Genetics and genomics of crop domestication

Plant Biotechnology and Agriculture

Volumn , Issue , 2012, Pages 3-18

  Heslop Harrison, J S ^a   Schwarzacher, Trude ^a  

^a UNIVERSITY OF LEICESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84873061954     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-12-381466-1.00001-8     Document Type: Chapter

References (89)

1. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society 2011, 161(2):105-121. Angiosperm Phylogeny Group.
2. Anhalt U.C.M., Heslop-Harrison J.S., Byrne S., Guillard A., Barth S. Segregation distortion in Lolium: Evidence for genetic effects. Theoretical Applied Genetics 2008, 117:297-306. doi: 10.1007/s00122-008-0774-7.
3. Anhalt U.C.M., Heslop-Harrison J.S., Piepho H.P., Byrne S., Barth S. Quantitative trait loci mapping for biomass yield traits in a Lolium inbred line derived F2 population. Euphytica 2009, 170:99-107. doi: 10.1007/s10681-009-9957-9.
4. Antonovics J., Bradshaw A.D., Turner R.G. Heavy metal tolerance in plants. Advances in ecological research 1971, 2-86. Academic Press, London. J.B. Cragg (Ed.).
5. Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature 408 6814 796 815 Available from: < >. http://www.dx.doi.org/10.1038/35048692/.
6. Argout X., Salse J., Aury J.M., Guiltinan M.J., Droc G., Gouzy J., et al. The genome of Theobroma cacao. Nature Genetics 2011, 43(2):101-108. Available from: < http://dx.doi.org/10.1038/ng.736/>, February.
7. Bailey J.P., Bímová K., Mandák B. The potential role of polyploidy and hybridisation in the further evolution of the highly invasive Fallopia taxa in Europe. Ecological Research 2007, 22:920-928.
8. Bassham James A., Calvin M. Photosynthesis 1955, Lawrence Berkeley National Laboratory, LBNL Paper UCRL-2853. Retrieved from: < http://escholarship.org/uc/item/0j6008b4/>.
9. Buckler E.S., Thornsberry J.M., Kresovich S. Molecular diversity, structure and domestication of grasses. Genetical Research 2001, 77(3):213-218. Available from: < http://view.ncbi.nlm.nih.gov/pubmed/11486504/>, June.
10. Caldwell K.S., Dvorak J., Lagudah E.S., Akhunov E., Luo M.C.C., Wolters P., et al. Sequence polymorphism in polyploid wheat and their D-genome diploid ancestor. Genetics 2004, 167(2):941-947. Available from: < http://dx.doi.org/10.1534/genetics.103.016303/>, June.
11. Charlesworth D. Evolution of plant breeding systems. Current Biology 2006, 16:R726-R735. September 5. 10.1016/j.cub.2006.07.068.
12. Chiu W.I., Niwa Y, Zeng W., Hirano T., Kobayashi H., Sheen J. Engineered GFP as a vital reporter in plants. Current Biology 1996, 6(3):325-330. Available from: < http://www.cell.com/current-biology/abstract/S0960-9822(02)00483-9/>, March.
13. Chory J., Ecker J.R., Briggs S., Caboche M., Coruzzi G.M., Cook D., et al. National Science Foundation-sponsored workshop report: "The 2010 project functional genomics and the virtual plant. A blueprint for understanding how plants are built and how to improve them". Plant Physiology 2000, 123:423-426. doi:10.1104/pp.123.2.423.
14. Cifuentes M., Eber F., Lucas M.O., Lode M., Chevre A.M., Jenczewski E. Repeated polyploidy drove different levels of crossover suppression between homoeologous chromosomes in Brassica napus allohaploids. The Plant Cell 2010, 22(7):2265-2276. Available from: < http://dx.doi.org/10.1105/tpc.109.072991/>, July.
15. Clark R.M., Linton E., Messing J., Doebley J.F. Pattern of diversity in the genomic region near the maize domestication gene tb1. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(3):700-707. Available from: < http://dx.doi.org/10.1073/pnas.2237049100/>, January.
16. Clottes, J. 2010. Chauvet Cave (ca. 30,000 B.C.). (2000). In Heilbrunn Timeline of Art History. New York: The Metropolitan Museum of Art. < > Accessed 09.10. http://www.metmuseum.org/toah/hd/chav/hd_chav.htm/.
