Dynamic Rearrangements Determine Genome Organization and Useful Traits in Soybean
Dynamic Rearrangements Determine Genome Organization and Useful Traits in Soybean
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DOI：
10.1104/pp.109.141739
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发表时间：
2009-11-01
期刊：
影响因子：
7.4
通讯作者：
Lee, Suk-Ha
中科院分区：
文献类型：
--
作者：
Kim, Kyung Do;Shin, Jin Hee;Lee, Suk-Ha
大豆（Glycine max）是一种古多倍体，其基因组经历了至少两轮多倍体和随后的二倍体事件。一些研究已经调查了相对较近的多倍体事件所产生的基因组结构变化，但由于重复后基因丢失的频率很高，因此对古代多倍体知之甚少。我们之前的研究，关于负责细菌性叶脓疱的区域，报道了最近全基因组重复事件产生的两个同源Rxp区域。在本研究中，我们鉴定了来自近期和古代多倍体事件的4个同源Rxp区域（1.96 ~ 4.60 Mb），这支持了大豆基因组的四重结构。在17号染色体（连锁组D2）上的预测基因中，71%的重复基因保存在最近的一个重复区域，21%和24%的重复基因保留在由古代多倍体形成的两个同源区域。此外，比较分析显示大豆和短角苜蓿的关系为2∶1，因为短角苜蓿没有发生大豆最近发生的多倍体事件。与大豆不同的是，短尾草同源区分化程度高，不存在同源性，说明两种植物的二倍体分化速率不同。我们的数据表明，尽管大豆基因组在古多倍体事件后经历了动态的基因组重排，但大豆的四个同源区域仍然存在广泛的同源性。此外，大豆不同染色体上的多个Rxp数量性状位点实际上由两轮多倍体事件产生的同源区域组成。
Soybean (Glycine max) is a paleopolyploid whose genome has gone through at least two rounds of polyploidy and subsequent diploidization events. Several studies have investigated the changes in genome structure produced by the relatively recent polyploidy event, but little is known about the ancient polyploidy due to the high frequency of gene loss after duplication. Our previous study, regarding a region responsible for bacterial leaf pustule, reported two homeologous Rxp regions produced by the recent whole-genome duplication event. In this study, we identified the full set of four homeologous Rxp regions (ranging from 1.96 to 4.60 Mb) derived from both the recent and ancient polyploidy events, and this supports the quadruplicated structure of the soybean genome. Among the predicted genes on chromosome 17 (linkage group D2), 71% of them were conserved in a recently duplicated region, while 21% and 24% of duplicated genes were retained in two homeologous regions formed by the ancient polyploidy. Furthermore, comparative analysis showed a 2: 1 relationship between soybean and Medicago truncatula, since M. truncatula did not undergo the recent polyploidy event that soybean did. Unlike soybean, M. truncatula homeologous regions were highly fractionated and their synteny did not exist, revealing different rates of diploidization process between the two species. Our data show that extensive synteny remained in the four homeologous regions in soybean, even though the soybean genome experienced dynamic genome rearrangements following paleopolyploidy events. Moreover, multiple Rxp quantitative trait loci on different soybean chromosomes actually comprise homeologous regions produced by two rounds of polyploidy events.