Abstract
The assessment of genetic diversity and population structure of a core collection would benefit to make use of these germplasm as well as applying them in association mapping. The objective of this study were to (1) examine the population structure of a rice core collection; (2) investigate the genetic diversity within and among subgroups of the rice core collection; (3) identify the extent of linkage disequilibrium (LD) of the rice core collection. A rice core collection consisting of 150 varieties which was established from 2260 varieties of Ting's collection of rice germplasm were genotyped with 274 SSR markers and used in this study. Two distinct subgroups (i.e. SG 1 and SG 2) were detected within the entire population by different statistical methods, which is in accordance with the differentiation of indica and japonica rice. MCLUST analysis might be an alternative method to STRUCTURE for population structure analysis. A percentage of 26% of the total markers could detect the population structure as the whole SSR marker set did with similar precision. Gene diversity and MRD between the two subspecies varied considerably across the genome, which might be used to identify candidate genes for the traits under domestication and artificial selection of indica and japonica rice. The percentage of SSR loci pairs in significant (P<0.05) LD is 46.8% in the entire population and the ratio of linked to unlinked loci pairs in LD is 1.06. Across the entire population as well as the subgroups and sub-subgroups, LD decays with genetic distance, indicating that linkage is one main cause of LD. The results of this study would provide valuable information for association mapping using the rice core collection in future.
Highlights
Rice (Oryza sativa L.) feeds more than 50% of the world’s population and is one of the most important crops in the world
The maximum of the ad hoc measure DK was observed for K = 2 (Figure S2a), which indicated that the entire population could be divided into two subgroups (i.e. SG 1 and SG 2)
admixed group (AD) is consisted of 7 indica-clined rice, 8 japonica-clined rice and 4 typical japonica rice
Summary
Rice (Oryza sativa L.) feeds more than 50% of the world’s population and is one of the most important crops in the world. Rice genetic resource is the primary material for rice breeding and makes a concrete contribution to global wealth creation and food security. China is well known as an origin center of cultivated rice, with abundant rice genetic resources. As early as 1920–1964, Ying Ting, An academician of Chinese academy of science, had collected more than 7128 rice landrace from all over China as well as some main rice cultivated countries. The collection is one of the earliest collections for rice germplasm resources in China and was named as Ting’s collection [1]. Rice landrace contain greater genetic diversity than elite cultivars and represent an intermediate stage in domestication between wild and elite cultivars [2]. Mining the elite genes within these rice landrace is of importance to the genetic improvement of cultivated rice
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