甘蓝型油菜株型与角果相关性状的QTL分析
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摘要
当前,选育株型得到改良、适合机械化生产的油菜新品种是我国油菜育种的主攻方向之一,而开展油菜株型相关性状的遗传研究和QTL定位工作,是实现分子标记辅助选育特异株型油菜新品种的基础。本研究以矮秆紧凑型甘蓝型油菜4942C-5和正常株型油菜8008及其构建的包含181个株系的DH群体为材料,对甘蓝型油菜株型及产量相关的16个性状进行了QTL定位和分析,主要结果如下：
1.甘蓝型油菜遗传图谱的构建及图谱比较基因组学信息
利用DH群体构建了一张包含1902个标记(AFLP标记160个,SSR标记253个,IP标记80个,SCAR标记3个及SNP标记1406个)的高密度遗传连锁图,包含20条连锁群(C1连锁群被分成两条连锁群),图谱总长2328.97cM,标记间平均图距1.46cM,与国际上已发表的遗传图谱有较好的一致性。此外,通过Blastn分析将456个拟南芥同源基因、549个白菜同源基因和421个甘蓝同源基因定位到甘蓝型油菜A基因组,212个拟南芥基因、209个白菜同源基因和250个甘蓝基因定位到甘蓝型油菜C基因组。以已鉴定的拟南芥24个保守区段为基础,利用比对到图谱上的拟南芥基因鉴定了63个共线性片段和82个插入片段。
2.共线性分析
结果均表现为A基因组的共线性优于C基因组。对甘蓝型油菜连锁群与对应甘蓝型油菜假染色体的共线性分析,甘蓝型油菜连锁群与对应白菜、甘蓝假染色体的共线性分析,甘蓝型油菜染色体与对应白菜、甘蓝假染色体的共线性分析这三个结果进行比较,就共线性强弱程度而言,前两个基本一致,第三个大都优于前两个,这可能表明某些连锁关系还有待进一步确认,也可能本研究材料这些区域存在着染色体重排,但都进一步证实了甘蓝型油菜源于白菜和甘蓝；就甘蓝型油菜连锁群(BnAl-BnA10, BnCl-BnC9)、甘蓝型油菜染色体(Bnl-Bn19)、白菜(BrAl-BrA10)和甘蓝(BoC1-BoC9)染色体的方向来看,BnAl-Bnl-BrAl、 BnA2-Bn2-BrA2、 BnA4-Bn4-BrA4、 BnA6-Bn6-BrA6、 BnA7-Bn7-BrA7、 BnC3-Bnl3-BoC3、 BnC4-Bn14-BoC4、 BnC8-Bn18-BoC8、 BnC9-Bn19-BoC9三者两两间方向都相同。共线性分析结果揭示的方向及共线性程度的强弱对利用其他作物基因组序列信息来解决甘蓝型油菜的实际问题奠定了基础。
3.DH群体频率分布与QTL定位
分析了DH群体16个性状在三个环境下的频率分布,结果表明大多数性状呈连续分布且存在多峰,偏离了标准正态分布。通过复合区间作图法(CIM)在全基因组进行QTL扫描分析,16个性状在三个环境中分别检测到117个、122个、98个QTL,共计337个QTL。利用不同性状逐一进行QTL元分析后,这337个QTL最终整合为234个,分配在甘蓝型油菜20条连锁群上。其中平均分枝长度(ALPB)检测到17个QTL,分布在A1、A3、A5、A6、A7和C1a连锁群,单个QTL解释的遗传变异为3.9-25.9%；主花序长度(LMI)检测到23个QTL,分布在A1、A3、 A5、A6、A7、C8和C9连锁群,单个QTL解释的遗传变异为4.7-25.5%；角果层长度(LSL)检测到10个QTL,分布在A1、A3、A6、A9、C3和C8连锁群,单个QTL解释的遗传变异为5.1-11.8%；分枝角果数(NSB)检测到9个QTL,分布在A1、A3、A9和C3连锁群,单个QTL解释的遗传变异为4.4-20.1%；一次有效分枝数(PB)检测到15个QTL,分布在A1、A4、A7、Cla、Clb、C2、C3和C4连锁群,单个QTL解释的遗传变异为4.7-15.1%；株高(PH)检测到15个QTL,分布在A1、A3、A6、A7、Clb和C9连锁群,单个QTL解释的遗传变异为0.7-32.2%；分枝角果密度(SDB)检测到24个QTL,分布在A1、A3、A5、A6、A7、A9、Cla、 Clb、C6、C7和C9连锁群,单个QTL解释的遗传变异为4.4-16.0%；主花序角果密度(SDMI)检测到10个QTL,分布在A3、A6、A7、Cla和C7连锁群,单个QTL解释的遗传变异为5.3-12.9%；角果长度(SL)检测到11个QTL,分布在A1、A7、A9和A10连锁群,单个QTL解释的遗传变异为2.4-60.0%；主花序角果数(SMI)检测到17个QTL,分布在A1、A2、A3、A5、A9和C1a连锁群,单个QTL解释的遗传变异为4.7-14.8%；每角果粒数(SN)检测到15个QTL,分布在A1、A6、 A7、A8、Cla、Clb、C3和C5连锁群,单个QTL解释的遗传变异为4.9-26.6%；单株角果数(SNPP)检测到9个QTL,分布在A1、A9和C3连锁群,单个QTL解释的遗传变异为4.8-24.3%；单株种子产量(SY)检测到10个QTL,分布在A1、 A3.A9.C3和C8连锁群,单个QTL解释的遗传变异为4.4-35.7%；总分枝长度(TLPB)检测到13个QTL,分布在A1、A3、A6、A9、Cla和C3连锁群,单个QTL解释的遗传变异为5.3-17.9%；千粒重(TSW)检测到16个QTL,分布在A1、A7、A9、 Cla、Clb、C8和C9连锁群,单个QTL解释的遗传变异为3.4-38.8%；角果层宽度(WSL)检测到20个QTL,分布在A1、A2、A3、A5、A7和A9连锁群,单个QTL解释的遗传变异为4.2-31.3%。
4.甘蓝型旁系同源保守区段内的QTL及同源QTL分析
第一轮元分析的234个QTL中有168个能定位到十字花科保守区段上,包括U、H、F、W、E、R、J、C、X、M、N、B、I、A共计14个保守区段。根据QTL的分布情况,在甘蓝型油菜基因组的旁系同源保守区段寻找同源QTL,结果8个性状包括一次有效分枝数、角果长度、角果层宽度、每角果粒数、千粒重、株高、主花序长度、种子产量共发现了8对同源QTL,这8对同源QTL分布在E、U、X、R保守区段。
