Xian-geng identification by SNP markers in Oryza sativa L.
摘要
<p id="C3">Asian cultivated rice (<italic>Oryza sativa</italic> L.) is divided into two subspecies of <italic>xian</italic> and <italic>geng</italic>. With the development of hybrid rice and utilization of interspecific heterosis, the boundaries between <italic>xian</italic> and <italic>geng</italic> 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 <italic>xian</italic>-<italic>geng</italic> specific SNP loci named as 4k-SNP and used the <italic>xian</italic>-<italic>geng</italic> index as an indicator for <italic>xian</italic>-<italic>geng</italic> identification. Furthermore, the 4k-SNP was reduced to 40-SNP (40 SNP loci) for <italic>indica</italic>/<italic>japonica</italic> 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<italic> xian</italic>-<italic>geng</italic> identification, 82 bred varieties were used in this study to compare the results of 40-SNP <italic>xian</italic>-<italic>geng</italic> identification and 4k-SNP identification. The result showed that the <italic>geng</italic> 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 (<italic>indica</italic>, <italic>aus</italic>, <italic>rayada</italic>, <italic>aromatic</italic>, <italic>tropical japonica</italic>, and <italic>temperate japonica</italic>), were used to compare the <italic>xian</italic>-<italic>geng</italic> identification results of 40-SNP with those of 4k-SNP and Cheng’s index. And the correlation coefficients of <italic>xian</italic>-<italic>geng</italic> 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 val