甘蓝型油菜含油量QTLs定位及候选基因筛选
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摘要
甘蓝型油菜是芸薹属植物中一种非常重要的油料作物并在世界范围内大面积的种植。甘蓝型油菜的含油量每期高一个百分点相当于产量期高2.3~2.5个百分点，所以研究甘蓝型油菜的含油量具有十分重要的意义。
本论文的主要研究内容如下：
1. DH群体的高低油混样转录组测序。根据DH高低油极端混样(高油混样是选择了DH群体含油量极端高的10个单株，低油混样是选择了DH群体含油量极端低的10个单株)转录组测序结果，得到了2730个差异表达基因，其中，1586个上调基因和1144个下调基因。
2.引物设计和多态性扩增。因为缺少多态性的标记，我们设计了2244对公共引物、5944对新开发的基因组来源的引物和443对新开发的与含油量有关的基因来源的引物。在亲本zy036和51070中扫了2244对公用引物、5944对新开发的基因组来源的引物和443对新开发的基因引物的多态性，分别鉴定出400(17.83%)、718(12.08%)和73(16.48%)对多态性引物。
3.遗传连锁图谱构建。利用DH群体构建了一个包括527个标记的遗传连锁图谱。这527个标记包括181个公用标记、298个新开发的基因组来源的标记和48个新开发的与含油量有关的基因标记。连锁图谱覆盖总长度是2,265.54cM，平均每条连锁群长度是119.34cM，标记之间的平均图距4.30cM。
4.含油量QTLs定位及候选基因筛选。利用WinQTL Cartographer2.5软件进行含油量QTLs检测，共检测到17个QTLs。通过QTL定位，估计的每个QTL解释含油量表型变异(R2)是9.15%~24.56%。每个QTL的加性效应是0.35~2.05。结合50个差异表达基因开发的基因来源的引物及17个含油量QTLs区间，共得到了7个含油量候选基因。
5.含油量与主花序产量及构成因子之间的相关性分析。实验表明: DH群体含油量与主花序产量、主花序有效角果数、每角粒数和千粒重之间没有明显的相关性(P>0.05)；共定位了13个主花序产量、10个主花序有效角果数、15个每角粒数和23个千粒重QTLs。
本论文的创新性如下：
1.用两个含油量差异很大(10个百分点)的甘蓝型油菜品种构建了DH群体，设计了许多新开发的基因组和基因来源引物，定位了含油量QTLs，并得到了高油QTLs，为甘蓝型油菜含油量和产量QTL性状的精细定位、基因克隆和分子标记辅助选择(MAS)奠定了基础。
2.通过把DH群体的高低油混样转录组测序得到的差异表达基因设计基因引物和含油量QTLs定位相结合，同步得到多个QTLs区间的多个含油量候选基因，为以后快速、高通量的寻找数量性状候选基因期供了可能性。
3.通过分析含油量与主花序产量及构成因子之间的相关性表明，含油量与主花序产量之间相关性不明显，说明可以同步期高油菜的含油量和产量。
Rapeseed (Brassica napus) is one of the most important oilseed crops, and it is cultivated over alarge area around the world. A1%increase in the seed oil content of rapeseed is equivalent to a2.3~2.5%increase in seed yield. Therefore, it is very important to improve the seed oil content inrapeseed.
The major research contents in the study are as follows:
1. Transcriptome sequencing of high-/low-oil content mixtures in DH population. A total of2370differentially expressed genes including1586up-regulated genes and1144down-regulatedgenes were detected. They were found according to the result of transcriptome sequencing ofextremely high-/low-oil content mixtures (10single plants of DH population with extremely high oilcontent were chosen as high-oil mixture and10single plants of DH population with extremely low oilcontent were chosen as low-oil mixture).
2. Primer design and primer polymorphism aplificatoin. To address the deficiency inpolymorphic markers, we designed2244pairs of publicly available primers,5944pairs of newlydeveloped genome-sourced primers, and443pairs newly developed primers related to oil-contentgenes. Primer screened for polymorphisms in the parents zy036and51070, for the2244pairs ofpublicly available primers,5944pairs of newly developed genome-sourced primers, and443pairs ofnewly developed primers related to oil-content genes,400(17.83%),718(12.08%), and73(16.48%)amplified polymorphisms.
