Molecular evolution of the rice blast resistance gene Pi-ta in invasive weedy rice in the USA

PLoS ONE

Volumn 6, Issue 10, 2011, Pages

  Lee, Seonghee ^a,b   Jia, Yulin ^c   Jia, Melissa ^c   Gealy, David R ^c   Olsen, Kenneth M ^d   Caicedo, Ana L ^e  

^a UNIVERSITY OF ARKANSAS   (United States)

^b PLANT BIOLOGY DIVISION   (United States)

^c AGRICULTURAL RESEARCH SERVICE   (United States)

^d WASHINGTON UNIVERSITY   (United States)

^e UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME 12; CONTROLLED STUDY; DNA FLANKING REGION; GENE FLOW; GENETIC MARKER; GENETIC ORGANIZATION; GENETIC VARIABILITY; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PI TA GENE; PLANT GENE; PLANT GENOME; RICE; RICE BLAST RESISTANCE GENE; SPECIES DIFFERENCE; UNITED STATES; WEEDY RICE; DNA SEQUENCE; GENETICS; PLANT DISEASE; WEED;

MAGNAPORTHE ORYZAE; ORYZA RUFIPOGON; ZIZANIA;

CELL RECEPTOR; PI TA PROTEIN, ORYZA SATIVA; PI-TA PROTEIN, ORYZA SATIVA; VEGETABLE PROTEIN;

EVOLUTION, MOLECULAR; GENES, PLANT; GENETIC VARIATION; ORYZA SATIVA; PLANT DISEASES; PLANT PROTEINS; PLANT WEEDS; RECEPTORS, CYTOPLASMIC AND NUCLEAR; SEQUENCE ANALYSIS, DNA; UNITED STATES;

EID: 80054744853     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0026260     Document Type: Article

References (39)

