Genome-wide SNP discovery and QTL mapping for fruit quality traits in inbred backcross lines (IBLs) of solanum pimpinellifolium using genotyping by sequencing

BMC Genomics

Volumn 18, Issue 1, 2017, Pages

  Celik, Ibrahim ^a   Gurbuz, Nergiz ^a   Uncu, Ali Tevfik ^a,b   Frary, Anne ^a   Doganlar, Sami ^a  

^a IZMIR INSTITUTE OF TECHNOLOGY   (Turkey)

^b NECMETTIN ERBAKAN UNIVERSITY   (Turkey)

Author keywords

Fruit weight; PH; Soluble solids content; Tomato genome

Indexed keywords

ALLELE; BREEDING; GENOME; GENOTYPE; HUMAN; HUMAN EXPERIMENT; MARKET; NEXT GENERATION SEQUENCING; NONHUMAN; PLANT YIELD; QUANTITATIVE TRAIT LOCUS MAPPING; SOLUBILITY; TOMATO; WILD SPECIES; CHROMOSOMAL MAPPING; CROSS BREEDING; FOOD QUALITY; FRUIT; GENETICS; GENOME-WIDE ASSOCIATION STUDY; HIGH THROUGHPUT SEQUENCING; PHENOTYPE; PLANT GENE; QUANTITATIVE TRAIT; SINGLE NUCLEOTIDE POLYMORPHISM; SOLANUM;

BREEDING; CHROMOSOME MAPPING; CROSSES, GENETIC; FOOD QUALITY; FRUIT; GENES, PLANT; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LYCOPERSICON ESCULENTUM; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT, HERITABLE; SOLANUM;

EID: 85008190868     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-016-3406-7     Document Type: Article

References (46)

