利用SNP标记进行水稻品种籼粳鉴定

Xian-geng identification by SNP markers in Oryza sativa L.

亚洲栽培稻(Oryza sativa L.)分为籼、粳2个亚种,随着杂交水稻的发展、种间杂种优势的利用,籼粳之间的界限变得越来越模糊。本研究利用3000份水稻种质资源信息,通过计算约2000万个单核苷酸多态性(single nucleotide polymorphism,SNP)位点的SNP-index值,进行籼粳特异SNP位点筛选,最终得到4084个籼粳特异SNP位点(4k-SNP);同时确定以籼粳指数作为水稻品种籼粳鉴定的指标。研究进一步采用大规模简单随机取样等统计分析方法对籼粳特异位点进行数据降维处理,将4k-SNP精简至40个SNP位点(40-SNP),用于水稻籼粳鉴定。为了验证40-SNP的籼粳鉴定效果,本研究一方面利用水稻生产上推广的82份选育品种,对40-SNP籼粳鉴定结果与4k-SNP鉴定结果进行比较,结果发现40-SNP与4k-SNP得出的粳型指数非常接近,相关系数为0.99;另一方面利用全球6类型(indica、aus、rayada、aromatic、tropicaljaponica、temperatejaponica)水稻品种共49份材料,对40-SNP籼粳鉴定结果与4k-SNP及程氏指数法籼粳鉴定结果进行比较,发现40-SNP与4k-SNP及程氏指数法籼粳鉴定结果的相关系数分别在0.98和0.86以上。这些结果证实了40-SNP对水稻品种籼粳鉴定的有效性及准确性。另外发现40-SNP对水稻6种亚群类型也有很好鉴别效果,其中indica的粳型指数<0.20,aus的粳型指数在0.20~0.40,rayada和aromatic的粳型指数在0.60~0.85之间,tropical japonica的粳型指数> 0.90,temperate japonica粳型指数最高,基本为1.00。本研究为研究水稻籼粳分化、杂种优势利用以及水稻种子管理条例制定等方面提供了数据支撑及理论基础。

Asian cultivated rice(Oryza sativa L.) is divided into two subspecies of xian and geng.With the development of hybrid rice and utilization of interspecific heterosis,the boundaries between xian and geng are becoming more and more vague.In this study,based on the SNP-index value of 20 million single nucleotide polymorphism(SNP) loci from 3000 rice germplasm resources,we captured 4084 xian-geng specific SNP loci named as 4 k-SNP and used the xian-geng index as an indicator for xian-geng identification.Furthermore,the 4 k-SNP was reduced to 40-SNP(40 SNP loci) for indica/japonica identification by using the statistical analysis methods such as large-scale simple random sampling based on the dimensionality reduction algorithms.To verify the effectiveness of 40-SNP on xian-geng identification,82 bred varieties were used in this study to compare the results of 40-SNP xian-geng identification and 4 k-SNP identification.The result showed that the geng index obtained from 40-SNP and 4 k-SNP were very close,and the correlation coefficient was 0.99.Moreover,a total of 49 varieties,belonging to six subgroups(indica,aus,rayada,aromatic,tropical japonica,and temperate japonica),were used to compare the xian-geng identification results of 40-SNP with those of 4 k-SNP and Cheng’s index.And the correlation coefficients of xian-geng identifications between 40-SNP and 4 k-SNP as well as between 40-SNP and Cheng’s index were above 0.98 and 0.86,between 40-SNP and 4 k-SNP as well as between 40-SNP and Cheng’s index were above 0.98 and 0.86,respectively.These results verified the validity and accuracy of 40-SNP on xian-geng identification in Oryza sativa L.In addition,40-SNP also had a good distinguishability for the six subgroups in rice,and the xian-geng index of indica,aus,rayada,aromatic,tropical japonica,and,temperate japonica was less than 0.20,0.20–0.40,0.60–0.85,more than 0.90,and 1.00,respectively.This study provides the data and theoretical basis for the differentiation of xian-geng and the utilization of heterosis and,formulation of seed management regulations.