Genetic diversity and population structure of a diverse set of rice germplasm for association mapping |
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Authors: | Liang Jin Yan Lu Peng Xiao Mei Sun Harold Corke Jinsong Bao |
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Institution: | (1) Institute of Nuclear Agricultural Sciences, Key Laboratory of Zhejiang Province and Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Zhejiang University, Hua Jiachi Campus, Hangzhou, 310029, People’s Republic of China;(2) School of Biological Sciences, The University of Hong Kong, Hong Kong, People’s Republic of China; |
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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. |
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