Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps.
Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps.
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DOI：
10.1534/g3.113.007153
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发表时间：
2013-11-06
期刊：
影响因子：
--
通讯作者：
Bryan GJ
中科院分区：
文献类型：
--
作者：
Sharma SK;Bolser D;de Boer J;Sønderkær M;Amoros W;Carboni MF;D'Ambrosio JM;de la Cruz G;Di Genova A;Douches DS;Eguiluz M;Guo X;Guzman F;Hackett CA;Hamilton JP;Li G;Li Y;Lozano R;Maass A;Marshall D;Martinez D;McLean K;Mejía N;Milne L;Munive S;Nagy I;Ponce O;Ramirez M;Simon R;Thomson SJ;Torres Y;Waugh R;Zhang Z;Huang S;Visser RG;Bachem CW;Sagredo B;Feingold SE;Orjeda G;Veilleux RE;Bonierbale M;Jacobs JM;Milbourne D;Martin DM;Bryan GJ
马铃薯是一种主要的全球粮食作物，最近对其基因组进行了测序。本文详细介绍了马铃薯参考基因组（DM）与一个新的基于序列标记的位点标记连锁图谱以及马铃薯及其近缘种番茄的其他物理和遗传图谱的整合。利用二倍体分离群体完成了DM基因组组装的初步锚定，用几种分子遗传标记对该群体进行了基因分型，构建了一个包含2469个标记位点的~936 cM连锁图谱。计算机锚定方法使用来自二倍体马铃薯基因型RH89-039-16 （RH）和番茄的遗传和物理图谱。这种结合的方法已经允许951个超级支架被排列成与12条马铃薯染色体相对应的假分子。这些伪分子代表了723 Mb基因组组合中的674 Mb（~93%）和39031个预测基因中的37482（~96%）。假分子内的超支架的顺序和取向与独立构建的高密度连锁图密切共线。通过对标记分布和物理位置的比较，可以发现重组较多和较少的区域，以及表现出明显分离扭曲的区域。这里提出的工作已经导致了马铃薯参考基因组超支架的染色体“假分子”的极大改进排序。
The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker−based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal “pseudomolecules”.
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影响因子：
64.8
作者：
Matsumoto, T;Wu, JZ;Sugiura, M
通讯作者：
Sugiura, M
DOI：
10.1101/sqb.2003.68.69
发表时间：
2003-01-01
期刊：
COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY
影响因子：
--
作者：
Fan, JB;Oliphant, A;Chee, MS
通讯作者：
Chee, MS
影响因子：
11.6
作者：
Fulton, TM;Van der Hoeven, R;Tanksley, SD
通讯作者：
Tanksley, SD
影响因子：
5.4
作者：
GEBHARDT, C;RITTER, E;SALAMINI, F
通讯作者：
SALAMINI, F
影响因子：
64.8
作者：
Kloosterman, Bjorn;Abelenda, Jose A.;Bachem, Christian W. B.
通讯作者：
Bachem, Christian W. B.