Molecular population genetics and agronomic alleles in seed banks: Searching for a needle in a haystack?

Journal of Experimental Botany

Volumn 60, Issue 9, 2009, Pages 2541-2552

  Prada, Dario ^a,b  

^a ROYAL BOTANIC GARDENS   (United Kingdom)

^b Pioneer Hi Bred Italia   (Italy)

Author keywords

Association mapping; Linkage disequilibrium; Plant genetic resources; Plant molecular genetics; Population stratification; Seed banking; Selective genes

Indexed keywords

AGRICULTURE; ALLELE; BREEDING; CROP; CROSS BREEDING; GENETICS; PLANT SEED; REVIEW;

AGRICULTURE; ALLELES; BREEDING; CROPS, AGRICULTURAL; CROSSES, GENETIC; SEEDS;

EID: 67649317045     PISSN: 00220957     EISSN: 14602431     Source Type: Journal    
DOI: 10.1093/jxb/erp130     Document Type: Review

References (85)

1. Antoniou AC, Easton DF. 2003. Polygenic inheritance of breast cancer: implications for design of association studies. Genetic Epidemiology 25, 190-202.
2. Balding DJ. 2006. A tutorial on statistical methods for population association studies. Nature Reviews Genetics 7, 781-791.
3. Barnaud A, Lacombe T, Doligez A. 2006. Linkage disequilibrium in cultivated grapevine, Vitis vinifera L. Theoretical and Applied Genetics 112, 708-716.
4. Barton N. 2000. Genetic hitchhiking. Philosophical Transactions of the Royal Society B, Biological Sciences 355, 1553-1562.
5. Brown AHD. 1989. The case for core collections. In: Brown AHD, Frankel OH, Marshall DR, Williams JT, eds. The use of plant genetic resources. Cambridge, UK: Cambridge University Press, 136-156. Brown AHD, Briggs JD. 1991. Sampling strategies for genetic variation in ex situ collections of endangered plant species. In: Falk DA, Holsinger KE, eds. Genetics and conservation of rare plants. New York, NY: Oxford University Press, 99-123.
6. Brown GR, Gill GP, Kuntz RJ, Langley CH, Neale DB. 2004. Nucleotide diversity and linkage disequilibrium in loblolly pine. Proceedings of the National Academy of Sciences, USA 42, 15255-15260.
7. Buckler ES, Thornsberry JM, Kresovich S. 2001. Molecular diversity, structure and domestication of grasses. Genetics Research 77, 213-218.
8. Caldwell KS, Russell J, Langridge P, Powell W. 2006. Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics 172, 557-567.
9. Camus-Kulandaivelu L, Veyrieras J-B, Madur D, Combes V, Fourmann M, Barraud S, Dubreuil P, Gouesnard B, Manicacci D, Charcosset A. 2006. Maize adaptation to temperate climate: relationship between population structure and polymorphism in the Dwarf8 gene. Genetics 172, 2449-2463.
10. Crossa J. 1989. Methodologies for estimating the sample size required for genetic conservation of outbreeding crops. Theoretical and Applied Genetics 77, 153-161.
11. Devlin B, Roeder K. 1999. Genomic control for association studies. Biometrics 55, 997-1004.
12. Doebley J, Stec A, Gustus C. 1995. teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics 141, 333-346.
13. Doebley J, Stec A, Hubbard L. 1997. The evolution of apical dominance in maize. Nature 386, 485-488.
14. Doebley JF, Gaut BS, Smith BD. 2006. The molecular genetics of crop domestication. Cell 127, 1309-1321.
15. Doney DL, Whitney ED. 1990. Genetic enhancement in Beta for disease resistance using wild relatives: a strong case for the value of genetic conservation. Economic Botany 44, 445-451.
16. Dvornyk V, Sirviö A, Mikkonen M, Savolainen O. 2002. Low nucleotide diversity at the pal1 locus in the widely distributed Pinus sylvestris. Molecular Biology and Evolution 19, 179-188.
17. Esquinas-Alcazar J. 2005. Protecting crop genetic diversity for food security: political, ethical and technical challenges. Nature Reviews Genetics 6, 946-953.
