To understand genetic structure and diversity of parental cultivars involved in China Mainland sugarcane breeding programs, 92 elite parents and 4 wild relatives were genotyped with 18 microsatellite DNA markers. The genetic similarity (GS) values among the cultivars ranged from 0.346 to 0.960 with an average of 0.533. Among the introduced cultivars, India accessions had the closest genetic distance to China Mainland accessions (0.447), while Australia accessions have the furthest distance (0.503). A comparison of allelic diversity among geographical origins showed that there were 22 China Mainland specific alleles, of which 28% were derived from native S. spontaneaum germplasm in China. Model-based genetic structure, clustering, and principal components analyses consistently revealed there were five groups within the 96 accessions. Groups 1, 2, 4, and 5 consisted of all cultivars and group 3 only contained wild germplasm. Group 2 was characterized as the Introduction group with 46 cultivars predominantly introduced from Australia, Taiwan of China, India, and USA. Groups 1, 4, and 5 consisted of cultivars mostly originated from China Mainland, defined as the Complex group, Yacheng lines group, and F134/CP72-1210 group, respectively, upon their pedigree. By understanding the genetic relationships among the parental cultivars, breeders can gain a rational basis for expanding the gene pool and select the best parental accessions for crossing.

China is one of the largest centers of genetic diversity of Oryza sativa L. and is the original centers of Oryza sativa L. subspecies japonica. Using a genetically representative core collection of 1 442 rice landraces of japonica in China, the genetic structure, differentiation, and geographic diversity were analyzed. The model-based structure analysis on varieties within three ecotypes revealed 16 eco-geographical types, which are partially accorded with some of the ecological zones in China. The differentiation of eco-geographical types contributed to the local ecological adaption and physical isolation, and maybe could be used to develop the heterotic groups of japonica. To facilitate the identification of different ecotypes and eco-geographical types, we provided the SSR character alleles of each ecotype or geographical eco-group and a rapid discriminated method based on these character alleles. Lastly, investigation on genetic diversity, genetic differentiation indicated that southwest region of China, including south of Yunnan Province, northwest of Guangxi Zhuang Autonomous Region, and southwest of Guizhou Province, possessed the highest genetic diversity and all the necessary conditions as a center of genetic diversity and should be the center of genetic diversity of rice landraces of japonica in China.