An association mapping approach to identify favourable alleles for tomato fruit quality breeding

BMC Plant Biology

Volumn 14, Issue 1, 2014, Pages

  Ruggieri, Valentino ^a   Francese, Gianluca ^b   Sacco, Adriana ^a   D'Alessandro, Antonietta ^b   Rigano, Maria Manuela ^a   Parisi, Mario ^b   Milone, Marco ^b   Cardi, Teodoro ^b   Mennella, Giuseppe ^b   Barone, Amalia ^a  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b Centro di Ricerca per l'Orticoltura   (Italy)

Author keywords

Candidate genes; Fruit quality; Genome wide association; Metabolite analysis; Mixed Linear Model; Solanum lycopersicum; SolCAP Infinium array

Indexed keywords

PLANT PROTEIN;

FRUIT; GENE LINKAGE DISEQUILIBRIUM; GENETICS; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; METABOLISM; PHENOTYPE; PHYSIOLOGY; QUANTITATIVE TRAIT LOCUS; SEASON; SINGLE NUCLEOTIDE POLYMORPHISM; TOMATO;

FRUIT; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; LINKAGE DISEQUILIBRIUM; LYCOPERSICON ESCULENTUM; PHENOTYPE; PLANT PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SEASONS;

EID: 84988689934     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/s12870-014-0337-9     Document Type: Article

References (64)

