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Genetics. Oct 2003; 165(2): 759–769.
PMCID: PMC1462795

Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.).

Abstract

To assess the usefulness of linkage disequilibrium mapping in an autogamous, domesticated species, we have characterized linkage disequilibrium in the candidate region for xa5, a recessive gene conferring race-specific resistance to bacterial blight in rice. This trait and locus have good mapping information, a tractable phenotype, and available sequence data, but no cloned gene. We sampled 13 short segments from the 70-kb candidate region in 114 accessions of Oryza sativa. Five additional segments were sequenced from the adjacent 45-kb region in resistant accessions to estimate the distance at which linkage disequilibrium decays. The data show significant linkage disequilibrium between sites 100 kb apart. The presence of the xa5 resistant reaction in two ecotypes and in accessions with different haplotypes in the candidate region may indicate multiple origins or genetic heterogeneity for resistance. In addition, genetic differentiation between ecotypes emphasizes the need for controlling for population structure in the design of linkage disequilibrium studies in rice.

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Selected References

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  • Olsen Kenneth M, Purugganan Michael D. Molecular evidence on the origin and evolution of glutinous rice. Genetics. 2002 Oct;162(2):941–950. [PMC free article] [PubMed]
  • Pritchard JK, Rosenberg NA. Use of unlinked genetic markers to detect population stratification in association studies. Am J Hum Genet. 1999 Jul;65(1):220–228. [PMC free article] [PubMed]
  • Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES., 4th Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11479–11484. [PMC free article] [PubMed]
  • Bhattramakki Dinakar, Dolan Maureen, Hanafey Mike, Wineland Robin, Vaske Dave, Register James C, 3rd, Tingey Scott V, Rafalski Antoni. Insertion-deletion polymorphisms in 3' regions of maize genes occur frequently and can be used as highly informative genetic markers. Plant Mol Biol. 2002 Mar-Apr;48(5-6):539–547. [PubMed]
  • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. [PubMed]
  • Blair Matthew W, Garris Amanda J, Iyer Anjali S, Chapman Brad, Kresovich Stephen, McCouch Susan R. High resolution genetic mapping and candidate gene identification at the xa5 locus for bacterial blight resistance in rice ( Oryza sativa L.). Theor Appl Genet. 2003 Jun;107(1):62–73. [PubMed]
  • Sasaki Takuji, Matsumoto Takashi, Yamamoto Kimiko, Sakata Katsumi, Baba Tomoya, Katayose Yuichi, Wu Jianzhong, Niimura Yoshihito, Cheng Zhukuan, Nagamura Yoshiaki, et al. The genome sequence and structure of rice chromosome 1. Nature. 2002 Nov 21;420(6913):312–316. [PubMed]
  • Shifman S, Darvasi A. The value of isolated populations. Nat Genet. 2001 Aug;28(4):309–310. [PubMed]
  • Buckler Edward S, 4th, Thornsberry Jeffry M. Plant molecular diversity and applications to genomics. Curr Opin Plant Biol. 2002 Apr;5(2):107–111. [PubMed]
  • Cavalli-Sforza LL, Edwards AW. Phylogenetic analysis. Models and estimation procedures. Am J Hum Genet. 1967 May;19(3 Pt 1):233–257. [PMC free article] [PubMed]
  • Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 2001 Aug;11(8):1441–1452. [PMC free article] [PubMed]
  • Feng Qi, Zhang Yujun, Hao Pei, Wang Shengyue, Fu Gang, Huang Yucheng, Li Ying, Zhu Jingjie, Liu Yilei, Hu Xin, et al. Sequence and analysis of rice chromosome 4. Nature. 2002 Nov 21;420(6913):316–320. [PubMed]
  • Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS. Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci U S A. 2001 Jul 31;98(16):9161–9166. [PMC free article] [PubMed]
  • Hagenblad Jenny, Nordborg Magnus. Sequence variation and haplotype structure surrounding the flowering time locus FRI in Arabidopsis thaliana. Genetics. 2002 May;161(1):289–298. [PMC free article] [PubMed]
  • Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov 11;22(22):4673–4680. [PMC free article] [PubMed]
  • Hudson RR, Kaplan NL. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics. 1985 Sep;111(1):147–164. [PMC free article] [PubMed]
  • Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES., 4th Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet. 2001 Jul;28(3):286–289. [PubMed]
  • Khush GS. Origin, dispersal, cultivation and variation of rice. Plant Mol Biol. 1997 Sep;35(1-2):25–34. [PubMed]
  • Lander ES. The new genomics: global views of biology. Science. 1996 Oct 25;274(5287):536–539. [PubMed]
  • Le Corre Valérie, Roux Fabrice, Reboud Xavier. DNA polymorphism at the FRIGIDA gene in Arabidopsis thaliana: extensive nonsynonymous variation is consistent with local selection for flowering time. Mol Biol Evol. 2002 Aug;19(8):1261–1271. [PubMed]
  • Nordborg Magnus, Tavaré Simon. Linkage disequilibrium: what history has to tell us. Trends Genet. 2002 Feb;18(2):83–90. [PubMed]

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