A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers.
A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers.
复制标题
整合了多个成分图谱和高通量多样性阵列技术 (DArT) 标记的高粱共识遗传图谱。
DOI：
10.1186/1471-2229-9-13
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发表时间：
2009-01-26
影响因子：
5.3
通讯作者：
Jordan DR
中科院分区：
文献类型：
--
作者：
Mace ES;Rami JF;Bouchet S;Klein PE;Klein RR;Kilian A;Wenzl P;Xia L;Halloran K;Jordan DR
基于DNA标记的高粱基因组作图开始于20世纪90年代初，在过去的十年中，已经发表了许多高粱的遗传连锁图谱，最初基于RFLP标记，最近的图谱包括AFLP和SSR，最近，多样性阵列技术（DArT）标记。必须将通过DArT产生的快速增长的遗传连锁数据与通过其他标记技术产生的高粱多个遗传连锁图相结合。在这里，我们报告共线性的六个独立的高粱成分的地图和整合这些成分的地图到一个单一的参考资源，包含常用的SSR，AFLP，和高通量DArT标记。使用MultiPoint软件构建六个组分图。所得到的地图的长度在910和1528厘米之间变化。分离在一个以上的群体中的498个标记的顺序是高度一致的6个单独的定位数据集之间。框架共识图谱使用“邻居”方法构建，包含10条高粱染色体上的251个整合的桥梁标记，跨度为1355.4 cM，平均密度为每5.4 cM一个标记，并用于其余标记的投影。总的来说，高粱共有图谱由总共1997个标记组成，这些标记定位到2029个独特的基因座（1190个DArT基因座和839个其他基因座），跨越1603.5cM，平均标记密度为1个标记/0.79cM。此外，还鉴定了35个多拷贝标记。平均而言，共有图谱上的每条染色体包含203个标记，其中58.6%是DArT标记。观察到DNA标记分布的非随机模式，具有一些明确的标记密集区和一些标记稀少区。最终的一致性图谱使我们能够绘制比任何单个图谱中可能的更多的标记，以获得更完整的高粱基因组覆盖范围，并填补单个图谱上的一些空白。除了个体组分图谱中标记顺序的总体一般一致性之外，使用差异比计算确定了本研究中使用的组分图谱中共同标记对之间的总体距离的良好一致性。所获得的一致性图谱可用作不同遗传背景下遗传研究的参考资源，此外还为不同标记技术之间的遗传信息传递以及DArT标记与其他基因组资源的整合提供了框架。DArT标记代表了一种负担得起的高通量标记系统，其在分子育种程序中具有很大的实用性，特别是在SNP阵列不可公开获得的作物如高粱中。
Sorghum genome mapping based on DNA markers began in the early 1990s and numerous genetic linkage maps of sorghum have been published in the last decade, based initially on RFLP markers with more recent maps including AFLPs and SSRs and very recently, Diversity Array Technology (DArT) markers. It is essential to integrate the rapidly growing body of genetic linkage data produced through DArT with the multiple genetic linkage maps for sorghum generated through other marker technologies. Here, we report on the colinearity of six independent sorghum component maps and on the integration of these component maps into a single reference resource that contains commonly utilized SSRs, AFLPs, and high-throughput DArT markers. The six component maps were constructed using the MultiPoint software. The lengths of the resulting maps varied between 910 and 1528 cM. The order of the 498 markers that segregated in more than one population was highly consistent between the six individual mapping data sets. The framework consensus map was constructed using a "Neighbours" approach and contained 251 integrated bridge markers on the 10 sorghum chromosomes spanning 1355.4 cM with an average density of one marker every 5.4 cM, and were used for the projection of the remaining markers. In total, the sorghum consensus map consisted of a total of 1997 markers mapped to 2029 unique loci (1190 DArT loci and 839 other loci) spanning 1603.5 cM and with an average marker density of 1 marker/0.79 cM. In addition, 35 multicopy markers were identified. On average, each chromosome on the consensus map contained 203 markers of which 58.6% were DArT markers. Non-random patterns of DNA marker distribution were observed, with some clear marker-dense regions and some marker-rare regions. The final consensus map has allowed us to map a larger number of markers than possible in any individual map, to obtain a more complete coverage of the sorghum genome and to fill a number of gaps on individual maps. In addition to overall general consistency of marker order across individual component maps, good agreement in overall distances between common marker pairs across the component maps used in this study was determined, using a difference ratio calculation. The obtained consensus map can be used as a reference resource for genetic studies in different genetic backgrounds, in addition to providing a framework for transferring genetic information between different marker technologies and for integrating DArT markers with other genomic resources. DArT markers represent an affordable, high throughput marker system with great utility in molecular breeding programs, especially in crops such as sorghum where SNP arrays are not publicly available.
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影响因子：
5.4
作者：
Boivin, K;Deu, M;Hamon, P
通讯作者：
Hamon, P
DOI：
10.1073/pnas.94.13.6809
发表时间：
1997-06-24
影响因子：
11.1
作者：
Gaut, BS;Doebley, JF
通讯作者：
Doebley, JF
影响因子：
6.9
作者：
Harris, Karen;Subudhi, P. K.;Mullet, John
通讯作者：
Mullet, John
DOI：
10.1073/pnas.0502365102
发表时间：
2005-09-13
影响因子：
11.1
作者：
Bowers, JE;Arias, MA;Paterson, AH
通讯作者：
Paterson, AH
影响因子：
5.4
作者：
BEAVIS, WD;GRANT, D
通讯作者：
GRANT, D