甘蓝型油菜与白菜比较作图和比较QTL研究
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摘要
分子标记的发展和大量遗传图谱的构建使不同物种间开展比较作图和比较QTL(Quantitative Trait Locus)的研究成为可能。比较作图可以作为一个有效的工具,将一个研究的比较透彻的物种中的信息和资源(像拟南芥、水稻等)转移到其它有待研究的物种中。这样不仅可以加快基因组的研究,又可以充分节省大量的人力和财力;同时,在比较作图的基础上,对同一性状在不同物种中(如芸苔属物种与拟南芥)开展QTLs比较分析,有利于深入了解复杂性状的遗传学基础。
实验室成员曾根据韩国已经测序的白菜A3、A9染色体的208个BACs信息设计和初步筛选的407对引物(其中SSR引物92对、IBP(Intron Based Polymorphism)引物315对)。本研究从中进一步筛选出对应于155个BACs的155对引物,将对应于104个BACs的64个IBP标记和44个SSR标记定位到TN DH遗传连锁图谱上,并利用实验室以前定位在图谱上的标记,重新构建了含有938个标记的甘蓝型油菜TN DH高密度遗传连锁图。该图谱包括472个SSR、64个IBP、41个AFLP、52个RFLP、97个SNP、57个SRAP和61个SSAP。
将法国的DY群体、RNSL群体以及其一个甘蓝型油菜整合图谱上的标记整合到TN DH遗传连锁图上,得到了包含1107个标记的甘蓝型油菜整合图谱。与TN DH遗传连锁图相比,整合图谱上增加了119个SSR、19个SNP和31个其它类型的标记;同时,将韩国公布的CK、JWF3P、VCS 3个白菜遗传图谱上的标记进行整合,得到一个包含658个标记的白菜整合图谱,含有439个SSR标记,145个IBP标记,48个RFLP标记和25个CAPS标记。通过对甘蓝型油菜/白菜整合图谱的比较分析以及图谱上的标记信息与拟南芥的比对,共发现了195个甘蓝型油菜/白菜整合图谱上的共同标记,其中10个为共同标记,138个为共BAC标记,47个根据拟南芥信息推测得到,为拟同源标记。根据甘蓝型油菜/白菜整合图谱的比较结果,推测甘蓝型油菜A基因组与白菜基因组间可能发生了24个染色体重排事件,其中有20个倒位和4个可能的片断缺失,没有明显的片断插入事件,重排涉及的片断长度(cM)占甘蓝型油菜A基因组的17.92%。
硫甙含量是衡量种子品质的一个重要性状。在白菜CK DH遗传连锁图A9连锁群上检测到了1个稳定出现的硫甙含量QTL。通过与实验室甘蓝型油菜TN DH遗传连锁图A9连锁群上检测到的1个多年多点重复出现的硫甙含量QTL比较,发现2个QTL位于同一个位置,因此可以利用白菜信息对甘蓝型油菜硫甙含量进行深入研究。
The progress in the development of molecular markers and construction of genetic linkage maps make it possible to carry out comparative genomics and comparative QTL (Quantitative Trait Locus) among species. Comparative mapping is one of effective strategies in utilizing genetic information from model plants with completed genomic sequences, such as Arabidopsis thaliana and rice, to their relatives because of its high efficiency on input and output. Meanwhile, comparative QTL analysis could be amplied in different species about the same trait, such as Brasscica species and other relatives of Arabidopsis, by an approach based on a comparative mapping. This approach facilicates the further research on the genetic basement about the complex traits.
407 primers including 92 SSR primer pairs and 315 IBP (Intron Based Polymorphism) primer pairs responding to 208 BACs of B.rapa were used for polymorphic assay between the parents of Brassica napus DH population (TNDH) by the partner of our lab. In this study, we do the further assay and select 155 polymorphic primer pairs responding to 155 BACs. And then, 64 IBP markers and 44 SSR primers were mapped onto the TN genetic linkage map which is responding to 104 BACs.After combined other available markers from our lab, a updated TN genetic linkage map was build up with a high density of molecular markers, containing 472 SSR markers, 64 IBP markers, 52 RFLP markers, 91 SNP markers, 57 SRAP markers and 61 SSAP markers. And then, a new Brassica napus consensus map was constructed based on the backbone of TN genetic map after integrated markers from the other public Brassica napus genetic maps such as DY, RNSL genetic linkage map and a consensus genetic linkage map, with a increasing of 119 SSR markers, 19 SNP markers and 31 other markers. At the same time, a new Brassica rapa consensus map was constructed based on the backbone of JWF3P genetic map after integrated markers from the other public Brassica rapa genetic maps such as CK and VCS genetic linkage map containing 658 markers including 439 SSR markers, 145 IBP markers, 48 RFLP markers and 25 CAPS markers.
Comparasion of the two consensus maps between A genome was performed, subsequently, based on 10 common markers, 138 common BAC markers between them and 47 pseudo-homologue markers were determined after they were compared with Arabidopsis genomic sequences, respectively. 24 chromosome rearrangements, account for 17.92% of the B.napus A genome, was found between this two divergented genomes, including 20 inversions and 4 indels, but distinct segment insertions/deletions.
