Genetic diversity in a collection of Italian long storage tomato landraces as revealed by SNP markers array

References

• Andreakis N, Giordano I, Pentangelo A, Fogliano V, Graziani G, Monti LM, Rao R. 2004. DNA fingerprinting and quality traits of Corbarino cherry-like tomato landraces. J Agric Food Chem. 52(11):3366–3371.10.1021/jf049963y
   PubMed Web of Science ®Google Scholar
• Bauchet G, Causse M. 2012. Genetic diversity in tomato (Solanum lycopersicum) and its wild relatives. In: Caliskan M, editor. Genetic diversity in plants. Rijeka, Croatia: InTechOpen; pp. 33–162.
   Google Scholar
• Blanca J, Cañizares J, Cordero L, Pascual L, Diez MJ, Nuez F. 2012. Variation revealed by SNP genotyping and morphology provides insight into the origin of the tomato. PLoS ONE. 7(10):e48198.10.1371/journal.pone.0048198
   PubMed Web of Science ®Google Scholar
• Casals J, Pascual L, Cañizares J, Cebolla-Cornejo J, Casañas F, Nuez F. 2012. Genetic basis of long shelf life and variability into Penjar tomato. Genet Resour Crop Ev. 59(2):219–229.10.1007/s10722-011-9677-6
   Web of Science ®Google Scholar
• Causse M, Desplat N, Pascual L, Le Paslier MC, Sauvage C, Bauchet G, Bérard A, Bounon R, Tchoumakov M, Brunel D, et al. 2013. Whole genome resequencing in tomato reveals variation associated with introgression and breeding events. BMC Genomics. 14(1):791.10.1186/1471-2164-14-791
   PubMedGoogle Scholar
• Chen J, Wang H, Shen H, Chai M, Li J, Qi M, Yang W. 2009. Genetic variation in tomato populations from four breeding programs revealed by single nucleotide polymorphism and simple sequence repeat markers. Sci Hort. 122:6–16.10.1016/j.scienta.2009.03.025
   Web of Science ®Google Scholar
• Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. 2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 6:80–92.10.4161/fly.19695
   PubMed Web of Science ®Google Scholar
• Conesa MA, Galmes J, Ochogavia JM, March J, Jaume J, Martorell A, Francis DM, Medrano H, Roce JKC, Cifre J. 2014. The postharvest tomato fruit quality of long shelf-life Mediterranean landraces is substantially influenced by irrigation regimes. Postharvest Biol Tec. 93:114–121.10.1016/j.postharvbio.2014.02.014
   Web of Science ®Google Scholar
• Du Z, Zhou X, Ling Y, Zhang Z, Su Z. 2010. AgriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 38:W64–W70.10.1093/nar/gkq310
   PubMed Web of Science ®Google Scholar
• Ercolano MR, Sacco A, Ferriello F, D’Alessandro R, Tononi P, Traini A, Barone A, Zago E, Chiusano ML, Buson G, et al. 2014. Patchwork sequencing of tomato San Marzano and Vesuviano varieties highlights genome-wide variations. BMC Genomics. 15:138.10.1186/1471-2164-15-138
   PubMed Web of Science ®Google Scholar
• Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 14(8):2611–2620.10.1111/mec.2005.14.issue-8
   PubMed Web of Science ®Google Scholar
• 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:e1367.10.1371/journal.pone.0001367
   PubMed Web of Science ®Google Scholar
• Hamilton JP, Sim SC, Stoffel K, Van Deynze A, Buell CR, Francis DM. 2012. Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis. Plant Genome. 5(1):17–29.10.3835/plantgenome2011.12.0033
   Web of Science ®Google Scholar
• Iovieno P, Punzo P, Guida G, Mistretta C, Van Oosten MJ, Nurcato R, Bostan H, Colantuono C, Costa A, Bagnaresi P, et al. 2016. Transcriptomic changes drive physiological responses to progressive drought stress and rehydration in tomato. Front Plant Sci. 7:371.
