Barcode System for Genetic Identification of Soybean [Glycine max (L.) Merrill] Cultivars Using InDel Markers Specific to Dense Variation Blocks.
Barcode System for Genetic Identification of Soybean [Glycine max (L.) Merrill] Cultivars Using InDel Markers Specific to Dense Variation Blocks.
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DOI：
10.3389/fpls.2017.00520
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发表时间：
2017
影响因子：
5.6
通讯作者：
Kim YH
中科院分区：
文献类型：
--
作者：
Sohn HB;Kim SJ;Hwang TY;Park HM;Lee YY;Markkandan K;Lee D;Lee S;Hong SY;Song YH;Koo BC;Kim YH
用于大豆[Glyine max(L.)Merrill]品种，插入/缺失(Indel)标记是目前首选的标记，因为它们易于使用，共显性和相对丰富。尽管INDELs具有重要的生物学意义，但对具有已证实的质量和重复性的INDELs的调查一直是有限的。在这项研究中，我们描述了基于Indel标记的大豆条码系统方法，每一种方法都是针对由于许多变异而导致的非随机重组的密集变异块(DVB)。首先，通过分析6个大豆品种(巴昆、森帕达尔2号、新木、大浦农、黄冈和威廉姆斯82)的全基因组数据，挖掘出2,274个VB，用于DVB特异的Indel标记。其次，在DVB地区确定了73,327个可能用于开发大豆条形码系统的INDELs。其中，通过凝胶电泳法从所有大豆品种中筛选出202个DVB特异INDELs，通过比较5个品种与参比品种的扩增产物的多态性，将其转化为2D条形码类型。最后，对147个大豆品种的标记多态性进行了评估，并详细介绍了区分大豆品种的大豆条形码系统。此外，通过对27个标记组合的大豆品种的洗牌模式的研究，可以快速地从染色体水平上识别DVBS的变化。特别是利用27个Indel标记对回交后代“新港”和轮回亲本“Sowon”进行了鉴定。这些结果表明，大豆条形码系统不仅可以最少地使用分子标记，而且可以比较来自不同来源的数据，因为不需要在新品种中进行等位基因入库。
For genetic identification of soybean [Glycine max (L.) Merrill] cultivars, insertions/deletions (InDel) markers have been preferred currently because they are easy to use, co-dominant and relatively abundant. Despite their biological importance, the investigation of InDels with proven quality and reproducibility has been limited. In this study, we described soybean barcode system approach based on InDel makers, each of which is specific to a dense variation block (dVB) with non-random recombination due to many variations. Firstly, 2,274 VBs were mined by analyzing whole genome data in six soybean cultivars (Backun, Sinpaldal 2, Shingi, Daepoong, Hwangkeum, and Williams 82) for transferability to dVB-specific InDel markers. Secondly, 73,327 putative InDels in the dVB regions were identified for the development of soybean barcode system. Among them, 202 dVB-specific InDels from all soybean cultivars were selected by gel electrophoresis, which were converted as 2D barcode types according to comparing amplicon polymorphisms in the five cultivars to the reference cultivar. Finally, the polymorphism of the markers were assessed in 147 soybean cultivars, and the soybean barcode system that allows a clear distinction among soybean cultivars is also detailed. In addition, the changing of the dVBs in a chromosomal level can be quickly identified due to investigation of the reshuffling pattern of the soybean cultivars with 27 maker sets. Especially, a backcross-inbred offspring, “Singang” and a recurrent parent, “Sowon” were identified by using the 27 InDel markers. These results indicate that the soybean barcode system enables not only the minimal use of molecular markers but also comparing the data from different sources due to no need of exploiting allele binning in new varieties.