Genetic Diversity of Shanlan Upland Rice (<i>Oryza sativa</i> L.) and Association Analysis of SSR Markers Linked to Agronomic Traits
Guofeng Yang, Yong Yang, Yali Guan, Zhixia Xu, Junyu Wang, Yong Yun, Xiaowei Yan, Qingjie Tang
Abstract
Shanlan upland rice, a kind of unique rice germplasm in Hainan Island, was used to evaluate genetic diversity and association between SSR markers and agronomic traits. A total of 239 alleles were detected in 57 Hainan upland rice varieties using 35 SSR markers, and the number of alleles per locus was 2‐19. The observed heterozygosity was 0.0655‐0.3115. The Shannon diversity index was 0.1352‐0.4827. The genetic similarity coefficient was 0.6736‐0.9707, and 46 varieties were clustered into one group, indicating that the genetic base of the Shanlan upland rice germplasm was narrow. A total of 25 SSR markers significantly related to plant height, effective panicle number per plant, panicle length, total grain number, filled grain number, seed rating rate, and 1000‐grain weight were obtained ( P < 0.01), with the percentage of the total variations explained ranging from 0.12% to 42.62%. RM208 explained 42.62% of the total variations in plant height of Shanlan upland rice. RM493 was significantly associated with 6 agronomic traits. We can speculate that RM208 may flank QTLs responsible for plant height and RM493 may flank QTLs playing a fundamental role in the intertwined regulatory network of agronomic traits of Shanlan upland rice.