5.多效性QTL及产量指示QTL
第二轮元分析整合结果表明共存在59个多效性QTL,这些多效性QTL涉及2-8个性状不等,为设计理想株型提供了依据。如mqA1.114将株型性状、株型兼角果性状、角果性状、单株产量整合到一起。本研究中检测到的10个种子产量QTL中的7个存在于多效性QTL中。在这7个与产量相关的多效性QTL中,mqA1.14、mqA9.4、mqC8.11的指示性状分别是主花序长度、主花序角果数和千粒重千粒重,而mqA1.5、 mqA1.9、mqC3.2和mqC3.4中没有一个QTL能作为单株产量的指示QTL。
6.株型与产量候选基因在图谱上的定位
连锁分析表明,依据拟南芥株型及籽粒相关基因TCP24、Sep1、AP1、STM、 LFY、ANT、AXR6、PIN1、AP3、REV,、TTG2、TT5设计的21对引物获得的26个标记可被定位到图谱的不同位置上,且在某些基因标记附近能检测到QTL,但这些QTL与候选基因是否存在着一定的联系还需进一步证实。同时,本研究还以定位到图谱上的拟南芥基因为桥梁,将玉米、水稻中株型及产量相关的重要基因定位到本研究构建的遗传图谱的大致位置上,结果有6个候选基因(GS5、ARGOS、MINI3、 CLAVATA1、DEP2、IPA1/OsSPL14)定位到遗传图谱的8个不同位置,其中与籽粒相关的基因GS5.ARGOS和MINI3被定位到附近有千粒重、每角果粒数、角果长度、籽粒产量性状相关QTL的位置上；与花/花序相关的拟南芥基因CLAVATA1被定位到A2连锁群的E保守区段,在此位置附近有一个主花序角果数的QTL；直立密穗基因DEP2被定位到A5连锁群F保守区段,在其附近有平均分枝长度和总分枝长度的QTL；水稻理想株型基因IPAl/OsSPL14被定位到A9连锁群N区段,相应位置定位了两个分枝角果密度的QTL。
At present, the breeding of rapeseed varieties with improved plant type and suitable for the mechanised production is one of the major directions of rapeseed breeding in China. The work on the genetic basis and QTL mapping of the traits associated with plant type could provide a basis for molecular marker assisted breeding of the new B. napus varieties with specific plant type. In this study, a population consisting of181DH lines, which was derived from F1microspore culture of a cross of the B. napus lines8008(normal plant type, high seed-yield per plant) and94942C-5(compact plant type, low seed-yield per plant), was used as the field test materials. Sixteen plant type-or yield-associated traits were analyzed, and the QTLs for these traits were mapped. The major results are as following:
1. The genetic map construction and comparative genomics information of B. napus
Using the double haploid population, a linkage map containing1904markers, including160AFLPs,254SSRs,79IPs,3SCARs and1048SNPs, was constructed. The resulting map consisted of20linkage groups (the C1was divided into two linkage groups), covering2328.97cM with an average of1.46cM between markers, with a considerable consistence to the previously published linkage maps. Moreover, the BLASTN analysis showed that456,549and421homologous genes from A. thaliana, B. rapa and B. oleracea respectively, could be mapped on A genome of B. napus. And212,209and250homologous genes from A. thaliana, B. rapa and B. oleracea respectively, could be mapped on C genome of B. napus. Based on the24identified conserved regions in A. thaliana,63sythenic blocks and82insertion fragments were identified by using the A. thaliana genes mapped on the genetic map of B. napus.
