Single-seeded InDel fingerprints in rice: An effective tool for indica-japonica rice classification and evolutionary studies
Single-seeded InDel fingerprints in rice: An effective tool for indica-japonica rice classification and evolutionary studies
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水稻单籽 InDel 指纹：籼粳稻分类和进化研究的有效工具
DOI：
10.1111/j.1759-6831.2011.00173.x
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发表时间：
2012-01-01
影响因子：
3.7
通讯作者：
Lu, Bao-Rong
中科院分区：
文献类型：
--
作者：
Liu, Ping;Cai, Xing-Xing;Lu, Bao-Rong
亚洲栽培水稻（Oryza sativa L.）是世界上重要的谷类作物，8000年前从其野生祖先驯化而来。亚洲栽培水稻在不同农业生态条件下的长期栽培和进化过程中，分化为籼稻亚种和粳稻亚种。需要一种有效的方法来鉴定水稻种质的籼粳性状，这是水稻遗传改良的必要条件。我们开发了一种结合从单个水稻种子中提取DNA和插入/删除（InDel）分子指纹图谱来确定水稻种质的籼粳性状的方法。利用单种子InDel指纹图谱（SSIF）对166个亚洲水稻品种、2个非洲水稻品种、30个野生水稻品种和42个杂草水稻品种进行了分析。结果表明，该方法能有效地确定水稻种质的籼粳性状。进一步分析表明，在大多数亚洲水稻品种和杂草水稻品种中，籼粳分化显著。相比之下，非洲稻品种和几乎所有野生稻品种都没有表现出这种分化。SSIF显示的栽培稻和野生稻样本的格局支持了我们之前的假设，即水稻在不同的农业生态条件下驯化后发生了籼粳分化。此外，水稻品种和杂草稻品种的差异模式表明，本研究中包括的杂草稻可能是内生起源（来自作物）。
Asian cultivated rice (Oryza sativa L.), an important cereal crop worldwide, was domesticated from its wild ancestor 8000 years ago. During its long-term cultivation and evolution under diverse agroecological conditions, Asian cultivated rice has differentiated into indica and japonica subspecies. An effective method is required to identify rice germplasm for its indica and japonica features, which is essential in rice genetic improvements. We developed a protocol that combined DNA extraction from a single rice seed and the insertion/deletion (InDel) molecular fingerprint to determine the indica and japonica features of rice germplasm. We analyzed a set of rice germplasm, including 166 Asian rice varieties, two African rice varieties, 30 accessions of wild rice species, and 42 weedy rice accessions, using the single-seeded InDel fingerprints (SSIF). The results show that the SSIF method can efficiently determine the indica and japonica features of the rice germplasm. Further analyses revealed significant indica and japonica differentiation in most Asian rice varieties and weedy rice accessions. In contrast, African rice varieties and nearly all the wild rice accessions did not exhibit such differentiation. The pattern of cultivated and wild rice samples illustrated by the SSIF supports our previous hypothesis that indica and japonica differentiation occurred after rice domestication under different agroecological conditions. In addition, the divergent pattern of rice cultivars and weedy rice accessions suggests the possibility of an endoferal origin (from crop) of the weedy rice included in the present study.