Combined linkage and association mapping of flowering time in Sunflower (Helianthus annuus L.)

Theoretical and Applied Genetics

Volumn 126, Issue 5, 2013, Pages 1337-1356

  Cadic, Elena ^a,b   Coque, Marie ^b,d   Vear, Felicity ^c   Grezes Besset, Bruno ^b   Pauquet, Jerôme ^b   Piquemal, Joël ^d   Lippi, Yannick ^a   Blanchard, Philippe ^e   Romestant, Michel ^f   Pouilly, Nicolas ^a   Rengel, David ^a   Gouzy, Jerôme ^a   Langlade, Nicolas ^a   Mangin, Brigitte ^g   Vincourt, Patrick ^a  

^a LABORATOIRE DES INTERACTIONS PLANTES MICROORGANISMES LIPM   (France)

^b BIOGEMMA SAS Domaine de Sandreau Mondonville   (France)

^c Diversity and Ecophysiology of Cereals   (France)

^d Syngenta Seeds SAS   (France)

^e Domaine de Sandreau   (France)

^f Domaine de Sandreau ^*  (France)

^g CEMAGREF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MAPPING;

ASSOCIATION MAPPING; HELIANTHUS ANNUUS; LINKAGE DISEQUILIBRIUM; PANEL STRUCTURES; QUANTITATIVE TRAIT LOCUS; RECOMBINANT INBRED LINES; SINGLE NUCLEOTIDE POLYMORPHISMS; STRUCTURE EFFECT;

PLANTS (BOTANY);

HELIANTHUS; HELIANTHUS ANNUUS;

PLANT DNA;

ARTICLE; CHROMOSOME MAP; FLOWER; GENE LINKAGE DISEQUILIBRIUM; GENETIC LINKAGE; GENETIC MARKER; GENETICS; GROWTH, DEVELOPMENT AND AGING; PHENOTYPE; PHYSIOLOGY; PLANT CHROMOSOME; PLANT GENE; QUANTITATIVE TRAIT LOCUS; SUNFLOWER;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; DNA, PLANT; FLOWERS; GENES, PLANT; GENETIC LINKAGE; GENETIC MARKERS; HELIANTHUS; LINKAGE DISEQUILIBRIUM; PHENOTYPE; QUANTITATIVE TRAIT LOCI;

EID: 84876710057     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-013-2056-2     Document Type: Article

References (79)

