利用功能分子标记分析甘蓝型油菜产量相关性状QTLs及其杂种优势遗传基础
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摘要
油菜是我国主要的油料作物，提高油菜籽产量和含油量以增加单位面积产油量是当前油菜研究和育种的首要目标。杂种优势利用是提高作物产量不可替代的最重要的途径，在油菜育种中已被广泛应用。与杂种优势利用取得的辉煌成绩相比，杂种优势机理的研究却远远滞后。已有研究表明，杂种和双亲间的差异表达基因与杂种优势的形成关系密切。但是，这些大量差异表达的基因是否与杂种优势或产量相关性状有关，目前尚不清楚。因此，将差异基因发展为功能标记并整合到图谱中，同时对重要农艺性状进行QTLs定位，从而确定差异表达基因与QTLs之间的关系，将在一定程度上有助于探讨杂种优势的遗传机理，促进甘蓝型油菜产量相关性状QTLs的克隆和利用。此外，模式植物拟南芥和水稻各个方面的研究都比较先进，甘蓝型油菜与模式植物的比较分析将有助于加快油菜上述各项研究的进程。
本研究以SI-1300和Eagle组配得到的F_2分离群体为基础，利用杂种和亲本的差异表达基因作标记构建的图谱为依托，对单株产量、单株角果总数等12个产量相关性状进行了QTLs定位和上位性分析，探讨了甘蓝型油菜杂种优势的机理，并利用本研究在甘蓝型油菜成功定位的功能分子标记开展了和其它作物的比较基因组学研究。主要结果如下：
1．根据杂种和亲本间的差异表达基因共设计了261对能扩增不同基因的引物对，其中247对引物序列在双亲SI-1300和Eagle中能扩增出清晰、明亮的条带。经过SSCP分析，111对引物的PCR扩增产物在双亲间能检测到清晰的多态性，共得到了177个功能分子标记。
2．根据Gene Ontology网站提供的分类信息，对能在双亲间扩增得到多态性的111个基因进行了分类。这些基因涉及了该分类标准的所有类别，共包括17大类，以初级代谢的基因最多。
3．以180个SSR标记、191个AFLP标记、152个SRAP标记和177个功能分子标记进行连锁遗传分析。在LOD≥3.0的条件下，共有582个标记进入连锁群，得到一张包含20个连锁群的甘蓝型油菜分子遗传图谱。该图谱总长2054.51 cM，标记间平均图距为3.53 cM。综合利用Piquemal等(2006)、Lowe等(2005)以及BBSRC网站等提供的油菜图谱中SSR标记的信息，对本研究中构建的油菜图谱与国际公认的图谱进行了初步比较。比较结果表明，该图谱中的19条连锁群可与公认的图谱(N1-N19)对应，仅是多出了1条连锁群(LG 20)。
4．12个产量相关性状均表现为正态分布。产量相关各性状在家系间的表型差异达到极显著水平，变异非常丰富。遗传力的变异范围为0.41～0.81。不同地点相同性状之间(除单株角果总数外)均存在极显著正相关性；同一地点不同性状之间的相关性也很明显。
5．利用复合区间作图法，在武汉和荆门两点共检测到影响12个性状的133个QTLs(LOD≥12.5)，其中有14个QTLs在两个地点都能被检测到。每个性状可以检测到7～15个QTLs不等。单个QTL可以解释的变异在3.02％～36.68％之间，平均为11.62％。涉及39个不同ESTs或基因的45个功能分子标记和产量及其相关性状有关，并且基础代谢的基因最多。
6．QTLs在连锁群上的分布并不是随机的，而成聚集分布，主要分布在N2和N7连锁群上；一些不同性状的QTLs定位在相同的区域，即存在一因多效或紧密连锁；高值亲本和低值亲本都包含对性状表现起增效作用(或减效作用)的等位基因；产量及其相关性状QTLs区域的相关位点表现了显性和超显性现象。
7．基因杂合性与性状值之间的相关系数表明，全基因组杂合性和性状之间并不存在显著相关。
8．利用169个共显性标记，对12个产量相关性状检测了全基因组所有可能的两位点互作对。取P＜0.01，12个性状在武汉和荆门两点分别检测到1093对和1121对极显著互作位点。经随机测验后，在武汉和荆门两点分别有297对和285对符合要求的位点对，共同的有6对。结果显示，油菜基因组中控制产量相关性状的互作位点数显著高于单一位点数。
9．本研究检测到的位点间互作有QTLs与非QTLs位点的互作和非QTLs位点与非QTLs位点间的互作，且后者类型占据了绝大多数。大多数位点的单独效应值一般都较小，但当两位点发生互作时，其效应值显著增大，成为显著影响性状表现的互作位点对；同一个位点可以与不同的位点互作，从而对同一性状产生影响，但效应值存在差异；相同的位点互作对可能影响不同的性状，即存在上位性互作的多效性。
10．单位点水平上的显性效应、超显性效应以及位点间的上位性互作效应都是甘蓝型油菜产量性状杂种优势的重要来源。
11．随机挑选10个功能标记的扩增产物测序。测序结果与原始序列比较分析发现，二者之间的相似程度极高，平均达到98％，最小的也有96％。说明扩增引物对原始序列进行了真实的扩增；随机挑选5对引物在双亲间的扩增差异片断进行回收、克隆并测序。对双亲间测序结果的比较发现，功能基因在双亲间的序列差异比较小。
12．利用TAIR网站的seqview软件，对整合到甘蓝型油菜遗传图谱的107个功能基因在拟南芥中的同源基因进行了电子定位。这些基因在拟南芥5条染色体上均有分布，共覆盖拟南芥基因组的110.95 MB。通过甘蓝型油菜和拟南芥之间的比较作图，本研究中共得到了21个共线性区域，涉及了油菜标记60个和拟南芥基因50个，这些共线性区域存在于甘蓝型油菜的15条连锁群上，并发现在拟南芥基因组上的每个共线性区域在油菜中存在1-7个拷贝。
