%A ZHENG Xiang-Hua, YE Jun-Hua, CHENG Chao-Ping, WEI Xing-Hua, YE Xin-Fu, YANG Yao-Long %T Xian-geng identification by SNP markers in Oryza sativa L. %0 Journal Article %D 2022 %J Acta Agronomica Sinica %R 10.3724/SP.J.1006.2022.02085 %P 342-352 %V 48 %N 2 %U {https://zwxb.chinacrops.org/CN/abstract/article_7269.shtml} %8 2022-02-12 %X

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 4k-SNP and used the xian-geng index as an indicator for xian-geng identification. Furthermore, the 4k-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 4k-SNP identification. The result showed that the geng index obtained from 40-SNP and 4k-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 4k-SNP and Cheng’s index. And the correlation coefficients of xian-geng identifications between 40-SNP and 4k-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.