甘蓝型油菜硼高效基因的定位
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摘要
作物高产养分高效是当今新形势下的重要育种目标。油菜是世界上继大豆之后第二大油料作物,而甘蓝型油菜占油菜种植面积的约80%。硼是植物生长发育所必需的微量元素营养之一,而世界上耕作土壤缺硼问题已成为许多作物产量提高的重要限制因子。甘蓝型油菜是需硼较多的作物,对缺硼非常敏感,缺硼容易导致“花而不实”,减少籽粒产量,严重时甚至不能形成产量。施用硼肥可以缓解作物缺硼问题,但是硼矿资源有限,而且过多施用硼肥可能会引起一些生态环境问题。有研究表明,不同甘蓝型油菜品种间硼效率性状存在着丰富的基因型差异。利用遗传学和分子生物学手段来改良甘蓝型油菜的硼效率性状,培育硼高效高产的品种是解决甘蓝型油菜缺硼问题的一条重要途径。本研究利用实验室已构建的甘蓝型油菜硼高效BQ DH群体为材料构建遗传连锁图,并通过三年的田间试验调查硼缺乏和硼正常条件下群体成熟期的籽粒产量及产量相关性状的表型变异。结合BQ DH遗传连锁图谱和群体表型进行了全基因组硼高效相关QTL定位与分析。取得的主要研究结果如下：
1.甘蓝型油菜硼高效BQ DH遗传连锁图谱的构建
收集并合成了文献中报道的以"BnGMS"和‘'BoGMS"命名的SSR标记引物1413对,本实验室根据白菜基因组A2、A3、A9的BAC序列设计了403对SSR标记引物,以及本研究根据白菜A2基因组序列自主开发设计的50对SSR引物,并在BQ DH群体中进行基因型分析。利用作图软件Joinmap4.0构建了一张含有486个分子标记的BQ DH遗传连锁图谱。图谱含有SSR标记468个,SRAP标记7个,GBM标记9个以及2个特异标记。图谱总长为1873.9cM,标记间的平均遗传图谱为3.86cM。
2. BQ DH群体及其亲本在不同硼水平下的表型变异
以BQ DH群体和亲本为材料进行了三年的田间试验调查了盛花-结荚果时期硼缺乏条件下的缺硼症状表型和成熟期不同硼水平条件下籽粒产量及产量相关性状的表型变异。对于盛花-结荚果期：硼高效亲本QY10在缺硼条件下仍能较正常的开花结果,没有表现出明显缺硼症状,受缺硼影响很小；硼低效亲本Bakow则开花结实受到明显的影响,叶片有明显的缺硼症状,对缺硼表现很敏感。表明QY10相对于Bakow具有更强的适应硼缺乏的能力。BQ DH群体之间则表现出了缺硼症状的表型分离,出现了从Ⅰ到V级的不同程度的应答表现。对于成熟期而言,缺硼条件下,硼高效亲本QY10相比于硼低效亲本Bakow在籽粒产量、株高、分枝数、每株荚果数、每荚果粒数和千粒重上均有显著差异。硼正常条件下,硼高效亲本QY10相比于硼低效亲本Bakow在籽粒产量、每株荚果数和千粒重上有明显差异。研究表明,两个硼水平下BQ DH群体的所有产量及产量相关性状均表现连续变异,并有超亲分离现象,说明了这些性状为数量性状,并同时受多基因控制。性状间的遗传相关性在同一硼水平下差异较大,方差分析发现,基因型、硼水平、环境以及他们之间的互作对6个调查性状均有显著影响。
3. BQ DH群体成熟期籽粒产量及产量相关性状和缺硼指数性状的QTL检测与分析
对BQ DH群体在三年田间试验中两个硼水平条件下的籽粒产量、株高、分枝数、每株荚果数、每荚粒数、千粒重和硼效率系数性状进行QTL定位分析,利用WinQTLCartographer2.5软件共检测到70个显著性QTL,分布于15条连锁群(A5, A8, C1, C2除外),其中,硼缺乏条件下30个,硼正常条件35个,硼效率系数性状检测到5个。单个QTL解释了4.15-23.16%的表型变异。7和16个QTL分别在三年和两年试验中被重复检测到。通过BioMercator2.1软件,将其他研究报道的29个籽粒产量及产量相关性状的QTL映射到BQ DH遗传连锁图上,并分别与本研究报道的16个相应性状的QTL相互重叠。对于缺硼指数性状,检测到了3个QTL,位于A7和C8连锁群上。
4. BQ DH群体成熟期籽粒产量及产量相关性状的上位性互作的检测与分析
利用QTLNetwork2.0软件对BQ DH群体中两个硼水平下6个性状及硼效率系数总共检测到32个上位性互作对,分布于全基因组(A8除外)上。单个互作对的表型贡献率范围为0.53-14.26%。这32个互作对当中大部分是两个没有单位点效应的位点之间的互作,表明除了单位点QTL外还存在着许多没有单位点加性效应位点之间的上位性互作参与了性状的调控。
5. BQ DH遗传连锁图谱与拟南芥基因组的比较作图及in silico定位
利用BQ DH遗传连锁图谱上已知序列信息的分子标记作为锚定标记,将该遗传图谱与拟南芥基因组比较作图,在BQ DH遗传连锁图谱上定位了20个共线性区段和123个保守岛。通过in silico定位最终将拟南芥中153个与籽粒产量及产量相关性状和硼吸收代谢相关的基因定位到BQ DH群体中的70个QTL的区间内,并发现有硼代谢相关的基因定位在低硼条件下的籽粒产量QTL区间内。这些QTL信息和候选基因为深入研究提供了丰富的信息。
6.甘蓝型油菜硼高效主效位点BnBE1的定位及其候选基因的预测分析
通过比较分析BQ F2群体、TN DH群体以及本研究的BQ DH群体等三个群体的A2染色体上检测到的硼高效QTL,结果表明,这三个群体中定位到的硼高效QTL相互重叠,正是BQ F2报道的BE1。因此将此位点定为甘蓝型油菜成熟期硼高效主效QTL BnBE1。并利用与甘蓝型油菜A基因组高度同源的白菜基因组信息对主效位点BnBE1预测出6个候选基因,它们是关于小分子转运基因以及拟南芥中硼通道转运蛋白AtNP5;1和AtNIP7;1在白菜基因组中的同源基因。
Nutrient efficient crops which produce higher yields per unit of nutrient applied or absorbed is a latest important breeding target. Rapeseed is the second important oil crop after soybean. Brassica napus was the most important member of rapeseed which occupies about80%of rapeseed area. Boron (B) is one of essential micro-nutrient for high plant growth. B deficiency becomes a various limiting factor of increasing crop yield in the world. B. napus which is in great demand of B shows very sensitive to B deficiency. B deficiency could lead to flowering without seed set and yield decrease even no seed setting. Application of borax fertilizers can alleviate the problem in some degree, but can also lead to