   PubMed Web of Science ®Google Scholar
• Kevany BM, Tieman DM, Taylor MG, Cin VD, Klee HJ. 2007. Ethylene receptor degradation controls the timing of ripening in tomato fruit. Plant Journal. 51(3):458–467.10.1111/j.1365-313X.2007.03170.x
   PubMed Web of Science ®Google Scholar
• Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 33(7):1870–1874.10.1093/molbev/msw054
   PubMed Web of Science ®Google Scholar
• Li J, Tao X, Li L, Mao L, Luo Z, Khan ZU, Ying T. 2016. Comprehensive RNA-Seq analysis on the regulation of tomato ripening by exogenous auxin. PLOS ONE 11(5):e0156453.10.1371/journal.pone.0156453
   PubMed Web of Science ®Google Scholar
• Lin T, Zhu G, Zhang J, Xu X, Yu Q, Zheng Z, Zhang Z, Lun Y, Li S, Wang X, et al. 2014. Genomic analyses provide insights into the history of tomato breeding. Nat Genet. 46(11):1220–1226.10.1038/ng.3117
   PubMed Web of Science ®Google Scholar
• Mazzucato A, Papa R, Bitocchi E, Mosconi P, Nanni L, Negri V, Picarella ME, Siligato F, Soressi GP, Tiranti B, et al. 2008. Genetic diversity, structure and marker-trait associations in a collection of Italian tomato (Solanum lycopersicum L.) landraces. Theor Appl Genet. 116(5):657–669.10.1007/s00122-007-0699-6
   PubMed Web of Science ®Google Scholar
• Mercati F, Leone M, Lupini A, Sorgonà A, Bacchi M, Abenavoli MR, Sunseri F. 2013. Genetic diversity and population structure of a common bean (Phaseolus vulgaris L.) collection from Calabria (Italy). Genet Resour Crop Ev. 60(3):839–852.10.1007/s10722-012-9879-6
   Web of Science ®Google Scholar
• Mercati F, Longo C, Poma D, Araniti F, Lupini A, Mammano MM, Fiore MC, Abenavoli MR, Sunseri M. 2015. Genetic variation of an Italian long shelf-life tomato (Solanum lycopersicon L.) collection by using SSR and morphological fruit traits. Genet Resour Crop Ev. 62:721–732.10.1007/s10722-014-0191-5
   Web of Science ®Google Scholar
• Monti LM, Santangelo E, Corrado G, Rao R, Soressi GP, Scarascia Mugnozza GT. 2004. Il “San Marzano”: problematiche e prospettive in relazione alla sua salvaguardia e alla necessità di interventi genetici. Agroindustria. 3:161–170.
   Google Scholar
• Mou W, Li D, Bu J, Jiang Y, Khan ZU, Luo Z, Mao L, Ying T. 2016. Comprehensive analysis of ABA effects on ethylene biosynthesis and signaling during tomato fruit ripening. PLoS ONE. 11(4): e0154072.10.1371/journal.pone.0154072
   PubMed Web of Science ®Google Scholar
• Moyle LC, Muir CD. 2010. Reciprocal insights into adaptation from agricultural and evolutionary studies in tomato. Evol Appl. 3(5–6):409–421.10.1111/j.1752-4571.2010.00143.x
   PubMed Web of Science ®Google Scholar
• Nakazato T, Bogonovich M, Moyle LC. 2008. Environmental factors predict adaptive phenotypic differentiation within and between two wild Andean tomatoes. Evolution. 62(4):774–792.10.1111/evo.2008.62.issue-4
   PubMed Web of Science ®Google Scholar
• Nei M. 1987. Molecular evolutionary genetics. New York (NY): Columbia University Press.
   Google Scholar
• Page RD. 1996. TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci. 12(4):357–358.
   PubMedGoogle Scholar
• Parisi M, Aversano R, Graziani G, Ruggieri V, Senape V, Sigillo L, Barone A. 2016. Phenotypic and molecular diversity in a collection of ‘Pomodoro di Sorrento’ Italian tomato landrace. Sci Hort. 203:143–151.10.1016/j.scienta.2016.02.038
   Web of Science ®Google Scholar
• Pritchard JK, Stephens M, Donelly P. 2000. Inference of population structure using multilocus genotype data. Genetics. 155(2):945–959.
   PubMed Web of Science ®Google Scholar
• Rick CM, Laterrot H, Philouze J. 1990. A revised key for the Lycopersicon species. Tomato Genet Cooperative Rep. 40:31.
   Google Scholar
• Ruggieri V, Francese G, Sacco A, D’Alessandro A, Rigano MM, Parisi M, Milone M, Cardi T, Mennella G, Barone A. 2014. An association mapping approach to identify favourable alleles for tomato fruit quality breeding. BMC Plant Biol. 14:17.10.1186/s12870-014-0337-9
   PubMed Web of Science ®Google Scholar
• Sacco A, Ruggieri V, Parisi M, Festa G, Rigano MM, Picarella ME, Mazzucato A, Barone A. 2015. Exploring a tomato landraces collection for fruit-related traits by the aid of a high-throughput genomic platform. PLoS ONE. 10(9):e0137139.10.1371/journal.pone.0137139
   PubMed Web of Science ®Google Scholar
• Seymour GB, Østergaard L, Chapman NH, Knapp S, Martin C. 2013. Fruit development and ripening. Ann Rev Plant Biol. 64:219–241.10.1146/annurev-arplant-050312-120057
   PubMed Web of Science ®Google Scholar
• Sharma M, Pandey GK. 2016. Expansion and function of repeat domain proteins during stress and development in plants. Front Plant Sci. 6:1218.
