长牡蛎基因区SNP标记规模开发及其在遗传育种研究中的应用
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摘要
牡蛎（Oyster）属软体动物门，瓣鳃纲，牡蛎科，广泛分布于亚洲、美洲、欧洲以及澳洲等世界各海域。牡蛎具有重要的生态和经济价值，也是研究得最为全面深入的海洋贝类之一，特别是随着牡蛎全基因组测序的完成，其逐步成为海洋贝类研究的模式种。我国于20世纪80年代开始人工养殖长牡蛎（Crassostreagigas），现已成为我国重要的海水养殖贝类。自从二十世纪以来，养殖长牡蛎经常受夏季大规模死亡，经济性状性能衰退等原因影响，造成长牡蛎养殖生产损失较大。培育高产、抗逆、质优的牡蛎一直是牡蛎产业和育种研究的重要目标。
随着分子生物学与基因组学的发展，牡蛎的育种研究也正在经历由传统的选择、杂交育种到基于基因组信息的分子育种的转变。基于基因组的分子育种核心内容是对基因型和表型多态性的研究，其中单核苷酸多态性（SNP）因其分布广（尤其是在基因区也有分布）、可实现高通量检测等优点，逐渐成为基因型检测的重要工具。通过牡蛎全基因组测序和转录组测序，我们对牡蛎基因组SNP和多态性进行了系统筛查评估，本研究以长牡蛎全基因组序列为参考，利用三个海区的长牡蛎转录组数据获得长牡蛎基因表达区的SNP位点信息，并结合高分辨率熔解曲线技术（HRM）构建一套适合于长牡蛎高杂合基因组特点的高通量SNP标记开发平台。利用该平台成功开发了长牡蛎基因区SNP标记1329个，分型效率达到65.2%。在获得分型的SNP标记中84%是转换类型，其中包括R32.5%，Y35.8%，K7%，M9%，另外还有16%为颠换类型，其中包括W10%，S6%。通过SNP标记的引物序列信息将开发的SNP标记在长牡蛎全基因组Scaffold上进行一一定位，发现上述所有SNP标记覆盖长牡蛎基因组中653个Scaffold，占整个基因组所有Scaffold的38.1%。在基因组数据上的进一步研究发现，所获得的SNP标记分布于864个基因上，这些基因涉及197个Kegg注释通路，其中包括代谢、应激、免疫、抗逆、调节、生殖以及机体构成等方面，几乎涵盖长牡蛎整个生命活动的所有组成部分。这些标记的开发为牡蛎重要性状的基因解析以及基因功能的验证提供了有力工具。
长牡蛎基因预测结果显示：长牡蛎HSP70家族呈现扩张状态，推测可能与长牡蛎对潮间带多变生活环境的适应相关。此外，高温也被证实是长牡蛎夏季死亡的一个重要因素。本研究根据长牡蛎基因组中预测的HSP70家族基因的88个成员的序列信息为依据，在上述转录组数据中获取相应的转录序列，并以此为参考开发HSP基因中的SNP标记，共获得43个可以正确分型的SNP标记。以青岛神汤沟海区的长牡蛎自然群体为材料，采取人工控制高温刺激的手段将受试牡蛎材料分为热刺激敏感群组和热刺激耐受群组。利用上述平台检测43个HSP70基因中的SNP标记在群体中的分离情况，统计分析其等位基因以及基因型的分离比例并进行高温抗逆相关性分析。发现2个位于HSP70基因中的SNP标记与高温抗逆具有显著相关性（p<0.05），其中一个标记（SNP863）的等位基因频率与高温抗逆表现出极显著相关性(p<0.01)。这说明该基因中标记的等位基因频率及基因型频率与长牡蛎感受高温刺激以及其高温耐受能力密切相关。这两个SNP标记的突变类型均为Y（C/T），SNP809标记在高温抗逆性群组中等位基因T以及基因型TT出现的频率更高，分别为64.70%、35.30%，而其高温敏感性群组中分别为40.60%、17.20%；然而在SNP863标记中等位基因C与基因型CC在高温抗逆性群组中出现的频率却占据了绝对优势分别为90.60%、81.2%，而其高温敏感性群组中分别为64.8%、42.2%，甚至在高温抗逆群组中根本没有出现TT基因型。这表明这两个SNP标记位点所在的基因在长牡蛎高温抗逆过程中可能有重要作用，并且其等位基因型和基因型与长牡蛎热刺激耐受相关。该结果为长牡蛎高温抗逆机制的进一步研究找到良好的切入点，也为长牡蛎抗高温新品种的选育方法的建立奠定了良好的基础。
本文还研究了一种基于精简基因组高通量测序技术的SNP标记开发方法，该方法的核心是利用精简过的基因组序列片段的双端测序的结果来获得SNP标记。利用该方法在一个长牡蛎F1家系中构建一张高密度遗传连锁图谱。该图谱共包含1584个SNP标记，图谱全长为737.34CM；最大连锁群包含336个SNP标记，最小连锁群包含61个SNP标记，标记间平均图距为0.47CM。将连锁图谱上的标记定位到长牡蛎基因组上，获得相应的对应关系，在1584个标记中共计有1242个标记能够定位在Scaffold上，占总图谱标记的78.41%；这些标记共分布于654个Scaffold上，这些SNP标记的Scaffold全长超过282M，约占所有Scaffold全长的1/2左右。该连锁图谱为基因组测序图谱Scaffold的排序以及长牡蛎QTL精细定位和基因解析等遗传连锁研究奠定基础。
此外，本研究还建立了基于物种间COI基因序列的SNP差异，并利用本实验室SNP标记开发平台，建立一种贝类近缘物种种质鉴定的方法。该方法借助于高分辨率溶解曲线来区分DNA条形码序列中的SNP差异从而达到种质鉴定的结果。利用COI基因上的一段序列片段设计产生的一对引物在我国海域常见的巨蛎属牡蛎的物种鉴定中体现出简单易行、明确直观、准确有效等突出的优越性。其次，本方法为一个开放体系，应用范围广泛，不仅可用于一种贝类物种鉴定，只要是基于DNA条形码序列水平上的差异能够区分的贝类物种均可以利用该方法来进行物种间的区分、鉴定。
Crassostrea gigas belongs to mollusks, widely distributed across the world inAsia, America, Europe and Australia. Crassostrea gigas started to be cultured inChina since1980s, and now become one of the important cultured mollusk of China.Summer mortality and the degenerationof production traits impact the aquacultureseriously in the past decades, which bring new requirements to the Crassostrea gigasbreeding. At the same times, the oyster is established to be the model species by thepromotion of whole genome sequencing, which lay the foundation to the molecularbreeding of oyster.
