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Population structure and association mapping on chromosome 7 using a diverse panel of Chinese germplasm of rice (Oryza sativa L.)

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The majority of 170 rice accessions used in this study were diverse landraces or varieties from a putative mini-core collection of Chinese germplasm along with some widely used parental lines in genetic analysis or breeding (a few from abroad). The population was genotyped using 84 SSR or InDel markers on chromosome 7 and 48 markers on other chromosomes. The phenotyping of heading date, plant height and panicle length were carried out in different locations for 2 years. Based on morphological characterization, distance-based clustering and model-based estimation of marker data, the population showed a predominant structure with two subpopulations in correspondence with indica and japonica subspecies. The estimation of linkage disequilibrium in 2 Mb windows varied along chromosome 7 and showed parallel changes with inter-subspecies differentiation of marker loci (Fst). Based on the mixed linear model considering population structure and family relatedness [i.e. the (Q + K) model], one to three associated markers (P ≤ 0.0001) per trait per experiment were scanned out on rice chromosome 7. Most significant loci were repeated for the data from both field experiments while two loci were associated with two or three traits. Marker-based allelic effects were shown in a couple of associated markers as examples. The application of association results in breeding program was also discussed.

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The authors are grateful to Dr. Zichao Li for providing us the rice accessions in the putative mini-core collection of Chinese rice germplasm. Two anonymous reviewers gave us many critical comments, based on that the manuscript was improved in several issues from its early version. This study was jointly supported by a grant from the Ministry of Agriculture of China (948-2006-R1), a grant from National Key Basic Research Program of China (973 Plan), a grant from the National Natural Science Foundation of China (30830071) and a grant from Shanghai Municipal Commission of Science and Technology.

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Correspondence to Hanwei Mei or Lijun Luo.

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Communicated by J. Yu.

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Wen, W., Mei, H., Feng, F. et al. Population structure and association mapping on chromosome 7 using a diverse panel of Chinese germplasm of rice (Oryza sativa L.). Theor Appl Genet 119, 459–470 (2009).

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  • Plant Height
  • Marker Locus
  • Association Mapping
  • Rice Chromosome
  • InDel Marker