   PubMed Web of Science ®Google Scholar
• Sim SC, Van Deynze A, Stoffel K, Douches DS, Zarka D, Ganal MW, Chetelat RT, Hutton SF, Scott JW, Gardner RG, et al. 2012. High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding. PLoS ONE. 7(9):e45520.10.1371/journal.pone.0045520
   PubMed Web of Science ®Google Scholar
• Sim SC, Kim M, Chung SM, Park Y. 2015. Assessing the genetic variation in cultivated tomatoes (Solanum lycopersicum L.) using genome-wide single nucleotide polymorphisms. Hortic Environ Biotec. 56(6):800–810.10.1007/s13580-015-0107-0
   Web of Science ®Google Scholar
• Siracusa L, Patanè C, Avola G, Ruberto G. 2012. Polyphenols as chemotaxonomic markers in Italian “long storage” tomato genotypes. J Agr Food Chem. 60(1):309–314.10.1021/jf203858y
   PubMed Web of Science ®Google Scholar
• Siracusa L, Patanè C, Rizzo V, Cosentino SL, Ruberto G. 2018. Targeted secondary metabolic and physico-chemical traits analysis to assess genetic variability within a germplasm collection of “long storage” tomatoes. Food Chem. 244:275–283.10.1016/j.foodchem.2017.10.043
   PubMed Web of Science ®Google Scholar
• Stich B, Melchinger AE, Frisch M, Maurer HP, Heckenberger M, Reif JC. 2005. Linkage disequilibrium in European elite maize germplasm investigated with SSRs. Theor Appl Genet. 111(4):723–730.10.1007/s00122-005-2057-x
   PubMed Web of Science ®Google Scholar
• Sunkar R, Zhu JK. 2004. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell. 16(8):2001–2019.10.1105/tpc.104.022830
   PubMed Web of Science ®Google Scholar
• Supek F, Bošnjak M, Škunca N, Šmuc T. 2011. REVIGO summarizes and visualizes long lists of Gene Ontology terms. PLoS ONE. 6(7):e21800.10.1371/journal.pone.0021800
   PubMed Web of Science ®Google Scholar
• The Tomato Genome Consortium. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 485:635–641.
   PubMed Web of Science ®Google Scholar
• Tranchida-Lombardo V, Aiese Cigliano R, Anzar I, Landi S, Palombieri S, Colantuoni C, Bostan H, Termolino P, Aversano R, Batelli G, et al. 2017. Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits. DNA Res. 25(2):149–160.
   Web of Science ®Google Scholar
• 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. 8:465.10.1186/1471-2164-8-465
   PubMed Web of Science ®Google Scholar
• Wang KL-C, Li H, Ecker JR. 2002. Ethylene biosynthesis and signaling networks. Plant Cell. 14:s131–s151.10.1105/tpc.001768
   PubMed Web of Science ®Google Scholar
• Williams C, Clair DA. 1993. Phenetic relationships and levels of variability detected by restriction fragment length polymorphism and random amplified polymorphic DNA analysis of cultivated and wild accessions of Lycopersicon esculentum. Genome. 36(3):619–630.10.1139/g93-083
   PubMed Web of Science ®Google Scholar
• Wilson RL, Kim H, Bakshi A, Binder BM. 2014. The ethylene receptors ETHYLENE RESPONSE1 and ETHYLENE RESPONSE2 have contrasting roles in seed germination of Arabidopsis during salt stress. Plant Physiol. 165(3):1353–1366.10.1104/pp.114.241695
   PubMed Web of Science ®Google Scholar
• Wu J, Wang J, Pan C, Guan X, Wang Y, Liu S, He Y, Chen J, Chen L, Lu G. 2014. Genome-wide identification of MAPKK and MAPKKK gene families in tomato and transcriptional profiling analysis during development and stress response. PLoS ONE. 9(7):e103032.10.1371/journal.pone.0103032
   PubMed Web of Science ®Google Scholar
• Xu R. 2014. Genome-wide analysis and identification of stress-responsive genes of the CCCH zinc finger family in Solanum lycopersicum. Mol Genet Genomics. 289(5): 965–979.
   PubMed Web of Science ®Google Scholar
• Zheng X, Levine D, Shen J, Gogarten SM, Laurie C, Weir BS. 2012. A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics. 28(24):3326–3328.10.1093/bioinformatics/bts606
   PubMed Web of Science ®Google Scholar