杂色鲍微卫星DNA标记筛选和广东沿海养殖群体遗传多样性分析
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摘要
20世纪80年代末杂色鲍因其生长较快而成为我国南方最主要的养殖鲍。在鲍养殖业迅速发展的同时,由于海洋环境污染,养殖群体遗传结构单一、近交机率增加,同时,海域养殖过度、养殖污染,赤潮频发等外在因素更是严重的制约了鲍养殖业可持续发展。如何增强鲍的抗逆能力,提高其品质和质量,改良种质资源状况已经成为当前我国重要的研究课题。随着分子生物学技术的不断发展完善,分子标记技术不仅用于遗传多样性调查和种群遗传结构分析,也为种质评价、鉴别、溯源提供了条件,同时,也为分子标记辅助育种技术体系的建立奠定了基础。
本论文以中国重要海洋经济贝类杂色鲍(Haliotis diversicolor Reeve)为对象,研究了杂色鲍微卫星标记的分离,分析了杂色鲍养殖群体的遗传多样性与遗传分化,主要研究结果如下:
(1)由于有关杂色鲍在公共数据库中的基因序列信息比较少,特别是EST序列,且有关杂色鲍的微卫星标记研究方面几乎是空白。故本实验室构建了杂色鲍的肌肉组织和内脏组织的cDNA文库,构建了一个高质量的cDNA文库。共测序获得了8016个表达序列标签(Expressed Sequence Tag, EST),经聚类分析共得到1087个contigs和3694个singletons序列,既4781个unigene序列。比对分析显示1882个EST序列在GenBank数据库中没有同源性,占EST总数的23.5%;2899个EST序列在数据库中有同源序列,占EST总数的36.2%。
(2)从4781个unigene序列中,经过软件筛选发现161个ESTs序列共含有173个微卫星,占整个EST序列的3.72%。双碱基重复序列110个,占63.6 % ;三碱基类型的47个,占约27.2 %.从161个含有微卫星的EST序列中初步选取141条序列用引物设计软件prime prime 5进行微卫星引物设计。其中51对序列由于没有足够的侧翼序列不能用来设计引物,共设计93对引物由上海生工合成。在93对引物中,78对引物扩增出微卫星条带,其他15对引物在不同的温度和Mg2+浓度下不能得到扩增产物(无扩增产物、杂带过多或只能在部分个体中出现扩增产物)。在这78对可扩增的引物中,有53对的扩增产物是预期片段,25对引物的产物远超过预期片段可能是错配的缘故。我们用这53对引物通过上述选取的8个个体用聚丙烯酰胺凝胶电泳来检测多态性。通过检测,19对引物具有多态性。用40个采集样品检测的结果显示每个位点的等位基因数从2个到16个不等,平均为7.84个;观测杂合度介于0.412-0.748之间,期望杂合度的变化范围为0.653-0.846。
(3)以7个养殖群体分别来自广东汕头(ST,36个体),汕尾(SW,36个体),惠东(HD,36个体),湛江(ZJ,36个)和徐闻(XW,36个体,深圳野生驯养(SY,36个体)和日本(RB,36个体。实验所采取汕头,汕尾和惠东养殖群体为汕头与日本千叶杂交一代群体的杂交群体。利用7个微卫星位点ZSB2 ,ZSB4,ZSB6,ZSB8,ZSB10,ZSB13和ZSB17的引物进行了遗传多样性和种群遗传结构分析,统计分析了等位基因数、基因频率、杂合度、平均多态信息含量等遗传参数,并检测了群体是否符合Hardy-Weinberg平衡的状况。结果显示:7个位点产生的等位基因数从8-16个不等,共检测到76个等位基因,平均每个位点10.87个。有效等位基因数目范围为3.8-10.8,平均观察杂合度范围0.472-0.914,平均期待杂合度范围为:0.748-0.920。7个群体的每个位点多态信息含量变化范围为0.645-0.889,PIC值均在0.500以上,表现为高多态。相比两个野生驯养的养殖群群体而言,其他5个养殖群体整体存在不同程度的遗传多样性的降低。本研究中Fst值的范围为0.013-0.167。两个野生驯养的养殖群体之间以及与养殖群体之间Fst值都大于0.08,表明两野生驯养的养殖群体与养殖群体之间都存在明显的遗传分化。养殖群体遗传距离与地理距离不相关,可能是杂色鲍人工养殖过程中各育苗厂之间亲鲍和苗种频繁交流交换所造成的结果.从总体上说,杂色鲍养殖群体目前仍具有较高的遗传多样性,遗传信息丰富,遗传变异大,可以作为良好的育种材料.