The development of molecular biology and genomics promote the transitionfrom the trational breeding to the molecular breeding, which focused on thegenotyping and phenotyping.. Whole genomic sequencing of the C. gigas make itpossible to screen and validate the SNPs.Three transcriptome were used to obtain theSNPs in the gene region, and a platform based on HRM was established to distinguishthe genotypes of the SNP. A total of1329SNP markers were validated based on thisplatform, accounting for65.2%of the total slected SNPs. And84%of the developedSNP markers are transition which contains32.5%R;35.8%Y;7%K and9%M, theremaining are transversion which contains10%W and6%S. The primers sequencewere used to locate the the SNPs to the genome and the1329SNP markers distributein653Scaffolds, accounted for38.1%of the whole genome..The obtained SNPmarkers are distributed in864genes of197KEGG path ways, and these path ways involve metabolism, stress, immune, resistance, adjustment, reproduction and bodycomposition of Crassostrea gigas. These developed SNP markers provide a goodfoundation for validation of the gene function and the phenotyping–genotyping of theeconomico traitss of the oyster..
The HSP70gene family is expanded in Crassostrea gigas compared to otherspecies, which may have a relationship to the adaption of intertidal zone life, andthere are studies showed a correlation between the summer mortality and the HSPgenes. A total of43SNP markers were developed from the88HSP70genes, and theSNP markers are genotyped in the high temperature-sensitive and high temperature-resistant group. Allele frequency and genotype frequency of all the markers in thetwo groups are counted and correlation analysis is performed to calculate thecorrelation between the alleles frequency and genotype frequency to the hightemperature resistance. Two SNP markers are found significant correlated to thetemperature resistance (p<0.05) and one SNP allele (SNP863) shows extremelysignificant correlation to the temperature resistance (p<0.01). This indicats that thegenes contained the markers play a very important role in high temperature resistanceof Crassostrea gigas. Both of the two SNP markers are Y, and the frequency of alleleT and genotype TT of the SNP809marker are high in the high temperature resistantgroups, while the frequency of allele C and genotype CC of SNP863marker are highin the high temperature resistance groups. The two markers provide a good startingpoint for the further mechanism research of high temperature resistance. And establishclear goals for the high temperature resisting new varieties of breeding.
A genetic map is established with SNP tags obtained by resequencing of areduced representation library in a F1family of Crassostrea gigas. The geneticlinkage map is composed of10linkage groups with total of1584SNP markers. Andthe total length of the genetic map is737.34cM. There are336markers in the largestlinkage group while there are61markers in the smallest one, and the average distancebetween markers on this map is0.47cM.78.41%(1242) SNP markers are mapped to654Scaffolds with the overall length over282M, which accounted for half of the whole genome. The establishment of the genetic map laid the foundation for QTLanalysis and chromosome mapping of scaffold.
