A sequence-based genetic linkage map as a reference for Brassica rapa pseudochromosome assembly.
A sequence-based genetic linkage map as a reference for Brassica rapa pseudochromosome assembly.
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DOI：
10.1186/1471-2164-12-239
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发表时间：
2011-05-14
期刊：
影响因子：
4.4
通讯作者：
Wu J
中科院分区：
文献类型：
--
作者：
Wang Y;Sun S;Liu B;Wang H;Deng J;Liao Y;Wang Q;Cheng F;Wang X;Wu J
芜菁甘蓝是一种重要的经济作物，也是研究多倍体化和极端形态进化的模式植物。跨国白菜基因组测序计划（BrGSP）于2003年启动。2008年，采用新一代测序技术对白菜基因组进行测序。一些关于白菜假染色体组装的图谱已经发表，但它们对基因组的覆盖不完整，将大约 73.6% 的支架锚定在染色体上。因此，需要一个新的遗传图谱来帮助假染色体组装。本研究涉及构建白菜型白菜（Brassica rapa）的参考遗传连锁图谱，形成最近测序工作产生的白菜基因组锚定序列支架的骨干。使用源自大白菜 (B. rapa ssp. pekinensis) DH 系 (Z16) 和快速循环自交系 (L144) 之间的 F1 杂交小孢子培养物的 119 个双单倍体 (DH) 系来构建连锁图谱。通过对两个亲本系进行重新测序，开发了基于 PCR 的插入/缺失 (InDel) 标记。该图谱总共包含 507 个标记，其中包括 415 个 InDels 和 92 个 SSR。使用与现有白菜连锁图相同的SSR标记进行比对和定向，可以识别出十个连锁群，指定为A01-A10。连锁图谱总长度为1234.2 cM，相邻标记位点之间的平均距离为2.43 cM。 A08 和 A09 的连锁基团长度范围分别为 71.5 cM 至 188.5 cM。使用开发的连锁图谱，152 个支架被锚定在染色体上，涵盖了白菜基因组的 82.9% 以上。结合之前获得的连锁图谱，183 个支架固定在染色体上，基因组的总覆盖率为 88.9%。该连锁图谱的开发对于基因组序列和遗传信息的整合至关重要，并为国际芸苔属研究界提供了有用的资源。
Brassica rapa is an economically important crop and a model plant for studies concerning polyploidization and the evolution of extreme morphology. The multinational B. rapa Genome Sequencing Project (BrGSP) was launched in 2003. In 2008, next generation sequencing technology was used to sequence the B. rapa genome. Several maps concerning B. rapa pseudochromosome assembly have been published but their coverage of the genome is incomplete, anchoring approximately 73.6% of the scaffolds on to chromosomes. Therefore, a new genetic map to aid pseudochromosome assembly is required. This study concerns the construction of a reference genetic linkage map for Brassica rapa, forming the backbone for anchoring sequence scaffolds of the B. rapa genome resulting from recent sequencing efforts. One hundred and nineteen doubled haploid (DH) lines derived from microspore cultures of an F1 cross between a Chinese cabbage (B. rapa ssp. pekinensis) DH line (Z16) and a rapid cycling inbred line (L144) were used to construct the linkage map. PCR-based insertion/deletion (InDel) markers were developed by re-sequencing the two parental lines. The map comprises a total of 507 markers including 415 InDels and 92 SSRs. Alignment and orientation using SSR markers in common with existing B. rapa linkage maps allowed ten linkage groups to be identified, designated A01-A10. The total length of the linkage map was 1234.2 cM, with an average distance of 2.43 cM between adjacent marker loci. The lengths of linkage groups ranged from 71.5 cM to 188.5 cM for A08 and A09, respectively. Using the developed linkage map, 152 scaffolds were anchored on to the chromosomes, encompassing more than 82.9% of the B. rapa genome. Taken together with the previously available linkage maps, 183 scaffolds were anchored on to the chromosomes and the total coverage of the genome was 88.9%. The development of this linkage map is vital for the integration of genome sequences and genetic information, and provides a useful resource for the international Brassica research community.
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影响因子：
2.9
作者：
Ching A;Caldwell KS;Jung M;Dolan M;Smith OS;Tingey S;Morgante M;Rafalski AJ
通讯作者：
Rafalski AJ
影响因子：
3.3
作者：
Kim, Jung Sun;Chung, Tae Young;Park, Beom-Seok
通讯作者：
Park, Beom-Seok
影响因子：
--
作者：
Cui XiuMin, Cui XiuMin;Dong YuXiu, Dong YuXiu;Jin, M. F.
通讯作者：
Jin, M. F.
影响因子：
12.3
作者：
Mun JH;Kwon SJ;Seol YJ;Kim JA;Jin M;Kim JS;Lim MH;Lee SI;Hong JK;Park TH;Lee SC;Kim BJ;Seo MS;Baek S;Lee MJ;Shin JY;Hahn JH;Hwang YJ;Lim KB;Park JY;Lee J;Yang TJ;Yu HJ;Choi IY;Choi BS;Choi SR;Ramchiary N;Lim YP;Fraser F;Drou N;Soumpourou E;Trick M;Bancroft I;Sharpe AG;Parkin IA;Batley J;Edwards D;Park BS
通讯作者：
Park BS
影响因子：
30.8
作者：
Daly, MJ;Rioux, JD;Lander, ES
通讯作者：
Lander, ES