13．在NCBI中利用Blastx查询水稻、玉米和小麦中位于油菜QTLs区间内功能标记序列的相似序列，大多数序列都能找到同源基因。在水稻中，对上述同源基因进行电子定位，并查找附近区域产量性状相关的QTLs，结果在部分水稻同源序列附近发现有与控制油菜类似性状相关的QTLs。
Bracissa napus is one of the most important oilseed crops in China. Now, the major object for breeders is to increase the oil production by increasing the yield and the oil content of rapeseed, and heterosis utilization, which is the most effective way to increase the yield and improve the quality in crops, have been widely used in B. napus. However, the molecular basis of heterosis is unclear until now. Some researches have shown that the differentially expressed genes between parents and hybrid are related to the heterosis. Nevertheless, it is unclear whether all the differentially expressed genes in hybrid are contributors to the heterosis or QTLs for traits, or some of them merely the results of hybridization. Therefore, such genes were developed to molecular functional markers, and were tested for their association with interested traits when they are integrated into a functional map of the genome and the QTLs of important agronomical traits have been located. This work will be helpful to the studies of the molecular basis of heterosis and facilitate the cloning and utilization of QTLs for important traits in B. napus. In addition, the comparative mapping between B. napus and model plants (Arabidopsis and flee) will accelerate above studies in rapeseed.
In this study, an F2 population of 184 individuals resulting from crossing "SI-1300×Eagle" was used for linkage analysis, and a molecular functional map was constructed using differentially expressed genes, where QTLs mapping were conducted for 12 yield-related traits. Furthermore, the genetic dissection of heterosis in B. napus was studied. In addition, the comparative mapping was done between B. napus and model plants, including Arabidopsis and rice. The major results are as follows:
1. A total of 261 PCR primer pairs were designed according to the differentially expressed genes between parents and hybrid. Of these, each of the majority (247) amplified a clear, strong and single band from the total genomic DNA of two parents when detected by 1.5% agarose gels. Using SSCP analysis, a total of 111 B. napus ESTs or genes showed polymorphisms between parents of the mapping population, providing 177 marker loci.