1. The Tomato consortium: The tomato genome sequence provides insights into fleshy fruit evolution. Nature 2012, 485(7400):635-641.
2. Hamilton JP, Sim S-C, Stoffel K, Van Deynze A, Buell CR, Francis DM: Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis. Plant Genome 2012, 5(1):17-29.
3. Merk HL, Yarnes SC, Van Deynze A, Tong N, Menda N, Mueller LA, Mutschler MA, Loewen SA, Myers JR, Francis DM: Trait diversity and potential for selection indices based on variation among regionally adapted processing tomato germplasm. J Am Soc Horticultural Sci 2012, 137(6):427-437.
4. Robbins MD, Sim S-C, Yang W, Van Deynze A, van der Knaap E, Joobeur T, Francis DM: Mapping and linkage disequilibrium analysis with a genomewide collection of SNPs that detect polymorphism in cultivated tomato. J Exp Bot 2011, 62(6):1831-1845.
5. Sim SC, Van Deynze A, Stoffel K, Douches DS, Zarka D, Ganal MW, Chetelat RT, Hutton SF, Scott JW, Gardner RG, Panthee DR, Mutschler M, Myers JR, Francis DM: High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding. PLoS One 2012, 7(9):e45520.
6. Sim S-C, Durstewitz G, Plieske J, Wieseke R, Ganal MW, Van Deynze A, Hamilton JP, Buell CR, Causse M, Wijeratne S, Francis DM: Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS One 2012, 7(7):e40563.
7. Hall D, Tegstrom C, Ingvarsson PK: Using association mapping to dissect the genetic basis of complex traits in plants. Brief Funct Genomics 2010, 9(2):157-165.
8. Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z, Costich DE, Buckler ES: Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 2009, 21(8):2194-2202.
9. Semagn K, Bjørnstad Å, Xu Y: The genetic dissection of quantitative traits in crops. Electron J Biotechnol 2010, 13:16-17.
10. Zhu C, Gore M, Buckler ES, Yu J: Status and prospects of association mapping in plants. Plant Genome J 2008, 1(1):5.
11. Yu J, Buckler ES: Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 2006, 17(2):155-160.
12. 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: Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2011, 2:467.
13. Mazzucato A, Papa R, Bitocchi E, Mosconi P, Nanni L, Negri V, Picarella ME, Siligato F, Soressi GP, Tiranti B, Veronesi F: Genetic diversity, structure and marker-trait associations in a collection of Italian tomato (Solanum lycopersicum L.) landraces. Theor Appl Genet 2008, 116(5):657-669.
14. Ranc N, Muños S, Xu J, Le Paslier M-C, Chauveau A, Bounon R, Rolland S, Bouchet J-P, Brunel D, Causse M: Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of solanum lycopersicum var. cerasiforme. G3: Genes Genomes Genet 2012, 2(8):853-864.
15. Xu J, Ranc N, Munos S, Rolland S, Bouchet JP, Desplat N, Le Paslier MC, Liang Y, Brunel D, Causse M: Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species. Theor Appl Genet 2013, 126(3):567-581.
16. Shirasawa K, Fukuoka H, Matsunaga H, Kobayashi Y, Kobayashi I, Hirakawa H, Isobe S, Tabata S: Genome-wide association studies using single nucleotide polymorphism markers developed by re-sequencing of the genomes of cultivated tomato. DNA Res 2013, 20(6):593-603.
17. Hirakawa H, Shirasawa K, Ohyama A, Fukuoka H, Aoki K, Rothan C, Sato S, Isobe S, Tabata S: Genome-wide SNP genotyping to infer the effects on gene functions in tomato. DNA Res 2013, 20(3):221-233.
18. Rodríguez GR, Kim HJ, van der Knaap E: Mapping of two suppressors of OVATE (sov) loci in tomato. Heredity 2013, 111(3):256-264.
19. Blanca J, Canizares J, Cordero L, Pascual L, Diez MJ, Nuez F: Variation revealed by SNP genotyping and morphology provides insight into the origin of the tomato. PLoS One 2012, 7(10):e48198.
20. Sauvage C, Segura V, Bauchet G, Stevens R, Thi Do P, Nikoloski Z, Fernie AR, Causse M: Genome wide association in tomato reveals 44 candidate loci for fruit metabolic traits. Plant Physiol 2014, 165(3):1120-1132.
21. Zhang N, Brewer MT, van der Knaap E: Fine mapping of fw3.2 controlling fruit weight in tomato. Theor Appl Genet 2012, 125(2):273-284.
22. Tomes ML, Quackenbush FW: Caro-red, a new provitamin a rich tomato. Economic Botany 1958, 12:256-260.
23. Bernardo R: Molecular markers and selection for complex traits in plants: learning from the last 20 years. Crop Sci 2008, 48(5):1649-1664.
24. Galeano C, Cortes A, Fernandez A, Soler A, Franco-Herrera N, Makunde G, Vanderleyden J, Blair M: Gene-based single nucleotide polymorphism markers for genetic and association mapping in common bean. BMC Genet 2012, 13(1):48.
25. Wang M, Sukumaran S, Barkley N, Chen Z, Chen C, Guo B, Pittman R, Stalker H, Holbrook C, Pederson G: Population structure and marker-trait association analysis of the US peanut (Arachis hypogaea L.) mini-core collection. Theor Appl Genet 2011, 123(8):1307-1317.
26. Gutierrez L, Cuesta-Marcos A, Castro A, von Zitzewitz J, Schmitt M, Hayes P: Association mapping of malting quality quantitative trait loci in winter barley: positive signals from small germplasm arrays. Plant Genome 2011, 4(3):256-272.
27. Atwell S, Huang YS, Vilhjalmsson BJ, Willems G, Horton M, Li Y, Meng D, 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 JD, Michael T, Nemri A, Roux F, Salt DE, Tang C, Todesco M, et al: Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 2010, 465(7298):627-631.
28. Raggi L, Tissi C, Mazzucato A, Negri V: Molecular polymorphism related to flowering trait variation in a Phaseolus vulgaris L. collection. Plant Sci 2014, 215-216:180-189.
29. Raiola A, Rigano MM, Calafiore R, Frusciante L, Barone A: Enhancing the health-promoting effects of tomato fruit for biofortified food. Mediators Inflamm 2014, 2014:16.
30. Di Matteo A, Sacco A, Anacleria M, Pezzotti M, Delledonne M, Ferrarini A, Frusciante L, Barone A: The ascorbic acid content of tomato fruits is associated with the expression of genes involved in pectin degradation. BMC Plant Biol 2010, 10:163.
31. Agius F, Gonzalez-Lamothe R, Caballero JL, Munoz-Blanco J, Botella MA, Valpuesta V: Engineering increased vitamin C levels in plants by overexpression of a D-galacturonic acid reductase. Nat Biotechnol 2003, 21(2):177-181.
