Genetic structure and differentiation of Oryza sativa L. in China revealed by microsatellites

Abstract

China is one of the largest centers of genetic diversity of Oryza sativa L. in the world. Using a genetically representative primary core collection of 3,024 rice landraces in China, we analyzed the genetic structure and intraspecific differentiation of O. sativa, and the directional evolution of SSR. The genetic structure was investigated by model-based structure analysis and construction of neighbor-joining phylogenetic tree. Comparison between genetic structure and predefined populations according to Ting's taxonomic system revealed a hierarchical genetic structure: two distinct subspecies, each with three ecotypes and different numbers of geo-ecogroups within each ecotype. Two subspecies evidently resulted from adaptation to different environments. The different cropping systems imposed on the subspecies led to further differentiation, but the variation within each subspecies resulted from different causes. Indica, under tropical-like or lowland-like environments, exhibited clear differentiation among seasonal ecotypes, but not among soil-watery ecotypes; and japonica showed clear differences between soil water regime ecotypes, but not among seasonal ecotypes. Chinese cultivated rice took on evident directional evolution in microsatellite allele size at several aspects, such as subspecies and geographical populations. Japonica has smaller allele sizes than indica, and this may partly be the result of their different domestication times. Allele size was also negatively correlated with latitude and altitude, and this may be interpreted by different mutation rates, selection pressures, and population size effects under different environments and cropping systems.

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

“…early (Ind.E), late (Ind.L) and intermediate (Ind.M) ecotypes [6]. However, the gradually increasing LnP(D) values after K=3 indicated subtle sub-structures in the 3 ecotypes [6]. In the present study, we conducted further independent simulations within each of the ecotypes to examine the possibility of more subtle sub-structures.…”

“…early (Ind.E), late (Ind.L) and intermediate (Ind.M) ecotypes [6]. However, the gradually increasing LnP(D) values after K=3 indicated subtle sub-structures in the 3 ecotypes [6].…”

“…These taxonomies were primarily based on morphological traits, which were mostly quantitative and controlled by polygenes, and were easily influenced by the environment. Using SSR markers and the primary core collection of rice germplasm resources in China, Zhang et al [6] divided indica into three ecotypes: Indica Early (Ind.E), Indica Late (Ind.L) and Indica Medium (Ind.M). Their results also indicated some subtle sub-structures within the three ecotypes.…”

“…Molecular markers have been widely applied to investigate the genetic structure, evolution and genetic diversity of rice germplasm resources [6,[12][13][14][15]. It is feasible to study the genetic structure and ecotypic classification within indica.…”

Otimização da utilização de marcadores moleculares microssatélites e sua aplicação em estudos com plantas daninhas

“…Ainda, o caráter codominante dos marcadores SSR permite a distinção entre homozigotos e heterozigotos (Varshney et al, 2005). Já a presença de múltiplos alelos por locus favorece a avaliação da diversidade genética de populações e subpopulações mesmo em espécies com alto grau de autogamia (Zhang et al, 2009), como a maioria das plantas daninhas. A análise de marcadores microssatélites consiste em reações de PCR convencional, seguida pela verificação dos resultados em gel de agarose, poliacrilamida ou através de eletroforese capilar automatizada (Menksen & Kahl, 2005).…”