Authors: Sujay Rakshit Arunita Rakshit Hideo Matsumura Yoshihiro Takahashi Yoshitaka Hasegawa Akiko Ito Takashige Ishii Naohiko T Miyashita Ryohei Terauchi
Publish Date: 2007/01/12
Volume: 114, Issue: 4, Pages: 731-743
Abstract
Polymorphism over ∼26 kb of DNA sequence spanning 22 loci and one region distributed on chromosomes 1 2 3 and 4 was studied in 30 accessions of cultivated rice Oryza sativa and its wild relatives Phylogenetic analysis using all the DNA sequences suggested that O sativa ssp indica and ssp japonica were independently domesticated from a wild species O rufipogon O sativa ssp indica contained substantial genetic diversity π = 00024 whereas ssp japonica exhibited extremely low nucleotide diversity π = 00001 suggesting the origin of the latter from a small number of founders O sativa ssp japonica contained a larger number of derived and fixed nonsynonymous substitutions as compared to ssp indica Nucleotide diversity and genealogical history substantially varied across the 22 loci A locus RLD15 on chromosome 2 showed a distinct genealogy with ssp japonica sequences distantly separated from those of O rufipogon and O sativa ssp indica Linkage disequilibrium LD was analyzed in two different regions LD in O rufipogon decays within 5 kb whereas it extends to ∼50 kb in O sativa ssp indicaSR conducted this work under financial support from Japanese Society for Promotion of Sciences Tokyo RT thanks B Till L Comai and S Henikoff Washington University Seatle USA for training him with TILLING technique We thank N Kurata National Institute of Genetics Mishima Japan for providing rice seeds and J Rozas University of Barcelona Spain for guiding us with the DnaSP program two anonymous reviewers and M Morgante University of Udine Italy for valuable comments to the earlier version of the manuscript This work was supported by the “Program for Promotion of Basic Research Activities for Innovative Biosciences” Japan “Iwate University 21st Century COE Program Establishment of ThermoBiosystem Research Program” and “JSPS grant no 18310136” to RTSupplementary Fig 1 Results of multilocus HKA test Contributions to the overall χ2 test static by the polymorphism and divergence observations for each locus Squares indicate divergence between African and Asian species and circles correspond to polymorphism within Asian species If the observed value was greater than the expected then the point is placed above the line otherwise it is placed below the line JPG 74 kb
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