Glucosinolate content is an important trait for seed quality of Brassica species. A stable conmon QTL which is determining of seed glucosinolate content was detected on A9 linkage group of both TN and CK genetic linkage map under different environments in different years. Comparative QTL indicates the QTL at the same position of B.rapa and B.napus. So we can do some further research about the QTL of glucosinolate content in B. napus using the information of B. rapa.
实验室成员曾根据韩国已经测序的白菜A3、A9染色体的208个BACs信息设计和初步筛选的407对引物(其中SSR引物92对、IBP(Intron Based Polymorphism)引物315对)。本研究从中进一步筛选出对应于155个BACs的155对引物,将对应于104个BACs的64个IBP标记和44个SSR标记定位到TN DH遗传连锁图谱上,并利用实验室以前定位在图谱上的标记,重新构建了含有938个标记的甘蓝型油菜TN DH高密度遗传连锁图。该图谱包括472个SSR、64个IBP、41个AFLP、52个RFLP、97个SNP、57个SRAP和61个SSAP。
将法国的DY群体、RNSL群体以及其一个甘蓝型油菜整合图谱上的标记整合到TN DH遗传连锁图上,得到了包含1107个标记的甘蓝型油菜整合图谱。与TN DH遗传连锁图相比,整合图谱上增加了119个SSR、19个SNP和31个其它类型的标记;同时,将韩国公布的CK、JWF3P、VCS 3个白菜遗传图谱上的标记进行整合,得到一个包含658个标记的白菜整合图谱,含有439个SSR标记,145个IBP标记,48个RFLP标记和25个CAPS标记。通过对甘蓝型油菜/白菜整合图谱的比较分析以及图谱上的标记信息与拟南芥的比对,共发现了195个甘蓝型油菜/白菜整合图谱上的共同标记,其中10个为共同标记,138个为共BAC标记,47个根据拟南芥信息推测得到,为拟同源标记。根据甘蓝型油菜/白菜整合图谱的比较结果,推测甘蓝型油菜A基因组与白菜基因组间可能发生了24个染色体重排事件,其中有20个倒位和4个可能的片断缺失,没有明显的片断插入事件,重排涉及的片断长度(cM)占甘蓝型油菜A基因组的17.92%。
硫甙含量是衡量种子品质的一个重要性状。在白菜CK DH遗传连锁图A9连锁群上检测到了1个稳定出现的硫甙含量QTL。通过与实验室甘蓝型油菜TN DH遗传连锁图A9连锁群上检测到的1个多年多点重复出现的硫甙含量QTL比较,发现2个QTL位于同一个位置,因此可以利用白菜信息对甘蓝型油菜硫甙含量进行深入研究。
The progress in the development of molecular markers and construction of genetic linkage maps make it possible to carry out comparative genomics and comparative QTL (Quantitative Trait Locus) among species. Comparative mapping is one of effective strategies in utilizing genetic information from model plants with completed genomic sequences, such as Arabidopsis thaliana and rice, to their relatives because of its high efficiency on input and output. Meanwhile, comparative QTL analysis could be amplied in different species about the same trait, such as Brasscica species and other relatives of Arabidopsis, by an approach based on a comparative mapping. This approach facilicates the further research on the genetic basement about the complex traits.
407 primers including 92 SSR primer pairs and 315 IBP (Intron Based Polymorphism) primer pairs responding to 208 BACs of B.rapa were used for polymorphic assay between the parents of Brassica napus DH population (TNDH) by the partner of our lab. In this study, we do the further assay and select 155 polymorphic primer pairs responding to 155 BACs. And then, 64 IBP markers and 44 SSR primers were mapped onto the TN genetic linkage map which is responding to 104 BACs.After combined other available markers from our lab, a updated TN genetic linkage map was build up with a high density of molecular markers, containing 472 SSR markers, 64 IBP markers, 52 RFLP markers, 91 SNP markers, 57 SRAP markers and 61 SSAP markers. And then, a new Brassica napus consensus map was constructed based on the backbone of TN genetic map after integrated markers from the other public Brassica napus genetic maps such as DY, RNSL genetic linkage map and a consensus genetic linkage map, with a increasing of 119 SSR markers, 19 SNP markers and 31 other markers. At the same time, a new Brassica rapa consensus map was constructed based on the backbone of JWF3P genetic map after integrated markers from the other public Brassica rapa genetic maps such as CK and VCS genetic linkage map containing 658 markers including 439 SSR markers, 145 IBP markers, 48 RFLP markers and 25 CAPS markers.
Comparasion of the two consensus maps between A genome was performed, subsequently, based on 10 common markers, 138 common BAC markers between them and 47 pseudo-homologue markers were determined after they were compared with Arabidopsis genomic sequences, respectively. 24 chromosome rearrangements, account for 17.92% of the B.napus A genome, was found between this two divergented genomes, including 20 inversions and 4 indels, but distinct segment insertions/deletions.
Glucosinolate content is an important trait for seed quality of Brassica species. A stable conmon QTL which is determining of seed glucosinolate content was detected on A9 linkage group of both TN and CK genetic linkage map under different environments in different years. Comparative QTL indicates the QTL at the same position of B.rapa and B.napus. So we can do some further research about the QTL of glucosinolate content in B. napus using the information of B. rapa.
引文
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