Comparative Relationships and Chromosome Evolution in Switchgrass (Panicum virgatum) and Its Genomic Model, Foxtail Millet (Setaria italica)
Comparative Relationships and Chromosome Evolution in Switchgrass (Panicum virgatum) and Its Genomic Model, Foxtail Millet (Setaria italica)
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DOI：
10.1007/s12155-014-9508-7
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发表时间：
2015-03-01
影响因子：
3.6
通讯作者：
Devos, Katrien M.
中科院分区：
文献类型：
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作者：
Daverdin, Guillaume;Bahri, Bochra A.;Devos, Katrien M.
开发了柳枝稷（Panicum virgatum L.）共识图谱，该图谱结合了来自两个作图群体的数据和来自该主要专性异交物种的双亲的整合重组数据。共识图谱由 1,321 个位点组成，跨度为 2,122 cM。对基因和基因组标记在连锁群长度上的分布的分析表明，基因标记在远端区域相对过多，而基因组标记在着丝粒周围区域相对过多。此外，位于远端和着丝粒周围区域的基因标记以相似的速度鉴定了密切相关的物种谷子（Setaria italica (L.) P. Beauv.）基因组中的直系同源物，但与远端区域相比，定位到着丝粒周围区域的基因组标记发现的直向同源物较少。由于跨物种序列保守性很大程度上限于基因，因此我们的数据表明，映射到远端区域的基因组标记比映射到着丝粒周围区域的基因组标记更有可能源自基因区域。柳枝稷共有图谱上的基因座与其在谷子基因组中的直系同源物之间的比较分析表明，这两个物种至少存在九个倒位和一个相互易位。将比较分析扩展到高粱表明，在过去 1300 万年中，大部分重排发生在谷子基因组中。染色体数目从穿心莲科的 10 条减少到黍科的 9 条，是通过一系列复杂的重排实现的，其中涉及与高粱 6、8 和 9 号染色体同源的三个祖先染色体，以及柳枝稷和谷子谱系中的 III 号和 VII 号染色体。将祖先 9 号染色体插入祖先 8 号染色体后，受体染色体的着丝粒丢失，并且伴随着重复 DNA 的丢失。柳枝稷-谷子比较图提供了在遗传分析中使用谷子作为柳枝稷替代品时需要考虑的重排指南。
A switchgrass (Panicum virgatum L.) consensus map was developed that combined data from two mapping populations and integrated recombination data from both parents of this largely obligate outcrossing species. The consensus map consisted of 1,321 loci and spanned 2,122 cM. An analysis of the distribution of genic and genomic markers across the length of a linkage group showed that genic markers were relatively overrepresented in distal regions, while genomic markers were relatively overrepresented in pericentromeric regions. Furthermore, genic markers located in distal and pericentromeric regions identified orthologs in the genome of the closely related species foxtail millet (Setaria italica (L.) P. Beauv.) at a similar rate, but fewer orthologs were found for genomic markers that mapped to pericentromeric regions compared to distal regions. Because cross-species sequence conservation is largely limited to genes, our data suggest that genomic markers that map to distal regions are more likely to be derived from genic regions than those that map to pericentromeric regions. A comparative analysis between loci on the switchgrass consensus map and their orthologs in the foxtail millet genome showed that the two species varied by at least nine inversions and one reciprocal translocation. Extending the comparative analysis to sorghum demonstrated that the majority of the rearrangements occurred in the foxtail millet genome in the past 13 million years. The reduction in chromosome number from 10 in the Andropogoneae to 9 in the Paniceae was achieved through a complex set of rearrangements involving three ancestral chromosomes orthologous to sorghum chromosomes 6, 8, and 9 and chromosomes III and VII in the lineage leading to switchgrass and foxtail millet. Upon insertion of ancestral chromosome 9 into ancestral chromosome 8, the centromere of the recipient chromosome was lost, and this was accompanied by a loss of repetitive DNA. The switchgrass-foxtail millet comparative map provides a guide of the rearrangements that need to be taken into account when using foxtail millet as a surrogate for switchgrass in genetic analyses.