17. Cong B., Liu J., Tanksley S.D. Natural alleles at a tomato fruit size quantitative trait locus differ by heterochronic regulatory mutations. Proceedings of the National Academy of Sciences of the United States of America 2002, 99(21):13606-13611. Available from: < http://dx.doi.org/10.1073/pnas.172520999/>, October.
18. Crawley M.J., Brown S.L. Seed limitation and the dynamics of feral Oilseed Rape on the M25 motorway. Proceedings of the Royal Society of London Series B: Biological Sciences 1995, 259(1354):49-54. Available from: < http://dx.doi.org/10.1098/rspb.1995.0008/>.
19. Damude H.G., Kinney A.J. Enhancing plant seed oils for human nutrition. Plant Physiology 2008, 147:962-968. doi:10.1104/pp.108.121681.
20. De Langhe E., Hřibová E., Carpentier S., Doležel J., Swennen R. Did backcrossing contribute to the origin of hybrid edible bananas?. Annals of Botany 2010, 106(6):849-857. Available from: < http://dx.doi.org/10.1093/aob/mcq187/>, December.
21. Doebley J. The genetics of maize evolution. Annual Review of Genetics 2004, 38(1):37-59. Available from: < http://dx.doi.org/10.1146/annurev.genet.38.072902.092425/>.
22. Doebley J.F., Gaut B.S., Smith B.D. The molecular genetics of crop domestication. Cell 2006, 127(7):1309-1321. Available from: < http://dx.doi.org/10.1016/j.cell.2006.12.006/>, December.
23. Doust A. Architectural evolution and its implications for domestication in grasses. Annals of Botany 2007, 100(5):941-950. Available from: < http://dx.doi.org/10.1093/aob/mcm040/>, October.
24. Dubcovsky J., Dvorak J. Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 2007, 316(5833):1862-1866. Available from: < http://dx.doi.org/10.1126/science.1143986/>, June.
25. Dwivedi S., Perotti E., Upadhyaya H., Ortiz R. Sexual and apomictic plant reproduction in the genomics era: Exploring the mechanisms potentially useful in crop plants. Sexual Plant Reproduction 2010, 23(4):265-279. Available from: < http://dx.doi.org/10.1007/s00497-010-0144-x/>, December.
26. FAOstat (2010). Production data relating to food and agriculture. < >. http://www.faostat.fao.org/.
27. FAO/IAEA mutant variety database (2010). < >. http://www.mvgs.iaea.org/aboutMutantVarieties.aspx/.
28. French-Italian Public Consortium for Grapevine Genome Characterization The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla Nature 449 463 468 doi:10.1038/nature06148.
29. Gailing O., Vornam B., Leinemann L., Finkeldey R. Genetic and genomic approaches to assess adaptive genetic variation in plants: Forest trees as a model. Physiologia Plantarum 2009, 137(4):509-519. December.
30. Gross B.L., Olsen K.M. Genetic perspectives on crop domestication. Trends in Plant Science 2010, 15(9):529-537. Available from: < http://dx.doi.org/10.1016/j.tplants.2010.05.008/>, September.
31. Guo J., Wang Y., Song C., Zhou J., Qiu L., Huang H., et al. A single origin and moderate bottleneck during domestication of soybean (Glycine max): Implications from microsatellites and nucleotide sequences. Annals of Botany 2010, 106(3):505-514. Available from: < http://dx.doi.org/10.1093/aob/mcq125/>, September.
32. Gurevitch J., Padilla D. Are invasive species a major cause of extinctions?. Trends in Ecology & Evolution 2004, 19(9):470-474. Available from: < http://dx.doi.org/10.1016/j.tree.2004.07.005/>, September.
33. Hammer K. Das Domestikations-syndrom. Kulturpflanze 1984, 32:11-34.
34. Harlan J., de Wet J. Some thoughts about weeds. Economic Botany 1965, 19(1):16-24. Available from: < http://dx.doi.org/10.1007/BF02971181/>, January.
35. Heaton E.A., Dohleman F.G., Long S.P. Meeting US biofuel goals with less land: The potential of Miscanthus. Global Change Biology 2008, 14:2000-2014.
36. Heslop-Harrison J.S. Exploiting novel germplasm. Australian Journal of Agricultural Research 2002, 53(8):873-879.
37. Heslop-Harrison J.S. Biotechnology of fruit and nut crops: Introduction. Biotechnology of Fruit and Nut Crops 2004, xix-xxiv. CABI. R.E. Litz (Ed.).