2. Based on the information from Gene Ontology website, these 111 ESTs or genes were grouped into 17 functional categories, and the largest group was allocated to the general metabolism.
3. One hundred and fifty-two sequence-related amplified polymorphism (SRAP) markers, 177 functional markers, 180 simple sequence repeat (SSR) markers, and 191 amplified fragment length polymorphism (AFLP) markers were used to construct a genetic linkage map of B. napus. Under the condition of LOD≥3.0, a total of 582 markers were assigned to 20 linkage groups (LGs). This map covered 2054.51 eM with average marker interval of 3.53 cM. The public information of microsatellites (SSR markers), derived from the Piquemal et.al (2005), Lowe et.al (2004), and BBSRC, contributed to establish the links between the map of Parkin et.al (1995) and ours. The results showed that most of LGs were aligned with the standard map (N1-NI9) except one LG.
4. All the 12 yield-related traits demonstrated the normal distribution. The highly significant variation among the 184 genotypes was observed for all the traits, and the heritability ranged from 0.41 for number of siliques on main infloresence (SMI) to 0.81 for height of primary effective branch (HPB). High correlation coefficients between the two locations were observed for most traits with the exception of number of seeds per silique (SS), And the coefficients between different traits in the same location are also high.
5. QTLs were detected for 12 yield-related traits in Wuhan and Jingmen, respectively. A total of 133 QTLs were identified, including 14 consistent ones across two locations. Seven to fifteen QTLs were found per trait and individual QTLs explained 3.02% 36..68% of the variance with an average of 11.62%. A total of 45 functional markers involved in 39 expressed sequence tags were linked with the QTLs of 12 traits, and the metabolic genes were the largest group.
6. The results of mapping QTLs showed that most of the QTLs were clustered, especially on LGs N2 and N7. Some QTLs related to different traits located in the similar region, which are tightly linked or pleiotropy. Both parents had QTLs with positive or negative effects on the same trait, and QTLs for yield-related traits which showed overdominant and dominant were detected in both locations.
7. The correlation coefficients between heterozygosity of the marker genotypes and trait measurements were small for all the traits and indicated that the lack of correlation between them.
8. All possible two-locus combinations were tested for t 2 yield-related traits using 169 codominant markers. With P＜0.01, 1093 and 1121 combinations which were significantly affected the traits were detected in Wuhan and Jingmen, respectively. Further conformation by randomization test revealed 297 and 285 two-locus interactions in Wuhan and Jingmen, respectively, whereas only six were common in both locations. The results showed that the number of two-locus combinations significantly affected the yield-related traits were greater than that of QTLs.
9. Interactions included the epistasis between QTLs and non-QTLs, and the one between non-QTLs. The later occupied the majority. The effect of individual locus of the interaction was small, whereas the significant effects to the trait were gotten when the two loci interacted. The same locus may have interaction with several other loci to affect the same trait, and the same two-locus interaction may affect several traits, like pleiotropy.
10. The dominant and overdominant effects at single locus level and the epistasis effects at multiple loci level are all the important sources of the genetic basis of heterosis in B. napus.
11. Ten amplified sequences for functional markers were cloned and sequenced. Comparing the sequence of cloned by us with the original one, we found that the similarity of them is average high to 98%, with the least 96%, which indicated that the designed primers can really amplify the original sequence. In addition, the sequences in both parents amplified by five functional primer pairs were randomly selected and sequenced. The comparation of the sequences between the parents showed the high similarity of the functional genes between cultivars.
12. The physical localizations of Arabidopsis genes corrponding to the 107 ones of B. napus intergrated to the map were determined by the seqview tool of TAIR. Alignment between the B. napus LGs and A. thaliana chromosomes revealed that genes localized on each five Arabidopsis chromosome and covered a total of 110.95 MB of Arabidopsis genome. Syntenic regions were sought between Arabidopsis and Brassica. A total of 21 conserved regions, involved in 60 functional markers and 50 genes of B. napus and Arabidopsis, respectively, were identified. These conserved regions were located at 15 LGs of B. napus, and each conserved region in Arabidopsis corresponded to 1-7 regions ofB. napus.
