油菜隐性细胞核雄性不育基因区段的比较分析与特异标记的开发
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摘要
甘蓝型油菜是由甘蓝和白菜杂交天然加倍后形成,基因组中包含A、C两个基因组的信息。由于A、C基因组是在大约400万年前由共同的芸薹属祖先分化而来,二者具有高度保守的基因组结构和微观共线性(Rana et al.,2004)。因此,甘蓝型油菜的遗传作图研究很可能会受到同源基因组的影响。从DNA序列水平上研究A、C基因组之间的变异,并在微观共线性良好的同源基因组之间区别二者,将为甘蓝型油菜的相关研究提供帮助。
9012AB是一种新的甘蓝型油菜隐性细胞核雄性不育材料,具有败育彻底,不育性稳定,恢复源广泛的特点,因此在三系配套育种中具有重要的利用价值。陈凤祥等对该材料的研究表明:其育性受到两对重叠隐性不育基因(ms3ms3、ms4ms4)和一对隐性上位抑制基因(rfrf)互作控制。何俊平等已将其中一个不育基因ms3精细定位在0.034cM的遗传区间。物理作图表明该区间最少由6个BAC克隆构成的一个完整的重叠群所覆盖,并利用亚克隆测序的方法获得其中包含目标基因的一个BAC克隆。为了进一步开发与Ms3紧密连锁的标记,并验证BAC克隆筛选的结果及比较该区间在甘蓝和白菜基因组之间的微观共线性关系,从而为Ms4的研究提供可能的便利,本研究从上述BAC克隆测序序列中随机选择20kb的区域在不同材料中进行比较测序并分析,获得如下主要结果:
1.根据20kb的区域设计18对引物,其扩增产物理论上能够构成一个完整的重叠群并完全覆盖该区间。利用这18对引物在9012A、9012B、白菜和甘蓝中扩增,扩增产物拼接后共得到三种材料52个区段序列信息。
2.对所得材料的区段序列进行比对分析发现,甘蓝型油菜Tapidor、9012A、9012B、白菜和甘蓝之间存在较好的微观共线性,且甘蓝型油菜9012A和白菜之间的相似性高,9012B、Tapidor和甘蓝之间的相似性高。参考模式植物拟南芥信息进一步基因预测发现:该区段3个对应基因方向相同,外显子区域一致且比较保守;内含子区段序列存在碱基的突变、插入或缺失。根据测序所得序列差异较大的区域,开发9012A和9012B之间6对多态性标记,白菜和甘蓝之间的多态性标记DM1和HWY。
3.经重组单株验证后,根据9012A和9012B之间序列差异开发的新标记在20,391个单株的分离群体中与ms3基因共分离。和原来的定位结果相比,虽然开发了新的标记,但并没有缩小包含ms3基因的物理区间。
4.根据白菜和甘蓝的序列差异,开发出在49份白菜和8份甘蓝之间存在稳定多态性的共显性标记2个。利用该标记筛选先前鉴定的甘蓝型油菜BAC克隆文库,发现标记在克隆中扩增产物与白菜基因组中大小和序列一致,而没有发现与甘蓝基因组中大小一致的克隆。而根据先前的研究,ms3基因定位于N19连锁群,对应甘蓝的第9染色体。据此推测,筛选到的BAC克隆事实上可能是ms3基因位于白菜基因组中的同源区。
5.利用BAC克隆开发出的SSR标记和本实验中开发的A、C基因组特异标记DM1在Ms4定位群体中进行多态性检测,发现所有标记在定位群体中与Ms4基因不连锁,暗示着Ms4基因可能根本就不是Ms3的一个同源基因,而是两个起源不同的基因。因此,以前认为Ms3和Ms4为重叠隐性基因的这一说法可能需要进一步论证。
Brassica napus is a polyploid resulting from the natural hybridization of B. rapa (containing the Brassica A genome) and B. oleracea (containing the Brassica C genome). The A and C genome differentiated from a common ancestor Brassica about 400 million years ago.They have highly conserve genome structure and high micro-collinearity (Rana et al., 2004), which may hamper the genetic mapping in Brassica napus.The research of the variance between A and C genomes on DNA sequence level can be used to distinguish homologous genomes between A and C genomes which have high microcollinearity, and therefore may provide some assistance of the research of Brassica napus.