38. Heslop-Harrison J.S. Genes in evolution: The control of diversity and speciation. Annals of Botany 2010, 106(3):437-438. Available from: < http://dx.doi.org/10.1093/aob/mcq168/>.
39. Heslop-Harrison J.S., Schwarzacher T. Domestication, genomics and the future for banana. Annals of Botany 2007, 100(5):1073-1084. doi: 10.1093/aob/mcm191.
40. Heslop-Harrison J.S., Schwarzacher T. Organisation of the plant genome in chromosomes. The Plant Journal 2011, 66(1):18-33. Available from: < http://dx.doi.org/10.1111/j.1365-313X.2011.04544.x/>.
41. Heyduck R.F., Baltensperger D.D., Nelson L.A., Graybosch R.A. Yield and agronomic traits of waxy proso in the central Great Plains. Crop Science 2008, 48(2):741-748. Available from: < http://dx.doi.org/10.2135/cropsci2007.02.0081/>.
42. Huang X.Q., Wolf M., Ganal M.W., Orford S., Koebner R.M.D., Röder M.S. Did modern plant breeding lead to genetic erosion in european winter wheat varieties?. Crop Science 2007, 47(1):343-349. Available from: < http://dx.doi.org/10.2135/cropsci2006.04.0261/>.
43. Hunt H.V., Vander Linden M., Liu X., Motuzaite-Matuzeviciute G., Colleridge S., Jones M.K. Millets across Eurasia: Chronology and context of early records of the genera Panicum and Setaria from archaeological sites in the Old World. Vegetation History and Archaeobotany 2008, 17:5-18.
44. Hyten D.L., Song Q., Zhu Y., Choi I.Y., Nelson R.L., Costa J.M., et al. Impacts of genetic bottlenecks on soybean genome diversity. Proceedings of the National Academy of Sciences 2006, 103(45):16666-16671. Available from: < http://dx.doi.org/10.1073/pnas.0604379103/> November.
45. Innan H., Kim Y. Detecting local adaptation using the joint sampling of polymorphism data in the parental and derived populations. Genetics 2008, 179(3):1713-1720. Available from: < http://dx.doi.org/10.1534/genetics.108.086835/> July.
46. Janick J. The origin of fruits, fruit growing, and fruit breeding. Plant Breeding Reviews 2005, 25:255-320.
47. Jarvis D.I., Hodgkin T. Wild relatives and crop cultivars: Detecting natural introgression and farmer selection of new genetic combinations in agroecosystems. Molecular Ecology 1999, 8:S159-S173.
48. Kell D.B. Breeding crop plants with deep roots: Their role in sustainable carbon, nutrient and water sequestration. Annals of Botany 2011, Sept. in press. < http://dx.doi.org/10.1093/aob/mcr175/>.
49. Kim J., Kim T.-G., Jung S.H., Kim J.-R., Park T., Heslop-Harrison P., et al. Evolutionary design principles of modules that control cellular differentiation: Consequences for hysteresis and multistationarity. Bioinformatics 2008, 24(13):1516-1522. doi: 10.1093/bioinformatics/btn229.
50. Kim T.H., Kim J., Heslop-Harrison P., Cho K.H. Evolutionary design principles and functional characteristics based on kingdom-specific network motifs. Bioinformatics 2010, < http://dx.doi.org/10.1093/bioinformatics/btq633/>.
51. King D., Heslop-Harrison J. S., & 23 other members of the GM Science Review Panel. (2003). GM science review: An open review of the science relevant to GM crops and food based on the interests and concerns of the public. < >. 296pp. http://www.gmsciencedebate.org.uk/.
52. King D., Heslop-Harrison J. S., & 25 other members of the GM Science Review Panel. (2004). GM science review: Second Report. An open review of the science relevant to GM crops and food based on the interests and concerns of the public. Full text from: < >. 116pp. http://www.gmsciencedebate.org.uk/.
53. Koornneef M., van Eden J., Hanhart C.J., Stam P., Braaksma F.J., Feenstra W.J. Linkage map of Arabidopsis thaliana. Journal of Heredity 1983, 74(4):265-272. Available from: < http://jhered.oxfordjournals.org/content/74/4/265.abstract/>, July.
54. Martin C., Ellis N., Rook F. Do transcription factors play special roles in adaptive variation?. Plant Physiology 2010, 154(2):506-511. Available from: < http://dx.doi.org/10.1104/pp.110.161331/>, October.
