Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species

Theoretical and Applied Genetics

Volumn 126, Issue 3, 2013, Pages 567-581

  Xu, Jiaxin ^a,b   Ranc, Nicolas ^b,d   Muños, Stéphane ^b,e   Rolland, Sophie ^b,f   Bouchet, Jean Paul ^b   Desplat, Nelly ^b   Le Paslier, Marie Christine ^c   Liang, Yan ^a   Brunel, Dominique ^c   Causse, Mathilde ^b  

^a NORTHWEST A F UNIVERSITY   (China)

^b Researches Center of Avignon   (France)

^c CENTRE NATIONAL DE GÉNOTYPAGE   (France)

^d Syngenta Seeds SAS   (France)

^e LABORATOIRE DES INTERACTIONS PLANTES MICROORGANISMES LIPM   (France)

^f AGROCAMPUS OUEST   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CULTIVATION; FRUITS; MAPPING; PLANTS (BOTANY); VALUE ENGINEERING;

ASSOCIATION ANALYSIS; ASSOCIATION MAPPING; GENETIC STRUCTURE; LINKAGE DISEQUILIBRIUM; PHENOTYPIC DIVERSITY; POPULATION STRUCTURES; QUANTITATIVE TRAIT LOCUS; SOLANUM LYCOPERSICUM;

QUALITY CONTROL;

LYCOPERSICON; LYCOPERSICON ESCULENTUM; LYCOPERSICON ESCULENTUM VAR. CERASIFORME; LYCOPERSICON PIMPINELLIFOLIUM; SOLANUM;

EID: 84874320505     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-012-2002-8     Document Type: Article

References (56)