3. Construction of the genetic linkage map. A genetic linkage map was constructed with527markers using our DH population. The map included181publicly available markers,298newlydeveloped genome-sourced markers and48newly developed markers related to oil-content genes.The total length of the19linkage groups was2,265.54cM, with an average length of119.34cM foreach linkage group and an average distance of4.30cM between markers.
4. Mapping of QTLs and screening of candidate genes for seed oil content.17QTLs for oilcontent were detected using software WinQTL Cartographer2.5. By QTL mapping, the mount ofphenotype variation (R2) in seed oil content explained by an individual QTL ranged from9.15%to24.56%. The additive effect of an individual QTL varied from0.35to2.05. Seven candidate genesrelated with oil content was found by combining the information of gene-sourced primers based on50differentially expressed genes with17oil content QTLs regions.
5. Analysis of correlation between oil content and yield of main inflorescence and itscomponents. It was shown that there were no significant correlation (P>0.05) between oil content andthe yield of main inflorescence, the number of effective siliques on main inflorescence, the number ofseeds per silique and thousand seeds weight.13QTLs of the yield of main inflorescence,10QTLs ofthe number of effective siliques on main inflorescence,15QTLs of the number of seeds per silique and23QTLs of thousand seeds weight were mapped.
The points of innovation in the study are as follows:
1. The B. napus DH population whose parents (10percentage points) with big difference in oilcontent were constructed. Many newly developed genome-and gene-sourced primers were designed.QTLs for oil content were detected, especially high-oil QTLs, which were laid foundation for finelyQTL mapping related to oil content and yield traits, genes cloning and molecular marker assistedselection (MAS) in B. napus.
2. Many candidate genes in many QTL regions could be detected at same time by combiningdesign of gene primers using differentially expressed genes obstaining from result of transcriptomesequencing of high-/low-oil content mixtures in DH population, which supplied possibility to findquickly candidate genes related to the quantitative traits with high-throughput.
3. It was shown that oil content and yield of main inflorescence had no significant correlationshipbetween each other by analysis of correlation between oil content and yield of main inflorescence andits components, which indicated that oil content and yield could be increased at same time.
本论文的主要研究内容如下：
1. DH群体的高低油混样转录组测序。根据DH高低油极端混样(高油混样是选择了DH群体含油量极端高的10个单株，低油混样是选择了DH群体含油量极端低的10个单株)转录组测序结果，得到了2730个差异表达基因，其中，1586个上调基因和1144个下调基因。
2.引物设计和多态性扩增。因为缺少多态性的标记，我们设计了2244对公共引物、5944对新开发的基因组来源的引物和443对新开发的与含油量有关的基因来源的引物。在亲本zy036和51070中扫了2244对公用引物、5944对新开发的基因组来源的引物和443对新开发的基因引物的多态性，分别鉴定出400(17.83%)、718(12.08%)和73(16.48%)对多态性引物。
3.遗传连锁图谱构建。利用DH群体构建了一个包括527个标记的遗传连锁图谱。这527个标记包括181个公用标记、298个新开发的基因组来源的标记和48个新开发的与含油量有关的基因标记。连锁图谱覆盖总长度是2,265.54cM，平均每条连锁群长度是119.34cM，标记之间的平均图距4.30cM。
4.含油量QTLs定位及候选基因筛选。利用WinQTL Cartographer2.5软件进行含油量QTLs检测，共检测到17个QTLs。通过QTL定位，估计的每个QTL解释含油量表型变异(R2)是9.15%~24.56%。每个QTL的加性效应是0.35~2.05。结合50个差异表达基因开发的基因来源的引物及17个含油量QTLs区间，共得到了7个含油量候选基因。
5.含油量与主花序产量及构成因子之间的相关性分析。实验表明: DH群体含油量与主花序产量、主花序有效角果数、每角粒数和千粒重之间没有明显的相关性(P>0.05)；共定位了13个主花序产量、10个主花序有效角果数、15个每角粒数和23个千粒重QTLs。
本论文的创新性如下：
1.用两个含油量差异很大(10个百分点)的甘蓝型油菜品种构建了DH群体，设计了许多新开发的基因组和基因来源引物，定位了含油量QTLs，并得到了高油QTLs，为甘蓝型油菜含油量和产量QTL性状的精细定位、基因克隆和分子标记辅助选择(MAS)奠定了基础。
2.通过把DH群体的高低油混样转录组测序得到的差异表达基因设计基因引物和含油量QTLs定位相结合，同步得到多个QTLs区间的多个含油量候选基因，为以后快速、高通量的寻找数量性状候选基因期供了可能性。
3.通过分析含油量与主花序产量及构成因子之间的相关性表明，含油量与主花序产量之间相关性不明显，说明可以同步期高油菜的含油量和产量。
Rapeseed (Brassica napus) is one of the most important oilseed crops, and it is cultivated over alarge area around the world. A1%increase in the seed oil content of rapeseed is equivalent to a2.3~2.5%increase in seed yield. Therefore, it is very important to improve the seed oil content inrapeseed.
