinations and fifteen microsatellite markers were polymorphic in either of the parents and segregated in the progeny. Among these segregating markers,100 were mapped to 13 linkage groups, six triplets and seven doublets of the male map, covering a total of 1142.2 cM. The total length of male framework map was 813.2 cM with an average marker spacing of 14.2 cM. And 75 markers were assigned to six linkage groups, seven triplets and thrirteen doublets of the female map, covering a total of 1115.8 cM. The total length of female framework map was 612.2 cM with an average marker spacing of 28.3 cM. None of the fifteen microsatellite markers was assigned to the genetic maps. The estimated genome length of P. fulvidraco was 1951.7 cM for the male and 2180.4 cM for the female, respectively. Genome coverage was estimated to be 41.67% and 28.08% for the female and male framework maps respectively, rising to 58.53% (male) and 51.18% (female) when associated markers were included.
The genetic maps presented here will serve as a basis for the construction of a high-resolution genetic map and mapping of economically important genes.
(1) FIASCO法开发黄颡鱼微卫星引物
物种特异性微卫星标记是对该物种开展各项遗传背景研究的基础。本研究采用FIASCO法对黄颡鱼微卫星引物进行了开发和筛选,实验中共挑取594个阳性克隆,77个克隆送出测序,75个测序成功获得完整序列,其中含有符合要求的微卫星重复序列(二核苷酸重序列复次数大于等于8,三核苷酸序列复次数大于等于6,四核苷酸序列复次数大于等于6)的克隆序列54个,占测序克隆总量的70.13%。
54个含有微卫星的序列共设计出43对引物,有20对引物能够稳定地扩增出预期大小的目的条带,多态性检测显示其中16个位点具有多态性,4个位点在检测群体中呈单态性。16个多态位点中有10个位点符合哈温平衡,其余6个位点经Bonferroni校正后显著偏离哈温平衡(P值为0.0000至0.0059)。16个多态性位点的等位基因数为3-11个,平均等位基因数5.4个；期望杂合度(He)范围为0.6372至0.8772,平均期望杂合度0.7521；观测杂合度为(Ho)范围为0.1250至0.9500,平均观测杂合度0.5990；多态信息含量(PIC)范围为0.3841至0.8809,平均多态信息含量0.6534。
(2)数据库搜索法筛选黄颡鱼微卫星标记
与物种功能基因相对应或本身就是功能基因一部分的Ⅰ型标记在鱼类的遗传学研究尤其是对具有良好经济性状的品种选育种中是非常有效的分子标记,本研究中利用GenBank公共数据库中搜索到的6条含有微卫星序列的黄颡鱼功能基因序列设计出9对引物,有5对引物可以扩增出稳定的目的条带。多态性检测结果显示,有3个位点具有多态性,位点EST01和EST07在检测群体呈单态性。3个微卫星位点的等位基因数为2-4个,观测杂合度为0.5750-0.9750,期望杂合度范围为0.4949-0.7516,多态信息含量在0.3693-0.6940之间,除位点EST06符合哈温平衡外,其余2个位点经Bonferroni校正后均显著偏离哈温平衡(P值分别为0.0000和0.0062)。3个多态性微卫星标记均为Ⅰ型微卫星标记。
(3)黄颡鱼野生群体遗传多样性和遗传结构的微卫星分析
遗传多样性和遗传结构是一个物种的重要特征,反映一个物种适应环境的能力和对环境变迁持续进化的潜力,同时也反映了生态适应进化、环境变迁与自然选择的效应。本研究利用8个微卫星标记对采自4个水系的12个野生黄颡鱼群体(共460个样本)进行了群体遗传多样性和遗传结构分析,12个黄颡鱼野生群体的期望杂合度(He)在0.6222-0.6940之间,观测杂合度(Ho)在0.4489-0.9611之间,等位基因丰度AR在3.2794-4.1543之间,有效等位基因数在3.1-4.4之间,多态信息含量PIC为0.4968-0.6378。12个黄颡鱼遗传多样性普遍处于较高水平,但采自珠江水系的西江群体XJR的遗传多样性最低,并在位点Pf428显示出单态性。
NJ聚类和UPGMA聚类结果均显示12个群体被分为3支：西江群体为独立的一支,巢湖群体CHL、黑龙江干流群体HLJR和洪泽湖群体HZL构成第二支,其余8个位于长江中下游的黄颡鱼群体组成了第三支,三个分支的划分恰好与各群体所处水系的位置相同。基于遗传距离DA构建的带有自展值的UPGMA聚类树也显示出相同的聚类结果。分子方差分析显示总变异的11.69%来自于三个黄颡鱼地理分支间的变异,6.02%来自于地理组群内群体间变异,而群体内变异占总变异的82.29%,黄颡鱼三个地理分支间的遗传分化系数为0.1771(P<0.001),遗传分化程度为中度。