environmental problem, and B ore resources are limited. It was reported that considerable genotypic variation exists among different cultivars in response to B deficiency in B. napus. So, developing B efficiency cultivars by genetics and biotechnology is a essential approach for improving B. napus in response to B deficiency. In this study, a genetic linkage map was constructed based on the B. napus BQ DH population which was developed by other members in our group. Three-year field trials with low and normal B treatments were conducted using the BQ DH population for investigating seed yield and yield-related traits. Quantitative trait locus (QTL) analysis for seed yield and yield-related traits under low B and normal B conditions using the BQ DH population was conducted. Main results are as follows:
1. Construction of B efficiency BQ DH genetic linkage map in B. napus
A total of1413SSR primers named "BnGMS" and "BoGMS" from other study reports,403SSR primers developed by our group according to sequenced BAC of A2, A3and A9and50SSR primers developed according to sequence of A2chromosome in Brassica rapa in this study were used for genotyping in the BQ DH population. A genetic linkage map named as BQ DH map was constructed based on the BQ DH population by software Joinmam4.0. BQ DH genetic map comprise a total of486molecular markers, including468SSR markers,7SRAP markers,9GBM markers and2other markers, which covers a total length of1873.9cM with an average interval of3.86cM between adjacent markers.
2. Phenotype variations of the BQ DH population and their parents under different B conditions
Trait associated with B deficiency symptom at the full-bloom stage and filling stage under low B condition, seed yield and yield-related traits under both B conditions were investigated by three-year field trials using the BQ DH population and its parents. For the trait associated with B deficiency symptom, B-efficient cultivar QY10showed almost normal flowering and seed setting and almost no B deficiency symptom, B-inefficient cultivar Bakow was seriously influenced by B deficiency in flowering and seed setting and leaves. It indicated that QY10has a stronger adaptability to B deficiency than Bakow. Abundant variation among the BQ DH population ranged from grade I to grade V was observed. At the mature stage, significant differences were observed between the two parents by seed yield, plant height, branch number, pod number per plant, seed number per pod and seed weight under low B condition. And significant differences were observed between the two parents by seed yield, pod number per plant and seed weight under normal B condition. All the traits investigated under both B conditions showed continuous phenotypic variation and significant transgressive segregation in both directions, indicating these traits are all quantitative traits and controlled by multiple genes. Correlations among all the traits under single B condition were different. ANOVA results suggested that genotype, B level, environment and the interactions among these variable had significant effect on the six measured traits.
