甘蓝型油菜亚基因组间杂种优势分子遗传基础研究
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摘要
将芸薹属中白菜型油菜(Brassic rapa,2n=2X=20, ArAr)的基因组片段导入到甘蓝型油菜(Brassic napus,2n=4X=38, AnAnCnCn)中,形成一类新型的甘蓝型油菜(New type Brassic napus,4X=38, Ar/nAr/nCnCn)。将新型的甘蓝型油菜与自然甘蓝型油菜(AnAnCnCn)杂交产生的杂交种Ar/nAnCnCn能表现出强大的杂种优势,这种优势我们称为亚基因组间杂种优势。多项研究已证实亚基因组间杂种优势的存在,但其产生的遗传机理仍未得到揭示。为了研究白菜基因组片段的渗透对甘蓝型油菜基因组的结构变异的影响,并揭示亚基因组间杂种优势产生的分子遗传机理,我们利用一个半冬性的甘蓝型油菜品种“华双3号”(简称H3,2n=38)与一个中国半冬性白菜型油菜品种“天门油菜白”(简称TM,2n=20)杂交,然后再与白菜型油菜回交,通过染色体观察和单粒传的方式衍生了一个由138个F8新型甘蓝型油菜株系组成的重组自交系群体(简称TH-RIL群体)。将TH-RIL每个株系与原始甘蓝型油菜亲本H3回交建立了一个回交群体(简称TH-BC)。将TH-RIL群体、TH-BC群体和两亲本(H3兼作对照)进行了两年一点的田间试验。考察了种子产量、每角果粒数、千粒重、地上部分生物学产量、开花期、株高、分枝数和含油量等8个性状,另外通过上述性状计算获得了单株角果数和产油量两个性状值。
通过表型数据分析结果表明,在TH-RIL群体中,新型甘蓝型油菜千粒重性状与自然甘蓝型油菜亲本相比,变化最为明显。有77.5%TH-RILs株系的千粒重超过H3；近一半的株系在株高、全株角果数和干物质重超过H3；有20.3%的株系在单株产量上超过H3；不足30%的株系在其他性状方面超过H3。这说明白菜基因组渗透到甘蓝型油菜后,能够对甘蓝型油菜产生较广泛的变异。在TH-BC群体中,亚基因组间杂种优势表现突出。中亲优势(Mid-parent heterosis, MPH)变异范围从0.0%(千粒重)到47.1%(产油量),而超亲优势(over parent heterosis, OPH)变异从-7.4%(分支数)到26.9%(产油量)。平均有97%左右的杂交组合的单株产量性状超过H3,群体平均产量中亲优势为28%。这说明,当白菜外源片段渗透到甘蓝型油菜时,表现比较明显的杂种优势。
利用545个SSR标记(289对引物扩增),28个IBAP(intron-based amplified polymorphism)标记,51个着丝粒特有的反转座子标记和248个非着丝粒特有的反转座子标记共872个多态性标记用来进行基因组结构变异分析和遗传图谱构建(命名为TH-RIL map)。构建了一个含有628个标记的新型甘蓝型油菜遗传图谱(TH map),包括A基因组上的10条连锁群,C基因组的7条连锁群(无C6和C7),其余的8条短连锁群无法与已发表的连锁群相对应。由于TH群体的C基因组供体仅来源于H3,部分C基因组上的连锁群的成功构建是由于部分同源染色体之间发生的同源重组而导致的。TH图谱总长为2272.8cM,标记之间平均遗传距离为3.9cM。
利用该群体进行基因组结构变异分析,新型甘蓝型油菜中一方面被导入了白菜特有的等位基因；另一方面渗透诱发了大量新的基因组结构变异,如等位基因的变异(不同于双亲的新带(N-type)的出现以及双亲共同带的消失(D-type))。分析表明新型甘蓝型油菜创建过程中可能有反转座子的激活。为了进一步验证反转座子的激活这一遗传现象,将TH-RIL群体中扩增出的92条新的反转座子片段进行克隆测序,通过与三个转座子数据库进行比对,获得含转座子片段的序列65条,说明这些片段的变异是由于转座子的激活而诱发。同时利用65条序列与芸薹属基因组信息进行比对,设计12个RBIP (retrotransposon-based insersion polymorphism)引物再次证实了其存在。通过基因GO (http://www.geneontology.org/)注释发现在65条新变异的序列中有45条变异序列涉及到功能基因,主要是与代谢,细胞加工和胁迫有关的基因。
利用QTL Cartographer V2.5分析软件对三套数据(RIL群体数据,BC群体数据和MPH数据)进行单位点的QTL扫描分析。9个性状共检测到了123个QTL,其中微效作用但可以重复检测到QTL(简称MR-QTL)有40个,达到显著水平QTL(简称SL-QTL)有83个。利用TH-RIL群体分析白菜基因组的渗透对新型甘蓝型油菜的作用,在TH-RIL群体中检测到58个QTL,有33个QTL定位在包含N-type等位点的区域,这些新检测到的QTL能解释64.2%的表型变异,并且大约40%的QTL对性状表现出正向作用。来源于白菜基因组的Ar等位基因的渗透也对产量和产量相关的性状产生重要影响,另外有6个QTL和1/5的单标记分析位点都来源于B. rapa亲本。