群体间遗传距离与地理直线距离的Mantel检测结果显示,12个黄颡鱼群体间的遗传距离(Nei氏无偏距离)与地理直线距离的对数之间无显著相关性(r=0.3937,R2=0.155,P=0.9200),黄颡鱼群体间的遗传距离不符合地理隔离模式。
(4)黄颡鱼遗传连锁图谱的构建
遗传连锁图谱的构建是黄颡鱼遗传学研究的一个重要方向,为进一步了解黄颡鱼基因组成、基因克隆及重要经济性状定位奠定基础,实现对黄颡鱼遗传改良和新品种培育提供资料。本研究利用81对AFLP引物组合产生的411个多态性位点和15个微卫星标记,以黄颡鱼单对亲本及其杂交F1代为作图群体,运用拟测交策略分别构建了黄颡鱼雌雄遗传连锁图谱。
在黄颡鱼雄性连锁图谱中,100个AFLP标记组成了13个连锁群(遗传标记数量大于4)、6个三联体和7个连锁对,总图距为1142.2 cM。其中框架图总长度为813.2 cM,连锁群长度为17.1 cM至194.2 cM,标记间平均间隔距离为15.6 cM。雌性连锁图谱中,由75个标记组成的6个连锁群,7个三联体,13个连锁对,总图距为1115.8 cM。其中框架图长度为612.2 cM,连锁群长度介于60.3 cM至160.0 cM之间,标记间平均间隔距离为22.3 cM。由雄性和雄性连锁图谱估算的黄颡鱼基因组长度分别为1951.7 cM和2180.4 cM。所构建的雄性和雌性黄颡鱼框架图谱覆盖率分别为41.67%和28.08%。如果将三联体和连锁对也考虑进去,雄性和雌性黄颡鱼图谱总覆盖率则分别为58.53%和51.18%。
Yellow catfish(Pelteobagrus fulvidraco Richardson), a member of the family Bagridae of order Siluriformes, is widely distributed in most of water systems in China. Due to its high-quality meat, yellow catfish has become increasing important as a high-value species in aquaculture. Basic knowledge on the genetic diversity, population structure and linkage map of yellow catfish is essential to the effective conservation of wild germ plasm resource, further studies of genetics and marker-assisted breeding in this species. Here, we developed microsatellite loci from yellow catfish, and estimated the genetic diversity and population structure of the yellow catfish for 12 wild populations (N = 460 individuals from ten lakes and two rivers) based on eight polymorphic microsatellite markers. Meanwhile, a primary genetic linkage map of yellow catfish was also constructed. The main contents include:
(1) Isolation of microsatellite loci from yellow catfish by FIASCO protocol
Twenty microsatellite loci from yellow catfish(Pelteobagrus fulvidraco Richardson) have been isolated using the fast isolation by AFLP of sequences containing repeats (FIASCO) protocol, sixteen loci were polymorphic and four ones were monomorphic. Those polymorphic loci were characterized by genotyping 40 individuals. The observed number of alleles ranged from 3 to 11 with an average of 5.4 of each locus. The expected and observed heterozygosities ranged from 0.6372 to 0.8770 with a mean value of 0.7521 and from 0.1250 to 0.9500 with a mean value of 0.5990, respectively. And the polymorphic information content indexes were varied from 0.3841 to 0.8809 with an average of 0.6534. Among these polymorphic microsatellite loci, ten ones conformed to Hardy-Weinberg Equilibrium. These microsatellite markers would be useful for investigating the genetic diversity and population structure of yellow catfish.