3. QTL detection for seed yield and yield-related traits and index of boron deficiency (GBD) in the BQ DH population
Seed yield, plant height, branch number, pod number per plant, seed number per pod and seed weight under both B conditions and B efficiency coefficient (BEC) were use for QTL mapping in the BQ DH population. A total of70putative QTLs distributing on15linkage groups (except for A5, A8, C1and C2) singly explaining4.15-23.16%of phenotypic variation were detected by software WinQTLCartographer2.5, including30QTLs under low B condition,35QTLs under normal B condition and5QTLs for BEC. Among these QTLs,7and16QTLs were identified across three and two trials, respectively. By BioMercator2.1,29QTLs for seed yield and yield-related traits from other populations were projected onto the BQ DH population, co-locating with16QTLs for the same trait. Three QTLs for GBD were detected distributing on A7and C8linkage groups.
4. Detection of epistatic interactions for seed yield and yield-related traits in the BQ DH population
Six measured traits under both B conditions and BEC were used to detect epistatic interactions in the BQ DH population by software QTLNetwork2.0. A total of32epistatic interactions distributing on the whole genome (except for A8) were detected, singly explaining0.53-14.26%of phenotypic variation. Most of them were the interactions between two loci without main-effect. It indicated that many epistatic interactions between two without main-effect loci are involved in regulating seed yield and yield-related traits under low and normal B conditions.
5. Comparative mapping between the BQ DH genetic linkage map and Arabidopsis genome and in silico mapping
The comparative mapping between B. napus and Arabidopsis was carried employing SSR and GBM markers with known sequence information as anchored markers based on identified24conserved chromosomal blocks on Arabidopsis genome. A total of20synteny blocks and123insertions fragment islands were identified. By in silico mapping,153genes associated with seed yield, yield-related traits and B metabolism were mapped to the confidence intervals of70putative QTLs in the BQ DH population. The information and candidate genes were benefit for further study.
6. Identification of B efficiency major locus BnBEl and prediction of candidate genes of BnBEl
Comparative analyzing the QTLs for B efficiency on A2linkage group in the BQ F2, TN DH and BQ DH populations, the QTLs for B efficiency of the three populations co-localize in the same genomic region, just was the reported BE1. And the major locus for B efficiency at the mature stage was designed as BnBEl. Six candidate genes of BnBE1were predicted using known B. rapa genome information, including small molecule transporter genes, and B. rapa homologous genes of AtNIP5;1and AtNIP7;1in Arabidopsis.
1.甘蓝型油菜硼高效BQ DH遗传连锁图谱的构建
收集并合成了文献中报道的以"BnGMS"和‘'BoGMS"命名的SSR标记引物1413对,本实验室根据白菜基因组A2、A3、A9的BAC序列设计了403对SSR标记引物,以及本研究根据白菜A2基因组序列自主开发设计的50对SSR引物,并在BQ DH群体中进行基因型分析。利用作图软件Joinmap4.0构建了一张含有486个分子标记的BQ DH遗传连锁图谱。图谱含有SSR标记468个,SRAP标记7个,GBM标记9个以及2个特异标记。图谱总长为1873.9cM,标记间的平均遗传图谱为3.86cM。
2. BQ DH群体及其亲本在不同硼水平下的表型变异
以BQ DH群体和亲本为材料进行了三年的田间试验调查了盛花-结荚果时期硼缺乏条件下的缺硼症状表型和成熟期不同硼水平条件下籽粒产量及产量相关性状的表型变异。对于盛花-结荚果期：硼高效亲本QY10在缺硼条件下仍能较正常的开花结果,没有表现出明显缺硼症状,受缺硼影响很小；硼低效亲本Bakow则开花结实受到明显的影响,叶片有明显的缺硼症状,对缺硼表现很敏感。表明QY10相对于Bakow具有更强的适应硼缺乏的能力。BQ DH群体之间则表现出了缺硼症状的表型分离,出现了从Ⅰ到V级的不同程度的应答表现。对于成熟期而言,缺硼条件下,硼高效亲本QY10相比于硼低效亲本Bakow在籽粒产量、株高、分枝数、每株荚果数、每荚果粒数和千粒重上均有显著差异。硼正常条件下,硼高效亲本QY10相比于硼低效亲本Bakow在籽粒产量、每株荚果数和千粒重上有明显差异。研究表明,两个硼水平下BQ DH群体的所有产量及产量相关性状均表现连续变异,并有超亲分离现象,说明了这些性状为数量性状,并同时受多基因控制。性状间的遗传相关性在同一硼水平下差异较大,方差分析发现,基因型、硼水平、环境以及他们之间的互作对6个调查性状均有显著影响。
