Bai Y, Lindhout P: Domestication and breeding of tomatoes: what have we gained and what can we gain in the future?. Ann Bot-London. 2007, 100: 1085-1094. 10.1093/aob/mcm150.
Article
Google Scholar
Grandillo S, Chetelat R, Knapp SK, Spooner DM, Peralta I, Cammareri M, Perez O, Termolino P, Tripode P, Chiusano ML, Ercolano MR, Fruschiante L, Monte L, Pignone D: Solanum section Lycopersicon. Wild crop relatives: Genomic and breeding resources, Volume 5. Edited by: Kole C. 2011, Berlin, Heidelberg: Springer-Verlag, 129-216.
Chapter
Google Scholar
Zago F: Buone varietà di pomodoro. L'Italia Agricola. 1912, 44: 110-456.
Google Scholar
Zago F: Varietà per la preparazione dei pelati. L'Italia Agricola. 1929, 66: 360-362.
Google Scholar
Ercolano MR, Carli P, Soria A, Cascone A, Fogliano V, Frusciante L, Barone A: Biochemical sensorial and genomic profiling of Italian tomato traditional varieties. Euphytica. 2008, 164: 571-582. 10.1007/s10681-008-9768-4.
Article
CAS
Google Scholar
Carli P, Barone A, Fogliano V, Frusciante L, Ercolano MR: Dissection of genetic and environmental factors involved in tomato organoleptic quality. BMC Plant Biol. 2011, 11: 58-10.1186/1471-2229-11-58.
Article
PubMed Central
PubMed
Google Scholar
Garcia-Martinez S, Corrado G, Ruiz-Martinez JJ, Rao R: Diversity and structure of a sample of traditional Italian and Spanish tomato accessions. Genet Resour Crop Evol. 2013, 60: 789-798. 10.1007/s10722-012-9876-9.
Article
CAS
Google Scholar
The Tomato Genome Consortium: The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 2012, 485: 635-641. 10.1038/nature11119.
Article
Google Scholar
Todd PM, Alba R: The tomato genome fleshed out. Nat Biotechnol. 2012, 30: 765-767. 10.1038/nbt.2319.
Article
Google Scholar
The 1000 Genomes Project Consortium: An integrated map of genetic variation from 1092 human genomes. Nature. 2012, 491: 56-65. 10.1038/nature11632.
Article
PubMed Central
Google Scholar
Cao J, Schneeberger K, Ossowski S, Günther T, Bender S, Fitz1 J, Koenig D, Lanz C, Stegle O, Lippert C, Wang X, Ott F, Müller J, Alonso-Blanco C, Borgwardt K, Schmid KJ, Weigel D: Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet. 2011, 43: 956-963. 10.1038/ng.911.
Article
CAS
PubMed
Google Scholar
Treangen TJ, Salzberg SL: Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet. 2011, 13: 36-46.
PubMed Central
PubMed
Google Scholar
Schneeberger K, Ossowski S, Ott F, Klein JD, Wang X, Lanz C, Smith LM, Cao J, Fitz J, Warthmann N, Henz SR, Huson DH, Weigel D: Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proc Natl Acad Sci USA. 2011, 108: 10249-10254. 10.1073/pnas.1107739108.
Article
CAS
PubMed Central
PubMed
Google Scholar
Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT, Kahles A, Bohnert R, Jean G, Derwent P, Kersey P, Belfield EJ, Harberd NP, Kemen E, Toomajian C, Kover PX, Clark RM, Rätsch G, Mott R: Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature. 2011, 477: 419-423. 10.1038/nature10414.
Article
CAS
PubMed
Google Scholar
Bevan M: Genomics: endless variation most beautiful. Nature. 2011, 477: 415-416. 10.1038/477415a.
Article
CAS
PubMed
Google Scholar
Jiménez-Gómez JM, Maloof JN: Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. BMC Plant Biol. 2009, 9: 85-10.1186/1471-2229-9-85.
Article
PubMed Central
PubMed
Google Scholar
Lunter G, Goodson M: Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res. 2011, 21: 936-939. 10.1101/gr.111120.110.
Article
CAS
PubMed Central
PubMed
Google Scholar
Gremme G, Brendel V, Sparks ME, Kurtz S: Engineering a software tool for gene structure prediction in higher organisms. Inf Softw Technol. 2005, 47: 965-978. 10.1016/j.infsof.2005.09.005.
Article
Google Scholar
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones S, Marra M: Circos: an information aesthetic for comparative genomics. Genome Res. 2009, 19: 1639-1645. 10.1101/gr.092759.109.
Article
CAS
PubMed Central
PubMed
Google Scholar
Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM: 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. 2012, 6: 80-92. 10.4161/fly.19695.
