Functional Gene Polymorphism to Reveal Species History: The Case of the CRTISO Gene in Cultivated Carrots

PLoS ONE

Volumn 8, Issue 8, 2013, Pages

  Soufflet Freslon, Vanessa ^a,b,c   Jourdan, Matthieu ^a,b,c   Clotault, Jérémy ^a,b,c   Huet, Sébastien ^a,b,c   Briard, Mathilde ^a,b,c   Peltier, Didier ^a,b,c   Geoffriau, Emmanuel ^a,b,c  

^a AGROCAMPUS OUEST   (France)

^b UNIVERSITÉ D'ANGERS   (France)

^c Universite d'Angers   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BALANCING SELECTION; CARROT; CONTROLLED STUDY; CRTISO GENE; CULTIVAR IDENTIFICATION; DNA POLYMORPHISM; FUNCTIONAL GENOMICS; GENE LINKAGE DISEQUILIBRIUM; GENE SEQUENCE; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; HAPLOTYPE; MICROSATELLITE MARKER; NONHUMAN; PLANT GENE; PLANT ROOT; SEQUENCE ANALYSIS; SPECIES IDENTIFICATION;

EID: 84881089721     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0070801     Document Type: Article

References (59)

1. Hudson R, (1990) Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology 7: 1-44.
2. Camus-Kulandaivelu L, Chevin L, Tollon-Cordet C, Charcosset A, Manicacci D, et al. (2008) Patterns of molecular evolution associated with two selective sweeps in the Tb1-Dwarf8 region in maize. Genetics 180 (2): 1107-1121.
3. Fu Z, Yan J, Zheng Y, Waburton ML, Crouch JH, et al. (2010) Nucleotide diversity and molecular evolution of the PSY1 gene in Zea mays compared to some other grass species. Theor Appl Genet 120: 709-720.
4. Mackevic V, (1929) The carrot of Afghanistan. Bull Appl Bot Genet Plant Breed 20: 517-562.
5. Banga O, (1963) Origin and distribution of the Western cultivated carrot. Genetica Agraria 17: 357-370.
6. Laufer B (1919) In:Sino-Iranica: Chinese contributions to the History of civilization in Ancient Iran with special reference to the History of cultivated plants and products. Field Museum of Natural History, Chicago 451-454.
7. Shinohara S (1984) Introduction and variety development in Japan. In: 4-7-7SAACEO (ed) Vegetable seed production technology of Japan elucidated with respective variety development histories, particulars. 273-282.
8. Clotault J, Geoffriau E, Lionneton E, Briard M, Peltier D, (2010) Carotenoid biosynthesis genes provide evidence of geographical subdivision and extensive linkage disequilibrium in the carrot. Theor Appl Genet 121: 659-72.
9. Baranski R, Maksylewicz-Kaul A, Nothnagel T, Cavagnaro PF, Simon PW, et al. (2011) Genetic diversity of carrot (Daucus carota L.) cultivars revealed by analysis of SSR loci. Genet Resour Crop Evol 59: 163-170.
10. Surles RL, Weng N, Simon PW, Tanumihardjo SA, (2004) Carotenoid profiles and consumer sensory evaluation of specialty carrots (Daucus carota L.) of various colors. J Agric Food Chem 52: 3417-3421.
11. Maass D, Arango J, Wust F, Beyer P, Welsch R, (2009) Carotenoid crystal formation in Arabidopsis and carrot roots caused by increased phytoene synthase Protein Levels. PLoS ONE 4: e6373.
12. Just BJ, Santos CAF, Yandell BS, Simon PW, (2009) Major QTL for carrot color are positionally associated with carotenoid biosynthetic genes and interact epistatically in a domesticated x wild carrot cross. Theor Appl Genet 119: 1155-69.
13. Hannoufa A, Hossain Z, (2012) Regulation of carotenoid accumulation in plants. Biocatalysis and Agricultural Biotechnology 1: 198-202.
14. Cunningham FX, Gantt E, (1998) Genes and enzymes of carotenoid biosynthesis in plants. Annu Rev Plant Physiol Plant Mol Biol 49: 557-583.
15. Hirschberg J, (2001) Carotenoid biosynthesis in flowering plants. Current Opinion in Plant Biology 4: 210-218.
16. Bartley GE, Scolnik PA, (1995) Plant carotenoids: pigments for photoprotection, visual attraction, and human health. The Plant cell 7: 1027-1038.
17. Isaacson T, Ronen G, Zamir D, Hirschberg J, (2002) Cloning of tangerine from tomato reveals a carotenoid isomerase essential for the production of beta-carotene and xanthophylls in plants. The Plant Cell 14: 333-342.
18. Park H, Kreunen SS, Cuttriss AJ, Della-Penna D, Pogson BJ, (2002) Identification of the carotenoid isomerase provides insight into carotenoid biosynthesis, prolamellar body formation, and photomorphogenesis. The Plant Cell 14: 321-332.
19. Just BJ, Santos CAF, Fonseca MEN, Boiteux LS, Oloizia BB, et al. (2007) Carotenoid biosynthesis structural genes in carrot (Daucus carota): isolation, sequence-characterization, single nucleotide polymorphism (SNP) markers and genome mapping. Theor Appl Genet 114: 693-704.
20. Isaacson T, Ohad I, Beyer P, Hirschberg J, (2004) Analysis in vitro of the enzyme CRTISO establishes a poly-cis-carotenoid biosynthesis pathway in plants. Plant Physiol 136: 4246-4255.
21. Fang J, Chai C, Qian Q, Li C, tang J, et al. (2008) Mutations of genes in synthesis of the carotenoid precursors of ABA lead to pre-harvest sprouting and photo-oxidation in rice. The Plant Journal 54: 177-189.
22. Galpaz N, Ronen G, Khalfa Z, Zamir D, Hirschberg J, (2006) A chromoplast-specific carotenoid biosynthesis pathway is revealed by cloning of the tomato white-flower locus. The Plant Cell 18: 1947-1960.