利用TH-BC群体和TH-MPH数据进行杂种优势分析,对在这两个群体中检测的66个QTL进行显性度分析,确定了63个QTL为从部分显性到超显性效应的杂种优势位点。其中包括7个部分显性,6个完全显性和50个超显性。所有的与杂种优势有关的等位基因将可以分成5类,Ar(直接来源于白菜型油菜),An(直接来源于甘蓝型油菜),An(间接来自于A基因组发生变异的等位点),Cn(间接来自于C基因组变异的等位点)和L(分布在未定位的连锁群的一类)。92.0%QTL(58个)分布在A基因组,作用最大的一类来源于新变异的等位点(A。),占总数的47.1%QTL(32),并且起正向作用的位点比例为56.3%；其次直接来源于白菜等位基因的(Ar)有22.1%QTL(15个),并且起正向作用的比例为86.7%(13个)。23.9%的QTL与转座子的激活有关,正负作用的比例大致相等。这说明转座子的激活可以诱导新的等位基因的产生,并且对表型产生一定的影响。
利用QTL mapper2.0软件进行上位性互作效应检测,从三套数据中共检测到了536个非等位基因互作对。在TH-BC和TH-MPH数据检测的372个互作对中,A-A亚基因组的互作比例最高,为71.4%；其次是A-C亚基因组的互作为26.5%和C-C互作(2.1%)。每个等位基因各来源于五类(Ar, An, An, Cn和L)中的一种,可组成15种类型的两位点互作。从互作模型看,比例最大的是Ar-An(20.8%),其次为An-An(19.3%),平均58.6%互作对产生正向作用。由此可知,从单位点和两位点模型来看,亚基因组间杂种优势首先来源于白菜基因组渗透到甘蓝型油菜中所产生的新的发生变异的等位基因的贡献,其次是直接来源于白菜等位基因的作用,并且正效应的比例略大于负效应。从遗传模式看,亚基因组间杂种优势遗传模式是上位性、显性和超显性效应多种效应的综合作用。
甘蓝型油菜为异源多倍体,A和C基因组的高度相似性(同源基因)为杂种优势固定的研究提供了有利条件。利用TH-RIL群体中检测的203个互作对来分析杂种优势,并存在6对部分同源染色体之间的互作,被认为是固定杂种优势对。TH-RIL群体中的固定杂种优势的研究可为直接提高新型甘蓝型油菜的表型,间接提高杂种优势提供理论基础。
在甘白杂交过程中,由白菜基因组渗透所诱导的等位基因的变异及转座子的激活,诱发新型甘蓝型油菜中大量新等位基因产生。这些新的等位基因所产生单位点效应,它们之间的互作效应,新等位基因与直接渗透的亲本等位基因之间的互作效应成为亚基因组间杂种优势利用的重要理论基础。甘蓝型油菜作为一个多倍体模式物种,其亚基因间杂种优势的机理研究和应用,对为其它物种的相关研究,特别是利用亲本种和近缘种改良栽培种的研究,具有重要的指导和借鉴意义。
Introgression of Brassica rapa genome (2n=2X=20, ArAr) into Brassica napus (2n=4X=38, AnAnCnCn) creates a type of new type B. napus (4X=38, Ar/nAr/nCnCn). A cross between the new type B. napus and natural B. napus produces stronger heterosis, which is nominated as intersubgenomic heterosis. There were previous ample experiments to prove its truth but molecular genetic mechanism of intersubgenomic heterosis was still not unveiled. To investigate the influence of B. rapa genomic introgression on B. napus genomic structural variations and molecular mechanism of intersubgenomic heterosis, we developed a recombination inbred line (RIL) population (called TH-RIL) of new type B. napus of138Fg lines derived from an fertile BC1F2individual with38chromosomes which came from a corss of H3(a semi-winter B. napus cultivar)/TM (a semi-winter B. rapa cultivar)//TM and its corresponding backcrossed F1population (TH-BC) created by crosses of each RIL and H3. Field trial was carried out at one location in China in two years. One hundred and thirty eight recombination inbred lines,138BC combinations and their two parents (also as controls) were planted to evaluate for yield and eight yield-related traits, including seed yield, seed number per pod, kio-seed weight, dry weight, flowering time, plant height, branch number per plant, and oil content. In addition, pod number per plant and oil yield were calculated.