(2) Development of type I makers of yellow catfish based on Public Data Base
Five microsatellite loci were obtained based on sequences of six microsatellite-containing genes by searching Genbank. Among these loci, three ones were polymorphic. The observed number of alleles ranged from 2 to 4. The expected and observed heterozygosities ranged from 0.4949 to 0.7516 and from 0.5750 to 0.9750, respectively. And the polymorphic information content indexes were varied from 0.3693 to 0.6940. Only one polymorphic loci conformed to Hardy-Weinberg Equilibrium. These typeⅠmarkers would play an important role in map construction, QTL analysis, gene mapping and marker-assisted selection of yellow catfish.
(3) Population structure and genetic diversity of the yellow catfish inferred from microsatellite markers
We estimated the genetic diversity and population structure of the yellow catfish for 12 wild populations (N=460 individuals from ten lakes and two rivers) based on eight polymorphic microsatellite markers. The expected and observed heterozygosities of these populations ranged from 0.6222 to 0.6940 and from 0.4489 to 0.9611, respectively. The mean number of alleles and the number of effective alleles were varied from 3.2794 to 4.1543 and from3.1 to 4.4, respectively. These genetic indices indicated the genetic diversity of wild yellow catfish populations was at a high level. However, the population XJR sampled from Xijiang River of Guangdong Province showed lowest level of genetic diversity and monomorphism at locus Pf428 was detected while other populations showing polymorphism at the locus.
Cluster analysis revealed three clusters that reflected geographical separation and isolation, for each cluster represented one geographic group. Population XJR being located in Xijiang River in southern China formed a separate cluster. The large cluster included almost all populations in the middle and lower reaches of Yangtze River Basin with only one exception (the population CHL). Population CHL and the other two populations (HLJR and HZL) whose sits belong to northern river system of China formed the third cluster. AMOVA showed that a major portion (82.29%) of the total genetic variation resulted from the within-populations component, while among geographic groups variation and the variance among population within groups accounted for 11.69% and 6.02% of the total genetic variation, respectively. The differenciation among three geographic groups were highly significant (FST=0.1771, P<0.001). However, when we further analyzed correlation between genetic and geographical distances with the Mantel test, the result showed no significant correlation between genetic and geographical distances (r=0.3937, R2=0.155, P=0.9200).
(4) A primary linkage map of yellow catfish based on AFLP and microsatellite markers
Genetic linkage map is useful for genetic improvement and selective breeding of yellow catfish. Linkage maps were constructed using an intraspecific F1cross and amplified fragment length polymorphism (AFLP) markers.411 AFLP markers produced from eighty-one selected AFLP primer combinations and fifteen microsatellite markers were polymorphic in either of the parents and segregated in the progeny. Among these segregating markers,100 were mapped to 13 linkage groups, six triplets and seven doublets of the male map, covering a total of 1142.2 cM. The total length of male framework map was 813.2 cM with an average marker spacing of 14.2 cM. And 75 markers were assigned to six linkage groups, seven triplets and thrirteen doublets of the female map, covering a total of 1115.8 cM. The total length of female framework map was 612.2 cM with an average marker spacing of 28.3 cM. None of the fifteen microsatellite markers was assigned to the genetic maps. The estimated genome length of P. fulvidraco was 1951.7 cM for the male and 2180.4 cM for the female, respectively. Genome coverage was estimated to be 41.67% and 28.08% for the female and male framework maps respectively, rising to 58.53% (male) and 51.18% (female) when associated markers were included.
The genetic maps presented here will serve as a basis for the construction of a high-resolution genetic map and mapping of economically important genes.
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