In the late 20th, Haliotis diversicolor become the most important farming abalone in southern China because of its rapid growth. As the marine environment, a single breeding population genetic structure, increase the probability of inbreeding, lack of fast growth, good quality and strong resistance new abalone breeding. Meanwhile, over-farmed, farming pollution, frequent red tides external factors is a serious constraint abalone aquaculture sustainable development. How to enhance the resilience of abalone and improve its quality and quality improvement of germplasm resources situation has become an important research topic in China. With molecular biology techniques developed molecular markers not only for the investigation of genetic diversity and population genetic structure, but also for germplasm evaluation, identification, traceability provides the conditions,also lay the foundation for Marker-assisted breeding system. In the present study, a panel of microsatellite markers were isolated and characterized, and analysis of cultured abalone populations genetic diversity. The results obtained here are as follows:
(1) As the Haliotis diversicolor in the public database of gene sequence information in relatively small, particularly EST sequences, and the Haliotis diversicolor of microsatellite markers research was virtually nonexistent. A complementary DNA (cDNA) library with total 8016 expressed sequence tags (ESTs) was constructed and sequenced from whole body of Haliotis diversicolor Reeve. A total of 8016 expressed sequence tags (ESTs) and clustered into 1087 contigs and 3694 singletons. Among the 4781 unique genes identified, 1882 (23.5%) genes had no significant matches to known sequences in public database. The remaining 2899 (36.2%) genes that exhibited homology with gnese of known functions. 161 ESTs sequences (3.72%)contain 173 microsatellite were found.
(2) 4781 unigenes were assembled from this dataset and screened for simple repeat sequences (SSRs) with at least 5 repeats for di-, tri-, tetra- and penta-, and 4 repeats for hexanucleotide repeats. Total 173 SSRs were found, and the number of di- and trinucleotide repeats are 110 (63.6%) and 47 (27.2 %) separately. Primers were designed according 93 SSR-containing ESTs with sufficient flanking sequences to acquire 78 (83.9%) successful polymerase chain reactions (PCRs) including 25 (32.1%) products longer than expected sizes probably due to introns. 53 pairs that produced expected fragments were screened for polymorphism between eight abalone individuals from three populations. 19 (35.8%) of them with polymorphism were examined in one population (40 individuals) to test the number of alleles. The number of alleles ranged from 2 to 16 with an average of 7.84. The observed heterozygosity ranged from 0.412 to 0.748 , and the expected heterozygosity ranged from 0.653 to 0.846.
(3)Genetic diversity of 7 cultured populations of the Haliotis diversicolor from Shantou, Shanwei, Huidong, Shenzhen, Zhanjiang, Xuwen (above all of Guangdong Province, China) was analyzed using seven microsatellite markers (ZSB2、ZSB4、ZSB6、ZSB8、ZSB10、ZSB13、ZSB17). Seventy-six alleles of these seven microsatellite loci were found in these seven populations. The observed number of alleles of these microsatellite loci was 8-16 in each population with the average number of alleles was 10.87, and the average effective number of alleles was 3.8-10.8. The observed population heterozygosity was 0.472-0.914 and the observed expected heterozygosity was 0.748-0.920. The polymorphism of the seven populations were all high, and the PIC of the pupations were 0.645-0.889 ( PIC >0.5). Compared two populations of wild domesticated breeding, the five breeding groups were of different degrees of overall reduction in genetic diversity. In this study, Fst values range from 0.013-0.167. Between the two wild domesticated breeding populations and between wild domesticated breeding and cultured populations Fst values are greater than 0.08, indicating that between wild domesticated breeding populations, and between wild domesticated breeding populations and cultured populations exist significant genetic differentiation. The results did not show the consistent relationship between the geographic and the genetic distances, suggesting the existence of exchanges of breeds and eggs between the hatcheriesthe abalone.Generally speaking, groups of abalone farming is still a high level of genetic diversity, these results provided a useful information for the selective breeding, germplast conservation and its application of Haliotis diversicolor.