1. Achard P, Renou JP, Berthomé R, Harberd NP, Genschik P (2008) Plant DELLAs restrain growth and promote survival of adversity by reducing the levels of reactive oxygen species. Curr Biol 18: 656-660.
2. Allard RW, Bradshaw AD (1964) Implications of genotype-environmental interactions in applied plant breeding. Crop Sci. 4: 503-508.
3. Andersen JR, Schrag T, Melchinger AE, Zein I, Lübberstedt T (2005) Validation of Dwarf8 polymorphisms associated with flowering time in elite European inbred lines of maize (Zea mays L.). Theor Appl Genet 111: 206-217.
4. Aranzana MJ, Kim S, Zhao K, Bakker E, Horton M et al (2005) Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1: e60.
5. Arcade A, Labourdette A, Falque M, Mangin B, Chardon F, Charcosset A, Joets J (2004) BioMercator: integrating genetic maps and QTL towards discovery of candidate genes. Bioinformatics 20: 2324-2326.
6. Atwell S, Huang YS, Vilhjalmsson BJ, Willems G, Horton M, Li Y et al (2010) Genome-wide association study of 107 traits in Arabidopsis thaliana inbred lines. Nature 465: 627-631.
7. Austin DF, Lee M, Veldboom LR, Hallauer AR (2000) Genetic mapping in maize hybrid progeny across testers and generations: grain yield and grain moisture. Crop Sci 40: 30-39.
8. Baack EJ, Sapir Y, Chapman MA, Burke JM, Rieseberg LH (2008) Selection on domestication traits and QTLs in crop-wild sunflower hybrids. Mol Ecol 17: 666-677.
9. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc B Met 57: 289-300.
10. Bert PF, Jouan I, Tourvielle de Labrouhe D, Serre F, Philippon J, Nicolas P, Vear F (2003) Comparative genetic analysis of quantitative traits in sunflower (Helianthus annuus L.). 3. Characterisation of QTL involved in developmental and agronomic traits. Theor Appl Genet 107: 181-189.
11. Blackman BK, Rasmussen DA, Strasburg JL, Raduski AR, Burke JM, Knapp SJ, Michaels SD, Rieseberg LH (2011) Contributions of flowering time genes to sunflower domestication and improvement. Genetics 187: 271-287.
12. Bouzidi MF, Badaoui S, Cambon F, Vear F, De Labrouche DT, Nicolas P, Mouzeyar S (2002) Molecular analysis of a major locus for resistance to downy mildew in sunflower with specific PCR-based markers. Theor Appl Genet 104: 600-952.
13. Bowers JE, Bachlava E, Brunick RL, Rieseberg LH, Knapp SJ, Burke JM (2012) Development of a 10, 000 locus genetic map of the sunflower genome based on multiple crosses. Genes Genomes Genetics 2: 721-729.
14. Brachi B, Faure N, Horton M, Flahauw E, Vazquez A et al (2010) Linkage and association mapping of Arabidopsis thaliana flowering time in nature. PLoS Genet 6: e1000940.
15. Breseghello F, Sorrells ME (2006) Association analysis as a strategy for improvement of quantitative traits in plants. Crop Sci 46: 1323-1330.
16. Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ et al (2009) The genetic architecture of maize flowering time. Science 325: 714-718.
17. Burke JM, Tang S, Knapp SJ, Rieseberg LH (2002) Genetic analysis of sunflower domestication. Genetics 161: 1257-1267.
18. Butler DG, Cullis BR, Gilmour AR, Gogel BJ (2007) ASReml-R reference manual. The State of Queensland, Department of Primary Industries and Fisheries, Brisbane.
19. Charcosset A, Mangin B, Moreau L, Combes L, Jourjon MF (2000) Heterosis in maize investigated using connected RIL populations. In: Quantitative genetics and breeding methods: the way ahead. INRA, Paris, pp 89-98.
20. Coque M, Mesnildrey S, Romestant M, et al (2008) Sunflower lines core collections for association studies and phenomics. In: Proceedings ASTA Conference, Cordoba.
21. Crouzillat D, De la Canal L, Perrault A, Ledoigt G, Vear F, Serieys H (1991) Cytoplasmic male sterility in sunflower: comparison of molecular biology and genetic studies. Plant Mol Biol 16: 415-426.
22. 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.
23. Famoso AN, Zhao K, Clark RT, Tung C, Wright MH, Kochian LV, McCouch SR (2011) Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping. PLoS Genet 7: e1002221.
24. Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54: 357-374.
25. Flint-Garcia SA, Thuillet A-C, Yu J, Pressoir G, Romero SM, Mitchell SE, Doebley J, Kresovich S, Goodman MM, Buckler ES (2005) Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J 44: 1054-1064.
