利用InDel标记鉴定水稻育种材料的籼粳属性

Identification of Indica-Japonica Attribute for Breeding Materials Using InDel Markers in Rice

准确高效鉴定水稻材料的籼粳属性对于开展水稻籼粳亚种间杂种优势利用有着重要意义。利用19对基于籼稻(9311)和粳稻(日本晴)全基因组DNA序列比对获得的差异片段而设计的特异插入/缺失(Insertion/Deletion,InDel)引物,对48份育种上常用的籼稻、粳稻和中间型材料(品种)进行了InDel标记的籼粳属性分析,利用DNA样品在这19对InDel位点上的籼型或粳型基因频率,结合聚类分析和主成分分析,确定了这些材料的籼粳属性,通过比对程氏指数法的籼粳鉴定结果检验了InDel分子标记法在水稻籼粳属性鉴定上的有效性。结果表明,InDel分子标记法与传统的程氏指数法的总体吻合率为89.58%,在典型籼稻或典型粳稻材料上两者的吻合率为100%;在具有复杂遗传背景的中间型材料上,InDel分子标记法比程氏指数法具有更高的准确性。因此,InDel分子标记法是真正鉴定籼粳的特异方法,比传统方法具有更高的灵敏性和准确度,可以用于籼粳属性鉴定及遗传分化研究。

It is greatly significant to identify indica or japonica accurately and efficiently for exploring the heterosis of indica-japonica inter-subspecies in rice breeding . In this paper, forty eight rice varieties including indica, japonica and intermediate type which commonly used in rice breeding were analyzed by 19 pairs of insertion/deletions （InDel） molecular markers, which were designed on the base of the comparative genomic DNA sequences between indica variety 9311 and japonica variety Nipponbare. Indica-japonica attribute of each rice variety was identified by calculating indica and japonica gene frequencies at the 19 InDel sites of each DNA sample, together with cluster analysis and principal component analysis （PCA）. Compared with the results of the Cheng^s index method the effectiveness of using InDel molecular markers to identify indica japonica in rice was verified. Results showed that the coincidence rate between InDel molecular marker method and traditional Cheng~ index method is 89.58% in identifying indica or japonica for all the tested materials, and 100% for the typical indica or japonica varieties. It hinted that InDel molecular marker method is more accurate than Cheng^s index method for the intermediate type materials with complicated genetic background. The results indicated that the InDel molecular marker method has higher resolution and accuracy compared with the traditional one, and the new method can be completely used to identify indica-japonica and genetic differentiation research in rice.