Article Crop Germplasm Resources

Chinese Science Bulletin

, Volume 58, Issue 3, pp 344-352

Open Access This content is freely available online to anyone, anywhere at any time.

Genetic structure and eco-geographical differentiation of cultivated Hsien rice (Oryza sativa L. subsp. indica) in China revealed by microsatellites

  • DongLing ZhangAffiliated withKey Laboratory of Crop Heterosis and Utilization of Ministry of Education, and Beijing Laboratory of Crop Genetic Improvement, China Agricultural University
  • , HongLiang ZhangAffiliated withKey Laboratory of Crop Heterosis and Utilization of Ministry of Education, and Beijing Laboratory of Crop Genetic Improvement, China Agricultural University Email author 
  • , YongWen QiAffiliated withKey Laboratory of Crop Heterosis and Utilization of Ministry of Education, and Beijing Laboratory of Crop Genetic Improvement, China Agricultural University
  • , MeiXing WangAffiliated withKey Laboratory of Crop Heterosis and Utilization of Ministry of Education, and Beijing Laboratory of Crop Genetic Improvement, China Agricultural University
  • , JunLi SunAffiliated withKey Laboratory of Crop Heterosis and Utilization of Ministry of Education, and Beijing Laboratory of Crop Genetic Improvement, China Agricultural University
  • , Li DingAffiliated withInstitute of Crop Science, Chinese Academy of Agricultural Sciences
  • , ZiChao LiAffiliated withKey Laboratory of Crop Heterosis and Utilization of Ministry of Education, and Beijing Laboratory of Crop Genetic Improvement, China Agricultural University Email author 

Abstract

Indica is not only an important rice subspecies widely planted in Asia and the rest of the world, but it is also the genetic background of the majority of hybrid varieties in China. Studies on genetic structure and genetic diversity in indica germplasm resources are important for the classification and utilization of cultivated rice in China. Using a genetically representative core collection comprising 1482 Chinese indica landraces, we analysed the genetic structure, geographic differentiation and diversity. Model-based structure analysis of varieties within three ecotypes revealed nine eco-geographical types partially accordant with certain ecological zones in China. Differentiation of eco-geographical types was attributed to local ecological adaption and physical isolation. These groups may be useful for developing heterotic groups of indica. To facilitate the identification of different ecotypes and eco-geographical types, we identified characteristic SSR alleles of each ecotype and eco-geographical type and a rapid index of discrimination based on characteristic alleles. The characteristic alleles and rapid discrimination index may guide development of heterotic groups, and selection of hybrid parents.

Keywords

population structure indica SSR