55. McClintock B., Kato T.A., Blumenschein A. Chromosome constitution of races of maize. Its significance in the interpretation of relationships between races and varieties in the Americas 1981, Colegio de Postgraduados, Chapingo, Mexico.
56. Millenium Ecosystem Assessment. (2010). Guide to the Millennium Assessment Reports. < >. http://www.maweb.org/en/Index.aspx/.
57. Molnár I., Cifuentes M., Schneider A., Benavente E., Molnar-Lang M. Association between simple sequence repeat-rich chromosome regions and intergenomic translocation breakpoints in natural populations of allopolyploid wild wheats. Annals of Botany 2011, 107(1):65-76. < http://dx.doi.org/10.1093/aob/mcq215/>, December.
58. Moose S.P., Mumm R.H. Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiology 2008, 147:969-977. doi: 10.1104/pp.108.118232.
59. Neale D.B. Genomics to tree breeding and forest health. Current Opinion in Genetics & Development 2007, 17(6):539-544. December.
60. Nielsen R., Williamson S., Kim Y., Hubisz M.J., Clark A.G., Bustamante C. Genomic scans for selective sweeps using SNP data. Genome Research 2005, 15(11):1566-1575. Available from: < http://dx.doi.org/10.1101/gr.4252305/>, November.
61. Papa R., Bellucci E., Rossi M., Leonardi S., Rau D., Gepts P., et al. Tagging the signatures of domestication in common bean (Phaseolus vulgaris) by means of pooled DNA samples. Annals of Botany 2007, 100(5):1039-1051. Available from: < http://dx.doi.org/10.1093/aob/mcm151/>, October.
62. Paris H.S., Daunay M.C., Janick J. The Cucurbitaceae and Solanaceae illustrated in medieval manuscripts known as the Tacuinum Sanitatis. Annals of Botany 2009, 103(8):1187-1205. Available from: < http://dx.doi.org/10.1093/aob/mcp055/>, June.
63. Paterson A.H., Lin Y.R., Li Z., Schertz K.F., Doebley J.F., Pinson S.R.M., et al. Convergent domestication of cereal crops by independent mutations. Science 1995, 269:1714-1718.
64. Richardson, J. A. (1975). Physical problems of growing plants on colliery waste. M. J. Chadwick & G. T. Goodman (Eds.), The Ecology of Resource Degradation and Renewal. The Fifteenth Symposium of the British Ecological Society, Leeds, 10-12 July 1973 (pp. 275-286). Oxford: Blackwell Scientific Publications.
65. Rieseberg L.H., Blackman B.K. Speciation genes in plants. Annals of Botany 2010, 106(3):439-455. Available from: < http://dx.doi.org/10.1093/aob/mcq126/>, September.
66. Rubin E.M. Genomics of cellulosic biofuels. Nature 2008, 454:841-845. doi: 10.1038/nature07190, August 14.
67. Saeidi H., Rahiminejad M.R., Heslop-Harrison J.S. Retroelement insertional polymorphisms, diversity and phylogeography within diploid, D-Genome Aegilops tauschii (Triticeae, Poaceae) sub-taxa in Iran. Annals of Botany 2008, 101(6):855-861. doi:10.1093/aob/mcn042.
68. Salamini F., Ozkan H., Brandolini A., Scafer-Pregl R., Martin W. Genetics and geography of wild cereal domestication in the near East. Nature Reviews Genetics 2002, 3:429.
69. Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y., et al. The genome sequence and structure of rice chromosome 1. Nature 2002, 420(6913):312-316. Available from: < http://dx.doi.org/10.1038/nature01184/>, November.
70. Schulze J., Stoll P., Widmer A., Erhardt A. Searching for gene flow from cultivated to wild strawberries in Central Europe. Annals of Botany 2011, 107(4):699-707. Available from: < http://dx.doi.org/10.1093/aob/mcr018/>.
71. Somerville C.R., Youngs, H., Taylor C., Davis S.C., Long S.P. Feedstocks for lignocellulosic biofuels. Science 2010, 790-792. doi: 10.1126/science.1189268.
72. Tang T., Lu J., Huang J., He J., McCouch S.R., Shen Y., et al. Genomic variation in rice: Genesis of highly polymorphic linkage blocks during domestication. PLoS Genetics 2006, 2(11):e199. Available from: < http://dx.doi.org/10.1371/journal.pgen.0020199/>, November.