3. BQ DH群体成熟期籽粒产量及产量相关性状和缺硼指数性状的QTL检测与分析
对BQ DH群体在三年田间试验中两个硼水平条件下的籽粒产量、株高、分枝数、每株荚果数、每荚粒数、千粒重和硼效率系数性状进行QTL定位分析,利用WinQTLCartographer2.5软件共检测到70个显著性QTL,分布于15条连锁群(A5, A8, C1, C2除外),其中,硼缺乏条件下30个,硼正常条件35个,硼效率系数性状检测到5个。单个QTL解释了4.15-23.16%的表型变异。7和16个QTL分别在三年和两年试验中被重复检测到。通过BioMercator2.1软件,将其他研究报道的29个籽粒产量及产量相关性状的QTL映射到BQ DH遗传连锁图上,并分别与本研究报道的16个相应性状的QTL相互重叠。对于缺硼指数性状,检测到了3个QTL,位于A7和C8连锁群上。
4. BQ DH群体成熟期籽粒产量及产量相关性状的上位性互作的检测与分析
利用QTLNetwork2.0软件对BQ DH群体中两个硼水平下6个性状及硼效率系数总共检测到32个上位性互作对,分布于全基因组(A8除外)上。单个互作对的表型贡献率范围为0.53-14.26%。这32个互作对当中大部分是两个没有单位点效应的位点之间的互作,表明除了单位点QTL外还存在着许多没有单位点加性效应位点之间的上位性互作参与了性状的调控。
5. BQ DH遗传连锁图谱与拟南芥基因组的比较作图及in silico定位
利用BQ DH遗传连锁图谱上已知序列信息的分子标记作为锚定标记,将该遗传图谱与拟南芥基因组比较作图,在BQ DH遗传连锁图谱上定位了20个共线性区段和123个保守岛。通过in silico定位最终将拟南芥中153个与籽粒产量及产量相关性状和硼吸收代谢相关的基因定位到BQ DH群体中的70个QTL的区间内,并发现有硼代谢相关的基因定位在低硼条件下的籽粒产量QTL区间内。这些QTL信息和候选基因为深入研究提供了丰富的信息。
6.甘蓝型油菜硼高效主效位点BnBE1的定位及其候选基因的预测分析
通过比较分析BQ F2群体、TN DH群体以及本研究的BQ DH群体等三个群体的A2染色体上检测到的硼高效QTL,结果表明,这三个群体中定位到的硼高效QTL相互重叠,正是BQ F2报道的BE1。因此将此位点定为甘蓝型油菜成熟期硼高效主效QTL BnBE1。并利用与甘蓝型油菜A基因组高度同源的白菜基因组信息对主效位点BnBE1预测出6个候选基因,它们是关于小分子转运基因以及拟南芥中硼通道转运蛋白AtNP5;1和AtNIP7;1在白菜基因组中的同源基因。
Nutrient efficient crops which produce higher yields per unit of nutrient applied or absorbed is a latest important breeding target. Rapeseed is the second important oil crop after soybean. Brassica napus was the most important member of rapeseed which occupies about80%of rapeseed area. Boron (B) is one of essential micro-nutrient for high plant growth. B deficiency becomes a various limiting factor of increasing crop yield in the world. B. napus which is in great demand of B shows very sensitive to B deficiency. B deficiency could lead to flowering without seed set and yield decrease even no seed setting. Application of borax fertilizers can alleviate the problem in some degree, but can also lead to environmental problem, and B ore resources are limited. It was reported that considerable genotypic variation exists among different cultivars in response to B deficiency in B. napus. So, developing B efficiency cultivars by genetics and biotechnology is a essential approach for improving B. napus in response to B deficiency. In this study, a genetic linkage map was constructed based on the B. napus BQ DH population which was developed by other members in our group. Three-year field trials with low and normal B treatments were conducted using the BQ DH population for investigating seed yield and yield-related traits. Quantitative trait locus (QTL) analysis for seed yield and yield-related traits under low B and normal B conditions using the BQ DH population was conducted. Main results are as follows:
1. Construction of B efficiency BQ DH genetic linkage map in B. napus
A total of1413SSR primers named "BnGMS" and "BoGMS" from other study reports,403SSR primers developed by our group according to sequenced BAC of A2, A3and A9and50SSR primers developed according to sequence of A2chromosome in Brassica rapa in this study were used for genotyping in the BQ DH population. A genetic linkage map named as BQ DH map was constructed based on the BQ DH population by software Joinmam4.0. BQ DH genetic map comprise a total of486molecular markers, including468SSR markers,7SRAP markers,9GBM markers and2other markers, which covers a total length of1873.9cM with an average interval of3.86cM between adjacent markers.