1. Agrama HA, Eizenga GC, Yan W (2007) Association mapping of yield and its components in rice cultivars. Mol Breed 19: 341-356.
2. Aranzana MJ, Kim S, Zhao KY, Bakker E, Horton M, Jakob K, Lister C, Molitor J, Shindo C, Tang CL, Toomajian C, Traw B, Zheng HG, Bergelson J, Dean C, Marjoram P, Nordborg M (2005) Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1: 531-539.
3. Atwell S, Huang YS, Vilhjalmsson BJ, Willems G, Horton M, Li Y, Meng DZ, Platt A, Tarone AM, Hu TT, Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, Brachi B, Chory J, Dean C, Debieu M, de Meaux J, Ecker JR, Faure N, Kniskern JM, Jones JDG, Michael T, Nemri A, Roux F, Salt DE, Tang CL, Todesco M, Traw MB, Weigel D, Marjoram P, Borevitz JO, Bergelson J, Nordborg M (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465: 627-631.
4. Barrero LS, Tanksley SD (2004) Evaluating the genetic basis of multiple-locule fruit in a broad cross section of tomato cultivars. Theor Appl Genet 109: 669-679.
5. Berard A, Le Paslier MC, Dardevet M, Exbrayat-Vinson F, Bonnin I, Cenci A, Haudry A, Brunel D, Ravel C (2009) High-throughput single nucleotide polymorphism genotyping in wheat (Triticum spp.). Plant Biotechnol J 7: 364-374.
6. Bergelson J, Roux F (2010) Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana. Nat Rev Genet 11: 867-879.
7. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633-2635.
8. Causse M, Saliba-Colombani V, Lecomte L, Duffe P, Rousselle P, Buret M (2002) QTL analysis of fruit quality in fresh market tomato: a few chromosome regions control the variation of sensory and instrumental traits. J Exp Bot 53: 2089-2098.
9. Causse M, Buret M, Robini K, Verschave P (2003) Inheritance of nutritional and sensory quality traits in fresh market tomato and relation to consumer preferences. J Food Sci 68: 2342-2350.
10. Causse M, Duffe P, Gomez MC, Buret M, Damidaux R, Zamir D, Gur A, Chevalier C, Lemaire-Chamley M, Rothan C (2004) A genetic map of candidate genes and QTLs involved in tomato fruit size and composition. J Exp Bot 55: 1671-1685.
11. Davies JN, Hobson GE (1981) The constituents of tomato fruit-the influence of environment, nutrition, and genotype. Crit Rev Food Sci Nutr 15: 205-280.
12. De La Vega FA, Lazaruk KD, Rhodes MD, Wenz MH (2005) Assessment of two flexible and compatible SNP genotyping platforms: TaqMan (R) SNP genotyping assays and the SNPlex (TM) genotyping system. Mutat Res Fundam Mol Mech Mutagen 573: 111-135.
13. Eshed Y, Zamir D (1995) An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics 141: 1147-1162.
14. 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.
15. Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54: 357-374.
16. Frary A, Nesbitt TC, Grandillo S, van der Knaap E, Cong B, Liu JP, Meller J, Elber R, Alpert KB, Tanksley SD (2000) fw2. 2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289: 85-88.
17. Fridman E, Pleban T, Zamir D (2000) A recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene. Proc Natl Acad Sci USA 97: 4718-4723.
18. Goldman IL, Paran I, Zamir D (1995) Quantitative trait locus analysis of a recombinant inbred line population derived from a Lycopersicon esculentum x Lycopersiconcheesmanii cross. Theor Appl Genet 90: 925-932.
19. Grandillo S, Tanksley SD (1996) QTL analysis of horticultural traits differentiating the cultivated tomato from the closely related species Lycopersicon pimpinellifolium. Theor Appl Genet 92: 935-951.
20. Hall D, Tegstrom C, Ingvarsson PK (2010) Using association mapping to dissect the genetic basis of complex traits in plants. Brief Funct Genomics 9: 157-165.
21. Hamblin MT, Warburton ML, Buckler ES (2007) Empirical comparison of simple sequence repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness. Plos One 2(12): e1367.
22. Hardy OJ, Vekemans X (2002) SPAGEDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2: 618-620.
23. Laval G, SanCristobal M, Chevalet C (2002) Measuring genetic distances between breeds: use of some distances in various short term evolution models. Genet Select Evol 34: 481-507.
24. Lecomte L, Saliba-Colombani V, Gautier A, Gomez-Jimenez MC, Duffe P, Buret M, Causse M (2004) Fine mapping of QTLs of chromosome 2 affecting the fruit architecture and composition of tomato. Mol Breed 13: 1-14.
25. Mamidi S, Chikara S, Goos RJ, Hyten DL, Annam D, Moghaddam SM, Lee RK, Cregan PB, McClean PE (2011) Genome-wide association analysis identifies candidate genes associated with iron deficiency chlorosis in soybean. Plant Genome 4: 154-164.
26. Mazzucato A, Papa R, Bitocchi E, Mosconi P, Nanni L, Negri V, Picarella ME, Siligato F, Soressi GP, Tiranti B, Veronesi F (2008) Genetic diversity, structure and marker-trait associations in a collection of Italian tomato (Solanum lycopersicum L.) landraces. Theor Appl Genet 116: 657-669.
27. Mezmouk S, Dubreuil P, Bosio M, Decousset L, Charcosset A, Praud S, Mangin B (2011) Effect of population structure corrections on the results of association mapping tests in complex maize diversity panels. Theor Appl Genet 122: 1149-1160.
28. Miller JC, Tanksley SD (1990) RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theor Appl Genet 80: 437-448.
