Similar traits, different genes? Examining convergent evolution in related weedy rice populations

Molecular Ecology

Volumn 22, Issue 3, 2013, Pages 685-698

  Thurber, Carrie S ^a   Jia, Melissa H ^b   Jia, Yulin ^b   Caicedo, Ana L ^a  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

^b USDA ARS Dale Bumpers National Rice Research Center   (United States)

Author keywords

flowering time; Oryza sativa; Quantitative trait loci; red rice; shattering

Indexed keywords

PLANT DNA;

CHROMOSOME MAP; CONFERENCE PAPER; DNA SEQUENCE; GENETIC MARKER; GENETICS; GENOTYPE; MOLECULAR EVOLUTION; PHENOTYPE; POPULATION GENETICS; QUANTITATIVE TRAIT LOCUS; RICE; WEED;

CHROMOSOME MAPPING; DNA, PLANT; EVOLUTION, MOLECULAR; GENETIC MARKERS; GENETICS, POPULATION; GENOTYPE; ORYZA SATIVA; PHENOTYPE; PLANT WEEDS; QUANTITATIVE TRAIT LOCI; SEQUENCE ANALYSIS, DNA;

ORYZA SATIVA; ZIZANIA;

EID: 84872448126     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12147     Document Type: Conference Paper

References (62)