Species identification are also studied in this research, a species identificationmethod based on the SNP genotyping platform for oyster is established. And a pair ofprimer from the DNA barcoding (COI) sequence is obtained with which can identifythe5species in Crassostrea at the same times. This method shows more simple, moreclearly, more precise and more effectively against the usual methods, and this is anopen system for species identification, all the shellfish species which can be identifiedby DNA barcoding can be identified by this method.
随着分子生物学与基因组学的发展，牡蛎的育种研究也正在经历由传统的选择、杂交育种到基于基因组信息的分子育种的转变。基于基因组的分子育种核心内容是对基因型和表型多态性的研究，其中单核苷酸多态性（SNP）因其分布广（尤其是在基因区也有分布）、可实现高通量检测等优点，逐渐成为基因型检测的重要工具。通过牡蛎全基因组测序和转录组测序，我们对牡蛎基因组SNP和多态性进行了系统筛查评估，本研究以长牡蛎全基因组序列为参考，利用三个海区的长牡蛎转录组数据获得长牡蛎基因表达区的SNP位点信息，并结合高分辨率熔解曲线技术（HRM）构建一套适合于长牡蛎高杂合基因组特点的高通量SNP标记开发平台。利用该平台成功开发了长牡蛎基因区SNP标记1329个，分型效率达到65.2%。在获得分型的SNP标记中84%是转换类型，其中包括R32.5%，Y35.8%，K7%，M9%，另外还有16%为颠换类型，其中包括W10%，S6%。通过SNP标记的引物序列信息将开发的SNP标记在长牡蛎全基因组Scaffold上进行一一定位，发现上述所有SNP标记覆盖长牡蛎基因组中653个Scaffold，占整个基因组所有Scaffold的38.1%。在基因组数据上的进一步研究发现，所获得的SNP标记分布于864个基因上，这些基因涉及197个Kegg注释通路，其中包括代谢、应激、免疫、抗逆、调节、生殖以及机体构成等方面，几乎涵盖长牡蛎整个生命活动的所有组成部分。这些标记的开发为牡蛎重要性状的基因解析以及基因功能的验证提供了有力工具。
长牡蛎基因预测结果显示：长牡蛎HSP70家族呈现扩张状态，推测可能与长牡蛎对潮间带多变生活环境的适应相关。此外，高温也被证实是长牡蛎夏季死亡的一个重要因素。本研究根据长牡蛎基因组中预测的HSP70家族基因的88个成员的序列信息为依据，在上述转录组数据中获取相应的转录序列，并以此为参考开发HSP基因中的SNP标记，共获得43个可以正确分型的SNP标记。以青岛神汤沟海区的长牡蛎自然群体为材料，采取人工控制高温刺激的手段将受试牡蛎材料分为热刺激敏感群组和热刺激耐受群组。利用上述平台检测43个HSP70基因中的SNP标记在群体中的分离情况，统计分析其等位基因以及基因型的分离比例并进行高温抗逆相关性分析。发现2个位于HSP70基因中的SNP标记与高温抗逆具有显著相关性（p<0.05），其中一个标记（SNP863）的等位基因频率与高温抗逆表现出极显著相关性(p<0.01)。这说明该基因中标记的等位基因频率及基因型频率与长牡蛎感受高温刺激以及其高温耐受能力密切相关。这两个SNP标记的突变类型均为Y（C/T），SNP809标记在高温抗逆性群组中等位基因T以及基因型TT出现的频率更高，分别为64.70%、35.30%，而其高温敏感性群组中分别为40.60%、17.20%；然而在SNP863标记中等位基因C与基因型CC在高温抗逆性群组中出现的频率却占据了绝对优势分别为90.60%、81.2%，而其高温敏感性群组中分别为64.8%、42.2%，甚至在高温抗逆群组中根本没有出现TT基因型。这表明这两个SNP标记位点所在的基因在长牡蛎高温抗逆过程中可能有重要作用，并且其等位基因型和基因型与长牡蛎热刺激耐受相关。该结果为长牡蛎高温抗逆机制的进一步研究找到良好的切入点，也为长牡蛎抗高温新品种的选育方法的建立奠定了良好的基础。
本文还研究了一种基于精简基因组高通量测序技术的SNP标记开发方法，该方法的核心是利用精简过的基因组序列片段的双端测序的结果来获得SNP标记。利用该方法在一个长牡蛎F1家系中构建一张高密度遗传连锁图谱。该图谱共包含1584个SNP标记，图谱全长为737.34CM；最大连锁群包含336个SNP标记，最小连锁群包含61个SNP标记，标记间平均图距为0.47CM。将连锁图谱上的标记定位到长牡蛎基因组上，获得相应的对应关系，在1584个标记中共计有1242个标记能够定位在Scaffold上，占总图谱标记的78.41%；这些标记共分布于654个Scaffold上，这些SNP标记的Scaffold全长超过282M，约占所有Scaffold全长的1/2左右。该连锁图谱为基因组测序图谱Scaffold的排序以及长牡蛎QTL精细定位和基因解析等遗传连锁研究奠定基础。
此外，本研究还建立了基于物种间COI基因序列的SNP差异，并利用本实验室SNP标记开发平台，建立一种贝类近缘物种种质鉴定的方法。该方法借助于高分辨率溶解曲线来区分DNA条形码序列中的SNP差异从而达到种质鉴定的结果。利用COI基因上的一段序列片段设计产生的一对引物在我国海域常见的巨蛎属牡蛎的物种鉴定中体现出简单易行、明确直观、准确有效等突出的优越性。其次，本方法为一个开放体系，应用范围广泛，不仅可用于一种贝类物种鉴定，只要是基于DNA条形码序列水平上的差异能够区分的贝类物种均可以利用该方法来进行物种间的区分、鉴定。
Crassostrea gigas belongs to mollusks, widely distributed across the world inAsia, America, Europe and Australia. Crassostrea gigas started to be cultured inChina since1980s, and now become one of the important cultured mollusk of China.Summer mortality and the degenerationof production traits impact the aquacultureseriously in the past decades, which bring new requirements to the Crassostrea gigasbreeding. At the same times, the oyster is established to be the model species by thepromotion of whole genome sequencing, which lay the foundation to the molecularbreeding of oyster.