29. Moonsamy PV, Bonella PL, Williams TC, Holcomb CL, Turenchalk GS, Blake LA, Hoglund BN, Rastrou M, Daigle DA, Simen BB, Goodridge D, Hillman G, Hamilton A, May AP, Erlich HA (2011) Use of the fluidigm (R) access array (TM) system provides simplified amplicon library preparation in next generation sequencing for high throughput hla genotyping. Hum Immunol 72: S142-S142.
30. Munos S, Ranc N, Botton E, Berard A, Rolland S, Duffe P, Carretero Y, Le Paslier MC, Delalande C, Bouzayen M, Brunel D, Causse M (2011) Increase in tomato locule number is controlled by two single-nucleotide polymorphisms located near Wuschel. Plant Physiol 156: 2244-2254.
31. Nemri A, Atwell S, Tarone AM, Huang YS, Zhao K, Studholme DJ, Nordborg M, Jones JD (2010) Genome-wide survey of Arabidopsis natural variation in downy mildew resistance using combined association and linkage mapping. Proc Natl Acad Sci USA 107: 10302-10307.
32. Nesbitt TC, Tanksley SD (2002) Comparative sequencing in the genus Lycopersicon: implications for the evolution of fruit size in the domestication of cultivated tomatoes. Genetics 162: 365-379.
33. Orsini E, Krchov LM, Uphaus J, Melchinger AE (2012) Mapping of QTL for resistance to first and second generation of European corn borer using an integrated SNP and SSR linkage map. Euphytica 183: 197-206.
34. Paterson AH, Damon S, Hewitt JD, Zamir D, Rabinowitch HD, Lincoln SE, Lander ES, Tanksley SD (1991) Mendelian factors underlying quantitative traits in tomato-comparison across species, generations, and environments. Genetics 127: 181-197.
35. Pindo M, Vezzulli S, Coppola G, Cartwright DA, Zharkikh A, Velasco R, Troggio M (2008) SNP high-throughput screening in grapevine using the SNPlex (TM) genotyping system. BMC Plant Biol 8: 128.
36. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38: 904-909.
37. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
38. Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5: 94-100.
39. Ranc N, Munos S, Santoni S, Causse M (2008) A clarified position for Solanum lycopersicum var. cerasiforme in the evolutionary history of tomatoes (solanaceae). BMC Plant Biol 8: 130.
40. Ranc N, Muños S, Xu J, Le Paslier MC, Chauveau A, Bounon R, Rolland S, Bouchet JP, Brunel D, Causse M (2012) Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of Solanum lycopersicum var. cerasiforme. Genes Genomes Genet 2: 853-864.
41. Robbins MD, Sim SC, Yang WC, van Deynze A, van der Knaap E, Joobeur T, Francis DM (2011) Mapping and linkage disequilibrium analysis with a genome-wide collection of SNPs that detect polymorphism in cultivated tomato. J Exp Bot 62: 1831-1845.
42. Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4: 137-138.
43. Saliba-Colombani V, Causse M, Langlois D, Philouze J, Buret M (2001) Genetic analysis of organoleptic quality in fresh market tomato 1. Mapping QTLs for physical and chemical traits. Theor Appl Genet 102: 259-272.
44. Sim S-C, Durstewitz G, Plieske J, Wieseke R, Ganal MW, van Deynze A, Hamilton JP, Robin Buell C, Causse M, Wijeratne S, Francis DM (2012) Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS One 7(7): e40563. doi: 10. 1371/journal. pone. 0040563.
45. Szalma SJ, Hostert BM, LeDeaux JR, Stuber CW, Holland JB (2007) QTL mapping with near-isogenic lines in maize. Theor Appl Genet 114: 1211-1228.
46. Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, Flint-Garcia S, Rocheford TR, McMullen MD, Holland JB, Buckler ES (2011) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43: U113-U159.
47. Tobler AR, Short S, Andersen MR, Paner TM, Briggs JC, Lambert SM, Wu PP, Wang Y, Spoonde AY, Koehler RT, Peyret N, Chen C, Broomer AJ, Ridzon DA, Zhou H, Hoo BS, Hayashibara KC, Leong LN, Ma CN, Rosenblum BB, Day JP, Ziegle JS, De La Vega FM, Rhodes MD, Hennessy KM, Wenz HM (2005) The SNPlex genotyping system: a flexible and scalable platform for SNP genotyping. J Biomol Tech (JBT) 16: 398-406.
48. van Berloo R, Zhu AG, Ursem R, Verbakel H, Gort G, van Eeuwijk FA (2008) Diversity and linkage disequilibrium analysis within a selected set of cultivated tomatoes. Theor Appl Genet 117: 89-101.
49. van der Knaap E, Tanksley SD (2001) Identification and characterization of a novel locus controlling early fruit development in tomato. Theor Appl Genet 103: 353-358.
50. van der Knaap E, Tanksley SD (2003) The making of a bell pepper-shaped tomato fruit: identification of loci controlling fruit morphology in Yellow Stuffer tomato. Theor Appl Genet 107: 139-147.
51. van Deynze A, Stoffel K, Buell CR, Kozik A, Liu J, van der Knaap E, Francis D (2007) Diversity in conserved genes in tomato. BMC Genomics 8: 465.
52. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93: 77-78.
53. Wang JK, Wan XY, Crossa J, Crouch J, Weng JF, Zhai HQ, Wan JM (2006) QTL mapping of grain length in rice (Oryza sativa L.) using chromosome segment substitution lines. Genet Res 88: 93-104.
54. 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.
55. Zhao H, Nettleton D, Soller M, Dekkers JCM (2005) Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between markers and QTL. Genet Res 86: 77-87.
56. Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam MR, Reynolds A, Mezey J, McClung AM, Bustamante CD, McCouch SR (2011) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2: 467.