本论文以中国重要海洋经济贝类杂色鲍(Haliotis diversicolor Reeve)为对象,研究了杂色鲍微卫星标记的分离,分析了杂色鲍养殖群体的遗传多样性与遗传分化,主要研究结果如下:
(1)由于有关杂色鲍在公共数据库中的基因序列信息比较少,特别是EST序列,且有关杂色鲍的微卫星标记研究方面几乎是空白。故本实验室构建了杂色鲍的肌肉组织和内脏组织的cDNA文库,构建了一个高质量的cDNA文库。共测序获得了8016个表达序列标签(Expressed Sequence Tag, EST),经聚类分析共得到1087个contigs和3694个singletons序列,既4781个unigene序列。比对分析显示1882个EST序列在GenBank数据库中没有同源性,占EST总数的23.5%;2899个EST序列在数据库中有同源序列,占EST总数的36.2%。
(2)从4781个unigene序列中,经过软件筛选发现161个ESTs序列共含有173个微卫星,占整个EST序列的3.72%。双碱基重复序列110个,占63.6 % ;三碱基类型的47个,占约27.2 %.从161个含有微卫星的EST序列中初步选取141条序列用引物设计软件prime prime 5进行微卫星引物设计。其中51对序列由于没有足够的侧翼序列不能用来设计引物,共设计93对引物由上海生工合成。在93对引物中,78对引物扩增出微卫星条带,其他15对引物在不同的温度和Mg2+浓度下不能得到扩增产物(无扩增产物、杂带过多或只能在部分个体中出现扩增产物)。在这78对可扩增的引物中,有53对的扩增产物是预期片段,25对引物的产物远超过预期片段可能是错配的缘故。我们用这53对引物通过上述选取的8个个体用聚丙烯酰胺凝胶电泳来检测多态性。通过检测,19对引物具有多态性。用40个采集样品检测的结果显示每个位点的等位基因数从2个到16个不等,平均为7.84个;观测杂合度介于0.412-0.748之间,期望杂合度的变化范围为0.653-0.846。
(3)以7个养殖群体分别来自广东汕头(ST,36个体),汕尾(SW,36个体),惠东(HD,36个体),湛江(ZJ,36个)和徐闻(XW,36个体,深圳野生驯养(SY,36个体)和日本(RB,36个体。实验所采取汕头,汕尾和惠东养殖群体为汕头与日本千叶杂交一代群体的杂交群体。利用7个微卫星位点ZSB2 ,ZSB4,ZSB6,ZSB8,ZSB10,ZSB13和ZSB17的引物进行了遗传多样性和种群遗传结构分析,统计分析了等位基因数、基因频率、杂合度、平均多态信息含量等遗传参数,并检测了群体是否符合Hardy-Weinberg平衡的状况。结果显示:7个位点产生的等位基因数从8-16个不等,共检测到76个等位基因,平均每个位点10.87个。有效等位基因数目范围为3.8-10.8,平均观察杂合度范围0.472-0.914,平均期待杂合度范围为:0.748-0.920。7个群体的每个位点多态信息含量变化范围为0.645-0.889,PIC值均在0.500以上,表现为高多态。相比两个野生驯养的养殖群群体而言,其他5个养殖群体整体存在不同程度的遗传多样性的降低。本研究中Fst值的范围为0.013-0.167。两个野生驯养的养殖群体之间以及与养殖群体之间Fst值都大于0.08,表明两野生驯养的养殖群体与养殖群体之间都存在明显的遗传分化。养殖群体遗传距离与地理距离不相关,可能是杂色鲍人工养殖过程中各育苗厂之间亲鲍和苗种频繁交流交换所造成的结果.从总体上说,杂色鲍养殖群体目前仍具有较高的遗传多样性,遗传信息丰富,遗传变异大,可以作为良好的育种材料.