The development of molecular biology and genomics promote the transitionfrom the trational breeding to the molecular breeding, which focused on thegenotyping and phenotyping.. Whole genomic sequencing of the C. gigas make itpossible to screen and validate the SNPs.Three transcriptome were used to obtain theSNPs in the gene region, and a platform based on HRM was established to distinguishthe genotypes of the SNP. A total of1329SNP markers were validated based on thisplatform, accounting for65.2%of the total slected SNPs. And84%of the developedSNP markers are transition which contains32.5%R;35.8%Y;7%K and9%M, theremaining are transversion which contains10%W and6%S. The primers sequencewere used to locate the the SNPs to the genome and the1329SNP markers distributein653Scaffolds, accounted for38.1%of the whole genome..The obtained SNPmarkers are distributed in864genes of197KEGG path ways, and these path ways involve metabolism, stress, immune, resistance, adjustment, reproduction and bodycomposition of Crassostrea gigas. These developed SNP markers provide a goodfoundation for validation of the gene function and the phenotyping–genotyping of theeconomico traitss of the oyster..
The HSP70gene family is expanded in Crassostrea gigas compared to otherspecies, which may have a relationship to the adaption of intertidal zone life, andthere are studies showed a correlation between the summer mortality and the HSPgenes. A total of43SNP markers were developed from the88HSP70genes, and theSNP markers are genotyped in the high temperature-sensitive and high temperature-resistant group. Allele frequency and genotype frequency of all the markers in thetwo groups are counted and correlation analysis is performed to calculate thecorrelation between the alleles frequency and genotype frequency to the hightemperature resistance. Two SNP markers are found significant correlated to thetemperature resistance (p<0.05) and one SNP allele (SNP863) shows extremelysignificant correlation to the temperature resistance (p<0.01). This indicats that thegenes contained the markers play a very important role in high temperature resistanceof Crassostrea gigas. Both of the two SNP markers are Y, and the frequency of alleleT and genotype TT of the SNP809marker are high in the high temperature resistantgroups, while the frequency of allele C and genotype CC of SNP863marker are highin the high temperature resistance groups. The two markers provide a good startingpoint for the further mechanism research of high temperature resistance. And establishclear goals for the high temperature resisting new varieties of breeding.
A genetic map is established with SNP tags obtained by resequencing of areduced representation library in a F1family of Crassostrea gigas. The geneticlinkage map is composed of10linkage groups with total of1584SNP markers. Andthe total length of the genetic map is737.34cM. There are336markers in the largestlinkage group while there are61markers in the smallest one, and the average distancebetween markers on this map is0.47cM.78.41%(1242) SNP markers are mapped to654Scaffolds with the overall length over282M, which accounted for half of the whole genome. The establishment of the genetic map laid the foundation for QTLanalysis and chromosome mapping of scaffold.
Species identification are also studied in this research, a species identificationmethod based on the SNP genotyping platform for oyster is established. And a pair ofprimer from the DNA barcoding (COI) sequence is obtained with which can identifythe5species in Crassostrea at the same times. This method shows more simple, moreclearly, more precise and more effectively against the usual methods, and this is anopen system for species identification, all the shellfish species which can be identifiedby DNA barcoding can be identified by this method.
引文
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