Article
CAS
PubMed Central
PubMed
Google Scholar
Choi Y, Sims GE, Murphy S, Miller JR, Chan AP: Predicting the functional effect of amino acid substitutions and indels. PLOSOne. 2012, 7: e46688-10.1371/journal.pone.0046688.
Article
CAS
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, and 1000 Genome Project Data Processing Subgroup: The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics. 2009, 25: 2078-2079. 10.1093/bioinformatics/btp352.
Article
PubMed Central
PubMed
Google Scholar
Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010, 26 (6): 841-842. 10.1093/bioinformatics/btq033.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology The Gene Ontology Consortium. Nat Genet. 2000, 25: 25-29. 10.1038/75556.
Article
CAS
PubMed Central
PubMed
Google Scholar
Conesa A, Götz S, García-Gómez JM, Teroll J, Talónl M, Roblesl M: Blast2GO: a universal tool for annotation visualization and analysis in functional genomics research. Bioinformatics. 2005, 21: 3674-3676. 10.1093/bioinformatics/bti610.
Article
CAS
PubMed
Google Scholar
Du Z, Zhou X, Ling Y, Zhang Z, Su Z: agriGO: a GO analysis toolkit for the agricultural community. Nucl Acids Res. 2012, 38: W64-W70.
Article
Google Scholar
Tipney H, Hunter L: An introduction to effective use of enrichment analysis software. Hum Genomics. 2010, 4: 202-206. 10.1186/1479-7364-4-3-202.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hamilton JP, Sim SC, Stoffel K: Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis. The Plant Genome. 2012, 5: 17-29. 10.3835/plantgenome2011.12.0033.
Article
CAS
Google Scholar
Sim SC, Robbins MD, Van Deynze A, Michel AP, Francis DM: Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L). Heredity. 2011, 106: 927-935. 10.1038/hdy.2010.139.
Article
CAS
PubMed Central
PubMed
Google Scholar
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. PLOSOne. 2012, 7: e45520-10.1371/journal.pone.0045520.
Article
CAS
Google Scholar
Blanca J, Cañizares J, Cordero L, Pascual L, Diez MJ, Nuez F: Variation revealed by SNP genotyping and morphology provides insight into the origin of the tomato. PLOSOne. 2012, 7: e48198-10.1371/journal.pone.0048198.
Article
CAS
Google Scholar
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. 10.1093/dnares/dst005. doi:10.1093/dnares/dst005
Article
CAS
PubMed Central
PubMed
Google Scholar
McHale LK, Haun WJ, Xu WW, Bhaskar PB, Anderson JE, Hyten DL, Gerhardt DJ, Jeddeloh JA, Stupar RM: Structural variants in the soybean genome localize to clusters of biotic stress-response genes. Plant Physiol. 2012, 159: 1295-1308. 10.1104/pp.112.194605.
Article
CAS
PubMed Central
PubMed
Google Scholar
Pavlidis P, Metzler D, Stephan W: Selective sweeps in multilocus models of quantitative traits. Genetics. 2012, 192: 225-239. 10.1534/genetics.112.142547.
Article
PubMed Central
PubMed
Google Scholar
Zhong S, Fei Z, Chen YR, Zheng Y, Huang M, Vrebalov J, McQuinn R, Gapper N, Liu B, Xiang J, Shao Y, Giovannoni JJ: Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol. 2013, 31: 154-159. 10.1038/nbt.2462.
Article
CAS
PubMed
Google Scholar
Klee HJ, Giovannoni JJ: Genetics and control of tomato fruit ripening and quality attributes. Annu Rev Genet. 2011, 45: 41-59. 10.1146/annurev-genet-110410-132507.
Article
CAS
PubMed
Google Scholar
Tsuchisaka A, Yu G, Jin H, Alonso JM, Ecker JR, Zhang X, Gao S, Theologis A: A combinatorial interplay among the 1-aminocyclopropane-1-carboxylate isoforms regulates ethylene biosynthesis in Arabidopsis thaliana. Genetics. 2009, 183: 979-1003. 10.1534/genetics.109.107102.
Article
CAS
PubMed Central
PubMed
Google Scholar
Matas A, Gapper N, Chung M, Giovannoni J, Rose JKC: Biology and genetic engineering of fruit maturation for enhanced quality and shelf-life. Curr Opin Biotech. 2009, 20: 197-203. 10.1016/j.copbio.2009.02.015.
Article
CAS
PubMed
Google Scholar
Ng PC, Henikoff S: Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet. 2006, 7: 61-80. 10.1146/annurev.genom.7.080505.115630.
Article
CAS
PubMed
Google Scholar