Genetic diversity and population structure of a diverse set of rice germplasm for association mapping

Abstract

Germplasm diversity is the mainstay for crop improvement and genetic dissection of complex traits. Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) in target populations is of great importance and a prerequisite for association mapping. In this study, 100 genome-wide simple sequence repeat (SSR) markers were used to assess genetic diversity, population structure, and LD of 416 rice accessions including landraces, cultivars and breeding lines collected mostly in China. A model-based population structure analysis divided the rice materials into seven subpopulations. 63% of the SSR pairs in these accessions were in LD, which was mostly due to an overall population structure, since the number of locus pairs in LD was reduced sharply within each subpopulation, with the SSR pairs in LD ranging from 5.9 to 22.9%. Among those SSR pairs showing significant LD, the intrachromosomal LD had an average of 25-50 cM in different subpopulations. Analysis of the phenotypic diversity of 25 traits showed that the population structure accounted for an average of 22.4% of phenotypic variation. An example association mapping for starch quality traits using both the candidate gene mapping and genome-wide mapping strategies based on the estimated population structure was conducted. Candidate gene mapping confirmed that the Wx and starch synthase IIa (SSIIa) genes could be identified as strongly associated with apparent amylose content (AAC) and pasting temperature (PT), respectively. More importantly, we revealed that the Wx gene was also strongly associated with PT. In addition to the major genes, we found five and seven SSRs were associated with AAC and PT, respectively, some of which have not been detected in previous linkage mapping studies. The results suggested that the population may be useful for the genome-wide marker-trait association mapping. This new association population has the potential to identify quantitative trait loci (QTL) with small effects, which will aid in dissecting complex traits and in exploiting the rich diversity present in rice germplasm.

Correlation among Agro-Morphological Variation and Genetic Diversity of Rice (<i>Oryza sativa </i>L.) under Drought Stress

“…The maximum genetic diversity is the most important criterion to select parental varieties for breeding because of increase the choice of desirable genotypes [26]. Findings of this study were similar to previous studies, in which the PIC values were from 0.16 to 0.78 for European Chinese rice collection of 416 accessions [24,27]. In addition, Chen et al [28] screened 300 rice accessions with 372 SNP markers for 0.358 of diversity and found that polymorphic was 0.285.…”

“…Studies by Garris et al [22] and Ram et al [23] showed that the number of alleles per locus, polymorphic information content and gene diversity were 4.8-14.0, 0.6-0.7, and 6.2-6.8, respectively. The average alleles per locus were 3.9 in 416 rice accessions collected from China [24].…”

Genetic diversity, population structure and association analysis in linseed (Linum usitatissimum L.)

“…As compared to biparental QTL mapping, association mapping increases the range of natural variation that can be exploited in a single experiment and potential genomic regions could be identified (Jin et al 2010). However, this method has chances of false positives mainly due to the population structure (Pritchard et al 2000) and familial relatedness (Yu et al 2006).…”

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

“…This study identified seven rice groups, three of which were defined as tropical japonica, one as temperate japonica, two as indica and one as aus in terms of Garris et al's (2005) classification. Numerous studies on rice cultivars at a local scale have also been conducted and found different subdivisions of rice germplasm (de Oliveira Borba et al, 2009;Zhang et al, 2009Zhang et al, , 2011bJin et al, 2010;Li et al, 2010). Thus, the genetic subdivision and classification of rice germplasm remain unclear, with three to seven major groups identified by different studies.…”

“…In the study by Garris et al (2005), only 15 accessions from mainland China were included and these were grouped into just two groups (indica and temperate japonica). Recent studies have provided convincing evidence that more than two distinct groups were present in Chinese rice germplasm (Zhang et al, 2009(Zhang et al, , 2011bHuang et al, 2010Huang et al, , 2012Jin et al, 2010), implying that greater sampling of Chinese rice cultivars is required for a better resolution of rice population genetics. Finally, as the largest rice genepool, the Chinese rice germplasm has been a focus of investigations for a long time.…”