Analysis of Genetic Diversity and Population Structure of Rice Cultivars from Korea, China and Japan using SSR Markers

• Published in: Genes & genomics Vol. 31; no. 4; pp. 283 - 292
• Main Authors: Zhao, Weiguo (Konkuk University, Seoul, Republic of Korea), Chung, J.W. (Konkuk University, Seoul, Republic of Korea), Ma, K.H. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea), Kim, T.S. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea), Kim, S.M. (Kongju National University, Yesan, Republic of Korea), Shin, D.I. (Kongju National University, Yesan, Republic of Korea), Kim, C.H. (Kongju National University, Yesan, Republic of Korea), Koo, H.M. (Kongju National University, Yesan, Republic of Korea), Park, Y.J. (Kongju National University, Yesan, Republic of Korea), E-mail: yjpark@kongju.ac.kr
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.08.2009; 한국유전학회
• Subjects: Animal Genetics and Genomics; Biomedical and Life Sciences; ESTRUCTURA DE LA POBLACION; genetic diversity; Human Genetics; Life Sciences; Microbial Genetics and Genomics; ORYZA SATIVA; Plant Genetics and Genomics; POPULATION STRUCTURE; SSR; STRUCTURE DE LA POPULATION; 생물학; population structure; genetic diversity; SSR
• ISSN: 1976-9571; 2092-9293
• DOI: 10.1007/BF03191201

A total of 29 simple sequence repeat (SSR) markers were used to analyze the genetic diversity of 150 accessions of cultivated nice (Oryza sativa L.) from Korea, China, and Japan. A total of 375 alleles were detected with an average of 12.9 per locus. The averaged values of gene diversity and polymorphism information content (PIC) for each SSR locus were 0.7001 and 0.6683, respectively. Alleles per locus in Korean rice were 8.8, whereas 8.1 and 7.2 alleles per locus were found in Chinese and Japanese rice, respectively. The mean gene diversity in Korean, Chinese, and Japanese rice was 0.6058, 0.6457, and 0.5174, respectively, whereas the mean PIC values for each SSR locus were 0.5759, 0.6138, and 0.4881, respectively. The genetic diversity of the Korean and Chinese cultivars was higher than that of the Japanese cultivars, and the genetic diversity of japonica was higher than that of indica. The model-based structure analysis revealed the presence of three subpopulations, which was basically consistent with clustering based on genetic distance. An AMOVA analysis showed that the between-population component of genetic variance was less than 22% in contrast to 78% for the within-population component. The overall F∧ST value was 0.2180, indicating a moderate differentiation among groups. The results could be used for designing effective breeding programs aimed at broadening the genetic bases of commercially grown varieties.