The phenotype data showed that compared with the better parent H3,77.5%of the RIL lines showed very obvious advantages on seed weight. Averagely almost half of the lines had advantages over H3in the respect of PH, SN and DW. The remaining traits, including OY, SY, PN, FT, were30%lower than H3in RIL lines. For SY trait,20.3%RIL lines exceeded H3. Such data demonstrated that the introgression of B. rapa into B. napus made phenotype have great variations. Middle parent heterosis (MPH) level ranged from SW (0.0%) to OY (47.1%) while the OPH ranged from BN (-7.4%) to OY (26.9%) while over-parent heterosis ranged from-7.4%(branch number) to26.9%(oil yield). About97%hybrid combinations exceeded H3for seed yield with an average of28%. This showed that when alien B. rapa genomic fragments were introgressed into B. napus, obvious heterosis appeared.
Analysis of genomic structural variation and genetic mapping were conducted with872different kinds of markers, including545SSR markers amplified by289SSR prier pairs,51centromere-specific retrotransposon (RTc) markers, and248noncentromere-specific retrotransposon (RTnc).
TH-RIL genetic map was constructed by628markers and has25linkage groups (LGs) covering2272.8cM with an average interval of3.9cM, including10LGs in A genome,7LGs in C genome except C6and C7, and8un-corresponding LGs with other published maps. The donor of C genome in TH-RILs only originated from C genome of H3, so partial C-genomic linkage groups could be successfully constructed because homoeologous recombination occurred between homoeologous chromosomes.
Through the analysis of genome-wide structural variation in the TH-RIL population, we found that new type B. napus contained B. rapa-specific alleles and numerous new alleles, such as the occurrence of N-type alleles (being present in some TH-RILs but absent in two parents) and D-type alleles (being present in two parents but absent in some TH-RILs). The analysis showed that retrotransposon markers were reactivated during the development of materials. Ninety two N-type varied bands were sequenced and analyzed by three transposon-specific databases. Sixty five sequences contained the transposon fragments, which showed that these genomic variations occurred by the induction of transposons. Finally, we detected12RBIP sites to confirm the occurrence of retrotransposon reactivation again. Go annotation toward sequenced65variants found that45variants were involved with functional genes, mainly including metabolism, cellular process and stress. The analysis of correlation coefficients showed that the novel sequence variation had significant impacts on the investigated traits.
Three data sets, including RIL population, BC population and middle parent heterosis data (MPH) were used to analyze QTL by QTL Cartographer V2.5software. A total of123QTL for yield and nine yield-related traits were identified with40repeatable micro-QTL (MR-QTL) and83significant-level (SL-QTL) over the threshold. Fifty eight QTLs were detected in TH-RIL population. Thirty-three of the41QTL were located in chromosomal varied regions that could explain the64.2%phenotypic variation, and two fifths of the QTL contributed positively to the improvement in the agronomic traits. B. rapa genomic fragment (Ar) also played a great role in seed yield and yield-related traits, and6QTL and1/5loci detected by single-marker analysis originated from B. rapa parent.