9012AB is a novel genic male sterility (GMS) material which has great potential in three line seed production, because of it's a series of advantages, such as complete sterility, high stability, sufficient restore lines, and so on. Genetic analysis indicated that the male sterility of 9012AB was controlled by two pairs of recessive duplicate sterile genes (ms3ms3 and ms4ms4) interacting with one pair of a recessive epistatic inhibitor gene (rfrf) (Chen et al., 1998). The previous study ( He et al., 2008) shown that the ms3 gene was fine mapped to a region of 0.034cM which including at least six BACs and the BAC clone which contained the target gene was identified by subclone sequencing. In order to develop ms3 mocular makers, confirm the results of BAC subclone and compare the micro-collinearity between B. oleracea and B. rapa, we randomly selected 20kb sequences on the basis of the subclone library for comparative sequencing and analyzing from differenent matirials, which can provide the theory basis and help for the mapping and cloning of ms4 gene. The major results were as follows:
1. A total of 18 primer pairs which were designed according to the 20kb sequences were used in 9012A、9012B、B. rapa and B. oleracea. The amplification products from these primer pairs could constitute a contig that can coverage this region completely in theory. Splicing the sequence of these amplification products, we obtained the the sequence information of these materials.
2. Based on the section sequence, we analyzed the microcollinearity of Tapidor、9012A、9012B、B. rapa and B. oleracea in the selective region. The results indicated that 9012A and B. rapa had the high sequence similarity, so as the 9012B、Tapidor and B. oleracea. Gene prediction of this region refer to the Arabidopsis genome sequence shown that this region included three highly conserved genes with the same direction. The sequences of the exons of those genes had little or no changes, however, the sequences of the introns of those genes had mutation, insertion or deletion. According to these significant differences, we developed six markers as to distinct 9012A and 9012B,markers named DM1 and HWY to distinct B. rapa and B. oleracea.
3. Five markers developed from 9012A and 9012B showed co-segregated with the target gene ms3 by tested recombination plants of 20,391 individuals. As a result, we did not reduce the physical region of the gene ms3, although five new markers were developed.
4. According to the different sequences between B. rapa and B. oleracea, Two codominant markers, which showed stable polymorphism in forty nine B. rapa and eight B. oleracea materials were developed. Then, we used the markers to identity the Brassica napus BAC library, which contained the target gene ms3. The amplified products with the same size and sequence information of B. rapa genome,were obtained, however, clone with the same size in B. oleracea genome was not found. According to the previous studies, ms3 gene located in the N19 linkage groups, which corresponding to B. oleracea chromosome of C9. It was speculated that the BAC clones we selected could be the homology region of ms3 in B. rapa.
5. We used the SSR markers from BAC clones and the A, C genome-specific markers to detect the polymorphism in ms4 mapping population. All markers were not linked with ms4 gene. It is suggested that the ms3 and ms4 were different homologous genes, so the statement about ms3 and ms4 were two pairs of recessive duplicate sterile genes needed to be further confirmed.
9012AB是一种新的甘蓝型油菜隐性细胞核雄性不育材料,具有败育彻底,不育性稳定,恢复源广泛的特点,因此在三系配套育种中具有重要的利用价值。陈凤祥等对该材料的研究表明:其育性受到两对重叠隐性不育基因(ms3ms3、ms4ms4)和一对隐性上位抑制基因(rfrf)互作控制。何俊平等已将其中一个不育基因ms3精细定位在0.034cM的遗传区间。物理作图表明该区间最少由6个BAC克隆构成的一个完整的重叠群所覆盖,并利用亚克隆测序的方法获得其中包含目标基因的一个BAC克隆。为了进一步开发与Ms3紧密连锁的标记,并验证BAC克隆筛选的结果及比较该区间在甘蓝和白菜基因组之间的微观共线性关系,从而为Ms4的研究提供可能的便利,本研究从上述BAC克隆测序序列中随机选择20kb的区域在不同材料中进行比较测序并分析,获得如下主要结果:
1.根据20kb的区域设计18对引物,其扩增产物理论上能够构成一个完整的重叠群并完全覆盖该区间。利用这18对引物在9012A、9012B、白菜和甘蓝中扩增,扩增产物拼接后共得到三种材料52个区段序列信息。
2.对所得材料的区段序列进行比对分析发现,甘蓝型油菜Tapidor、9012A、9012B、白菜和甘蓝之间存在较好的微观共线性,且甘蓝型油菜9012A和白菜之间的相似性高,9012B、Tapidor和甘蓝之间的相似性高。参考模式植物拟南芥信息进一步基因预测发现:该区段3个对应基因方向相同,外显子区域一致且比较保守;内含子区段序列存在碱基的突变、插入或缺失。根据测序所得序列差异较大的区域,开发9012A和9012B之间6对多态性标记,白菜和甘蓝之间的多态性标记DM1和HWY。
3.经重组单株验证后,根据9012A和9012B之间序列差异开发的新标记在20,391个单株的分离群体中与ms3基因共分离。和原来的定位结果相比,虽然开发了新的标记,但并没有缩小包含ms3基因的物理区间。
4.根据白菜和甘蓝的序列差异,开发出在49份白菜和8份甘蓝之间存在稳定多态性的共显性标记2个。利用该标记筛选先前鉴定的甘蓝型油菜BAC克隆文库,发现标记在克隆中扩增产物与白菜基因组中大小和序列一致,而没有发现与甘蓝基因组中大小一致的克隆。而根据先前的研究,ms3基因定位于N19连锁群,对应甘蓝的第9染色体。据此推测,筛选到的BAC克隆事实上可能是ms3基因位于白菜基因组中的同源区。