1. Webster TM, (2000) The southern states 10 most common and troublesome weeds in rice. Proceedings Southern Weed Science Society 53: 247-274.
2. Gross BL, Reagon M, Hsu SC, Caicedo AL, Jia Y, et al. (2010) Seeing red: the origin of grain pigmentation in US weedy rice. Molecular Ecology 19: 3380-3393.
3. Gross BL, Skare KJ, Olsen KM, (2009) Novel Phr1 mutations and the evolution of phenol reaction variation in US weedy rice (Oryza sativa L.). New Phytologist 184: 842-850.
4. Londo JP, Schaal BA, (2007) Origins and population genetics of weedy red rice in the USA. Molecular Ecology 16: 4523-4535.
5. Reagon M, Thurber CS, Gross BL, Olsen KM, Jia Y, et al. (2010) Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice. BMC Evolutionary Biology 10: 180.
6. Thurber CS, Reagon M, Gross BL, Olsen KM, Jia Y, et al. (2010) Molecular evolution of shattering loci in U.S. weedy rice. Molecular Ecology 19: 3271-3284.
7. Ellstrand NC, Prentice HC, Hancock JF, (1999) Gene flow and introgression from domesticated plants into their wild relatives. Annual Review of Ecology, Evolution, and Systematics 30: 539-563.
8. Lu BA, Snow AA, (2005) Gene flow from genetically modified rice and its environmental consequences. Bioscience 55: 669-678.
9. Shivrain VK, Burgos NR, Moldenhauer KK, McNew RW, Baldwin TL, (2006) Characterization of spontaneous crosses between Clearfield rice (Oryza sativa) and red rice (Oryza sativa). Weed Technology 20: 576-584.
10. Shivrain VK, Burgos NR, Rajguru SN, Anders MM, Moore JW, et al. (2007) Gene flow between Clearfield™ rice and red rice. Crop Protection 26: 349-356.
11. Gealy DR, Agrama HA, Eizenga GC, (2009) Exploring genetic and spatial structure of U.S. weedy red rice (Oryza sativa) in relation to rice relatives worldwide. Weed Science 57: 627-643.
12. Chen LJ, Lee DS, Song ZP, Suh HS, Lu B, (2004) Gene flow from cultivated rice (Oryza sativa) to its weedy and wild relatives. Annals of Botany 93: 67-73.
13. Jia Y, (2009) Artificial introgression of a large chromosome fragment around the rice blast resistance gene Pi-ta in backcross progeny and several elite rice cultivars. Heredity 103: 333-339.
14. Jia Y, Bryan GT, Farrall L, Valent B, (2003) Natural variation at the Pi-ta rice blast resistance locus. Phytopathology 93: 1452-1459.
15. Moldenhauer KAK, Lee FN, Norman RJ, Helms RS, Wells BR, et al. (1990) Registration of 'Katy' rice. Crop Science 30: 747-748.
16. Jia, Y, Wang Z, Singh P, (2002) Development of dominant rice blast resistance Pi-ta gene markers. Crop Science 42: 2145-2149.
17. Rybka K, Myamoto M, Ando I, Saito A, Kawasaki S, (1997) High resolution mapping of the indica-derived rice blast resistance genes: II. Pi-ta2 and Pi-ta and a consideration of their origin. Molecular Plant Microbe Interaction 10: 517-524.
18. Jia Y, Redus M, Wang Z, Rutger JN, (2004) Development of a SNLP marker for the Pi-ta blast resistance gene by tri-primer PCR. Euphytica 138: 97-105.
19. Moldenhauer KAK, Lee FN, Gibbons JW, Bernhardt JL, Norman RJ, et al. (2007) Registration of 'Ahrent' rice. Crop Science 47: 446-447.
20. Bryan GT, Wu KS, Farrall L, Jia Y, Hershey HP, et al. (2000) A single amino-acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta. Plant Cell 12: 2033-2045.
21. Jia Y, McAdams SA, Bryan GT, Hershey HP, Valent B, (2000) Direct interaction of resistance gene and avirulence gene products confers rice blast resistance. The EMBO Journal 19: 4004-4014.
22. Huang C, Hwang S, Chiang Y, Lin T, (2008) Molecular evolution of the Pi-ta gene resistant to rice blast in wild rice (Oryza rufipogon). Genetics 179: 1527-1538.
23. Lee S, Costanzo S, Jia Y, Olsen KM, Caicedo AL, (2009) Evolutionary dynamics of the genomic region around the blast resistance gene Pi-ta in AA genome Oryza species. Genetics 183: 1315-1325.
24. Wang X, Jia Y, Shu QY, Wu D, (2008) Haplotype diversity at the Pi-ta locus in cultivated rice and its wild relatives. Phytopathology 98: 1305-1311.
25. Jia Y, Martin R, (2008) Identification of a new locus, Ptr(t), required for rice blast resistance gene Pi-ta-mediated resistance. Molecular Plant-Microbe Interactions 21: 396-403.
26. Jia Y, Wang X, Costanzo S, Lee S, (2009) Understanding the coevolution of rice blast resistance gene Pi-ta and Magnaporthe oryzae avirulence gene AVR-Pita, pp. 137-147 in Advances in Genetics, Genomics and Control of Rice Blast Disease, edited by Wang GL, Valent B. Springer Science.
27. Shen JH, Araki L, Chen JQ, Chen, Tian D, (2006) Unique evolutionary mechanism in R-genes under the presence/absence polymorphism in Arabidopsis thaliana. Genetics 172: 1243-1250.
28. Gealy DR, Mitten DH, Rutger JN, (2003) Gene flow between red rice (Oryza sativa) and herbicide-resistant rice (O. sativa): implications for weed management. Weed Technology 17: 627-645.
29. Gealy DR, Yan W, Rutger JN, (2006) Red rice (Oryza sativa) plant types affect growth, coloration, and flowering characteristics of first- and second-generation crosses with rice. Weed Technology 20: 839-852.
30. Rajguru SN, Burgos NR, Shivrain VK, Stewart JM, (2005) Mutations in red rice ALS gene associated with resistance to imazethapyr. Weed Science 53: 567-577.
31. Messeguer J, Marfa V, Catala MM, Guiderdoni E, Mele E, (2004) A field study of pollen-mediated gene flow from Mediterranean GM rice to conventional rice and the red rice weed. Molecular Breeding 13: 103-112.
32. Rozas J, Sánchez-DelBarrio JC, Messegyer X, Rozas R, (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.
33. Hill WG, Robertson A, (1968) Linkage disequilibrium in finite populations. Theoretical and Applied Genetics 38: 226-231.
34. Lewontin RC, (1964) The interaction of selection and linkage. I. Generalconsiderations: heterotic models. Genetics 49: 49-67.
35. Sabeti PC, Reich DE, Higgins JM, Levine HZP, Richter DJ, et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
36. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.
37. Falush D, Stephens M, Pritchard JK, (2003) Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
38. Falush D, Stephens M, Pritchard JK, (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes 7: 574-578.
39. Pritchard JK, Stephens M, Donnelly PJ, (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.