High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis.
High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis.
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DOI：
10.1371/journal.pone.0033821
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Flavell R
中科院分区：
文献类型：
--
作者：
Ma XF;Jensen E;Alexandrov N;Troukhan M;Zhang L;Thomas-Jones S;Farrar K;Clifton-Brown J;Donnison I;Swaller T;Flavell R
我们利用测序基因分型技术(GBS)建立了中国芒属的高分辨率连锁图谱，首次鉴定了所有19个连锁群。这一结果在技术上意义重大，因为芒属有一个非常大的高度杂合的基因组，但到目前为止还没有或有限的基因组学信息。包含来自两个亲本连锁图谱的标记的复合连锁图谱由3,745个SNP标记组成，分布在19个连锁群上，覆盖2396 cM，平均分辨率为0.64 cM。中华根结线虫与高粱、玉米、水稻和短柱花属植物基因组的比较基因组学分析表明，与其他物种相比，高粱与芒属植物的同源关系最近。比较结果表明，除LG8外，所有19个中华根结线虫连锁对齐到一条高粱染色体上，可能是由于基因组复制后发生了染色体融合事件。这些数据还揭示了与高粱相关的其他几种染色体重排，包括中华根结线虫LG8中高粱共线染色体7的两个端粒着丝粒倒位和高粱共线染色体LG7和LG8中高粱共线染色体4号染色体的两个偏着丝粒倒位。这一结果首次清楚地证明了二倍体中华绒螯蟹是由两个亚基因组组成的四倍体起源。这一完整的、高分辨率的复合连锁图谱不仅将为新的QTL发现提供有用的资源，而且还将使现有的其他物种基因组资源的丰富得以合理部署，以改良芒属作为一种高生物量能源作物。此外，它对即将进行的芒属全基因组测序的基因组序列拼接也具有一定的参考价值。
We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the M. sinensis composite linkage map to the genomes of sorghum, maize, rice, and Brachypodium distachyon indicate that sorghum has the closest syntenic relationship to Miscanthus compared to other species. The comparative results revealed that each pair of the 19 M. sinensis linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7), presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of M. sinensis and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of M. sinensis. The results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of Miscanthus as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus.
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影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
3.7
作者：
Baxter SW;Davey JW;Johnston JS;Shelton AM;Heckel DG;Jiggins CD;Blaxter ML
通讯作者：
Blaxter ML
影响因子：
4.4
作者：
Chutimanitsakun Y;Nipper RW;Cuesta-Marcos A;Cistué L;Corey A;Filichkina T;Johnson EA;Hayes PM
通讯作者：
Hayes PM
影响因子：
5.4
作者：
Atienza, SG;Satovic, Z;Martín, A
通讯作者：
Martín, A
影响因子：
5.4
作者：
Atienza, SG;Satovic, Z;Martín, A
通讯作者：
Martín, A