13. The genes which were located in the QTLs regions in B. napus were used to search Genbank by BLASTX to achieve the homologous sequence in rice, maize and wheat. The results showed that most have similar sequences. Furthermore, the homologous sequences in rice were mapped by in-silico way, and the QTLs were searched around this gene. The regions where some genes located were found the QTLs for the similar trait in rice compared to B. napus.
本研究以SI-1300和Eagle组配得到的F_2分离群体为基础，利用杂种和亲本的差异表达基因作标记构建的图谱为依托，对单株产量、单株角果总数等12个产量相关性状进行了QTLs定位和上位性分析，探讨了甘蓝型油菜杂种优势的机理，并利用本研究在甘蓝型油菜成功定位的功能分子标记开展了和其它作物的比较基因组学研究。主要结果如下：
1．根据杂种和亲本间的差异表达基因共设计了261对能扩增不同基因的引物对，其中247对引物序列在双亲SI-1300和Eagle中能扩增出清晰、明亮的条带。经过SSCP分析，111对引物的PCR扩增产物在双亲间能检测到清晰的多态性，共得到了177个功能分子标记。
2．根据Gene Ontology网站提供的分类信息，对能在双亲间扩增得到多态性的111个基因进行了分类。这些基因涉及了该分类标准的所有类别，共包括17大类，以初级代谢的基因最多。
3．以180个SSR标记、191个AFLP标记、152个SRAP标记和177个功能分子标记进行连锁遗传分析。在LOD≥3.0的条件下，共有582个标记进入连锁群，得到一张包含20个连锁群的甘蓝型油菜分子遗传图谱。该图谱总长2054.51 cM，标记间平均图距为3.53 cM。综合利用Piquemal等(2006)、Lowe等(2005)以及BBSRC网站等提供的油菜图谱中SSR标记的信息，对本研究中构建的油菜图谱与国际公认的图谱进行了初步比较。比较结果表明，该图谱中的19条连锁群可与公认的图谱(N1-N19)对应，仅是多出了1条连锁群(LG 20)。
4．12个产量相关性状均表现为正态分布。产量相关各性状在家系间的表型差异达到极显著水平，变异非常丰富。遗传力的变异范围为0.41～0.81。不同地点相同性状之间(除单株角果总数外)均存在极显著正相关性；同一地点不同性状之间的相关性也很明显。
5．利用复合区间作图法，在武汉和荆门两点共检测到影响12个性状的133个QTLs(LOD≥12.5)，其中有14个QTLs在两个地点都能被检测到。每个性状可以检测到7～15个QTLs不等。单个QTL可以解释的变异在3.02％～36.68％之间，平均为11.62％。涉及39个不同ESTs或基因的45个功能分子标记和产量及其相关性状有关，并且基础代谢的基因最多。
6．QTLs在连锁群上的分布并不是随机的，而成聚集分布，主要分布在N2和N7连锁群上；一些不同性状的QTLs定位在相同的区域，即存在一因多效或紧密连锁；高值亲本和低值亲本都包含对性状表现起增效作用(或减效作用)的等位基因；产量及其相关性状QTLs区域的相关位点表现了显性和超显性现象。
7．基因杂合性与性状值之间的相关系数表明，全基因组杂合性和性状之间并不存在显著相关。
8．利用169个共显性标记，对12个产量相关性状检测了全基因组所有可能的两位点互作对。取P＜0.01，12个性状在武汉和荆门两点分别检测到1093对和1121对极显著互作位点。经随机测验后，在武汉和荆门两点分别有297对和285对符合要求的位点对，共同的有6对。结果显示，油菜基因组中控制产量相关性状的互作位点数显著高于单一位点数。
9．本研究检测到的位点间互作有QTLs与非QTLs位点的互作和非QTLs位点与非QTLs位点间的互作，且后者类型占据了绝大多数。大多数位点的单独效应值一般都较小，但当两位点发生互作时，其效应值显著增大，成为显著影响性状表现的互作位点对；同一个位点可以与不同的位点互作，从而对同一性状产生影响，但效应值存在差异；相同的位点互作对可能影响不同的性状，即存在上位性互作的多效性。
10．单位点水平上的显性效应、超显性效应以及位点间的上位性互作效应都是甘蓝型油菜产量性状杂种优势的重要来源。
11．随机挑选10个功能标记的扩增产物测序。测序结果与原始序列比较分析发现，二者之间的相似程度极高，平均达到98％，最小的也有96％。说明扩增引物对原始序列进行了真实的扩增；随机挑选5对引物在双亲间的扩增差异片断进行回收、克隆并测序。对双亲间测序结果的比较发现，功能基因在双亲间的序列差异比较小。
12．利用TAIR网站的seqview软件，对整合到甘蓝型油菜遗传图谱的107个功能基因在拟南芥中的同源基因进行了电子定位。这些基因在拟南芥5条染色体上均有分布，共覆盖拟南芥基因组的110.95 MB。通过甘蓝型油菜和拟南芥之间的比较作图，本研究中共得到了21个共线性区域，涉及了油菜标记60个和拟南芥基因50个，这些共线性区域存在于甘蓝型油菜的15条连锁群上，并发现在拟南芥基因组上的每个共线性区域在油菜中存在1-7个拷贝。
13．在NCBI中利用Blastx查询水稻、玉米和小麦中位于油菜QTLs区间内功能标记序列的相似序列，大多数序列都能找到同源基因。在水稻中，对上述同源基因进行电子定位，并查找附近区域产量性状相关的QTLs，结果在部分水稻同源序列附近发现有与控制油菜类似性状相关的QTLs。
