Genetic signature of rice domestication shown by a variety of genes

Journal of Molecular Evolution

Volumn 68, Issue 4, 2009, Pages 393-402

  Zhang, Yuanli ^a   Wang, Jiao ^a   Zhang, Xiaohui ^a   Chen, Jian Qun ^a   Tian, Dacheng ^a   Yang, Sihai ^a  

^a NANJING UNIVERSITY   (China)

Author keywords

Genetic variation; NBS LRR genes; Two directional selection

Indexed keywords

NUCLEOTIDE;

ARTICLE; CONTROLLED STUDY; DOMESTICATION; GENE LOCUS; GENETIC POLYMORPHISM; GENETIC VARIABILITY; MOLECULAR EVOLUTION; NONHUMAN; RICE;

AGRICULTURE; BASE SEQUENCE; CHI-SQUARE DISTRIBUTION; FOUNDER EFFECT; GENES, PLANT; GENETIC SPECIATION; IMMUNITY, INNATE; LINEAR MODELS; MUTATION; ORYZA SATIVA; PHYLOGENY; PLANT DISEASES; POLYMORPHISM, GENETIC; SELECTION (GENETICS); SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

JAPONICA; ORYZA RUFIPOGON; ZIZANIA;

EID: 64949176033     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-009-9217-6     Document Type: Article

References (38)

1. RL Allen PD Bittner-Eddy LJ Grenville-Briggs JC Meitz AP Rehmany 2004 Host-parasite coevolutionary conflict between Arabidopsis and downy mildew Science 306 1957 1960
2. A Amante-Bordeos LA Stich R Nelson RD Dalmacio NP Oliva 1992 Transfer of bacterial blight and blast resistance from the tetraploid wild rice Oryza minuta to cultivated rice Theor Appl Genet 84 345 354
3. EG Bakker C Toomajian M Kreitman J Bergelson 2006 A genome-wide survey of R gene polymorphisms in Arabidopsis Plan Cell 18 1803 1818
4. EG Bakker MB Traw C Toomajian M Kreitman J Bergelson 2008 Low levels of polymorphism in genes that control the activation of defense response in Arabidopsis thaliana Genetics 178 2031 2043
5. DS Brar GS Khush 1997 Alien introgression in rice Plant Mol Biol 35 35 47
6. J Ding H Araki Q Wang P Zhang S Yang JQ Chen D Tian 2007 Highly asymmetric rice genomes BMC Genomics 8 154
7. J Ding W Zhang Z Jing JQ Chen D Tian 2007 Unique pattern of R-gene variation within populations in Arabidopsis Mol Genet Genomics 277 619 629
8. J Elli P Dodds T Pryor 2000 Structure function and evolution of plant disease resistance genes Curr Opin Plant Biol 3 278 284
9. RR Hudson 2000 A new statistic for detecting genetic differentiation Genetics 155 2011 2014
10. H Jiang C Wang L Ping D Tian S Yang 2007 Pattern of LRR nucleotide variation in plant resistance genes Plant Sci 173 253 261
11. C Li A Zhou T Sang 2006 Rice domestication by reducing shattering Science 311 1936 1939
12. G Liu G Lu L Zeng GL Wang 2002 The two broad-spectrum blast resistance genes, Pi9(t) and Pi2(t), are physically linked on rice chromosome 6 Mol Genet Genomics 267 472 480
13. JP Londo YC Chiang KH Huang TY Chiang BA Schaal 2006 Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa Proc Natl Acad Sci USA 103 9578 9583
14. M Lynch TJ Crease 1990 The analysis of population survey data on DNA sequence variation Mol Biol Evol 7 377 394
15. J Ma JL Bennetzen 2004 Rapid recent growth and divergence of rice nuclear genomes Proc Natl Acad Sci U S A 101 12404 12410
16. BC Meyers S Kaushik RS Nandety 2005 Evolving disease resistance genes Curr Opin Plant Biol 8 129 134
17. AS Moffat 2001 Finding new ways to fight plant diseases Science 292 2270 2273
18. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York, NY
19. Z Nimchuk T Eulgem BF Holt III JL Dangl 2003 Recognition and response in the plant immune system Annu Rev Genet 37 579 609
20. J Ross-Ibarra PL Morrell BS Gaut 2007 Plant domestication, a unique opportunity to identify the genetic basis of adaptation Proc Natl Acad Sci U S A 104 8641 8648
21. J Rozas JC Sánchez-DelBarrio X Messeguer R Rozas 2003 DnaSP, DNA polymorphism analyses by the coalescent and other methods Bioinformatics 19 2496 2497
22. T Sang S Ge 2007 The puzzle of rice domestication J Intergr Plant Biol 49 760 768
23. G Second 1982 Origin of the genetic diversity of cultivated rice (Oryza spp.): Study of the polymorphism scored at 40 isozyme loci Jpn J Genet 57 25 57
24. Z Song B Li J Chen B-R Lu 2005 Genetic diversity and conservation of common wild rice (Oryza rufipogon) in china Plant Species Biol 20 83 92
25. X Sun Y Zhang S Yang JQ Chen B Hohn D Tian 2008 Insertion DNA promotes ectopic recombination during meiosis in Arabidopsis Mol Biol Evol 25 2079 2083
26. K Tamura J Dudley M Nei S Kumar 2007 MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software, version 4.0 Mol Biol Evol 24 1596 1599
27. T Tang J Lu J Huang J He SR McCouch Y Shen 2006 Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication PLoS Genet 2 el99
28. JD Thompson DG Higgins TJ Gibson 1994 CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-speciWc gap penalties, and weight matrix choice Nucleic Acids Res 22 4673 4680
29. D Tian Q Wang P Zhang H Araki S Yang M Kreitman T Nagylaki T Hudson J Bergelson JQ Chen 2008 Single-nucleotide mutation rate increases close to indels in eukaryotes Nature 455 105 108
30. C Vitte T Ishii F Lamy D Brar O Panaud 2004 Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.) Mol Genet Genomics 272 504 511
31. Wang X, Sun C (1996) The origin and differentiation of Chinese cultivated rice. China Agricultural University Press, Beijing
32. GA Watterson 1975 On the number of segregating sites in genetic models without recombination Theor Pop Biol 7 256 276
33. Weir BS (1996) Genetic data analysis II, 2nd edn. Sinauer, Sunderland, MA
34. S Yang Z Feng X Zhang K Jiang X Jin Y Hang JQ Chen D Tian 2006 Genome-wide investigation on the genetic variations of rice disease resistance genes Plant Mol Biol 62 181 193
35. S Yang T Gu C Pan Z Feng J Ding Y Hang JQ Chen D Tian 2008 Genetic variation of NBS-LRR class resistance genes in rice lines Theor Appl Genet 116 165 177
36. T Zhou Y Wang JQ Chen H Araki Z Jing K Jiang J Shen D Tian 2004 Genome-wide identification of NBS genes in rice reveals significant expansion of divergent non-TIR NBS Genes Mol Genet Genomics 271 402 415
37. Q Zhu S Ge 2005 Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes New Phytol 167 249 265
38. Q Zhu X Zheng J Luo BS Gaut S Ge 2007 Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: Severe bottleneck during domestication of rice Mol Biol Evol 24 875 888