Screening of Indica-Japonica Specific Molecular Markers and Establishment of Discrimination System

Objective Accurate differentiation of indica-japonica nature in rice is of great importance in the aspects of advantage utilization and evolutionary studies of indica-japonica subspecies hybrids. Molecular markers designed based on nucleotide sequence differences between indica rice and japonica rice have been widely used to discriminate indica-japonica in rice. However, it remains unclear whether these published molecular markers for indica-japonica discrimination still show indica-japonica specificity in experimental materials with diverse genetic backgrounds; moreover, the current indica-japonica discrimination is mostly based on the comparison between the line to be tested and two control varieties, which cannot reflect the indica-japonica similarity between the line to be tested and the indica (japonica) subspecies population. Therefore, it is necessary to screen a set of molecular markers that can show indica-japonica specificity in all diverse genetic materials and to establish an indica-japonica group discrimination system to objectively discriminate indica-japonica in rice.

Method In the Rice Diversity Germplasm Platform 2 (RDP2), which represents the genetic diversity of rice in the world, 92 rice varieties (lines) we selected that retained population genetic diversity based on the genotypes of 70000 SNP molecular markers, and screened 51 pairs of previously reported molecular markers for indica-japonica discrimination; and selected 5 indica rice and 5 japonica rice to form indica and japonica discrimination groups based on the clustering results of indica-japonica-specific molecular markers, and used indica discrimination values to quantify rice indica-japonica.

Result Twenty-four pairs of indica-japonicaspecific molecular markers were screened out of 51 pairs (both indica/japonica rice clusters showed specific band types with a frequency of higher than 69.5%), which were evenly distributed on 12 chromosomes of rice. Based on the banding results of the indica-japonica-specific molecular markers, a clustering analysis of indica-japonica nature was performed. Ninety-two varieties (lines) could be divided into 2 clusters of indica and japonica rice; and the clustering results were in perfect consitant with the known indica-japonica nature of these varieties (lines). Based on the clustering results, a cluster discrimination system was constructed and indica discrimination values were calculated for 10 randomly selected varieties (lines). Among them, there were 1 indica-leaning line, 1 japonica-leaning line, 4 indica lines and 4 japonica lines, and the quantitative discrimination of their indica-japonica nature was accurately achieved.

Conclusion In this study, we screened a set of molecular markers for indica-japonica identification in materials with rich genetic background, and established an indica-japonica discrimination system based on indica-japonica clusters, which can be used to discriminate indica-japonica of rice efficiently and accurately.