2. Phenotype variations of the BQ DH population and their parents under different B conditions
Trait associated with B deficiency symptom at the full-bloom stage and filling stage under low B condition, seed yield and yield-related traits under both B conditions were investigated by three-year field trials using the BQ DH population and its parents. For the trait associated with B deficiency symptom, B-efficient cultivar QY10showed almost normal flowering and seed setting and almost no B deficiency symptom, B-inefficient cultivar Bakow was seriously influenced by B deficiency in flowering and seed setting and leaves. It indicated that QY10has a stronger adaptability to B deficiency than Bakow. Abundant variation among the BQ DH population ranged from grade I to grade V was observed. At the mature stage, significant differences were observed between the two parents by seed yield, plant height, branch number, pod number per plant, seed number per pod and seed weight under low B condition. And significant differences were observed between the two parents by seed yield, pod number per plant and seed weight under normal B condition. All the traits investigated under both B conditions showed continuous phenotypic variation and significant transgressive segregation in both directions, indicating these traits are all quantitative traits and controlled by multiple genes. Correlations among all the traits under single B condition were different. ANOVA results suggested that genotype, B level, environment and the interactions among these variable had significant effect on the six measured traits.
3. QTL detection for seed yield and yield-related traits and index of boron deficiency (GBD) in the BQ DH population
Seed yield, plant height, branch number, pod number per plant, seed number per pod and seed weight under both B conditions and B efficiency coefficient (BEC) were use for QTL mapping in the BQ DH population. A total of70putative QTLs distributing on15linkage groups (except for A5, A8, C1and C2) singly explaining4.15-23.16%of phenotypic variation were detected by software WinQTLCartographer2.5, including30QTLs under low B condition,35QTLs under normal B condition and5QTLs for BEC. Among these QTLs,7and16QTLs were identified across three and two trials, respectively. By BioMercator2.1,29QTLs for seed yield and yield-related traits from other populations were projected onto the BQ DH population, co-locating with16QTLs for the same trait. Three QTLs for GBD were detected distributing on A7and C8linkage groups.
4. Detection of epistatic interactions for seed yield and yield-related traits in the BQ DH population
Six measured traits under both B conditions and BEC were used to detect epistatic interactions in the BQ DH population by software QTLNetwork2.0. A total of32epistatic interactions distributing on the whole genome (except for A8) were detected, singly explaining0.53-14.26%of phenotypic variation. Most of them were the interactions between two loci without main-effect. It indicated that many epistatic interactions between two without main-effect loci are involved in regulating seed yield and yield-related traits under low and normal B conditions.
5. Comparative mapping between the BQ DH genetic linkage map and Arabidopsis genome and in silico mapping
The comparative mapping between B. napus and Arabidopsis was carried employing SSR and GBM markers with known sequence information as anchored markers based on identified24conserved chromosomal blocks on Arabidopsis genome. A total of20synteny blocks and123insertions fragment islands were identified. By in silico mapping,153genes associated with seed yield, yield-related traits and B metabolism were mapped to the confidence intervals of70putative QTLs in the BQ DH population. The information and candidate genes were benefit for further study.
6. Identification of B efficiency major locus BnBEl and prediction of candidate genes of BnBEl
Comparative analyzing the QTLs for B efficiency on A2linkage group in the BQ F2, TN DH and BQ DH populations, the QTLs for B efficiency of the three populations co-localize in the same genomic region, just was the reported BE1. And the major locus for B efficiency at the mature stage was designed as BnBEl. Six candidate genes of BnBE1were predicted using known B. rapa genome information, including small molecule transporter genes, and B. rapa homologous genes of AtNIP5;1and AtNIP7;1in Arabidopsis.
引文
1.丁广大,杨美,李兴美.甘蓝型油菜分子标记在重组自交系群体中的偏分离分析,中国农业科技导报,2012,14(2)：56-61
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