2. Synteny analysis
The results indicated that the synteny in A genome was better than that in C genome. Alignments of linkage groups in B. napus to pseudochromosomes in B. napus, linkage group in B. napus to the pseudochromosomes in B. rapa and B. oleracea, and the pseudochromosomes in B. napus to pseudochromosomes in B. rapa and B. oleracea showed that the synteny extents in the first two alignments were equivalent and the synteny extent in the third alignment was mostly better than that in in the first two alignments. These results suggested that though the linkage relationship between some loci on the genetic map constructed in this study maybe needs further confirmation, or it is possible that chromosomal rearrangement really exits in these regions, the results from synteny analysis still fully confirmed the fact that B. napus is derived from B. rapa and B. oleracea. Considering the arrangement directions in the linkage groups in B. napus (BnA1-BnA10, BnC1-BnC9), the pseudochromosomes in B. napus (Bnl-Bnl9), B. rapa (BrA1-BrA10) and B. oleracea (BoC1-BoC9), the consistent direction was found in each element of the trisomes of BnAl-Bnl-BrAl, BnA2-Bn2-BrA2, BnA4-Bn4-BrA4, BnA6-Bn6-BrA6, BnA7-Bn7-BrA7, BnC3-Bn13-BoC3, BnC4-Bn14-BoC4, BnC8-Bnl8-BoC8, BnC9-Bnl9-BoC9. The information on direction and synteny extent could provide a basis for the revolution of the practical problem in B. napus by utilizing the genome sequence information from other crops.
3. Frequency distribution in DH population
The frequency distribution of the16traits in the DH population was analyzed in three environments. The results indicated that most traits showed a multimodal continuous distribution, deviating from the standard normal distribution. Using the composite interval mapping (MCIM), a genome-wide scan for QTLs was conducted. A total of337QTLs for the16traits were detected in three environments (117QTLs in11WH,122QTLs in12WH,98QTLs in11EZ). After meta-analysis was conducted for each trait, the337QTLs were consolidated into234QTLs covering20LGs. Seventeen QTLs controlling average length of primary branches (ALPB) were identified on6LGs:A1, A3, A5, A6, A7and Cla, with the individual QTL explaining3.9-25.9%of the phenotypic variation. For length of main inflorescence (LMI),10QTLs were detected on LGs Al, A3, A5, A6, A7, C8and C9, with the individual QTL explaining4.7-25.5%of the phenotypic variation. For the length of silique layer (LSL),10QTLs were detected on LGs A1, A3, A6, A9, C3and C8, with the individual QTL explaining5.1-11.8%of the phenotypic variation. Nine QTLs for number of siliques on branches (NSB) were assigned on four LGs: A1, A3, A9and C3, with the individual QTL accounting for4.4-20.1%of the phenotypic variation. For the number of primary branches (PB),15QTLs were detected on LGs Al, A4, A7, Cla, Clb, C2, C3and C4, with the individual QTL explaining4.7-15.1%of the phenotypic variation. Fifteen QTLs controlling plant height (PH) were detected on6LGs:A1, A3, A6, A7, Clb and C9, with the individual QTL explaining0.7-32.2%of the phenotypic variation. Twenty-four QTLs for silique density of branches (SDB) were assigned on11LGs:A1, A3, A5, A6, A7, A9, Cla, Clb, C6, C7and C9, with the individual QTL accounting for4.4-16.0%of the phenotypic variation. For silique density on main inflorescence (SDMI), 10QTLs were detected on LGs A3, A6, A7, Cla, and C7, with the individual QTL explaining5.3-12.9%of the phenotypic variation. For silique length (SL),11QTLs were detected on LGs Al, A7, A9and A10, with the individual QTL explaining2.4-60.0%of the phenotypic variation. Seventeen QTLs controlling number of siliques on main inflorescence (SMI) were detected on6LGs:Al, A2, A3, A5, A9and Cla, with the individual QTL explaining4.7-14.8%of the phenotypic variation. For number