1. Arendt J, Reznick D, (2007) Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation? Trends in Ecology & Evolution, 23, 26-32.
2. Asano K, Takashi T, Miura K, et al,. (2007) Genetic and Molecular Analysis of Utility of sd1 Alleles in Rice Breeding. Breeding Science, 57, 53-58.
3. Basu C, Halfhill MD, Mueller TC, Stewart CN Jr, (2004) Weed genomics: new tools to understand weed biology. Trends in Plant Science, 9, 391-398.
4. Bres-Patry C, Lorieuz M, Clement G, Bangratz M, Ghesquiere A, (2001) Heredity and genetic mapping of domestication-related traits in a temperate japonica weedy rice. Theoretical and Applied Genetics, 102, 118-126.
5. Cai HW, Morishima H, (2000) Genomic regions affecting seed shattering and seed dormancy in rice. Theoretical and Applied Genetics, 100, 840-846.
6. Cai HW, Morishima H, (2002) QTL clusters reflect character associations in wild cultivated rice. Theoretical and Applied Genetics, 104, 1217-1228.
7. Cai H-Y, Diao S, He Y-G, et al,. (2012) Genetic and physical mapping of qHY-8, a pleiotropic QTL for heading date and yield-related traits in rice. Euphytica, 184, 109-118.
8. Caicedo AL, Purugganan MD, (2005) Comparative plant genomics. Frontiers and prospects. Plant Physiology, 138, 545-547.
9. Caicedo AL, Williamson SH, Hernandez RD, et al,. (2007) Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genetics, 3, e163.
10. Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR, (1997) Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theoretical and Applied Genetics, 95, 553-567.
11. Delouche JC, Burgos NR, Gealy DR, et al,. (2007) Weedy rices- origin, biology, ecology and control (ed. FAO). FAO, Rome, Italy.
12. Ellstrand NC, Heredia SM, Leak-Garcia JA, et al,. (2010) Crops gone wild: evolution of weeds and invasives from domesticated ancestors. Evolutionary Applications, 3, 494-504.
13. Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S, (2005) Genetic structure and diversity in Oryza sativa L. Genetics, 169, 1631-1638.
14. Gu X-Y, Kianian SF, Hareland GA, Hoffer BL, Foley ME, (2005) Genetic analysis of adaptive syndromes interrelated with seed dormancy in weedy rice (Oryza sativa). Theoretical and Applied Genetics, 110, 1108-1118.
15. Harlan JR, DeWet JM, (1965) Some thoughts about weeds. Economic Botany, 19, 16-24.
16. Hodin J, (2000) Plasticity and constraints in development and evolution. Journal of Experimental Zoology, 288, 1-20.
17. Lee S-J, Oh C-S, Suh J-P, McCouch SR, Ahn S-N, (2005) Identification of QTLs for domestication-related and agronomic traits in an Oryza sativa × O. rufipogon BC1F7 population. Plant Breeding, 124, 209-219.
18. Li C, Zhou A, Sang T, (2006a) Genetic analysis of rice domestication syndrome with the wild annual species, Oryza nivara. New Phytologist, 170, 185-194.
19. Li C, Zhou A, Sang T, (2006b) Rice domestication by reducing shattering. Science, 311, 1936-1939.
20. Li S-B, Zhang Z-H, Hu Y, et al,. (2006c) Genetic dissection of developmental behavior of crop growth rate and its relationships with yield and yield related traits in rice. Plant Science, 170, 911-917.
21. Lin Z, Griffith ME, Li X, et al,. (2007) Origin of seed shattering in rice (Oryza sativa L.). Planta, 226, 11-20.
22. Londo JP, Schaal BA, (2007) Origins and population genetics of weedy red rice in the USA. Molecular Ecology, 16, 4523-4535.
23. Manceau M, Domingues VS, Linnen CR, Rosenblum EB, Hoekstra HE, (2010) Convergence in pigmentation at multiple levels: mutations, genes and function. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 365, 2439-2450.
24. Manichaikul A, Palmer AA, Sen S, Broman KW, (2007) Significance threshold for quantitative trait locus mapping under selective genotyping. Genetics, 177, 1963-1966.
25. McCouch SR, Teytelman L, Xu Y, et al,. (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Research, 9, 199-207.
26. Monna L, Kitazawa N, Yoshino R, et al,. (2002) Positional cloning of rice semidwarfing gene, sd-1: rice "green revolution gene" encodes a mutant enzyme involved in gibberellin synthesis. DNA Research, 9, 11-17.
27. Noldin JA, Chandler JM, McCauley GN, (1999) Red rice (Oryza sativa) biology. I. Characterization of red rice ecotypes. Weed Technology, 13, 12-18.
28. Olsen KM, Caicedo AL, Jia Y, (2007) Evolutionary genomics of weedy rice in the USA. Journal of Integrative Plant Biology, 49, 811-816.
29. Panaud O, Chen X, McCouch SR, (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Molecular and General Genetics, 252, 597-607.
30. Powles SB, Yu Q, (2010) Evolution in action: plants resistant to herbicides. Annual Review of Plant Biology, 61, 317-347.
31. Purugganan MD, Fuller DQ, (2009) The nature of selection during plant domestication. Nature, 457, 843-848.
32. Reagon M, Thurber CS, Gross BL, et al,. (2010) Genomic patterns of nucleotide diversity in parallel populations of U.S. weedy rice. BMC Evolutionary Biology, 10, 180.
