Development of Simple Sequence REPEAT Markers for Genetic Diversity Analysis Based on the cDNA Sequences of Chinese Yam (Dioscorea spp.)

Chinese yam, with its rich taste and high nutritive value, has remained an essential part of Chinese cuisine. As China is rich in yam germplasm resources, understanding the genetic diversity of local varieties, which is important for the proper management, conservation, variety improvement, and sustainable utilization of yam germplasms, is crucial. In this study, an Illumina Hi-seq 2500 sequencing (Illumina, San Diego, CA, USA) system was used to sequence cDNA libraries of root, stem, and leaf tissues of Chinese yam; 14,450 unigenes containing SSR sites were identified from the transcriptome dataset. About half of the SSRs were mononucleotides and approximately 23% were dinucleotides and trinucleotides. In addition, 100 SSR primers were randomly designed for PCR and polymorphism verification. A total of 32 yam materials used in the study were identified by 24 primer pairs. Based on the Qinling-Huaihe River line, the northern and southern germplasms were divided into different taxa, but no clear geographical pattern was observed in the southern germplasms. The 32 germplasms were also divided into three categories using a clustering analysis, with samples in the same group possessing similar morphological characters. These 24 newly identified SSR markers can provide the basis for the genetic identification, diversity analysis, and marker-assisted selection breeding of Dioscoreaceae.