of seeds per silique (SN),15QTLs were detected on8LGs:Al, A6, A7, A8, Cla, Clb, C3and C5, with the individual QTL explaining4.9-26.6%of the phenotypic variation. Nine QTLs for silique number per plant (SNPP) were assigned on3LGs:Al, A9and C3, with the individual QTL accounting for4.8-24.3%of the phenotypic variation. For seeds yield per plant (SY),10QTLs were identified on5LGs: A1, A3, A9, C3and C8, with the individual QTL explaining4.4-35.7%of the phenotypic variation. Thirteen QTLs for total length of primary branches (TLPB) were assigned on6LGs:A1, A3, A6, A9, Cla and C3, with the individual QTL accounting for5.3-17.9%of the phenotypic variation. For and thousand seed weight (TSW),16QTLs were detected on7LGs:Al, A7, A9, Cla, Clb, C8and C9, with the individual QTL explaining3.4-38.8%of the phenotypic variation. Twenty QTLs for silique the width of silique layer (WSL) were assigned on6LGs:Al, A2, A3, A7and A9, with the individual QTL accounting for4.2-31.3%of the phenotypic variation.
4. QTLs and homologous QTLs mapped in paralogous conserved blocks in B. napus.
One hundred and sixty-eight of the234QTLs identified by the first round meta-analysis could be mapped in silico in the14conserved crucifer blocks (U, H, F, W, E, R, J, C, X, M, N, B, I and A). Eight pairs of homologous QTLs for PB, SL, WSL, SN, TSW, PH, LMI and SY were found in paralogous conserved blocks E, U, X and R in B. napus.
5. Pleiotropic QTLs and indicator-QTLs for yield
The integrated results from the second round meta-analysis showed that there were59pleiotropic QTLs, and each of them was associated with2to8traits for designing ideal plant architecture. For example, mqA1.14integrated the traits on plant architecture traits, plant architecture and silique-traits, silique traits and seed yield together. Seven of ten QTLs detected in this study for seed yield were identified as pleiotropic QTLs. Among these pleiotropic QTLs, indicator traits of mqA1.14, mqA9.4and mqC8.1were length of main inflorescence, number of siliques on main inflorescence and thousand seeds weight, respectively, but no a QTL could be regarded as yield-indicator QTL in mqA1.5, mqA1.9, mqC3.2and mqC3.4.
6. The mapping of candidate genes governing plant type and yield traits on the genetic map
Linkage analysis showed that26markers, which derived from21primer pairs designed by the A. thaliana genes governing plant type and seed traits (TCP24, Sepl, API, STM, LFY, ANT, AXR6, PIN1, AP3, REV, TTG2and TT5), could be mapped at the different locations on this genetic map. Nearby some genic-markers, QTLs could be detected. However, the correlation between these QTLs and the candidate genes needs further confirmation. Using the A. thaliana genes mapped on the genetic map in this study as a bridge, some important genes governing plant type and yield component traits in rice and corn were roughly mapped on the genetic map in this study. The results showed that6candidate genes(GS5, ARGOS, MINI3, CLAVATA1, DEP2and IPAl/OsSPL14) could be mapped at eight locations. Among these candidate genes, GS5, ARGOS and MINI3which controlling seed component traits were mapped at the locations neighboring QTLs for thousand seeds weight (TSW), the number of seeds per silique (SN), silique length (SL) and seed yield (SY). The A. thaliana gene CLAVATA1, which governs flower/inflorescence traits, was mapped in the E conserved blocks neighboring a QTL for number of siliques on main inflorescence (SMI) on LG A2. The dense and erect panicle gene DEP2was mapped in the F conserved blocks neighboring QTLs for average length of primary branches (ALPB) and total length of primary branches (TLPB) on LG A5. The rice ideal plant architecture gene IPA1/OsSPL14was mapped in the N conserved blocks neighboring two QTLs for silique density of branches (SDB) on LG A9.