23. Li Q, Farre G, Naqvi S, Breitenbach J, Sanahuja G, et al. (2010) Cloning and functional characterization of the maize carotenoid isomerase and β-carotene hydroxylase genes and their regulation during endosperm maturation. Transgenic Res 19: 1053-1068.
24. Chai C, Fang J, Liu Y, Tong H, Gong Y, et al. (2011) ZEBRA2, encoding a carotenoid isomerase, is involved in photoprotection in rice. Plant Mol Biol 75: 211-221.
25. Clotault J, Peltier D, Soufflet-Freslon V, Briard M, Geoffriau E, (2012) Differential selection on carotenoid biosynthesis genes as a function of gene position in the metabolic pathway: a study on the carrot and dicots. PLoS ONE 7(6): e38724.
26. Briard M, Le Clerc V, Grzebelus D, Senalik D, Simon PW, (2000) Modified protocols for rapid carrot genomic DNA extraction and AFLP™ analysis using silver stain or radioisotopes. Plant Molecular Biology Reporter 18: 235-241.
27. Cavagnaro PF, Chung S-M, Manin S, Yildiz M, Ali A, et al. (2011) Microsatellite isolation and marker development in carrot- genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae. BMC Genomics 12: 386.
28. 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.
29. Evanno G, Regnaut S, Goudet J, (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620.
30. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (1996-2004) GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5171, Université de Montpellier II, Montpellier (France).
31. Goudet J, (1995) FSTAT (Version 1.2): A computer program to calculate F-statistics. Journal of Heredity 86: 485-486.
32. Weir BS, Cockerham CC, (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
33. Drummond AJ, Ashton B, Buxton S (2011). Geneious v5.1 created by Biomatters. Available from: http://www.geneious.com.
34. Dutheil J, Gaillard S, Bazin E, Glémin S, Ranwez V, et al. (2006) Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. BMC Bioinformatics 7: 188.
35. Thompson JD, Higgins DG, Gibson TJ, (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680.
36. Librado P, Rozas J, (2009) DnaSP v5: software for comprehensive analysis of DNA polymorphism data. Bioinformatics (Oxford, England) 25: 1451-1452.
37. Watterson GA, (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7: 256-276.
38. Nei M (1987) Molecular evolutionary genetics, Columbia University Press, New York, 512 p.
39. Bandelt HJ, Forster P, Röhl A, (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16: 37-48.
40. Gupta PK, Rustgi S, Kulwal PL, (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57: 461-485.
41. Flint-Garcia SA, Thornsberry JM, Buckler ES, (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54: 357-374.
42. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, et al. (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633-2635.
43. Tajima F, (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
44. Eyre-Walker A, Gaut RL, Hilton H, Feldman DL, Gaut BS, (1998) Investigation of the bottleneck leading to the domestication of maize. PNAS 95: 4441-4446.
45. Clotault J, Thuillet AC, Buiron M, De Mita S, Couderc et al, (2011) Evolutionary history of pearl millet (Pennisetum glaucum [L.] R. Br.) and selection on flowering genes since its domestication. Mol Biol Evol 29: 1199-1212.
46. Hudson RR, (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
47. De Mita S, Siol M, (2012) EggLib: processing, analysis and simulation tools for population genetics and genomics. BMC genetics 13: 27.
48. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, et al. (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 98: 11479-11484.
49. Stein M, Nothnagel Th, (1995) Some remarks on carrot breeding (Daucus carota sativus Hoffm.). Plant Breeding 114: 1-11.
50. Ingvarsson PK, (2008) Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula. Genetics 180: 329-340.
51. Xing Y, Frei U, Schejbel B, Asp T, Lübberstedt T, (2007) Nucleotide diversity and linkage disequilibrium in 11 expressed resistance candidate genes in Lolium perenne. BMC Plant Biology 7: 43.
52. Stenzel A, Lu T, Koch W, Hampe J, Guenther S, et al. (2004) Patterns of linkage disequilibrium in the MHC region on human chromosome 6p. Hum Genet 114: 377-385.
53. Smith AV, Thomas DJ, Munro HM, Abecasis GR, (2005) Sequence features in regions of weak and strong linkage disequilibrium. Genome Res 15: 1519-1534.
54. Zhu Q, Zheng X, Luo J, Gaut BS, Ge S, (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.
55. Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF, et al. (2005) The effects of artificial selection on the maize genome. Science 308: 1310-1314.
56. Iorizzo M, Senalik DA, Ellison SL, Grzebelus D, Cavagnaro PF, et al. (2013) Genetic structure and domestication of carrot (Daucus carota subsp. sativus) (Apiaceae). American Journal of Botany 100: 930-938.
57. Charlesworth D, (2006) Balancing selection and its effects on sequences in nearby genome regions. PLoS Genet 2 (4): e64.
58. Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, et al. (2007) Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet 3: 1745-1756.
59. Simon PW, Freeman RE, Vieira JV, Boiteux LS, Briard M et al. (2008) Carrot. In: Prohens J, Nuez F (eds) Springer New York, 327-357.