Bracissa napus is one of the most important oilseed crops in China. Now, the major object for breeders is to increase the oil production by increasing the yield and the oil content of rapeseed, and heterosis utilization, which is the most effective way to increase the yield and improve the quality in crops, have been widely used in B. napus. However, the molecular basis of heterosis is unclear until now. Some researches have shown that the differentially expressed genes between parents and hybrid are related to the heterosis. Nevertheless, it is unclear whether all the differentially expressed genes in hybrid are contributors to the heterosis or QTLs for traits, or some of them merely the results of hybridization. Therefore, such genes were developed to molecular functional markers, and were tested for their association with interested traits when they are integrated into a functional map of the genome and the QTLs of important agronomical traits have been located. This work will be helpful to the studies of the molecular basis of heterosis and facilitate the cloning and utilization of QTLs for important traits in B. napus. In addition, the comparative mapping between B. napus and model plants (Arabidopsis and flee) will accelerate above studies in rapeseed.
In this study, an F2 population of 184 individuals resulting from crossing "SI-1300×Eagle" was used for linkage analysis, and a molecular functional map was constructed using differentially expressed genes, where QTLs mapping were conducted for 12 yield-related traits. Furthermore, the genetic dissection of heterosis in B. napus was studied. In addition, the comparative mapping was done between B. napus and model plants, including Arabidopsis and rice. The major results are as follows:
1. A total of 261 PCR primer pairs were designed according to the differentially expressed genes between parents and hybrid. Of these, each of the majority (247) amplified a clear, strong and single band from the total genomic DNA of two parents when detected by 1.5% agarose gels. Using SSCP analysis, a total of 111 B. napus ESTs or genes showed polymorphisms between parents of the mapping population, providing 177 marker loci.
2. Based on the information from Gene Ontology website, these 111 ESTs or genes were grouped into 17 functional categories, and the largest group was allocated to the general metabolism.
