Integration of linkage maps for the Amphidiploid Brassica napus and comparative mapping with Arabidopsis and Brassica rapa.
Integration of linkage maps for the Amphidiploid Brassica napus and comparative mapping with Arabidopsis and Brassica rapa.
复制标题
将链球菌甘蓝纳普斯的连锁图与拟南芥和甘蓝铜rapa进行比较映射的整合。
DOI：
10.1186/1471-2164-12-101
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发表时间：
2011-02-09
期刊：
影响因子：
4.4
通讯作者：
King GJ
中科院分区：
文献类型：
--
作者：
Wang J;Lydiate DJ;Parkin IA;Falentin C;Delourme R;Carion PW;King GJ
大量代表芸苔属染色体的遗传连锁图谱为研究芸苔科作物性状和基因组进化提供了潜在的平台。然而，现有地图的调整仍然是一项重大挑战。这些遗传图谱的整合将提高遗传分辨率，并提供一种在序列标记的基因座之间导航的手段，并且随着这些基因组序列变得可用，提供连续的基因组序列。我们报告了第一个全基因组整合的芸苔属地图的基础上，涉及整理全基因组的基因型数据的序列标记标记的自动化管道上三个广泛使用的双二倍体甘蓝型油菜（2n = 38）人口。从每个群体的合并图中选择代表性标记，并生成骨架箱图。然后将三个种群的骨架图结合起来，为每个LG生成一个综合地图，比较两种不同的方法，一种封装在JoinMap中，另一种封装在MergeMap中。使用JoinMap生成BnaWAIT_01_2010a整合遗传图谱，包括定位到2，196个基因座上的5，162个遗传标记，总遗传长度为1，792 cM。每0.82 cM，对应于515 Kbp的一个基因座的图密度增加了至少三倍的原始图内的基因座和标记密度。在B。在油菜整合图谱中，我们鉴定了103个相对于拟南芥保守的共线性块，包括5个以前未报道的块。BnaWAIT_01_2010a图谱用于研究从芜菁的组分A基因组产生的基因组序列支架的顺序的完整性和保守性。我们的研究结果提供了一个全面的遗传整合的B。本研究从一系列来源获得了甘蓝型油菜基因组信息，预计将为油菜和油菜籽的研究提供有价值的信息。
The large number of genetic linkage maps representing Brassica chromosomes constitute a potential platform for studying crop traits and genome evolution within Brassicaceae. However, the alignment of existing maps remains a major challenge. The integration of these genetic maps will enhance genetic resolution, and provide a means to navigate between sequence-tagged loci, and with contiguous genome sequences as these become available. We report the first genome-wide integration of Brassica maps based on an automated pipeline which involved collation of genome-wide genotype data for sequence-tagged markers scored on three extensively used amphidiploid Brassica napus (2n = 38) populations. Representative markers were selected from consolidated maps for each population, and skeleton bin maps were generated. The skeleton maps for the three populations were then combined to generate an integrated map for each LG, comparing two different approaches, one encapsulated in JoinMap and the other in MergeMap. The BnaWAIT_01_2010a integrated genetic map was generated using JoinMap, and includes 5,162 genetic markers mapped onto 2,196 loci, with a total genetic length of 1,792 cM. The map density of one locus every 0.82 cM, corresponding to 515 Kbp, increases by at least three-fold the locus and marker density within the original maps. Within the B. napus integrated map we identified 103 conserved collinearity blocks relative to Arabidopsis, including five previously unreported blocks. The BnaWAIT_01_2010a map was used to investigate the integrity and conservation of order proposed for genome sequence scaffolds generated from the constituent A genome of Brassica rapa. Our results provide a comprehensive genetic integration of the B. napus genome from a range of sources, which we anticipate will provide valuable information for rapeseed and Canola research.