1.甘蓝型油菜遗传图谱的构建及图谱比较基因组学信息
利用DH群体构建了一张包含1902个标记(AFLP标记160个,SSR标记253个,IP标记80个,SCAR标记3个及SNP标记1406个)的高密度遗传连锁图,包含20条连锁群(C1连锁群被分成两条连锁群),图谱总长2328.97cM,标记间平均图距1.46cM,与国际上已发表的遗传图谱有较好的一致性。此外,通过Blastn分析将456个拟南芥同源基因、549个白菜同源基因和421个甘蓝同源基因定位到甘蓝型油菜A基因组,212个拟南芥基因、209个白菜同源基因和250个甘蓝基因定位到甘蓝型油菜C基因组。以已鉴定的拟南芥24个保守区段为基础,利用比对到图谱上的拟南芥基因鉴定了63个共线性片段和82个插入片段。
2.共线性分析
结果均表现为A基因组的共线性优于C基因组。对甘蓝型油菜连锁群与对应甘蓝型油菜假染色体的共线性分析,甘蓝型油菜连锁群与对应白菜、甘蓝假染色体的共线性分析,甘蓝型油菜染色体与对应白菜、甘蓝假染色体的共线性分析这三个结果进行比较,就共线性强弱程度而言,前两个基本一致,第三个大都优于前两个,这可能表明某些连锁关系还有待进一步确认,也可能本研究材料这些区域存在着染色体重排,但都进一步证实了甘蓝型油菜源于白菜和甘蓝；就甘蓝型油菜连锁群(BnAl-BnA10, BnCl-BnC9)、甘蓝型油菜染色体(Bnl-Bn19)、白菜(BrAl-BrA10)和甘蓝(BoC1-BoC9)染色体的方向来看,BnAl-Bnl-BrAl、 BnA2-Bn2-BrA2、 BnA4-Bn4-BrA4、 BnA6-Bn6-BrA6、 BnA7-Bn7-BrA7、 BnC3-Bnl3-BoC3、 BnC4-Bn14-BoC4、 BnC8-Bn18-BoC8、 BnC9-Bn19-BoC9三者两两间方向都相同。共线性分析结果揭示的方向及共线性程度的强弱对利用其他作物基因组序列信息来解决甘蓝型油菜的实际问题奠定了基础。
3.DH群体频率分布与QTL定位
分析了DH群体16个性状在三个环境下的频率分布,结果表明大多数性状呈连续分布且存在多峰,偏离了标准正态分布。通过复合区间作图法(CIM)在全基因组进行QTL扫描分析,16个性状在三个环境中分别检测到117个、122个、98个QTL,共计337个QTL。利用不同性状逐一进行QTL元分析后,这337个QTL最终整合为234个,分配在甘蓝型油菜20条连锁群上。其中平均分枝长度(ALPB)检测到17个QTL,分布在A1、A3、A5、A6、A7和C1a连锁群,单个QTL解释的遗传变异为3.9-25.9%；主花序长度(LMI)检测到23个QTL,分布在A1、A3、 A5、A6、A7、C8和C9连锁群,单个QTL解释的遗传变异为4.7-25.5%；角果层长度(LSL)检测到10个QTL,分布在A1、A3、A6、A9、C3和C8连锁群,单个QTL解释的遗传变异为5.1-11.8%；分枝角果数(NSB)检测到9个QTL,分布在A1、A3、A9和C3连锁群,单个QTL解释的遗传变异为4.4-20.1%；一次有效分枝数(PB)检测到15个QTL,分布在A1、A4、A7、Cla、Clb、C2、C3和C4连锁群,单个QTL解释的遗传变异为4.7-15.1%；株高(PH)检测到15个QTL,分布在A1、A3、A6、A7、Clb和C9连锁群,单个QTL解释的遗传变异为0.7-32.2%；分枝角果密度(SDB)检测到24个QTL,分布在A1、A3、A5、A6、A7、A9、Cla、 Clb、C6、C7和C9连锁群,单个QTL解释的遗传变异为4.4-16.0%；主花序角果密度(SDMI)检测到10个QTL,分布在A3、A6、A7、Cla和C7连锁群,单个QTL解释的遗传变异为5.3-12.9%；角果长度(SL)检测到11个QTL,分布在A1、A7、A9和A10连锁群,单个QTL解释的遗传变异为2.4-60.0%；主花序角果数(SMI)检测到17个QTL,分布在A1、A2、A3、A5、A9和C1a连锁群,单个QTL解释的遗传变异为4.7-14.8%；每角果粒数(SN)检测到15个QTL,分布在A1、A6、 A7、A8、Cla、Clb、C3和C5连锁群,单个QTL解释的遗传变异为4.9-26.6%；单株角果数(SNPP)检测到9个QTL,分布在A1、A9和C3连锁群,单个QTL解释的遗传变异为4.8-24.3%；单株种子产量(SY)检测到10个QTL,分布在A1、 A3.A9.C3和C8连锁群,单个QTL解释的遗传变异为4.4-35.7%；总分枝长度(TLPB)检测到13个QTL,分布在A1、A3、A6、A9、Cla和C3连锁群,单个QTL解释的遗传变异为5.3-17.9%；千粒重(TSW)检测到16个QTL,分布在A1、A7、A9、 Cla、Clb、C8和C9连锁群,单个QTL解释的遗传变异为3.4-38.8%；角果层宽度(WSL)检测到20个QTL,分布在A1、A2、A3、A5、A7和A9连锁群,单个QTL解释的遗传变异为4.2-31.3%。
4.甘蓝型旁系同源保守区段内的QTL及同源QTL分析
第一轮元分析的234个QTL中有168个能定位到十字花科保守区段上,包括U、H、F、W、E、R、J、C、X、M、N、B、I、A共计14个保守区段。根据QTL的分布情况,在甘蓝型油菜基因组的旁系同源保守区段寻找同源QTL,结果8个性状包括一次有效分枝数、角果长度、角果层宽度、每角果粒数、千粒重、株高、主花序长度、种子产量共发现了8对同源QTL,这8对同源QTL分布在E、U、X、R保守区段。
5.多效性QTL及产量指示QTL
