Population structure and genetic diversity of Chinese yams based on SNP molecular markers

Yams (Dioscorea opposita Thunb.) are a medicinal and edible crop, and an important export vegetable in China; however, their sources are complicated, and their varieties mixed. This study used 21 agronomic traits and single nucleotide polymorphism (SNP) markers to analyze the population structure and genetic diversity of 28 Chinese yam germplasm resources from across the country. The results showed that the distribution of agronomic traits at different levels was uneven and variation was abundant; the coefficient of variation of the bulbil weight was the largest (52.95%). In addition, 147,177 high-quality SNP sites were identified after effective filter screening. Population genetic structure analysis showed that the 28 accessions could be divided into 3 groups. In addition, phylogenetic analysis revealed that most individuals were genetically distant from each other, with a low degree of kinship and high genetic diversity. Pop28 (Taigu Zhongyang) showed the highest level of genetic diversity, whereas pop11 (Fujian yam) showed the lowest. The population differentiation index (Fst) of the 28 Chinese yam germplasm resources ranged from 0.103 to 0.902, and most showed high genetic differentiation. Furthermore, gene flow occurred mainly within Shanxi Province. This study revealed the population structure and genetic diversity of Chinese yam germplasm resources, laying a foundation for their development and utilization in the future.