The heterosis analysis was performed using the TH-BC and TH-RIL data sets. By the analysis of dominant degree,63(54.6%) of66QTL belonged to heterosis-related QTL, including7partial dominance loci,6full dominance loci and50over dominance loci. In total,92.0%QTL (58) were distributed in A genome. Based on allele origin, five types of allele Ar (directly derived from B. rapa), An (directly derived from B. napus), An and Cn (indirectly produced by B. rapa introgression in A genome and C genome, respectively, and L (unmapped alleles). As the first factor,47.1%QTL (32) originated from novel varied alleles (An) in A subgenome with56.3%(18) loci of32QTL conducting favorable effect, then next to15QTL (22.1%) from Ar with86.7%(13) of15derived Ar loci arising positive effect. Furthermore,14.1%QTL were mapped in the rearrangement region and80%of these loci play a positive role while23.9%loci of QTL were involved with retrotransposon reactivity and52.9%among them performed a positive function. This indicated that the retrotransposon reactivity could induce new allelic emergence which indirectly played a great role in phenotype traits.
Additionally,536interacting pairs of epistatic effect were also found by QTL mapper2.0software. For epistasis,372interaction pairs detected in TH-BC and TH-MPH data sets were identified and A-A subgenomic interaction ranked the first (71.4%), then followed by A-C interaction (26.5%) and the remained C-C interaction (2.1%). Since there was five allelic origins (Ar, An, An, Cn and L),15interacted patterns could be detected among interaction of five origins. The most important interacted modes were Ar-An (20.8%) and An-An (19.3%) which averagely58.6%loci produced a positive effect. It suggested that intersubgenomic heterosis were mainly rooted in An induced B. rapa genome introgression into B. napus and direct-effect Ar genome by the dissecting of whether single QTL or two-QTL interaction which slightly more than half of alleles worked as a positive function. The genetic mode of intersubgenomic heterosis was a comprehensive function of epistasis, dominant effect, and over dominant effect.
B. napus was an allopolyploid species and the higher homology between A and C genome provided the beneficial foundation for fixed heterosis study. We detected203interacted pairs in RIL population to analyze heterosis fixation. Six interacted pairs between homoeologous genomic fragments were considered as fixed heterosis loci which may be resulted from chromosomal rearrangements. The investigation of fixed heterosis could directly improve the performance of new type B. napus and indirectly enhance intersubgenomic heterosis.
An emergence of lots of novel alleles and chromosomal rearrangements induced by interspecific hybridization of B. napus and B. rapa makes new type B. napus significantly distinct from natural B. napus at alleles and genomic structure. Each pair of newly-detected alleles in an intersugenomic hybrid displayed dominance or over dominance alone. A wealth of alleles, allelic combination and allelic interaction which less occurred in an inter-variety hybrid, constitute the origin of intersubgenomic heterosis. It may be the essence of intersubgenomic heterosis merging epistasis and dominance effect from partial dominance to over dominance. B. napus, as a model crop of the study of polyploid, intersubgenomic heterosis and fixed heterosis, could play a great referenced role for guiding the research and breeding of other crops.