第二轮元分析整合结果表明共存在59个多效性QTL,这些多效性QTL涉及2-8个性状不等,为设计理想株型提供了依据。如mqA1.114将株型性状、株型兼角果性状、角果性状、单株产量整合到一起。本研究中检测到的10个种子产量QTL中的7个存在于多效性QTL中。在这7个与产量相关的多效性QTL中,mqA1.14、mqA9.4、mqC8.11的指示性状分别是主花序长度、主花序角果数和千粒重千粒重,而mqA1.5、 mqA1.9、mqC3.2和mqC3.4中没有一个QTL能作为单株产量的指示QTL。
6.株型与产量候选基因在图谱上的定位
连锁分析表明,依据拟南芥株型及籽粒相关基因TCP24、Sep1、AP1、STM、 LFY、ANT、AXR6、PIN1、AP3、REV,、TTG2、TT5设计的21对引物获得的26个标记可被定位到图谱的不同位置上,且在某些基因标记附近能检测到QTL,但这些QTL与候选基因是否存在着一定的联系还需进一步证实。同时,本研究还以定位到图谱上的拟南芥基因为桥梁,将玉米、水稻中株型及产量相关的重要基因定位到本研究构建的遗传图谱的大致位置上,结果有6个候选基因(GS5、ARGOS、MINI3、 CLAVATA1、DEP2、IPA1/OsSPL14)定位到遗传图谱的8个不同位置,其中与籽粒相关的基因GS5.ARGOS和MINI3被定位到附近有千粒重、每角果粒数、角果长度、籽粒产量性状相关QTL的位置上；与花/花序相关的拟南芥基因CLAVATA1被定位到A2连锁群的E保守区段,在此位置附近有一个主花序角果数的QTL；直立密穗基因DEP2被定位到A5连锁群F保守区段,在其附近有平均分枝长度和总分枝长度的QTL；水稻理想株型基因IPAl/OsSPL14被定位到A9连锁群N区段,相应位置定位了两个分枝角果密度的QTL。
At present, the breeding of rapeseed varieties with improved plant type and suitable for the mechanised production is one of the major directions of rapeseed breeding in China. The work on the genetic basis and QTL mapping of the traits associated with plant type could provide a basis for molecular marker assisted breeding of the new B. napus varieties with specific plant type. In this study, a population consisting of181DH lines, which was derived from F1microspore culture of a cross of the B. napus lines8008(normal plant type, high seed-yield per plant) and94942C-5(compact plant type, low seed-yield per plant), was used as the field test materials. Sixteen plant type-or yield-associated traits were analyzed, and the QTLs for these traits were mapped. The major results are as following:
1. The genetic map construction and comparative genomics information of B. napus
Using the double haploid population, a linkage map containing1904markers, including160AFLPs,254SSRs,79IPs,3SCARs and1048SNPs, was constructed. The resulting map consisted of20linkage groups (the C1was divided into two linkage groups), covering2328.97cM with an average of1.46cM between markers, with a considerable consistence to the previously published linkage maps. Moreover, the BLASTN analysis showed that456,549and421homologous genes from A. thaliana, B. rapa and B. oleracea respectively, could be mapped on A genome of B. napus. And212,209and250homologous genes from A. thaliana, B. rapa and B. oleracea respectively, could be mapped on C genome of B. napus. Based on the24identified conserved regions in A. thaliana,63sythenic blocks and82insertion fragments were identified by using the A. thaliana genes mapped on the genetic map of B. napus.
