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Alternative TitleMarker development and genetic mapping in common carp and population genetics in two Hypophthalmichthys fishes
Thesis Advisor童金苟
Degree Grantor中国科学院水生生物研究所
Place of Conferral水生生物研究所
Keyword分子标记 鲤(Cyprinus Carpio) 遗传图谱 鲢(Hypophthalmichthys Molitrix) 鳙(H. Nobilis) 遗传结构 遗传瓶颈 杂交渐渗
Abstract鲤科鱼类是世界养殖产量最高的鱼类类群,更是我国淡水养殖业的支柱。分子标记技术的发展极大地促进了鱼类遗传学研究与育种实践,然而鲤科鱼类的分子标记开发及应用研究仍处于起步阶段。本论文围绕鲤科鱼类的分子标记开发及应用这一主题,开展了以下几方面的工作。 鲤(Cyprinus carpio)由于四倍体起源、遗传标记少等原因,遗传作图较其他鱼类更为困难。本文利用AFLP和微卫星标记技术和单倍体作图策略成功构建了鲤的遗传图谱。图谱由64个连锁群组成,共定位了699个AFLP和20个微卫星标记,总图距达到5506.9cM,标记间的平均间隔为7.66 cM。分析显示各个标记均匀、随机地分布在不同连锁群上,但是部分连锁群上存在AFLP 标记簇。为了将已有的鲤基因或EST定位到图谱上,本研究还利用生物信息学手段从公共数据库中发掘得到了一批鲤的SNP位点,并在中国常见鲤群体中对部分位点展开了小规模的验证。研究发现鲤基因组存在大量的SNP变异,而不同鲤群体的SNP等位基因频率差别较大。因而在应用到遗传作图之前,有必要在给定的样本中检验这些候选的SNP位点的有效性。 鲢(Hypophthalmichthys molitrix)和鳙(H. nobilis)是我国传统的养殖鱼类,然而最近几十年来我国的鲢、鳙自然资源发生了严重的衰退。为了更有效地保护和利用鲢鳙资源,迫切需要开展鲢鳙的分子群体遗传学研究。本文通过构建鳙基因组富集文库,分离得到一批在鲢、鳙中表现为多态的新的微卫星标记。结合已公开报道的鲢、鳙微卫星标记,本文分析了长江中游洞庭湖、鄱阳湖和石首江段的鲢、鳙群体遗传结构。研究发现长江中游鲢、鳙群体的遗传多样性较低,群体间有一定程度的遗传分化, 并且可以检测到遗传瓶颈。其中鳙的遗传多样性更低,而分化程度更高。上述结果说明过去几十年人类活动所引起的长江鲢、鳙种群萎缩已经对这些群体,特别是鳙的遗传结构产生了显著影响。生境的变迁及人工杂种的逃逸等原因都有可能引起鲢、鳙的杂交、渐渗,本研究显示长江中游鲢、鳙并未发生大规模的种间杂交、渐渗。本文分析的样本采于三峡工程蓄水前,其研究结果可供今后研究和评估长江中游及其他区域的鲢、鳙种质资源状况参考。 EST来源的微卫星标记(EST-SSR)在基因组学和分子育种研究中有较大价值,因为它们来自于基因组的编码区,常常可以通过同源搜索初步了解其功能。目前这类标记主要作为大规模EST测序计划的副产物,通过对EST序列数据的生物信息学发掘而得到。但是,目前只有少数鲤科鱼类有大量的EST序列。本研究以稀有鮈鲫(Gobiocyrpis Rarus)为例,提出了一种名为cDNA-FIASCO的开发EST-SSR标记的新方法。研究结果显示,对于尚没有大量EST数据的鱼类该方法是一种快速开发EST-SSR标记的有效途径。
Other AbstractCyprinids are the most important cultivated fish group in term of production, especially in China. The DNA marker technology has had a revolutionary impact on fish genetics and breeding since 1980s, but its applications in the studies of genetic and breeding in Cyprinids is still in its infancy. As far as DNA marker development and applications in Cyprinids were concerned, the following studies were carried out in this dissertation. Due to the tetraploid origin and lack of genetic markers, genetic mapping in common carp (Cyprinus carpio) is more difficult than in other fishes. By using AFLP and microsatellite (SSR) marker technology and gynogenetic haploids, a genetic linkage map of common carp was generated. The map reported here contains 699 AFLP and 20 microsatellite markers. It spans 5506.9 cM in 64 linkage groups, for an average marker spacing of 7.66cM. The correlation analysis indicates that markers in this map are randomly distributed among different linkage groups, but the normality test on interval map distances suggests the occurrence of AFLP marker clusters. In order to add gene and/or EST on the map, a large number of SNPs were identified by bioinformatic approach from public EST database of C. carpio. In a pilot study, some randomly selected SNPs were characterized in the common carp samples from China. The results show that carp genome harbors a large number of SNP variations, and allele frequencies of SNPs vary in different common carp populations or strains. Therefore, before these SNPs are added into the map and used in the marker-assisted breeding, their validation and variation should be tested in the given carp population or strain. Silver carp (Hypophthalmichthys molitrix), together with the closely related bighead carp (H. nobilis), are among the most important freshwater foodfishes in China. However, depression of natural resources of these river-lake migratory fishes has become a severe problem in China. To more efficiently protect and exploit resources, studies on molecular population genetics of bighead carp and silver carp are urgently necessary. In this study, a set of novel polymorphic microsatellite markers of these two species were developed from an enriched genomic library of H. nobilis. Twenty-five polymorphic microsatellite loci (including previously available markers) were applied to investigate the genetic diversity and population structure of silver carp and bighead carp from Dongting Lake, Poyang Lake, and the Shishou section of the Yangtze River in China. Low genetic diversity, moderate population differentiation and genetic bottlenecks within silver carp and bighead carp were observed. Bighead carp was characterized by higher level of population differentiation and lower gene diversity than silver carp. These results suggest that recent demographic declines caused by human activity during last few decades have had tremendous impacts on the genetic structure of Hypophthalmichthys spp., especially to bighead carp. However, it does not appear that extensive hybridization or introgression between bighead and silver carps, which might result from habitat change or escape of hybrids from aquaculture, is occurring in the middle reaches of the Yangtze River. As samples of Hypophthalmichthys spp. in this study were collected before 2003when Three Gorges Dam (TGD) began to impound and alter river flow, the present study might act as a reference for future genetic studies of silver carp and bighead carp in middle reaches of the Yangtze River as well as other regions. EST-derived microsatellite markers are becoming very important in studies of genomics and molecular breeding, because they represent coding regions of the genome and putative function can often be deduced by homology searches. As byproducts of the EST projects, EST-SSR markers are usually developed from the EST databases by bioinformatics method. However, so far large amount of EST sequences are available only in limited cyprinid species. In a case study in rare minnow (Gobiocyrpis Rarus), an FIASCO-based strategy which could be called as cDNA-FIASCO was proposed. The results demonstrate that this novel method is highly efficient for the fast isolation of EST-SSRs from a fish species in which EST sequences are not abundant.
Document Type学位论文
Recommended Citation
GB/T 7714
程磊. 分子标记开发及鲤遗传作图和鲢鳙群体遗传分析[D]. 水生生物研究所. 中国科学院水生生物研究所,2009.
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