Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information.
Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information.
复制标题
异源四倍体棉花基因组组装：高密度分子遗传连锁图与 DNA 序列信息的整合
DOI：
10.1186/1471-2164-13-539
复制
发表时间：
2012-10-09
期刊：
影响因子：
4.4
通讯作者：
Wangzhen G
中科院分区：
文献类型：
--
作者：
Zhao L;Yuanda L;Caiping C;Xiangchao T;Xiangdong C;Wei Z;Hao D;Xiuhua G;Wangzhen G
棉花是世界上最重要的天然纺织纤维和重要的油料作物。对棉花基因组的破译将为该物种的研究和利用提供最终的参考和资源。高密度遗传图谱与基因组序列信息的整合将在很大程度上加快棉花全基因组组装的进程。本文更新了异源四倍体栽培棉高密度种间遗传连锁图谱。在我们之前公布的2247个基因座的图谱上，又增加了1167个标记基因座。利用基因信息开发的插入-缺失(Indel)、单核苷酸多态(SNP)和反转录转座子-微卫星扩增多态(REMAP)三种新标记用于提高图谱密度。更新后的图谱包含26个连锁群的3,414个座位，覆盖3,667.62 cM，平均座位间距离为1.08 cM。此外，利用3324个信息性的基于序列的标记和公开的棉属DNA序列信息完成了全基因组序列分析。共有413,113个EST和195个BAC序列被3324个基于序列的标记物理锚定和聚类。其中，来自棉属不同物种的14243个EST和188个BAC被聚在一起，并特异性地锚定在高密度遗传图谱上。从2,111个EST聚类和63个BAC中挖掘出2,748个候选Uniges用于功能标注和分类。将337个与纤维品质性状相关的EST/基因与132个已报道的棉花纤维品质数量性状基因座进行整合，证实了这些基因在纤维品质中的重要作用。不同棉种间以及四倍体棉花A-和D-亚基因组之间存在较高水平的序列保守性，表明棉属直系和近缘基因座具有共同的进化起源。本研究将为棉花四倍体基因组拼接、优良农艺性状相关基因的克隆以及进一步的比较基因组分析提供有价值的基因组资源。
Cotton is the world’s most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. Integration of high-density genetic maps with genomic sequence information will largely accelerate the process of whole-genome assembly in cotton. In this paper, we update a high-density interspecific genetic linkage map of allotetraploid cultivated cotton. An additional 1,167 marker loci have been added to our previously published map of 2,247 loci. Three new marker types, InDel (insertion-deletion) and SNP (single nucleotide polymorphism) developed from gene information, and REMAP (retrotransposon-microsatellite amplified polymorphism), were used to increase map density. The updated map consists of 3,414 loci in 26 linkage groups covering 3,667.62 cM with an average inter-locus distance of 1.08 cM. Furthermore, genome-wide sequence analysis was finished using 3,324 informative sequence-based markers and publicly-available Gossypium DNA sequence information. A total of 413,113 EST and 195 BAC sequences were physically anchored and clustered by 3,324 sequence-based markers. Of these, 14,243 ESTs and 188 BACs from different species of Gossypium were clustered and specifically anchored to the high-density genetic map. A total of 2,748 candidate unigenes from 2,111 ESTs clusters and 63 BACs were mined for functional annotation and classification. The 337 ESTs/genes related to fiber quality traits were integrated with 132 previously reported cotton fiber quality quantitative trait loci, which demonstrated the important roles in fiber quality of these genes. Higher-level sequence conservation between different cotton species and between the A- and D-subgenomes in tetraploid cotton was found, indicating a common evolutionary origin for orthologous and paralogous loci in Gossypium. This study will serve as a valuable genomic resource for tetraploid cotton genome assembly, for cloning genes related to superior agronomic traits, and for further comparative genomic analyses in Gossypium.
登录
查看更多内容
影响因子：
5.4
作者：
Guo, Wangzhen;Wang, Wei;Zhang, Tianzhen
通讯作者：
Zhang, Tianzhen
影响因子：
3.1
作者：
Han, ZG;Guo, WZ;Zhang, TZ
通讯作者：
Zhang, TZ
影响因子：
5.4
作者：
Han, ZG;Wang, CB;Zhang, TZ
通讯作者：
Zhang, TZ
影响因子：
5.8
作者：
Arcade, A;Labourdette, A;Joets, J
通讯作者：
Joets, J
影响因子：
--
作者：
Endrizzi, J. E.;Turcotte, E. L.;Kohel, R. J.
通讯作者：
Kohel, R. J.