Study Of SSR Markers On Identification Of Japonica Rice Varieties Authorized By Jiangsu Government

Rice is the one of the most important food crops in Jiangsu Province with more than 2.2 million hectares annually, and of them more than 1.87 million hectares plant japonica rice varieties. Development and application of elite japonica rice varieties are therefore directly associated with the food security of Jiangsu Province. Due to lack of high efficient method on identifying rice varieties, the illegal issues are frequently happened during the processes of authorization, widespread, business and management of rice vaireties, which severely affect the improvement of variety innovation and the application of elite variety. In the present study, we employed SSR (simple sequence repeat) markers to identify japonica rice varieties that authorized by Jiangsu Government in recent years, and developed a set of core-SSR markers which are able to distinguish Jiangsu japonica rice varieties. The main conclusions of the study are as follows:1. The sets of 24 and 48 SSR (Simple sequence repeat) markers respectively reported in Industrial standards of Agriculture Ministry "NY/T-1433-2007" (named 2007-version) and "NY/T-1433-2014" (named 2014-version) for rice variety identification were confirmed not able to identify all Jiangsu japonica rice varieties tested in the present study..Seventeen out of 86 japonica rice varieties, from the new-variety regional trial of Jiangsu Province of 2013, could not be distinguished by the 24 SSR markers in 2007-version, and two of them were not distinguished by the 48 SSR markers in 2014-version. Total of 46 japonica rice varieties, authorized by Jiangsu Government from 2009 to 2014, were further employed to test the 48 SSR markers in 2014-version on variety identifying. We found that the 48 SSR markers were capable of distinguishing most of the varieties tested but not on the two varieties, Nanjing 49 and Yandao 12. For the 48 SSR markers,16 of them had no polymorphism among the 46 varieties, and 21 of them had PIC value exceeding 0.25 and only 5 markers had PIC value exceeding 0.5, which indicated the polymorphism of 48 SSR markers were low in the 46 japonica rice varieties tested.2. The Jiangsu japonica rice varieties exhibited narrow genetic basis and low genetic diviesity. The 121 out of 714 SSR markers were developed which showed polymorphism on the 12 japonica varieties selected, and plus 32 polymorphic SSR markers in 2014-version, total of 153 polymorphic SSR markers were emplolyed to evaluated the genetic diversity of the 46 rice varieties. The results showed that the lowest genetic similarity coefficient among 46 rice varieties was 0.566, demonstrating that the varieties had narrow genetic bases with low genetic diversity. The average genetic similar coefficient of varieties in the type of Zhongshu Zhongjing were significantly higher than those of the varieties in other three ecotypes, indicating that the Zhongshu Zhongjing varieties had more narrow genetic base. For different rice ecotypes, Chishu Zhongjing and Zaoshu Wanjing showed highest genetic similar coefficient, while Zhongshu Zhongjing and Zhongshu Wanjing exhibited lowest.3. We developed 52 core-SSR markers that are able to identify Jiangsu japonica rice varieties and preliminarily estabilished the SSR fingerprints of 46 varieties using the developed core-SSR markers. On the base of 46 varieties×153 SSR markers genotype data, the markers’ distribution in rice genome and each marker’s PIC (polymorphic information content) value, we preliminarily developed 52 SSR markers as the core-SSR markers to identify Jiangsu japonica rice variety. In the population of the 46 varieties,52 core-SSR markers totally detected 132 alleles with average 2.54 alleles per marker detected, and the PIC values of 23 and 13 of the core-SSR markers were more than 0.25 and 0.5, respectively, which indicated that the core-SSR markers had relatively high polymorphism and rich allelic variation. The SSR fingerprints of the 46 varieties on 52 core-SSR markers loci were estabilished, and any of two varieties exhibited at least 3 differential loci, which indicated that the 52 core-SSR markers are of high ability to identify japonica rice varieties of Jiangsu Province.