3. One hundred and fifty-two sequence-related amplified polymorphism (SRAP) markers, 177 functional markers, 180 simple sequence repeat (SSR) markers, and 191 amplified fragment length polymorphism (AFLP) markers were used to construct a genetic linkage map of B. napus. Under the condition of LOD≥3.0, a total of 582 markers were assigned to 20 linkage groups (LGs). This map covered 2054.51 eM with average marker interval of 3.53 cM. The public information of microsatellites (SSR markers), derived from the Piquemal et.al (2005), Lowe et.al (2004), and BBSRC, contributed to establish the links between the map of Parkin et.al (1995) and ours. The results showed that most of LGs were aligned with the standard map (N1-NI9) except one LG.
4. All the 12 yield-related traits demonstrated the normal distribution. The highly significant variation among the 184 genotypes was observed for all the traits, and the heritability ranged from 0.41 for number of siliques on main infloresence (SMI) to 0.81 for height of primary effective branch (HPB). High correlation coefficients between the two locations were observed for most traits with the exception of number of seeds per silique (SS), And the coefficients between different traits in the same location are also high.
5. QTLs were detected for 12 yield-related traits in Wuhan and Jingmen, respectively. A total of 133 QTLs were identified, including 14 consistent ones across two locations. Seven to fifteen QTLs were found per trait and individual QTLs explained 3.02% 36..68% of the variance with an average of 11.62%. A total of 45 functional markers involved in 39 expressed sequence tags were linked with the QTLs of 12 traits, and the metabolic genes were the largest group.
6. The results of mapping QTLs showed that most of the QTLs were clustered, especially on LGs N2 and N7. Some QTLs related to different traits located in the similar region, which are tightly linked or pleiotropy. Both parents had QTLs with positive or negative effects on the same trait, and QTLs for yield-related traits which showed overdominant and dominant were detected in both locations.
7. The correlation coefficients between heterozygosity of the marker genotypes and trait measurements were small for all the traits and indicated that the lack of correlation between them.
8. All possible two-locus combinations were tested for t 2 yield-related traits using 169 codominant markers. With P＜0.01, 1093 and 1121 combinations which were significantly affected the traits were detected in Wuhan and Jingmen, respectively. Further conformation by randomization test revealed 297 and 285 two-locus interactions in Wuhan and Jingmen, respectively, whereas only six were common in both locations. The results showed that the number of two-locus combinations significantly affected the yield-related traits were greater than that of QTLs.
9. Interactions included the epistasis between QTLs and non-QTLs, and the one between non-QTLs. The later occupied the majority. The effect of individual locus of the interaction was small, whereas the significant effects to the trait were gotten when the two loci interacted. The same locus may have interaction with several other loci to affect the same trait, and the same two-locus interaction may affect several traits, like pleiotropy.
10. The dominant and overdominant effects at single locus level and the epistasis effects at multiple loci level are all the important sources of the genetic basis of heterosis in B. napus.
11. Ten amplified sequences for functional markers were cloned and sequenced. Comparing the sequence of cloned by us with the original one, we found that the similarity of them is average high to 98%, with the least 96%, which indicated that the designed primers can really amplify the original sequence. In addition, the sequences in both parents amplified by five functional primer pairs were randomly selected and sequenced. The comparation of the sequences between the parents showed the high similarity of the functional genes between cultivars.
12. The physical localizations of Arabidopsis genes corrponding to the 107 ones of B. napus intergrated to the map were determined by the seqview tool of TAIR. Alignment between the B. napus LGs and A. thaliana chromosomes revealed that genes localized on each five Arabidopsis chromosome and covered a total of 110.95 MB of Arabidopsis genome. Syntenic regions were sought between Arabidopsis and Brassica. A total of 21 conserved regions, involved in 60 functional markers and 50 genes of B. napus and Arabidopsis, respectively, were identified. These conserved regions were located at 15 LGs of B. napus, and each conserved region in Arabidopsis corresponded to 1-7 regions ofB. napus.
13. The genes which were located in the QTLs regions in B. napus were used to search Genbank by BLASTX to achieve the homologous sequence in rice, maize and wheat. The results showed that most have similar sequences. Furthermore, the homologous sequences in rice were mapped by in-silico way, and the QTLs were searched around this gene. The regions where some genes located were found the QTLs for the similar trait in rice compared to B. napus.
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