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首页> 美国卫生研究院文献>Breeding Science >Genome-wide indel markers shared by diverse Asian rice cultivars compared to Japanese rice cultivar ‘Koshihikari’
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Genome-wide indel markers shared by diverse Asian rice cultivars compared to Japanese rice cultivar ‘Koshihikari’

机译：与日本水稻品种越光相比亚洲不同水稻品种共有的全基因组插入缺失标记

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摘要

Insertion-deletion (indel) polymorphisms, such as simple sequence repeats, have been widely used as DNA markers to identify QTLs and genes and to facilitate rice breeding. Recently, next-generation sequencing has produced deep sequences that allow genome-wide detection of indels. These polymorphisms can potentially be used to develop high-accuracy polymerase chain reaction (PCR)-based markers. Here, re-sequencing of 5 indica, 2 aus, and 3 tropical japonica cultivars and Japanese elite cultivar ‘Koshihikari’ was performed to extract regions containing large indels (10–51 bp) shared by diverse cultivars. To design indel markers for the discrimination of genomic regions between ‘Koshihikari’ and other diverse cultivars, we subtracted the indel regions detected in ‘Koshihikari’ from those shared in other cultivars. Two sets of indel markers, KNJ8-indel (shared in eight or more cultivars, including ‘Khao Nam Jen’ as a representative tropical japonica cultivar) and C5-indel (shared in five to eight cultivars), were established, with 915 and 9,899 indel regions, respectively. Validation of the two marker sets by using 23 diverse cultivars showed a high PCR success rate (≥95%) for 83.3% of the KNJ8-indel markers and 73.9% of the C5-indel markers. The marker sets will therefore be useful for the effective breeding of Japanese rice cultivars.
机译：插入-缺失（插入/缺失）多态性（例如简单的序列重复）已广泛用作DNA标记，以鉴定QTL和基因并促进水稻育种。最近，下一代测序产生了可用于全基因组检测插入缺失的深度序列。这些多态性可潜在地用于开发基于高精度聚合酶链反应（PCR）的标记。在这里，对5个in稻，2个aus和3个热带粳稻品种和日本优良品种“越光”进行了重新测序，以提取包含不同品种共有的大indels（10-51 bp）的区域。为了设计用于区分“越光”和其他不同品种之间的基因组区域的插入缺失标记，我们从其他栽培品种共有的区域中减去在“越光”中检测到的插入缺失区域。建立了两组插入缺失标记，KNJ8-indel（共有八个或更多品种，包括代表热带粳稻的'Khao Nam Jen'）和C5-插入缺失（共享了五至八个品种），分别为915和9,899。插入区。通过使用23个不同的品种对两个标记集进行验证，显示83.3％的KNJ8-indel标记和73.9％的C5-indel标记具有很高的PCR成功率（≥95％）。因此，标记物组对于日本水稻品种的有效育种将是有用的。

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