The major research contents in the study are as follows:
1. Transcriptome sequencing of high-/low-oil content mixtures in DH population. A total of2370differentially expressed genes including1586up-regulated genes and1144down-regulatedgenes were detected. They were found according to the result of transcriptome sequencing ofextremely high-/low-oil content mixtures (10single plants of DH population with extremely high oilcontent were chosen as high-oil mixture and10single plants of DH population with extremely low oilcontent were chosen as low-oil mixture).
2. Primer design and primer polymorphism aplificatoin. To address the deficiency inpolymorphic markers, we designed2244pairs of publicly available primers,5944pairs of newlydeveloped genome-sourced primers, and443pairs newly developed primers related to oil-contentgenes. Primer screened for polymorphisms in the parents zy036and51070, for the2244pairs ofpublicly available primers,5944pairs of newly developed genome-sourced primers, and443pairs ofnewly developed primers related to oil-content genes,400(17.83%),718(12.08%), and73(16.48%)amplified polymorphisms.
3. Construction of the genetic linkage map. A genetic linkage map was constructed with527markers using our DH population. The map included181publicly available markers,298newlydeveloped genome-sourced markers and48newly developed markers related to oil-content genes.The total length of the19linkage groups was2,265.54cM, with an average length of119.34cM foreach linkage group and an average distance of4.30cM between markers.
4. Mapping of QTLs and screening of candidate genes for seed oil content.17QTLs for oilcontent were detected using software WinQTL Cartographer2.5. By QTL mapping, the mount ofphenotype variation (R2) in seed oil content explained by an individual QTL ranged from9.15%to24.56%. The additive effect of an individual QTL varied from0.35to2.05. Seven candidate genesrelated with oil content was found by combining the information of gene-sourced primers based on50differentially expressed genes with17oil content QTLs regions.
5. Analysis of correlation between oil content and yield of main inflorescence and itscomponents. It was shown that there were no significant correlation (P>0.05) between oil content andthe yield of main inflorescence, the number of effective siliques on main inflorescence, the number ofseeds per silique and thousand seeds weight.13QTLs of the yield of main inflorescence,10QTLs ofthe number of effective siliques on main inflorescence,15QTLs of the number of seeds per silique and23QTLs of thousand seeds weight were mapped.
The points of innovation in the study are as follows:
1. The B. napus DH population whose parents (10percentage points) with big difference in oilcontent were constructed. Many newly developed genome-and gene-sourced primers were designed.QTLs for oil content were detected, especially high-oil QTLs, which were laid foundation for finelyQTL mapping related to oil content and yield traits, genes cloning and molecular marker assistedselection (MAS) in B. napus.
2. Many candidate genes in many QTL regions could be detected at same time by combiningdesign of gene primers using differentially expressed genes obstaining from result of transcriptomesequencing of high-/low-oil content mixtures in DH population, which supplied possibility to findquickly candidate genes related to the quantitative traits with high-throughput.
3. It was shown that oil content and yield of main inflorescence had no significant correlationshipbetween each other by analysis of correlation between oil content and yield of main inflorescence andits components, which indicated that oil content and yield could be increased at same time.
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