73. Tanksley S.D., McCouch S.R. Seed banks and molecular maps: Unlocking genetic potential from the wild. Science 1997, 277(5329):1063-1066. Available from: < http://dx.doi.org/10.1126/science.277.5329.1063/>, August.
74. Tian Z., Wang X., Lee R., Li Y., Specht J.E., Nelson R.L., et al. Artificial selection for determinate growth habit in soybean. Proceedings of the National Academy of Sciences 2010, 107(19):8563-8568. Available from: < http://dx.doi.org/10.1073/pnas.1000088107/>, May.
75. Varshney R.K., Hoisington D.A., Tyagi A.K. Advances in cereal genomics and applications in crop breeding. Trends in Biotechnology 2006, 24(11):490-499. doi: 10.1016/j.tibtech.2006.08.006.
76. Vaughan D.A., Balázs E., Heslop-Harrison J.S. From crop domestication to super-domestication. Annals of Botany 2007, 100(5):893-901. doi: 10.1093/aob/mcm224.
77. Vigouroux Y., Mitchell S., Matsuoka Y., Hamblin M., Kresovich S., Smith J.S.C., et al. An analysis of genetic diversity across the maize genome using microsatellites. Genetics 2005, 169(3):1617-1630. Available from: < http://dx.doi.org/10.1534/genetics.104.032086/>, March.
78. Wang H., Nussbaum-Wagler T., Li B., Zhao Q., Vigouroux Y., Faller M., et al. The origin of the naked grains of maize. Nature 2005, 436(7051):714-719. Available from: < http://dx.doi.org/10.1038/nature03863/>, August.
79. Wang J.X., Gao T.G., Knapp S. Ancient Chinese literature reveals pathways of eggplant domestication. Annals of Botany 2008, 102(6):891-897. Available from: < http://dx.doi.org/10.1093/aob/mcn179/>, December.
80. Weeden N.F. Genetic changes accompanying the domestication of pisum sativum: Is there a common genetic basis to the "Domestication Syndrome" for Legumes?. Annals of Botany 2007, 100(5):1017-1025. Available from: < http://dx.doi.org/10.1093/aob/mcm122/>, October.
81. Wouw M.van de, van Hintum T., Kik C., van Treuren R., Visser B. Genetic diversity trends in twentieth century crop cultivars: A meta analysis. TAG Theoretical and Applied Genetics Theoretische und angxewandte Genetik 2010, 120(6):1241-1252. Available from: < http://dx.doi.org/10.1007/s00122-009-1252-6/>, April.
82. Wright S.I., Bi I.V., Schroeder S.G., Yamasaki M., Doebley J.F., McMullen M.D., et al. The effects of artificial selection on the maize genome. Science 2005, 308(5726):1310-1314. Available from: < http://dx.doi.org/10.1126/science.1107891/>, May.
83. Yamasaki M., Tenaillon M.I., Vroh Bi I, Schroeder S.G., Sanchez-Villeda H., Doebley J.F., et al. A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. The Plant Cell 2005, 17(11):2859-2872. Available from: < http://dx.doi.org/10.1105/tpc.105.037242/>y.
84. Yamasaki M., Wright S.I., McMullen M.D. Genomic screening for artificial selection during domestication and improvement in maize. Annals of Botany 2007, 100(5):967-973. Available from: < http://dx.doi.org/10.1093/aob/mcm173/>, October.
85. Yano M. Genetic and molecular dissection of naturally occurring variation. Current Opinion in Plant Biology 2001, 4:130-135.
86. Ye X., Al-Babili S., Klöti A., Zhang J., Lucca P., Beyer P., et al. Engineering the provitamin A (beta-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm. Science 2000, 287(5451):303-305. doi:10.1126/science.287.5451.303.
87. Zeder M.A. Documenting domestication: New genetic and archaeological paradigms 2006, University of California Press.
88. Zhang Y., Wang J., Zhang X., Chen J.Q., Tian D., Yang S. Genetic signature of rice domestication shown by a variety of genes. Journal of Molecular Evolution 2009, 68(4):393-402. Available from: < http://dx.doi.org/10.1007/s00239-009-9217-6/>, April.
89. Zhu Q., Zheng X., Luo J., Gaut B.S., Ge S. Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: Severe bottleneck during domestication of rice. Molecular Biology and Evolution 2007, 24(3):875-888. Available from: < http://dx.doi.org/10.1093/molbev/msm005/>, March.