18. Eyre-Walker A, Gaut RL, Hilton H, Feldman DL, Gaut BS. 1998. Investigation of the bottleneck leading to the domestication of maize. Proceedings of the National Academy of Sciences, USA 95, 4441-4446.
19. FAO. 1997. The state of the world's plant genetic resources for food and agriculture. http://www.fao.org/WAICENT/FAOINFO/AGRICULT/ AGP/AGPS/Pgrfa/pdf/swrfull.pdf.
20. Fay JC, Wu CI. 2000. Hitchhiking under positive Darwinian selection. Genetics 155, 1405-1413.
21. Flint-Garcia SA, Thornsberry JM, Buckler ES. 2003. Structure of linkage disequilibrium in plants. Annual Reviews in Plant Biology 54, 357-374.
22. Flint-Garcia SA, Thuillet AC, Romero SM, Mitchell S, Doebley J, Kresovich S, Goodman MM, Buckler ES. 2005. Maize association population: a high resolution platform for QTL dissection. The Plant Journal 44, 1054-1064.
23. Forrester JW. 1961. Industrial dynamics. Cambridge, MA: MIT Press.
24. Frankel OH. 1984. Genetic perspectives of germplasm conservation. In: Arber W, Llimensee K, Peacock WJ, Starlinger P, eds. Genetic manipulation: impact on man and society. Cambridge, UK: Cambridge University Press, 161-170.
25. Frary A, Nesbitt TC, Frary A, et al. 2000. fw22: a quantitative trait locus key to the evolution of tomato fruit size. Science 289, 85-88.
26. Fu YX, Li WH. 1993. Statistical tests of neutrality of mutations. Genetics 133, 693-709.
27. Gonzalez-Martinez SC, Wheeler NC, Ersoz E, Nelson CD, Neale DB. 2007. Association genetics in Pinus taeda L.I. Wood property traits. Genetics 175, 399-409.
28. Grandillo S, Ku HM, Tanksley SD. 1999. Identifying the loci responsible for natural variation in fruit size and shape in tomato. Theoretical and Applied Genetics 99, 978-987.
29. Gupta PK, Rustgi S, Kulwal PL. 2005. Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Molecular Biology 57, 461-485.
30. Halliburton R. 2004. Introduction to population genetics. Upper Saddle River, NJ: Pearson-Prentice-Hall.
31. Hamblin MT, Casa AM, Sun H, Murray SC, Paterson AH, Aquadro CF, Kresovich S. 2006. Challenges of detecting directional selection after a bottleneck: lessons from Sorghum bicolor. Genetics 173, 953-964.
32. Harlan JR. 1975. Crops and man. Madison, WI: American Society of Agronomy.
33. Hirschhorn JN, Daly MJ. 2005. Genome-wide association studies for common diseases and complex traits. Nature Reviews Genetics 6, 95-108.
34. Hoisington D, Khairallah M, Reeves T, Ribaut J-M, Skovmand B, Taba S, Warburton M. 1999. Plant genetic resources: what can they contribute toward increased crop productivity? Proceedings of the National Academy of Sciences, USA 96, 5937-5943.
35. Hudson RR. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18, 337-338.
36. Hudson RR, Kreitman M, Aguade M. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116, 153-159.
37. Hyten DL, Song Q, Zhu Y, Choi I, Nelson RL, Costa JM, Specht JE, Shoemaker RC, Perry BC. 2006. Impacts of genetic bottlenecks on soybean genome diversity. Proceedings of the National Academy of Sciences, USA 103, 16666-16671.
38. Ingvarsson PK. 2005. Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae). Genetics 169, 945-953.
39. Jarvis DI, Hodgkin T. 1999. Wild relatives and crop cultivars: detecting natural introgression and farmer selection of new genetic combinations in agroecosystems. Molecular Ecology 8, 159-173.
40. Johnson R. 2004. Marker-assisted selection. Plant Breeding Reviews 24, 293-309.
41. Jones H, Leigh FJ, Mackay I, Bower MA, Smith LMJ, Charles MP, Jones G, Jones MK, Brown TA, Powell W. 2008. Population-based resequencing reveals that the flowering time adaptation of cultivated barley originated east of the Fertile Crescent. Molecular Biology and Evolution 25, 2211-2219. Kimura M. 1968. Evolutionary rate at the molecular level. Nature 217, 624-626.