32. Hemavathi, Upadhyaya CP, Young KE, Akula N, Kim H, Heung JJ, Oh OM, Aswath CR, Chun SC, Kim DH, Park SW: Over-expression of strawberry d-galacturonic acid reductase in potato leads to accumulation of vitamin C with enhanced abiotic stress tolerance. Plant Sci 2009, 177(6):659-667.
33. Fantini E, Falcone G, Frusciante S, Giliberto L, Giuliano G: Dissection of tomato lycopene biosynthesis through virus-induced gene silencing. Plant Physiol 2013, 163(2):986-998.
34. Rodriguez-Villalon A, Gas E, Rodriguez-Concepcion M: Phytoene synthase activity controls the biosynthesis of carotenoids and the supply of their metabolic precursors in dark-grown Arabidopsis seedlings. Plant J 2009, 60(3):424-435.
35. Liu YS, Gur A, Ronen G, Causse M, Damidaux R, Buret M, Hirschberg J, Zamir D: There is more to tomato fruit colour than candidate carotenoid genes. Plant Biotechnol J 2003, 1(3):195-207.
36. Warpeha KM, Lateef SS, Lapik Y, Anderson M, Lee B-S, Kaufman LS: G-Proteincoupled receptor 1, G-protein Ga-subunit 1, and prephenate dehydratase 1 are required for blue light-induced production of phenylalanine in etiolated arabidopsis. Plant Physiol 2006, 140(3):844-855.
37. Floss DS, Walter MH: Role of carotenoid cleavage dioxygenase 1 (CCD1) in apocarotenoid biogenesis revisited. Plant Signal Behav 2009, 4(3):172-175.
38. Chatterjee C, Paul M, Xie L, van der Donk WA: Biosynthesis and mode of action of lantibiotics. Chem Rev 2005, 105(2):633-684.
39. Gao Y, Zeng Q, Guo J, Cheng J, Ellis BE, Chen J-G: Genetic characterization reveals no role for the reported ABA receptor, GCR2, in ABA control of seed germination and early seedling development in Arabidopsis. Plant J 2007, 52(6):1001-1013.
40. Chen JG, Ellis BE: GCR2 is a new member of the eukaryotic lanthionine synthetase component C-like protein family. Plant Signal Behav 2008, 3(5):307-310.
41. Gomez C, Conejero G, Torregrosa L, Cheynier V, Terrier N, Ageorges A: In vivo grapevine anthocyanin transport involves vesicle-mediated trafficking and the contribution of anthoMATE transporters and GST. Plant J 2011, 67(6):960-970.
42. Di Matteo A, Ruggieri V, Sacco A, Rigano MM, Carriero F, Bolger A, Fernie AR, Frusciante L, Barone A: Identification of candidate genes for phenolics accumulation in tomato fruit. Plant Sci 2013, 205-206:87-96.
43. Frary A, Gol D, Keles D, Okmen B, Pinar H, Sigva H, Yemenicioglu A, Doganlar S: Salt tolerance in Solanum pennellii: antioxidant response and related QTL. BMC Plant Biol 2010, 10(1):58.
44. Causse M, Duffe P, Gomez MC, Buret M, Damidaux R, Zamir D, Gur A, Chevalier C, Lemaire-Chamley M, Rothan C: A genetic map of candidate genes and QTLs involved in tomato fruit size and composition. J Exp Bot 2004, 55(403):1671-1685.
45. Grandillo S, Ku HM, Tanksley SD: Identifying the loci responsible for natural variation in fruit size and shape in tomato. Theor Appl Genet 1999, 99(6):978-987.
46. Lippman Z, Tanksley SD: Dissecting the genetic pathway to extreme fruit size in tomato using a cross between the small-fruited wild species Lycopersicon pimpinellifolium and L. esculentum var. Giant Heirloom. Genetics 2001, 158(1):413-422.
47. 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: Increase in tomato locule number is controlled by two single-nucleotide polymorphisms located near WUSCHEL. Plant Physiol 2011, 156(4):2244-2254.
48. Huang Z, van der Knaap E: Tomato fruit weight 11.3 maps close to fasciated on the bottom of chromosome 11. Theor Appl Genet 2011, 123(3):465-474.
49. Foolad MR: Genome mapping and molecular breeding of tomato. Int J Plant Genomics 2007, 2007: Article ID 64358, 52 pages. doi: 10.1155/2007/64358.
50. Saliba-Colombani V, Causse M, Langlois D, Philouze J, Buret M: Genetic analysis of organoleptic quality in fresh market tomato. 1. mapping QTLs for physical and chemical traits. Theor Appl Genet 2001, 102(2-3):259-272.
51. Fulton TM, Bucheli P, Voirol E, López J, Pétiard V, Tanksley SD: Quantitative trait loci (QTL) affecting sugars, organic acids and other biochemical properties possibly contributing to flavor, identified in four advanced backcross populations of tomato. Euphytica 2002, 127(2):163-177.
52. Chen GP, Wilson ID, Kim SH, Grierson D: Inhibiting expression of a tomato ripening-associated membrane protein increases organic acids and reduces sugar levels of fruit. Planta 2001, 212(5-6):799-807.
53. Antanaitis BC, Aisen P, Lilienthal HR, Roberts RM, Bazer FW: The novel "g' =1.74" EPR spectrum of pink and purple uteroferrin. J Biol Chem 1980, 255(23):11204-11209.
54. SCAR Agro-Food Tomato Working Group: Measurement of the quality of tomatoes. In Recommendations of an EEC working group. Edited by Eccher Zerbini P, Gorini F, Polesello A. Milan: IVTPA; 1991.
55. Ishida BK, Ma J, Chan B: A simple, rapid method for HPLC analysis of lycopene isomers. Phytochem Anal 2001, 12(3):194-198.
56. Singleton VL, Rossi JA: Colorimetry of total phenolics with phosphomolybdic-phosphotungstic acid reagents. Am J Enology Viticulture 1965, 16(3):144-158.
57. Team RDC: R: A Language and Environment for Statistical Computing; 2005.
58. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES: TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 2007, 23(19):2633-2635.
59. Breseghello F, Sorrells ME: Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 2006, 172(2):1165-1177.
60. Pritchard JK, Stephens M, Donnelly P: Inference of population structure using multilocus genotype data. Genetics 2000, 155(2):945-959.
61. Evanno G, Regnaut S, Goudet J: Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 2005, 14(8):2611-2620.
62. Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES: A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 2006, 38(2):203-208.
63. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D: The structure of haplotype blocks in the human genome. Science 2002, 296(5576):2225-2229.
64. Barrett JC, Fry B, Maller J, Daly MJ: Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 2005, 21(2):263-265.