5.利用BAC克隆开发出的SSR标记和本实验中开发的A、C基因组特异标记DM1在Ms4定位群体中进行多态性检测,发现所有标记在定位群体中与Ms4基因不连锁,暗示着Ms4基因可能根本就不是Ms3的一个同源基因,而是两个起源不同的基因。因此,以前认为Ms3和Ms4为重叠隐性基因的这一说法可能需要进一步论证。
Brassica napus is a polyploid resulting from the natural hybridization of B. rapa (containing the Brassica A genome) and B. oleracea (containing the Brassica C genome). The A and C genome differentiated from a common ancestor Brassica about 400 million years ago.They have highly conserve genome structure and high micro-collinearity (Rana et al., 2004), which may hamper the genetic mapping in Brassica napus.The research of the variance between A and C genomes on DNA sequence level can be used to distinguish homologous genomes between A and C genomes which have high microcollinearity, and therefore may provide some assistance of the research of Brassica napus.
9012AB is a novel genic male sterility (GMS) material which has great potential in three line seed production, because of it's a series of advantages, such as complete sterility, high stability, sufficient restore lines, and so on. Genetic analysis indicated that the male sterility of 9012AB was controlled by two pairs of recessive duplicate sterile genes (ms3ms3 and ms4ms4) interacting with one pair of a recessive epistatic inhibitor gene (rfrf) (Chen et al., 1998). The previous study ( He et al., 2008) shown that the ms3 gene was fine mapped to a region of 0.034cM which including at least six BACs and the BAC clone which contained the target gene was identified by subclone sequencing. In order to develop ms3 mocular makers, confirm the results of BAC subclone and compare the micro-collinearity between B. oleracea and B. rapa, we randomly selected 20kb sequences on the basis of the subclone library for comparative sequencing and analyzing from differenent matirials, which can provide the theory basis and help for the mapping and cloning of ms4 gene. The major results were as follows:
1. A total of 18 primer pairs which were designed according to the 20kb sequences were used in 9012A、9012B、B. rapa and B. oleracea. The amplification products from these primer pairs could constitute a contig that can coverage this region completely in theory. Splicing the sequence of these amplification products, we obtained the the sequence information of these materials.
2. Based on the section sequence, we analyzed the microcollinearity of Tapidor、9012A、9012B、B. rapa and B. oleracea in the selective region. The results indicated that 9012A and B. rapa had the high sequence similarity, so as the 9012B、Tapidor and B. oleracea. Gene prediction of this region refer to the Arabidopsis genome sequence shown that this region included three highly conserved genes with the same direction. The sequences of the exons of those genes had little or no changes, however, the sequences of the introns of those genes had mutation, insertion or deletion. According to these significant differences, we developed six markers as to distinct 9012A and 9012B,markers named DM1 and HWY to distinct B. rapa and B. oleracea.
3. Five markers developed from 9012A and 9012B showed co-segregated with the target gene ms3 by tested recombination plants of 20,391 individuals. As a result, we did not reduce the physical region of the gene ms3, although five new markers were developed.
4. According to the different sequences between B. rapa and B. oleracea, Two codominant markers, which showed stable polymorphism in forty nine B. rapa and eight B. oleracea materials were developed. Then, we used the markers to identity the Brassica napus BAC library, which contained the target gene ms3. The amplified products with the same size and sequence information of B. rapa genome,were obtained, however, clone with the same size in B. oleracea genome was not found. According to the previous studies, ms3 gene located in the N19 linkage groups, which corresponding to B. oleracea chromosome of C9. It was speculated that the BAC clones we selected could be the homology region of ms3 in B. rapa.
5. We used the SSR markers from BAC clones and the A, C genome-specific markers to detect the polymorphism in ms4 mapping population. All markers were not linked with ms4 gene. It is suggested that the ms3 and ms4 were different homologous genes, so the statement about ms3 and ms4 were two pairs of recessive duplicate sterile genes needed to be further confirmed.
引文
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