26. Fusari CM, Lia VV, Hopp HE, Heinz RA, Paniego NB (2008) Identification of single nucleotide polymorphisms and analysis of linkage disequilibrium in sunflower elite inbred lines using the candidate gene approach. BMC Plant Biol 8: 7.
27. Fusari CM, Rienzo JA, Troglia C (2012) Association mapping in sunflower for Sclerotinia head rot resistance. BMC Plant Biol 12: 93.
28. Gallais A (1984) An analysis of heterosis vs. inbreeding effects with an autotetraploid cross-fertilized plant Medicago sativa L. Genetics 106: 123-137.
29. Gaut BS, Long AD (2003) The lowdown on linkage disequilibrium. Plant Cell 15: 1502-1506.
30. Gentzbittel L, Zhang YX, Vear F, Griveau B, Nicolas P (1994) RFLP studies of genetic relationships among inbred lines of the cultivated sunflower, Helianthus annuus L.: evidence for distinct restorer and maintainer germplasm pools. Theor Appl Genet 89: 419-425.
31. Hallauer AR, Miranda JB (1988) Quantitative genetics in maize breeding. Iowa State Univ Press, Ames.
32. Hill WG, Weir BS (1988) Variances and covariances of squared linkage disequilibria in finite populations. Theor Popul Biol 33: 54-78.
33. Holland JB (2004) Implementation of molecular markers for quantitative traits in breeding programs-challenges and opportunities. In: Fischer T, Turner N, Angus J, McIntyre L, Robertson M, Borrell A, Lloyd D (eds) New directions for a diverse planet: proceedings for the 4th international crop science congress. Brisbane, Australia.
34. Horne EC, Kumpatla SP, Patterson KA, Gupta M, Thompson SA (2004) Improved high-throughput sunflower and cotton genomic DNA extraction and PCR fidelity. Plant Mol Biol Rep 22: 83a-83i.
35. Ingvarsson PK (2005) Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae). Genetics 169: 945-953.
36. Jourjon MF, Jasson S, Marcel J, Ngom B, Mangin B (2005) MCQTL: multi-allelic QTL mapping in multi-cross design. Bioinformatics 21: 128-130.
37. Jung M, Ching A, Bhattramakki D, Dolan M, Tingey S et al (2004) Linkage disequilibrium and sequence diversity in a 500-kbp region around the adh1 locus in elite maize germplasm. Theor Appl Genet 109: 681-689.
38. Kane NC, Gill N, King MG, Bowers JE, Berges H et al (2011) Progress towards a reference genome for sunflower. Botany 89: 429-437.
39. Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, Daly MJ, Eskin E (2008) Efficient control of population structure in model organism association mapping. Genetics 178: 1709-1723.
40. Kolkman JM, Berry ST, Leon AJ, Slabaugh MB, Tang S, Gao W et al (2007) Single nucleotide polymorphisms and linkage disequilibrium in sunflower. Genetics 177: 457-468.
41. Lander ES, Botstein DB (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
42. Leon AJ, Andrade FH, Lee M (2000) Genetic mapping of factors affecting quantitative variation for flowering in sunflower. Crop Sci 40: 404-407.
43. Leon AJ, Lee M, Andrade FH (2001) Quantitative trait loci for growing degree days to flowering and photoperiod response in Sunflower (Helianthus annuus L.). Theor Appl Genet 102: 497-503.
44. Luna A, Nicodemus KK (2007) snp. plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package. Bioinformatics 23: 774-776.
45. Mackay TFC (2001) The genetic architecture of quantitative traits. Annu Rev Genet 35: 303-339.
46. Mackay I, Powell W (2007) Methods for linkage disequilibrium mapping in crops. Trends Plant Sci 12: 57-63.
47. Maenhout S, De Baets B, Haesaert G (2009) Marker-based estimation of the coefficient of coancestry in hybrid breeding programmes. Theor Appl Genet 118: 1181-1192.
48. Mandel JR, Dechaine JM, Marek LF, Burke JM (2011) Genetic diversity and population structure in cultivated sunflower and a comparison to its wild progenitor, Helianthus annuus L. Theor Appl Genet 123: 693-704.
49. Mangin B, Siberchicot A, Nicolas S, Doligez A, This P et al (2011) Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness. Heredity 108: 285-291.
50. Maynard Smith J, Haigh J (1974) The hitch-hiking effect of a favorable gene. Genet Res 23: 23-35.
51. Melchinger AE, Utz HF, Schon CC (1998) Quantitative trait locus (QTL) mapping using different testers and independent population samples in maize reveals low power of QTL detection and large bias in estimates of QTL effects. Genetics 149: 383-403.
52. Mestries E, Gentzbittel L, Labrouhe DT, Nicolas P, Vear F, Am S (1998) Analyses of quantitative trait loci associated with resistance to Sclerotinia sclerotiorum in sunflowers (Helianthus annuus L.) using molecular markers. Mol Breed 4: 215-226.