2. Synteny analysis
The results indicated that the synteny in A genome was better than that in C genome. Alignments of linkage groups in B. napus to pseudochromosomes in B. napus, linkage group in B. napus to the pseudochromosomes in B. rapa and B. oleracea, and the pseudochromosomes in B. napus to pseudochromosomes in B. rapa and B. oleracea showed that the synteny extents in the first two alignments were equivalent and the synteny extent in the third alignment was mostly better than that in in the first two alignments. These results suggested that though the linkage relationship between some loci on the genetic map constructed in this study maybe needs further confirmation, or it is possible that chromosomal rearrangement really exits in these regions, the results from synteny analysis still fully confirmed the fact that B. napus is derived from B. rapa and B. oleracea. Considering the arrangement directions in the linkage groups in B. napus (BnA1-BnA10, BnC1-BnC9), the pseudochromosomes in B. napus (Bnl-Bnl9), B. rapa (BrA1-BrA10) and B. oleracea (BoC1-BoC9), the consistent direction was found in each element of the trisomes of BnAl-Bnl-BrAl, BnA2-Bn2-BrA2, BnA4-Bn4-BrA4, BnA6-Bn6-BrA6, BnA7-Bn7-BrA7, BnC3-Bn13-BoC3, BnC4-Bn14-BoC4, BnC8-Bnl8-BoC8, BnC9-Bnl9-BoC9. The information on direction and synteny extent could provide a basis for the revolution of the practical problem in B. napus by utilizing the genome sequence information from other crops.
3. Frequency distribution in DH population
The frequency distribution of the16traits in the DH population was analyzed in three environments. The results indicated that most traits showed a multimodal continuous distribution, deviating from the standard normal distribution. Using the composite interval mapping (MCIM), a genome-wide scan for QTLs was conducted. A total of337QTLs for the16traits were detected in three environments (117QTLs in11WH,122QTLs in12WH,98QTLs in11EZ). After meta-analysis was conducted for each trait, the337QTLs were consolidated into234QTLs covering20LGs. Seventeen QTLs controlling average length of primary branches (ALPB) were identified on6LGs:A1, A3, A5, A6, A7and Cla, with the individual QTL explaining3.9-25.9%of the phenotypic variation. For length of main inflorescence (LMI),10QTLs were detected on LGs Al, A3, A5, A6, A7, C8and C9, with the individual QTL explaining4.7-25.5%of the phenotypic variation. For the length of silique layer (LSL),10QTLs were detected on LGs A1, A3, A6, A9, C3and C8, with the individual QTL explaining5.1-11.8%of the phenotypic variation. Nine QTLs for number of siliques on branches (NSB) were assigned on four LGs: A1, A3, A9and C3, with the individual QTL accounting for4.4-20.1%of the phenotypic variation. For the number of primary branches (PB),15QTLs were detected on LGs Al, A4, A7, Cla, Clb, C2, C3and C4, with the individual QTL explaining4.7-15.1%of the phenotypic variation. Fifteen QTLs controlling plant height (PH) were detected on6LGs:A1, A3, A6, A7, Clb and C9, with the individual QTL explaining0.7-32.2%of the phenotypic variation. Twenty-four QTLs for silique density of branches (SDB) were assigned on11LGs:A1, A3, A5, A6, A7, A9, Cla, Clb, C6, C7and C9, with the individual QTL accounting for4.4-16.0%of the phenotypic variation. For silique density on main inflorescence (SDMI), 10QTLs were detected on LGs A3, A6, A7, Cla, and C7, with the individual QTL explaining5.3-12.9%of the phenotypic variation. For silique length (SL),11QTLs were detected on LGs Al, A7, A9and A10, with the individual QTL explaining2.4-60.0%of the phenotypic variation. Seventeen QTLs controlling number of siliques on main inflorescence (SMI) were detected on6LGs:Al, A2, A3, A5, A9and Cla, with the individual QTL explaining4.7-14.8%of the phenotypic variation. For number of seeds per silique (SN),15QTLs