通过表型数据分析结果表明,在TH-RIL群体中,新型甘蓝型油菜千粒重性状与自然甘蓝型油菜亲本相比,变化最为明显。有77.5%TH-RILs株系的千粒重超过H3；近一半的株系在株高、全株角果数和干物质重超过H3；有20.3%的株系在单株产量上超过H3；不足30%的株系在其他性状方面超过H3。这说明白菜基因组渗透到甘蓝型油菜后,能够对甘蓝型油菜产生较广泛的变异。在TH-BC群体中,亚基因组间杂种优势表现突出。中亲优势(Mid-parent heterosis, MPH)变异范围从0.0%(千粒重)到47.1%(产油量),而超亲优势(over parent heterosis, OPH)变异从-7.4%(分支数)到26.9%(产油量)。平均有97%左右的杂交组合的单株产量性状超过H3,群体平均产量中亲优势为28%。这说明,当白菜外源片段渗透到甘蓝型油菜时,表现比较明显的杂种优势。
利用545个SSR标记(289对引物扩增),28个IBAP(intron-based amplified polymorphism)标记,51个着丝粒特有的反转座子标记和248个非着丝粒特有的反转座子标记共872个多态性标记用来进行基因组结构变异分析和遗传图谱构建(命名为TH-RIL map)。构建了一个含有628个标记的新型甘蓝型油菜遗传图谱(TH map),包括A基因组上的10条连锁群,C基因组的7条连锁群(无C6和C7),其余的8条短连锁群无法与已发表的连锁群相对应。由于TH群体的C基因组供体仅来源于H3,部分C基因组上的连锁群的成功构建是由于部分同源染色体之间发生的同源重组而导致的。TH图谱总长为2272.8cM,标记之间平均遗传距离为3.9cM。
利用该群体进行基因组结构变异分析,新型甘蓝型油菜中一方面被导入了白菜特有的等位基因；另一方面渗透诱发了大量新的基因组结构变异,如等位基因的变异(不同于双亲的新带(N-type)的出现以及双亲共同带的消失(D-type))。分析表明新型甘蓝型油菜创建过程中可能有反转座子的激活。为了进一步验证反转座子的激活这一遗传现象,将TH-RIL群体中扩增出的92条新的反转座子片段进行克隆测序,通过与三个转座子数据库进行比对,获得含转座子片段的序列65条,说明这些片段的变异是由于转座子的激活而诱发。同时利用65条序列与芸薹属基因组信息进行比对,设计12个RBIP (retrotransposon-based insersion polymorphism)引物再次证实了其存在。通过基因GO (http://www.geneontology.org/)注释发现在65条新变异的序列中有45条变异序列涉及到功能基因,主要是与代谢,细胞加工和胁迫有关的基因。
利用QTL Cartographer V2.5分析软件对三套数据(RIL群体数据,BC群体数据和MPH数据)进行单位点的QTL扫描分析。9个性状共检测到了123个QTL,其中微效作用但可以重复检测到QTL(简称MR-QTL)有40个,达到显著水平QTL(简称SL-QTL)有83个。利用TH-RIL群体分析白菜基因组的渗透对新型甘蓝型油菜的作用,在TH-RIL群体中检测到58个QTL,有33个QTL定位在包含N-type等位点的区域,这些新检测到的QTL能解释64.2%的表型变异,并且大约40%的QTL对性状表现出正向作用。来源于白菜基因组的Ar等位基因的渗透也对产量和产量相关的性状产生重要影响,另外有6个QTL和1/5的单标记分析位点都来源于B. rapa亲本。
利用TH-BC群体和TH-MPH数据进行杂种优势分析,对在这两个群体中检测的66个QTL进行显性度分析,确定了63个QTL为从部分显性到超显性效应的杂种优势位点。其中包括7个部分显性,6个完全显性和50个超显性。所有的与杂种优势有关的等位基因将可以分成5类,Ar(直接来源于白菜型油菜),An(直接来源于甘蓝型油菜),An(间接来自于A基因组发生变异的等位点),Cn(间接来自于C基因组变异的等位点)和L(分布在未定位的连锁群的一类)。92.0%QTL(58个)分布在A基因组,作用最大的一类来源于新变异的等位点(A。),占总数的47.1%QTL(32),并且起正向作用的位点比例为56.3%；其次直接来源于白菜等位基因的(Ar)有22.1%QTL(15个),并且起正向作用的比例为86.7%(13个)。23.9%的QTL与转座子的激活有关,正负作用的比例大致相等。这说明转座子的激活可以诱导新的等位基因的产生,并且对表型产生一定的影响。
利用QTL mapper2.0软件进行上位性互作效应检测,从三套数据中共检测到了536个非等位基因互作对。在TH-BC和TH-MPH数据检测的372个互作对中,A-A亚基因组的互作比例最高,为71.4%；其次是A-C亚基因组的互作为26.5%和C-C互作(2.1%)。每个等位基因各来源于五类(Ar, An, An, Cn和L)中的一种,可组成15种类型的两位点互作。从互作模型看,比例最大的是Ar-An(20.8%),其次为An-An(19.3%),平均58.6%互作对产生正向作用。由此可知,从单位点和两位点模型来看,亚基因组间杂种优势首先来源于白菜基因组渗透到甘蓝型油菜中所产生的新的发生变异的等位基因的贡献,其次是直接来源于白菜等位基因的作用,并且正效应的比例略大于负效应。从遗传模式看,亚基因组间杂种优势遗传模式是上位性、显性和超显性效应多种效应的综合作用。
甘蓝型油菜为异源多倍体,A和C基因组的高度相似性(同源基因)为杂种优势固定的研究提供了有利条件。利用TH-RIL群体中检测的203个互作对来分析杂种优势,并存在6对部分同源染色体之间的互作,被认为是固定杂种优势对。TH-RIL群体中的固定杂种优势的研究可为直接提高新型甘蓝型油菜的表型,间接提高杂种优势提供理论基础。
在甘白杂交过程中,由白菜基因组渗透所诱导的等位基因的变异及转座子的激活,诱发新型甘蓝型油菜中大量新等位基因产生。这些新的等位基因所产生单位点效应,它们之间的互作效应,新等位基因与直接渗透的亲本等位基因之间的互作效应成为亚基因组间杂种优势利用的重要理论基础。甘蓝型油菜作为一个多倍体模式物种,其亚基因间杂种优势的机理研究和应用,对为其它物种的相关研究,特别是利用亲本种和近缘种改良栽培种的研究,具有重要的指导和借鉴意义。