42. Knowler WC, Williams RC, Pettitt DJ, Steinberg AG. 1988. Gm3;5,13,14 and type 2 diabetes mellitus: an association in American Indians with genetic admixture. The American Journal of Human Genetics 43, 520-526.
43. Krutovsky KV, Neale DB. 2005. Nucleotide diversity and linkage disequilibrium in cold-hardiness- and wood quality-related candidate genes in Douglas fir. Genetics 171, 2029-2041.
44. Mackay I, Powell W. 2007. Methods for linkage disequilibrium mapping in crops. Trends in Plant Science 12, 57-63.
45. Malosetti M, van der Linden CG, Vosman B, van Eeuwijk FA. 2007. A mixed-model approach to association mapping using pedigree information with an illustration of resistance to Phytophthora infestans in potato. Genetics 175, 879-889.
46. Marshall DR, Brown AHD. 1975. Optimum sampling strategies in genetic conservation. In: Frankel OH, Hawkes JG, eds. Crop genetic resources for today and tomorrow. Cambridge, UK: Cambridge University Press, 53-80.
47. McVean G, Spencer CCA. 2006. Scanning the human genome for signals of selection. Current Opinion in Genetics and Development 16, 624-629.
48. Morrell PL, Lundy KE, Clegg MT. 2003. Distinct geographic patterns of genetic diversity are maintained in wild barley (Hordeum vulgare ssp. spontaneum) despite migration. Proceedings of the National Academy of Sciences, USA 100, 10812-10817.
49. Morton NE. 1998. Significance levels in complex inheritance. The American Journal of Human Genetics 62, 690-697.
50. Nordborg M, Hu TT, Ishino Y, et al. 2005. The pattern of polymorphism in Arabidopsis thaliana. Public Library of Sciences Biology 3, e196.
51. Palaisa K, Morgante M, Tingey S, Rafalski A. 2004. Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep. Proceedings of the National Academy of Sciences, USA 101, 9885-9890.
52. Parmesan C, Yohe G. 2003. A globally coherent fingerprint of climate change impacts across natural systems. Nature 421, 37-42.
53. Paterson AH, Damon S, Hewitt JD, Zamir D, Rabinowitch HD, Lincoln ES, Lander ES, Tanksley SD. 1991. Mendelian factors underlying quantitative traits in tomato: comparison across species, generations and environments. Genetics 127, 181-197.
54. Peng J, Richards DE, Hartley NM, et al. 1999. 'Green revolution' genes encode mutant gibberellin response modulators. Nature 400, 256-261.
55. Piffanelli P, Ramsay L, Waugh R, Benabdelmouna A, D'Hont A, Hollricher K, Jorgensen JH, Schulze-Lefert P, Panstruga R. 2004. A barley cultivation- associated polymorphism conveys resistance to powdery mildew. Nature 430, 887-891.
56. Ponting RC, Drayton MC, Cogan NOI, Dobrowolski MP, Spangenberg GC, Smith KF, Forster JW. 2007. SNP discovery, validation, haplotype structure and linkage disequilibrium in full-length herbage nutritive quality genes of perennial ryegrass (Lolium perenne L.). Molecular Genetics and Genomics 278, 585-597.
57. Pritchard JK, Stephens M, Donnelly P. 2000a. Inference of population structure using multilocus genotype data. Genetics 155, 945-959.
58. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P. 2000b. Association mapping in structured populations. The American Journal of Human Genetics 67, 170-181.
59. Putterill J, Laurie R, Macknight R. 2004. It's time to flower: the genetic control of flowering time. BioEssays 26, 363-373.
60. Rajaram S, Mann CE, Ortiz-Ferrara G, Mujeeb-Kazi A. 1983. Adaptation, stability and high yield potential of certain 1B/1R CIMMYT wheats. In: Sakamoto S, ed. Proceedings of the 6th international wheat genetics symposium. Kyoto: Japan, 613-621.
61. Risch NJ. 2000. Searching for genetic determinants in the new millennium. Nature 405, 847-856.
