Exploring a tomato landraces collection for fruit-related traits by the aid of a high-throughput genomic platform

PLoS ONE

Volumn 10, Issue 9, 2015, Pages

  Sacco, Adriana ^a   Ruggieri, Valentino ^a   Parisi, Mario ^b   Festa, Giovanna ^b   Rigano, Maria Manuela ^a   Picarella, Maurizio Enea ^c   Mazzucato, Andrea ^c   Barone, Amalia ^a  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

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

^c UNIVERSITY OF TUSCIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME; FRUIT; FRUIT SIZE; GENE FREQUENCY; GENETIC MARKER; LANDRACE; MORPHOLOGICAL TRAIT; PHYLOGENETIC TREE; PLANT YIELD; PRINCIPAL COMPONENT ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STRUCTURE ANALYSIS; TOMATO; CHROMOSOMAL MAPPING; CLUSTER ANALYSIS; GENETIC VARIATION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; GENOTYPE; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PHENOTYPE; PLANT CHROMOSOME; PLANT GENOME; QUANTITATIVE TRAIT LOCUS;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; CLUSTER ANALYSIS; FRUIT; GENETIC VARIATION; GENOME, PLANT; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; GENOTYPE; LYCOPERSICON ESCULENTUM; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS; QUANTITATIVE TRAIT LOCI;

EID: 84947556751     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0137139     Document Type: Article

References (59)

