A core collection and mini core collection of Oryza sativa L. in China

Abstract

The extent of and accessibility to genetic variation in a large germplasm collection are of interest to biologists and breeders. Construction of core collections (CC) is a favored approach to efficient exploration and conservation of novel variation in genetic resources. Using 4,310 Chinese accessions of Oryza sativa L. and 36 SSR markers, we investigated the genetic variation in different sized sub-populations, the factors that affect CC size and different sampling strategies in establishing CC. Our results indicated that a mathematical model could reliably simulate the relationship between genetic variation and population size and thus predict the variation in large germplasm collections using randomly sampled populations of 700-1,500 accessions. We recommend two principles in determining the CC size: (1) compromising between genetic variation and genetic redundancy and (2) retaining the main types of alleles. Based on the most effective scheme selected from 229 sampling schemes, we finally developed a hierarchical CC system, in which different population scales and genetic diversities allow a flexible use of genetic resources. The CC, comprising 1.7% (932) of the accessions in the basic collection, retained more than 85% of both the SSR and phenotypic variations. A mini core collection, comprising 0.3% (189) of the accessions in the basic collection, retained 70.65% of the SSR variation and 76.97% of the phenotypic variation, thus providing a rational framework for intensive surveys of natural variation in complex traits in rice genetic resources and hence utilization of variation in rice breeding.

Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

“…According to six diagnostic characters, Cheng (1985) further classified Chinese rice into Hsein, Hsein-cline, Keng-cline and Keng, whereas Ting (1957) developed a five-level taxonomic system for Chinese germplasm, in which rice cultivars were divided into Hsien and Keng subspecies, two seasonal types (early/medium and late sown), two drought-tolerant (or watery regime) types (lowland and upland) and two endosperm types (waxy and non-waxy) and other cultivars. In addition to the Hsien and Keng classification, the other four types of divisions were mainly based on ecological or habitat features and were not supported by subsequent investigations, particularly molecular approaches (Zhang et al, 2009(Zhang et al, , 2011a. By screening 3024 Chinese landraces, for example, Zhang et al (2009) found clear differentiation within two subspecies, that is, the subdivision among seasonal types within Indica and differentiation between drought-tolerant types within Japonica.…”

“…We also calculated the F ST value between three subgroups within Chinese Indica and found relatively low differentiation between them (F ST ¼ 0.076-0.132), consistent with the finding that subdivision was less apparent within Chinese Indica. We further estimated the genetic diversity of the 184 Chinese cultivars that were identified to belong to the core collection (Zhang et al 2011a). We found that the number of alleles in the core collection is lower than that in total samples, particularly for tropical japonica (9.5 vs 5.5).…”

“…The cultivars included 747 landraces and 79 modern varieties, and represent different seasonal (early, medium and late), drought-tolerant (lowland and upland) and endosperm (waxy and non-waxy) types (Table 1, Supplementary Table S1). In addition, we constructed a set of 153 'global' accessions that included 43 representative Chinese accessions (recognized in Zhang et al, 2009;2011a) and 110 accessions representing rice germplasm from countries other than China. The latter accessions consisted of the major rice groups identified by Glaszmann (1987) and Garris et al (2005) and were obtained from the Germplasm Resource Center of the International Rice Research Institute (Supplementary Table S2).…”

“…We sampled 153 diverse global rice cultivars representing all major groups identified in previous studies (Glaszmann, 1987;Garris et al, 2005;Zhang et al, 2009Zhang et al, , 2011a to analyse the population genetic structure and the genetic affinities among major sub-populations of rice. We first used STRUCTURE, a model-based approach to calculate the genetic component of each accession and subdivide all cultivars into clusters.…”

Fine mapping of the awn gene on chromosome 4 in rice by association and linkage analyses

“…In this study, the population used for association mapping consisted of 303 cultivated rice varieties in a rice mini core collection (including 204 Chinese varieties [22] and 99 varieties from other countries, Table S1). The awnness of each variety was evaluated in Sanya (18°09′N) and Hangzhou (29°44′N) in 2006 and in Beijing (39°56′N) in 2009.…”