53. Mir RR, Kumar N, Jaiswal V, Girdharwal N, Prasad M, Balyan HS, Gupta PK (2012) Genetic dissection of grain weight in bread wheat through quantitative trait locus interval and association mapping. Mol Breed 29: 963-972.
54. Mokrani L, Gentzbittel L, Azanza F, Fitamant L, Al-Chaarani G, Sarrafi A (2002) Mapping and analysis of quantitative trait loci for grain oil and agronomic traits using AFLP and SSR in sunflower (Helianthus annuus L.). Theor Appl Genet 106: 149-156.
55. Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z, Costich DE, Buckler ES (2009) Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21: 2194-2220.
56. Nordborg M, Weigel D (2008) Next-generation genetics in plants. Nature 456: 720-723.
57. Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng H, Bakker E, Calabrese P, Gladstone J, Goyal R, Jakobsson M, Kim S, Morozov Y, Padhukasahasram B, Plagnol V, Rosenberg NA, Shah C, Wall J, Wang J, Zhao K, Kalbfleisch T, Schultz V, Kreitman M, Bergelson J (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 3: e196.
58. Patterson N, Price AL, Reich D (2006) Population structure and Eigen analysis. PLoS Genet 2: e190.
59. Poormohammad Kiani S, Maury P, Nouri L, Ykhlef N, Grieu P, Sarrafi A (2009) QTL analysis of yield-related traits in sunflower under different water treatments. Plant Breeding 128: 363-373.
60. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
61. R Development Core Team (2012) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. ISBN 3-900051-07-0.
62. Rafalski JA (2002) Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant Sci 162: 329-333.
63. Raman H, Raman R, Eckermann P et al (2012) Genetic and physical mapping of flowering time loci in canola (Brassica napus L.). Theor Appl Genet 126: 119-132.
64. Rieseberg LH, Willis JH (2007) Plant speciation. Science 317: 910-914.
65. Sarnowski TJ, Świez S, Pawlikowska K, Kaczanowski S, Jerzmanowski A (2002) AtSWI3B, an Arabidopsis homolog of SWI3, a core subunit of yeast Swi/Snf chromatin remodeling complex, interacts with FCA, a regulator of flowering time. Nucl Acids Res 30: 3412-3421.
66. Shen CH, Krishnamurthy R, Yeh KW (2009) Decreased l-ascorbate content mediating bolting is mainly regulated by the galacturonate pathway in Oncidium. Plant Cell Physiol 50: 935-946.
67. Sun TP (2010) Gibberellin-GID1-DELLA: a pivotal regulatory module for plant growth and development. Plant Physiol 154: 567-570.
68. Sun G, Zhu C, Kramer MH, Yang SS, Song W, Piepho HP, Yu J (2010) Variation explained in mixed-model association mapping. Heredity 105: 333-340.
69. Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF et al (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci USA 98: 9161-9166.
70. Thornsberry JM, Goodman MM, Doebley J et al (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nature genet 28: 286-289.
71. Tian F et al (2011) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43: 159-162.
72. Vear F, Serre F, Jouan-Dufournel, Bert I, Roche PF, Walser SP, de Labrouhe DT, Vincourt P (2008) Inheritance of quantitative resistance to downy mildew (Plasmopara halstedii) in sunflower (Helianthus annuus L.). Euphytica 164: 561-570.
73. Vincourt P, As Sadi F, Bordat A, Langlade N, Gouzy J, Pouilly N, Lippi Y, Serre F, Godiard L, Tourvieille de Labrouhe D, Vear F (2012) Consensus mapping of major resistance genes and independent QTL for quantitative resistance to sunflower downy mildew. Theor Appl Genet 5: 909-920.
74. Wills DM, Burke JM (2007) Quantitative trait locus analysis of the early domestication of sunflower. Genetics 176: 2589-2599.
75. Wright S (1951) The genetic structure of populations. Ann Eugen 15: 323-354.
76. Xu L, Zhao Z, Dong A et al (2008) Di-and tri-but not monomethylation on histone H3 lysine 36 marks active transcription of genes involved in flowering time regulation and other processes in Arabidopsis thaliana. Mol Cell Biol 28: 1348-1360.
77. Yan J, Warburton ML, Crouch J (2011) Association mapping for enhancing maize (Zea mays L.) genetic improvement. Crop Sci 51: 433-449.
78. Yu JM, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38: 203-208.
79. Zhao K, Aranzana MJ, Kim S, Lister C, Shindo C, Tang C, Toomajian C, Zheng H, Dean C, Marjoram P, Nordborg M (2007) An Arabidopsis example of association mapping in structured samples. PLoS Genet 3: e4.