62. Salamini F, Ozkan H, Brandolini A, Schafer R, Martin W. 2005. Genetics and geography of wild cereal domestication in the near east. Nature Reviews Genetics 3, 429-441.
63. Savitsky H. 1960. Meiosis in an F1 hybrid between a Turkish wild beet (Beta vulgaris ssp. maritima) and Beta procumbens. Journal of the American Society for Sugar Beet Technology 11, 49-67.
64. Sawers RJH, Sheehan MJ, Brutnell TP. 2005. Cereal phytochromes: targets of selection, targets for manipulation? Trends in Plant Sciences 10, 138-143.
65. Schoen DJ, Brown AHD. 2001. The conservation of wild plant species in seed banks. BioScience 51, 960-966.
66. Sharbel TF, Haubold B, Mitchell-Olds T. 2000. Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe. Molecular Ecology 9, 2109-2118.
67. Skøt L, Humphreys J, Humphreys MO, Thorogood D, Gallagher J, Sanderson R, Armstead IP, Thomas ID. 2007. Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.). Genetics 177, 535-547.
68. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-595.
69. Tanksley SD, McCouch SR. 1997. Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277, 1063-1066.
70. This P, Lacombe T, Cadle-Davidson M, Owens CL. 2007. Wine grape (Vitis vinifera L.) color associates with allelic variation in the domestication gene VvmybA1. Theoretical and Applied Genetics 114, 723-730.
71. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES. 2001. Dwarf8 polymorphisms associate with variation in flowering time. Nature Genetics 28, 286-289.
72. Thumma BR, Nolan MF, Evans R, Moran GF. 2005. Polymorphisms in Cinnamoyl CoA Reductase (CCR) are associated with variation in microfibril angle in Eucalyptus spp. Genetics 171, 1257-1265.
73. van Hintum TJL, Brown AHD, Spillane C, Hodgkin T. 2000. Core collections of plant genetic resources. IPGRI Technical Bulletin No 3. Rome, Italy: International Plant Genetic Resources Institute.
74. Way MJ. 2003. Collecting seed from non-domesticated plants for long-term conservation. In: Smith RD, Dickie JB, Linington SH, Pritchard HW, Probert RJ, eds. Seed conservation: turning science into practice. London, UK: Royal Botanic Gardens Kew, 163-201.
75. Weber A, Clark RM, Vaughn L, Sanchez-Gonzalez J-J, Yu J, Yandell BS, Bradbury P, Doebley J. 2007. Major regulatory genes in maize contribute to standing variation in teosinte (Zea mays ssp. parviglumis). Genetics 177, 2349-2359.
76. Wright SI, Gaut BS. 2005. Molecular population genetics and the search for adaptive evolution in plants. Molecular Biology and Evolution 22, 506-519.
77. Wright SI, Vroh-Bi I, Schroeder SG, Yamasaki M, Doebley JF, McMullen MD, Gaut BS. 2005. The effects of artificial selection on the maize genome. Science 308, 1310-1314.
78. Yamasaki M, Tenaillon MI, Vroh-Bi I, Schroeder S, Sanchez- Villeda H, Doebley J, Gaut BS, McMullen MD. 2005. A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. The Plant Cell 17, 2859-2872.
79. 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.
80. Yin X, Struik PC, Kropff MJ. 2004. Role of crop physiology in predicting gene-to-phenotype relationships. Trends in Plant Science 9, 426-432.
81. Yu J, Pressoir G, Briggs WH, et al. 2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics 38, 203-208.
82. Yu J, Buckler ES. 2006. Genetic association mapping and genome organization of maize. Current Opinion in Biotechnology 17, 155-160.
83. Zhao K, Aranzana MJ, Kim S, et al. 2007. An Arabidopsis example of association mapping in structured samples. Public Library of Sciences Genetics 3, e4.
84. Zhu C, Gore M, Buckler ES, Yu J. 2008. Status and prospects of association mapping in plants. The Plant Genome 1, 5-20.
85. Zondervan KT, Cardon LR. 2004. The complex interplay among factors that influence allelic association. Nature Reviews Genetics 5, 89-100.