1. Foolad MR. Genome mapping and molecular breeding of tomato. Internat. J. Plant Genom. 2007;1-52.
2. Food and Agriculture Organization of the United Nations Statistics Division website. Available: http:// faostat3.fao.org/home/.
3. Bauchet G, Causse M. Genetic Diversity in Tomato (Solanumlycopersicum) and Its Wild Relatives, Genetic Diversity in Plants, Prof.MahmutCaliskan (Ed.), ISBN: 978-953-51-0185-7; 2012.
4. Dies MJ, Nuez F. Tomato. In: Prohens J., Nuez F. (Ed.), Vegetables II. Hand-book of Plant Breeding. Springer, New York, pp. 249-326; 2008.
5. Tanksley SD. The genetic, developmental, and molecular bases of fruit size and shape variation in tomato. The Plant Cell. 2004; 16: (1) S181-S189.
6. Rick CM. Tomato resources of South America reveal many genetic treasures. Diversity. 1991; 7: 54-56.
7. Garcia-Martinez S, Andreani L, Garcia-Gusano M, Geuna F, Ruiz JJ. Evaluation of amplified fragment length polymorphism and simple sequence repeats for tomato germplasm fingerprinting: utility for grouping closely related traditional cultivars. Genome. 2006; 49 (6): 648-656. PMID: 16936844
8. Bailey LH, Tracy WW, Kyle EJ, Watts RL. Tomato. In: Bailey LH (Ed) The standard cyclopedia of horticulture. The Macmillan Company, New York, pp 3353-3359; 1960.
9. Corrado G, Caramante M, Piffanelli P, Rao R. Genetic diversity in Italian tomato landraces: Implications for the development of a core collection. Sci. Hortic. 2014;http://dx.doi.org/10.1016/j.scienta.2014.01. 027.
10. Andreakis N, Giordano I, Pentangelo A, Fogliano V, Graziani G, Monti LM, et al. DNA fingerprinting and quality traits of Corbarino cherry-like tomato landraces. J. Agr. Food. Chem. 2004; 52: 3366-3377.
11. Carelli PM, Gerald LTS, Grazziotin GF, Echeverrigaray S. Genetic diversity among Brazilian cultivars and landraces of tomato Lycopersiconesculentum Mill. revealed by RAPD markers. Genet. Resour. Crop. Evol. 2006; 53: 395-400.
12. Carbonell-Barrachina AA, Agustí A, Ruiz JJ. Analysis of flavor volatile compounds by dynamic headspace in traditional and hybrid cultivars of Spanish tomatoes. Eur. Food Res. Technol. 2006; 222(5-6): 536-542.
13. Mazzucato A, Papa R, Bitocchi E, Mosconi P, Nanni L, Negri V, et al. Genetic diversity, structure and marker-trait associations in a collection of Italian tomato (Solanumlycopersicum L) landraces. Theor. Appl. Genet. 2008; 116: 657-669. doi: 10.1007/s00122-007-0699-6 PMID: 18193185
14. Mazzucato A, Ficcadenti N, Caioni M, Mosconi P, Piccini E, Sanampudi VRR, et al. Genetic diversity and distinctiveness in tomato (Solanumlycopersicum L) landraces: the Italian case study of 'A peraAbruzzese'. Sci. Hortic. 2010; 125: 55-62.
15. Gonçalves LS, Rodrigues R, do Amaral AT Júnior, Karasawa M, Sudré CP. Heirloom tomato gene bank: assessing genetic divergence based on morphological, agronomic and molecular data using a Ward-modified location model. Genet. Mol. Res. 2009; 8: 364-374. PMID: 19440972
16. Labate JA, Robertson LD, Baldo AM. Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanumlycopersicum L.). Heredity. 2009; 103(3): 257-267. doi: 10. 1038/hdy.2009.58 PMID: 19436327
17. Terzopoulos PJ, Walters SA, Bebeli PJ. Evaluation of Greek tomato landrace populations for heterogeneity of horticultural traits. Eur. J. Hortic. Sci. 2009; 74: 24-29.
18. Rodriguez GR, Kim HJ, van der Knaap E. Mapping of two suppressors of OVATE (sov) loci in tomato. Heredity. 2013; 111: 256-264. doi: 10.1038/hdy.2013.45 PMID: 23673388
19. Sim SC, Robbins MD, Chilcott C, Zhu T, Francis DM. Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanumlycopersicum L.) reveals patterns of SNP variation associated with breeding. BMC Genomics. 2009; 10: 466. doi: 10.1186/1471-2164-10-466 PMID: 19818135
20. Robbins MD, Sim S- C, Yang W, Van Deynze A, van der Knaap E, Joobeur T, et al. Mapping and linkage disequilibrium analysis with a genome-wide collection of SNPs that detect polymorphism in cultivated tomato. J. Exp. Bot. 2011; 62(6): 1831-1845. doi: 10.1093/jxb/erq367 PMID: 21193580
21. Shirasawa K, Isobe S, Hirakawa H, Asamizu E, Fukuoka H, Just D, et al. SNP discovery and linkage map construction in cultivated tomato. DNA Res. 2010; 17: 381-91. doi: 10.1093/dnares/dsq024 PMID: 21044984
22. Hamilton JP, Sim SC, Stoffel K, Van Deynze A, Buell CR, Francis DM. Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis. The Plant Genome. 2012; 5(1): 17-29.
23. Sim SC, Durstewitz G, Plieske J, Wieseke R, Ganal MW, Van Deynze A, et al. Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS One. 2012; 7(7): e40563. doi: 10.1371/journal.pone.0040563 PMID: 22802968
24. Ruggieri V, Francese G, Sacco A, D'Alessandro A, Rigano MM, Parisi M, et al. An association mapping approach to identify favourable alleles for tomato fruit quality breeding. BMC Plant Biol. 2014; 14: 337 doi: 10.1186/s12870-014-0337-9 PMID: 25465385
25. R Development Core Team. 2012 R: A Language and Environment for Statistical Computing. Vienne, Austria: R Foundation for Statistical Computing.
26. Futterer J, Gisel A, Iglesias V, Kloti A, Kost B, Mittelsten-Scheid O, et al. Standard molecular techniques for the analysis of transgenic plants. p. 215-218. In: Potrykus I.; Spangenberg G, (Ed.) Gene transfer to plants. Springer-Verlag, New York, USA; 1995.
27. 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. PMID: 17586829
28. Liu K, Muse SV. PowerMarker: Integrated analysis environment for genetic marker data. Bioinformatics. 2005; 21(9): 2128-9. PMID: 15705655
29. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000; 155(2): 945-959. PMID: 10835412
30. Earl DA, vonHoldt BM. STRUCTURE HARVESTER: a website and program for visualizing STRUC-TURE output and implementing the Evanno method. Conserv. Genet. Resour. 2012; 4(2): 359-361.
31. Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 2005; 14: 2611-2620. PMID: 15969739