33. Reagon M, Thurber CS, Olsen KM, Jia Y, Caicedo AL, (2011) The long and the short of it: SD1 polymorphism and the evolution of growth trait divergence in U.S. weedy rice. Molecular Ecology, 20, 3743-3756.
34. Remigereau M-S, Lakis G, Rekima S, et al,. (2011) Cereal domestication and evolution of branching: evidence for soft selection in the Tb1 orthologue of Pearl Millet (Pennisetum glaucum [L.] R. Br.). PLoS ONE, 6, e22404.
35. Rompler H, Rohland N, Lalueza-Fox C, et al,. (2006) Nuclear gene indicates coat-color polymorphism in Mammoths. Science, 313, 62.
36. Schluter D, Clifford EA, Nemethy M, McKinnon JS, (2004) Parallel evolution and inheritance of quantitative traits. American Naturalist, 163, 809-822.
37. Septiningsih EM, Prasetiyono J, Lubis E, et al,. (2003) Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theoretical and Applied Genetics, 107, 1419-1432.
38. Shen Y-J, Jiang H, Jin J-P, et al,. (2004) Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiology, 135, 1198-1205.
39. Shivrain VK, Burgos NR, Gealy DR, Sales MA, Smith KL, (2009) Gene flow from weedy red rice (Oryza sativa L.) to cultivated rice and fitness of hybrids. Pest Management Science, 65, 1124-1129.
40. Shivrain VK, Burgos NR, Agrama HA, et al,. (2010) Genetic diversity of weedy red rice (Oryza sativa) in Arkansas, USA. Weed Research, 50, 289-302.
41. Smith SD, Rausher MD, (2011) Gene loss and parallel evolution contribute to species difference in flower color. Molecular Biology and Evolution, 28, 2799-2810.
42. Steiner CC, Rompler H, Boettger LM, Shoneberg T, Hoekstra HE, (2008) The genetic basis of phenotypic convergence in beach mice: similar pigment patterns but different genes. Molecular Biology and Evolution, 26, 35-45.
43. Stinchcombe JR, Hoekstra HE, (2008) Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity, 100, 158-170.
44. Takahashi Y, Teshima KM, Yokoi S, Innan H, Shimamoto K, (2009) Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of flowering time in cultivated rice. Proceedings of the National Academy Sciences, USA, 106, 4555-4560.
45. Tan WD, Gan FF, Chang TC, (2004) Using normal quantile plot to select an appropriate transformation to achieve normality. Computational Statistics and Data Analysis, 45, 609-619.
46. Thomson MJ, Tai TH, McClung AM, et al,. (2003) Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theoretical and Applied Genetics, 107, 479-493.
47. Thurber CS, Reagon M, Gross BL, et al,. (2010) Molecular evolution of shattering loci in U.S. weedy rice. Molecular Ecology, 19, 3271-3284.
48. Thurber CS, Hepler P, Caicedo AL, (2011) Timing is everything: early degradation of abscission layer may lead to increased shattering in U.S. weedy rice. BMC Plant Biology, 11, 14.
49. Tilquin P, Coppieters W, Elsen JM, et al,. (2001) Statistical power of QTL mapping methods applied to bacteria counts. Genetical Research, 78, 303-316.
50. Vaughan LK, Ottis BV, Prazak-Havey AM, et al,. (2001) Is all red rice found in commercial rice really Oryza sativa? Weed Science, 49, 468-476.
51. Wang S, Basten CJ, Zeng Z-B, (2012) Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC. (http://statgen.ncsu.edu/qtlcart/WQTLCart.htm)
52. Wei X, Xu J, Guo H, et al,. (2010) DTH8 suppresses flowering in rice, influencing plant height and yield potential simultaneously. Plant Physiology, 153, 1747-1758.
53. Xiao JH, Li J, Grandillo S, et al,. (1998) Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon. Genetics, 150, 899-909.
54. Xu NW, Xu S, Ehlers J, (2009) Estimating the broad-sense heritability of early growth cowpea. International Journal of Plant Genomics, doi: 10.1155/2009/984521.
55. Yan W-H, Wang P, Chen H-X, et al,. (2011) A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice. Molecular Plant, 4, 319-330.
56. Yano M, Harushima Y, Nagamura Y, et al,. (1997) Identification of quantitative trait loci controlling heading date in rice using a high-density linkage map. Theoretical and Applied Genetics, 95, 1025-1032.
57. Yano M, Katayose Y, Ashikari M, et al,. (2000) Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. The Plant Cell, 12, 2473-2483.
58. Yoon H-S, Baum DA, (2004) Transgenic study of parallelism in plant morphological evolution. Proceedings of the National Academy of Sciences, USA, 101, 6524-6529.
59. Zhang L-B, Zhu Q, Wu Z-Q, et al,. (2009) Selection on grain shattering genes and rates of rice domestication. New Phytologist, 184, 708-720.
60. Zhang L, Wang S, Li H, et al,. (2010) Effects of missing marker and segregation distortion on QTL mapping in F2 populations. Theoretical and Applied Genetics, 121, 1071-1082.
61. Zhu B-F, Si L, Wang Z, et al,. (2011) Genetic control of a transition from black to straw-white seed hull in rice domestication. Plant Physiology, 155, 1301-1311.
62. Zhu Y, Ellstrand NC, Lu B-R, (2012) Sequence polymorphism in wild, weedy, and cultivated rice suggest seed-shattering locus sh4 played a minor role in Asian rice domestication. Ecology and Evolution, 2, 2106-2113.