Introgression of Brassica rapa genome (2n=2X=20, ArAr) into Brassica napus (2n=4X=38, AnAnCnCn) creates a type of new type B. napus (4X=38, Ar/nAr/nCnCn). A cross between the new type B. napus and natural B. napus produces stronger heterosis, which is nominated as intersubgenomic heterosis. There were previous ample experiments to prove its truth but molecular genetic mechanism of intersubgenomic heterosis was still not unveiled. To investigate the influence of B. rapa genomic introgression on B. napus genomic structural variations and molecular mechanism of intersubgenomic heterosis, we developed a recombination inbred line (RIL) population (called TH-RIL) of new type B. napus of138Fg lines derived from an fertile BC1F2individual with38chromosomes which came from a corss of H3(a semi-winter B. napus cultivar)/TM (a semi-winter B. rapa cultivar)//TM and its corresponding backcrossed F1population (TH-BC) created by crosses of each RIL and H3. Field trial was carried out at one location in China in two years. One hundred and thirty eight recombination inbred lines,138BC combinations and their two parents (also as controls) were planted to evaluate for yield and eight yield-related traits, including seed yield, seed number per pod, kio-seed weight, dry weight, flowering time, plant height, branch number per plant, and oil content. In addition, pod number per plant and oil yield were calculated.
The phenotype data showed that compared with the better parent H3,77.5%of the RIL lines showed very obvious advantages on seed weight. Averagely almost half of the lines had advantages over H3in the respect of PH, SN and DW. The remaining traits, including OY, SY, PN, FT, were30%lower than H3in RIL lines. For SY trait,20.3%RIL lines exceeded H3. Such data demonstrated that the introgression of B. rapa into B. napus made phenotype have great variations. Middle parent heterosis (MPH) level ranged from SW (0.0%) to OY (47.1%) while the OPH ranged from BN (-7.4%) to OY (26.9%) while over-parent heterosis ranged from-7.4%(branch number) to26.9%(oil yield). About97%hybrid combinations exceeded H3for seed yield with an average of28%. This showed that when alien B. rapa genomic fragments were introgressed into B. napus, obvious heterosis appeared.
Analysis of genomic structural variation and genetic mapping were conducted with872different kinds of markers, including545SSR markers amplified by289SSR prier pairs,51centromere-specific retrotransposon (RTc) markers, and248noncentromere-specific retrotransposon (RTnc).
TH-RIL genetic map was constructed by628markers and has25linkage groups (LGs) covering2272.8cM with an average interval of3.9cM, including10LGs in A genome,7LGs in C genome except C6and C7, and8un-corresponding LGs with other published maps. The donor of C genome in TH-RILs only originated from C genome of H3, so partial C-genomic linkage groups could be successfully constructed because homoeologous recombination occurred between homoeologous chromosomes.