32. Sol Genomics Network website. Available: www.Solgenomics.net.
33. Voorrips RE. MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered. 2002; 93: 77-78. PMID: 12011185
34. Rick CM, Holle M. Andean Lycopersiconesculentum var. cerasiforme: Genetic variation and its evolutionary significance. Econ. Bot. 1990; 44(3): 69-78.
35. Williams CE, St. Clair DA. Phenetic relationships and levels of variability detected by restriction fragment length polymorphism and random amplified polymorphic DNA analysis of cultivated and wild accessions of Lycopersiconesculentum. Genome. 1993; 36: 619-630. PMID: 18470012
36. 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. doi: 10. 1371/journal.pone.0048198 PMID: 23118951
37. Ranc N, Muños S, Santoni S, Causse M. A clarified position for Solanumlycopersicum var. cerasiforme in the evolutionary history of tomatoes (Solanaceae). BMC Plant Biol. 2008; 8: 130. doi: 10.1186/1471-2229-8-130 PMID: 19099601
38. Blanca J, Montero-Pau J, Sauvage C, Bauchet G, Illa E, Díez MJ, et al. Genomic variation in tomato, from wild ancestors to contemporary breeding accessions. BMC Genomics. 2015; 16: 257 doi: 10. 1186/s12864-015-1444-1 PMID: 25880392
39. Corrado G, Piffanelli P, Caramante M, Coppola M, Rao R. SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato. BMC Genomics. 2013; 14: 835. doi: 10.1186/1471-2164-14-835 PMID: 24279304
40. Shirasawa K, Fukuoka H, Matsunaga H, Kobayashi Y, Kobayashi I, Hirakawa H, et al. Genome-wide association studies using single nucleotide polymorphism markers developed by re-sequencing of the genomes of cultivated tomato. DNA Res.2013; 20: 593-603. doi: 10.1093/dnares/dst033 PMID: 23903436
41. Lin T, Zhu G, Zhang J, Xu X, Yu Q, Zheng Z, et al. Genomic analyses provide insights into the history of tomato breeding. Nat. Genet.2014; 46: 1220-1226. doi: 10.1038/ng.3117 PMID: 25305757
42. Sim SC, Robbins MD, Van Deynze A, Michel AP, Francis DM. Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanumlycopersicum L.). Heredity. 2011; 106: 927-935. doi: 10.1038/hdy.2010.139 PMID: 21081965
43. Sauvage C, Segura V, Bauchet G, Stevens R, Thi Do P, Nikoloski Z, et al. Genome wide association in tomato reveals 44 candidate loci for fruit metabolic traits.Plant Physiol. 2014; 165(3): 1120-1132.PMID: 24894148
44. Xu J, Ranc N, Munos S, Rolland S, Bouchet JP, Desplat N, et al. Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species.Theor. Appl. Genet. 2013; 126 (3): 567-581. doi: 10.1007/s00122-012-2002-8 PMID: 23124430
45. Ranc N, Muños S, Xu J, Le Paslier MC, Chauveau A, Bounon R, et al. Genome-wide association mapping in tomato (Solanumlycopersicum) is possible using genome admixture of Solanumlycopersicum var. cerasiforme.G3: Genes Genomes Genet. 2012; 2(8): 853-864.
46. Causse M, Duffe P, Gomez MC, Buret M, Damidaux R, Zamir D, et al. A genetic map of candidate genes and QTLs involved in tomato fruit size and composition. J. Exp. Bot. 2004; 55(403): 1671-1685. PMID: 15258170
47. Bergelson J, Roux F. Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana. Nat. Rev. Genet. 2010; 11: 867-879. doi: 10.1038/nrg2896 PMID: 21085205
48. Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price AH, et al. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryzasativa. Nat. Commun. 2011; 2: 467. doi: 10. 1038/ncomms1467 PMID: 21915109
49. Rodríguez GR, Muños S, Anderson C, Sim SC, Michel A, Causse M, et al. Distribution of SUN, OVATE, LC, and FAS in the tomato germplasm and the relationship to fruit shape diversity. Plant Physiol. 2011; 156: 275-285. doi: 10.1104/pp.110.167577 PMID: 21441384
50. Huang ZJ, Van Houten J, Gonzalez G, Xiao H, van der Knaap E. Genome-wide identification, phylogeny and expression analysis of SUN, OFP and YABBY gene family in tomato. Mol. Genet. Genomics. 2013; 288: 111-129. doi: 10.1007/s00438-013-0733-0 PMID: 23371549
51. Chusreeaeom K, Ariizumi T, Asamizu E, Okabe Y, Shirasawa K, Ezura H. Regulatory change in cell division activity and genetic mapping of a tomato (Solanumlycopersicum L.) elongated-fruit mutant. Plant Biotech. 2014; 31: 149-158. doi: 10.5511/plantbiotechnology.14.0204a
52. Barrero LS, Cong B, Wu F, Tanksley SD. Developmental characterization of the fasciated locus and mapping of Arabidopsis candidate genes involved in the control of floral meristem size and carpel number in tomato. Genome. 2006; 49: 991-1006 doi: 10.1139/G06-059 PMID: 17036074
53. Munos S, Ranc N, Botton E, Berard A, Rolland S, Duffe P, et al. Increase in tomato locule number is controlled by two single-nucleotide polymorphisms located near WUSCHEL. Plant Physiol. 2011; 156: 2244-2254 doi: 10.1104/pp.111.173997 PMID: 21673133
54. Lippman Z, Tanksley SD. Dissecting the genetic pathway to extreme fruit size in tomato using a cross between the small-fruited wild species Lycopersiconpimpinellifolium and L. esculentum var. Giant Heirloom. Genetics. 2001; 158: 413-422. PMID: 11333249
55. vanderKnaap E, Chakrabarti M, Chu YH, Clevenger JP, Illa-Berenguer E, Huang Z, et al. What lies beyond the eye: the molecular mechanisms regulating tomato fruit weight and shape. Front Plant Sci. 2014; 5: 227. doi: 10.3389/fpls.2014.00227 PMID: 24904622
56. Wu S, Xiao H, Cabrera A, Meulia T, van Der Knaap E. SUN regulates vegetative and reproductive organ shape by changing cell division patterns. Plant Physiol. 2011; 157: 1175-1186 doi: 10.1104/pp. 111.181065 PMID: 21921117
57. Leseberg CH, Eissler CL, Wang X, Johns MA, Duvall MR, Mao L. Interaction study of MADS-domain proteins in tomato. J. Exp. Bot. 2008; 59: 2253-65. doi: 10.1093/jxb/ern094 PMID: 18487636
58. Grandillo S, Ku HM, Tanksley SD. Identifying loci responsible for natural variation in fruit size and shape in tomato. Theor, Appl. Genet. 1999; 99: 978-987.
59. 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: 465-474. doi: 10.1007/s00122-011-1599-3 PMID: 21541852