In the late 20th, Haliotis diversicolor become the most important farming abalone in southern China because of its rapid growth. As the marine environment, a single breeding population genetic structure, increase the probability of inbreeding, lack of fast growth, good quality and strong resistance new abalone breeding. Meanwhile, over-farmed, farming pollution, frequent red tides external factors is a serious constraint abalone aquaculture sustainable development. How to enhance the resilience of abalone and improve its quality and quality improvement of germplasm resources situation has become an important research topic in China. With molecular biology techniques developed molecular markers not only for the investigation of genetic diversity and population genetic structure, but also for germplasm evaluation, identification, traceability provides the conditions,also lay the foundation for Marker-assisted breeding system. In the present study, a panel of microsatellite markers were isolated and characterized, and analysis of cultured abalone populations genetic diversity. The results obtained here are as follows:
(1) As the Haliotis diversicolor in the public database of gene sequence information in relatively small, particularly EST sequences, and the Haliotis diversicolor of microsatellite markers research was virtually nonexistent. A complementary DNA (cDNA) library with total 8016 expressed sequence tags (ESTs) was constructed and sequenced from whole body of Haliotis diversicolor Reeve. A total of 8016 expressed sequence tags (ESTs) and clustered into 1087 contigs and 3694 singletons. Among the 4781 unique genes identified, 1882 (23.5%) genes had no significant matches to known sequences in public database. The remaining 2899 (36.2%) genes that exhibited homology with gnese of known functions. 161 ESTs sequences (3.72%)contain 173 microsatellite were found.
(2) 4781 unigenes were assembled from this dataset and screened for simple repeat sequences (SSRs) with at least 5 repeats for di-, tri-, tetra- and penta-, and 4 repeats for hexanucleotide repeats. Total 173 SSRs were found, and the number of di- and trinucleotide repeats are 110 (63.6%) and 47 (27.2 %) separately. Primers were designed according 93 SSR-containing ESTs with sufficient flanking sequences to acquire 78 (83.9%) successful polymerase chain reactions (PCRs) including 25 (32.1%) products longer than expected sizes probably due to introns. 53 pairs that produced expected fragments were screened for polymorphism between eight abalone individuals from three populations. 19 (35.8%) of them with polymorphism were examined in one population (40 individuals) to test the number of alleles. The number of alleles ranged from 2 to 16 with an average of 7.84. The observed heterozygosity ranged from 0.412 to 0.748 , and the expected heterozygosity ranged from 0.653 to 0.846.
(3)Genetic diversity of 7 cultured populations of the Haliotis diversicolor from Shantou, Shanwei, Huidong, Shenzhen, Zhanjiang, Xuwen (above all of Guangdong Province, China) was analyzed using seven microsatellite markers (ZSB2、ZSB4、ZSB6、ZSB8、ZSB10、ZSB13、ZSB17). Seventy-six alleles of these seven microsatellite loci were found in these seven populations. The observed number of alleles of these microsatellite loci was 8-16 in each population with the average number of alleles was 10.87, and the average effective number of alleles was 3.8-10.8. The observed population heterozygosity was 0.472-0.914 and the observed expected heterozygosity was 0.748-0.920. The polymorphism of the seven populations were all high, and the PIC of the pupations were 0.645-0.889 ( PIC >0.5). Compared two populations of wild domesticated breeding, the five breeding groups were of different degrees of overall reduction in genetic diversity. In this study, Fst values range from 0.013-0.167. Between the two wild domesticated breeding populations and between wild domesticated breeding and cultured populations Fst values are greater than 0.08, indicating that between wild domesticated breeding populations, and between wild domesticated breeding populations and cultured populations exist significant genetic differentiation. The results did not show the consistent relationship between the geographic and the genetic distances, suggesting the existence of exchanges of breeds and eggs between the hatcheriesthe abalone.Generally speaking, groups of abalone farming is still a high level of genetic diversity, these results provided a useful information for the selective breeding, germplast conservation and its application of Haliotis diversicolor.
引文
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