Through the analysis of genome-wide structural variation in the TH-RIL population, we found that new type B. napus contained B. rapa-specific alleles and numerous new alleles, such as the occurrence of N-type alleles (being present in some TH-RILs but absent in two parents) and D-type alleles (being present in two parents but absent in some TH-RILs). The analysis showed that retrotransposon markers were reactivated during the development of materials. Ninety two N-type varied bands were sequenced and analyzed by three transposon-specific databases. Sixty five sequences contained the transposon fragments, which showed that these genomic variations occurred by the induction of transposons. Finally, we detected12RBIP sites to confirm the occurrence of retrotransposon reactivation again. Go annotation toward sequenced65variants found that45variants were involved with functional genes, mainly including metabolism, cellular process and stress. The analysis of correlation coefficients showed that the novel sequence variation had significant impacts on the investigated traits.
Three data sets, including RIL population, BC population and middle parent heterosis data (MPH) were used to analyze QTL by QTL Cartographer V2.5software. A total of123QTL for yield and nine yield-related traits were identified with40repeatable micro-QTL (MR-QTL) and83significant-level (SL-QTL) over the threshold. Fifty eight QTLs were detected in TH-RIL population. Thirty-three of the41QTL were located in chromosomal varied regions that could explain the64.2%phenotypic variation, and two fifths of the QTL contributed positively to the improvement in the agronomic traits. B. rapa genomic fragment (Ar) also played a great role in seed yield and yield-related traits, and6QTL and1/5loci detected by single-marker analysis originated from B. rapa parent.
The heterosis analysis was performed using the TH-BC and TH-RIL data sets. By the analysis of dominant degree,63(54.6%) of66QTL belonged to heterosis-related QTL, including7partial dominance loci,6full dominance loci and50over dominance loci. In total,92.0%QTL (58) were distributed in A genome. Based on allele origin, five types of allele Ar (directly derived from B. rapa), An (directly derived from B. napus), An and Cn (indirectly produced by B. rapa introgression in A genome and C genome, respectively, and L (unmapped alleles). As the first factor,47.1%QTL (32) originated from novel varied alleles (An) in A subgenome with56.3%(18) loci of32QTL conducting favorable effect, then next to15QTL (22.1%) from Ar with86.7%(13) of15derived Ar loci arising positive effect. Furthermore,14.1%QTL were mapped in the rearrangement region and80%of these loci play a positive role while23.9%loci of QTL were involved with retrotransposon reactivity and52.9%among them performed a positive function. This indicated that the retrotransposon reactivity could induce new allelic emergence which indirectly played a great role in phenotype traits.
Additionally,536interacting pairs of epistatic effect were also found by QTL mapper2.0software. For epistasis,372interaction pairs detected in TH-BC and TH-MPH data sets were identified and A-A subgenomic interaction ranked the first (71.4%), then followed by A-C interaction (26.5%) and the remained C-C interaction (2.1%). Since there was five allelic origins (Ar, An, An, Cn and L),15interacted patterns could be detected among interaction of five origins. The most important interacted modes were Ar-An (20.8%) and An-An (19.3%) which averagely58.6%loci produced a positive effect. It suggested that intersubgenomic heterosis were mainly rooted in An induced B. rapa genome introgression into B. napus and direct-effect Ar genome by the dissecting of whether single QTL or two-QTL interaction which slightly more than half of alleles worked as a positive function. The genetic mode of intersubgenomic heterosis was a comprehensive function of epistasis, dominant effect, and over dominant effect.
B. napus was an allopolyploid species and the higher homology between A and C genome provided the beneficial foundation for fixed heterosis study. We detected203interacted pairs in RIL population to analyze heterosis fixation. Six interacted pairs between homoeologous genomic fragments were considered as fixed heterosis loci which may be resulted from chromosomal rearrangements. The investigation of fixed heterosis could directly improve the performance of new type B. napus and indirectly enhance intersubgenomic heterosis.
An emergence of lots of novel alleles and chromosomal rearrangements induced by interspecific hybridization of B. napus and B. rapa makes new type B. napus significantly distinct from natural B. napus at alleles and genomic structure. Each pair of newly-detected alleles in an intersugenomic hybrid displayed dominance or over dominance alone. A wealth of alleles, allelic combination and allelic interaction which less occurred in an inter-variety hybrid, constitute the origin of intersubgenomic heterosis. It may be the essence of intersubgenomic heterosis merging epistasis and dominance effect from partial dominance to over dominance. B. napus, as a model crop of the study of polyploid, intersubgenomic heterosis and fixed heterosis, could play a great referenced role for guiding the research and breeding of other crops.
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