were detected on8LGs:Al, A6, A7, A8, Cla, Clb, C3and C5, with the individual QTL explaining4.9-26.6%of the phenotypic variation. Nine QTLs for silique number per plant (SNPP) were assigned on3LGs:Al, A9and C3, with the individual QTL accounting for4.8-24.3%of the phenotypic variation. For seeds yield per plant (SY),10QTLs were identified on5LGs: A1, A3, A9, C3and C8, with the individual QTL explaining4.4-35.7%of the phenotypic variation. Thirteen QTLs for total length of primary branches (TLPB) were assigned on6LGs:A1, A3, A6, A9, Cla and C3, with the individual QTL accounting for5.3-17.9%of the phenotypic variation. For and thousand seed weight (TSW),16QTLs were detected on7LGs:Al, A7, A9, Cla, Clb, C8and C9, with the individual QTL explaining3.4-38.8%of the phenotypic variation. Twenty QTLs for silique the width of silique layer (WSL) were assigned on6LGs:Al, A2, A3, A7and A9, with the individual QTL accounting for4.2-31.3%of the phenotypic variation.
4. QTLs and homologous QTLs mapped in paralogous conserved blocks in B. napus.
One hundred and sixty-eight of the234QTLs identified by the first round meta-analysis could be mapped in silico in the14conserved crucifer blocks (U, H, F, W, E, R, J, C, X, M, N, B, I and A). Eight pairs of homologous QTLs for PB, SL, WSL, SN, TSW, PH, LMI and SY were found in paralogous conserved blocks E, U, X and R in B. napus.
5. Pleiotropic QTLs and indicator-QTLs for yield
The integrated results from the second round meta-analysis showed that there were59pleiotropic QTLs, and each of them was associated with2to8traits for designing ideal plant architecture. For example, mqA1.14integrated the traits on plant architecture traits, plant architecture and silique-traits, silique traits and seed yield together. Seven of ten QTLs detected in this study for seed yield were identified as pleiotropic QTLs. Among these pleiotropic QTLs, indicator traits of mqA1.14, mqA9.4and mqC8.1were length of main inflorescence, number of siliques on main inflorescence and thousand seeds weight, respectively, but no a QTL could be regarded as yield-indicator QTL in mqA1.5, mqA1.9, mqC3.2and mqC3.4.
6. The mapping of candidate genes governing plant type and yield traits on the genetic map
Linkage analysis showed that26markers, which derived from21primer pairs designed by the A. thaliana genes governing plant type and seed traits (TCP24, Sepl, API, STM, LFY, ANT, AXR6, PIN1, AP3, REV, TTG2and TT5), could be mapped at the different locations on this genetic map. Nearby some genic-markers, QTLs could be detected. However, the correlation between these QTLs and the candidate genes needs further confirmation. Using the A. thaliana genes mapped on the genetic map in this study as a bridge, some important genes governing plant type and yield component traits in rice and corn were roughly mapped on the genetic map in this study. The results showed that6candidate genes(GS5, ARGOS, MINI3, CLAVATA1, DEP2and IPAl/OsSPL14) could be mapped at eight locations. Among these candidate genes, GS5, ARGOS and MINI3which controlling seed component traits were mapped at the locations neighboring QTLs for thousand seeds weight (TSW), the number of seeds per silique (SN), silique length (SL) and seed yield (SY). The A. thaliana gene CLAVATA1, which governs flower/inflorescence traits, was mapped in the E conserved blocks neighboring a QTL for number of siliques on main inflorescence (SMI) on LG A2. The dense and erect panicle gene DEP2was mapped in the F conserved blocks neighboring QTLs for average length of primary branches (ALPB) and total length of primary branches (TLPB) on LG A5. The rice ideal plant architecture gene IPA1/OsSPL14was mapped in the N conserved blocks neighboring two QTLs for silique density of branches (SDB) on LG A9.
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