1. Chen FQ, Foolad MR, Hyman J, Clair DAS, Beelaman RB. Mapping of QTLs for lycopene and other fruit traits in a Lycopersicon esculentum × L. pimpinellifolium cross and comparison of QTLs across tomato species. Mol Breed. 1999;5(3):283-99.
2. 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):413-22.
3. Doganlar S, Frary A, Ku HM, Tanksley SD. Mapping quantitative trait loci in inbred backcross lines of Lycopersicon pimpinellifolium (LA1589). Genome. 2002;45(6):1189-202.
4. Sharma A, Zhang L, Niño-Liu D, Ashrafi H, Foolad MR. A Solanum lycopersicum × Solanum pimpinellifolium linkage map of tomato displaying genomic locations of R-genes, RGAs, and candidate resistance/defense-response ESTs. Int J Plant Genomics. 2008;2008:1-18.
5. Sun YD, Liang Y, Wu JM, Li YZ, Cui X, Dynamic QL, QTL. analysis for fruit lycopene content and total soluble solid content in a Solanum lycopersicum x S. pimpinellifolium cross. Genet Mol Res. 2012;11(4):3696-710.
6. Top O, Bar C, Ökmen B, Özer DY, Rusçuklu D, Tamer N, Frary A, Doganlar S. Exploration of three solanum species for improvement of antioxidant traits in tomato. HortSci. 2014;49(8):1003-9.
7. Bernacchi D, Beck-Bunn T, Eshed Y, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley SD. Advanced backcross QTL analysis in tomato: I. Identification of QTLs for traits of agronomic importance from Lycopersicon hirsutum. Theor Appl Genet. 1998;97:381-97.
8. Collard BC, Mackill DJ. Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc Lond B Biol Sci. 2008;363(1491):557-72.
9. Foolad MR. Genome mapping and molecular breeding of tomato. Int J Plant Genomics. 2007;2007:64358.
10. Sol Genomics Network Database. Boyce Thompson Institute for Plant Research. 2016. http://solgenomics.net. Accessed 15 Jun 2016.
11. Kazusa Tomato Genomics Database. Kazusa-kamatari. Japan: Kisarazu; 2016. http://www.kazusa.or.jp/tomato/. Accessed 15 Jun 2016.
12. Sim SC, Durstewitz G, Plieske J, Wieseke R, Ganal MW, Deynze AV, 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.
13. Salinas M, Capel C, Alba JM, Mora B, Cuartero J, Fernández-Muñoz R, Lozano R, Capel J. Genetic mapping of two QTL from the wild tomato Solanum pimpinellifolium L. controlling resistance against two-spotted spider mite (Tetranychus urticae Koch). Theor Appl Genet. 2013;126(1):83-92.
14. Capel C, Fernández del Carmen A, Alba JM, Lima-Silva V, Hernández-Gras F, Salinas M, Boronat A, Angosto T, Botella MA, Fernández-Muñoz R, Granell A, Capel J, Lozano R. Wide-genome QTL mapping of fruit quality traits in a tomato RIL population derived from the wild-relative species Solanum pimpinellifolium L. Theor Appl Genet. 2015;128(10):2019-35.
15. Chen AL, Liu CY, Chen CH, Wang JF, Liao YC, Chang CH, Tsai MH, Hwu KK, Chen KY. Reassessment of QTLs for late blight resistance in the tomato accession L3708 using a restriction site associated DNA (RAD) linkage map and highly aggressive isolates of Phytophthora infestans. PLoS One. 2012;9(5):e96417.
16. Causse M, Desplat N, Pascual L, Le Paslier MC, Sauvage C, Bauchet G, Bérard A, Bounon R, Tchoumakov M, Brunel D, Bouchet JP. Whole genome resequencing in tomato reveals variation associated with introgression and breeding events. BMC Genomics. 2013;14(791):1-14.
17. Kim JE, Oh SK, Lee JH, Lee BM, Jo SH. Genome-wide SNP calling using next generation sequencing data in tomato. Mol Cells. 2014;37(1):36-42.
18. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 2011;6:e19379.
19. Kumar S, Banks TW, Cloutier S. SNP discovery through next-generation sequencing and its applications. Int J Plant Genomics. 2012;2012:1-14.
20. Huang X, Han B. Natural variations and genome-wide association studies in crop plants. Annu Rev Plant Biol. 2013;65:531-51.
21. Lin M, Cai S, Wang S, Liu S, Zhang G, Bai G. Genotyping-by-sequencing (GBS) identified SNP tightly linked to QTL for pre-harvest sprouting resistance. Theor Appl Genet. 2015;128(7):1385-95.
22. Spindel J, Wright M, Chen C, Cobb J, Gage J, Harrington S, Lorieux M, Ahmadi N, McCouch S. Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. Theor Appl Genet. 2013;126(11):2699-716.
23. Romay MC, Millard MJ, Glaubitz JC, Peiffer JA, Swarts KL, Casstevens TM, Elshire RJ, Acharya CB, Mitchell SE, Flint-Garcia SA, McMullen MD, Holland JB, Buckler ES, Gardner CA. Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biol. 2013;14(6):R55.
24. Tanksley SD, Nelson JC. Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet. 1996;92(2):191-203.
25. Grandillo S, Tanksley SD. QTL analysis of horticultural traits differentiating the cultivated tomato from the closely related species Lycopersicon pimpinellifolium. Theor Appl Genet. 1996;92(8):935-51.
26. 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):259-72.
27. Prudent M, Causse M, Génard M, Tripodi P, Grandillo S, Bertin N. Genetic and physiological analysis of tomato fruit weight and composition: influence of carbon availability on QTL detection. J Exp Bot. 2009;60(3):923-37.
28. 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):978-87.
29. Doyle JJ, Doyle JE. Isolation of plant DNA from fresh tissue. Focus. 1990;12:13-5.
30. Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, Sun Q, Buckler ES. TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS One. 2014;9:e90346.
31. Tomato (S. lycopersicum) genome. 2014. ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/assembly/build_2.50/. Accessed 16 Jun 2016.
32. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357-9.
33. Voorrips RE. MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered. 2002;93:77-8.
34. Joehanes R, Nelson JC. QGene 4.0 an extensible Java QTL-analysis platform. Bioinformatics. 2008;24:2788-9.
35. Churchill GA, Doerge RW. Empirical threshold values for quantitative trait mapping. Genetics. 1994;138:963-97.
36. Norusis MJ. PASW statistics 18 guide to data analysis. 1st ed. New Jersey: Prentice Hall Press; 2010.
37. Poland JA, Rife TW. Genotyping-by-sequencing for plant breeding and genetics. Plant Genome. 2012;5(3):92-102.
38. Okmen B, Sigva HO, Gurbuz N, Ulger M, Frary A, Doganlar S. Quantitative trait loci (QTL) analysis for antioxidant and agronomically important traits in tomato (Lycopersicon esculentum). Turk J Agric For. 2011;35:501-14.
39. Fulton TM, Beck-Bunn T, Emmatty D, Eshed Y, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley SD. QTL analysis of an advanced backcross of Lycopersicon peruvianum to the cultivated tomato and comparisons with QTLs found in other wild species. Theor Appl Genet. 1997;95:881-94.
40. Fulton TM, Grandillo S, Beck-Bunn T, Fridman E, Frampton A, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley SD. Advanced backcross QTL analysis of a Lycopersicon esculentum × Lycopersicon parviflorum cross. Theor Appl Genet. 2000;100:1025-42.
41. Oltman AE, Jervis SM, Drake MA. Consumer attitudes and preferences for fresh market tomatoes. J Food Sci. 2014;79:2091-7.
42. Frary A, Nesbitt TC, Grandillo S, Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanksley SD. fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science. 2000;289(5476):85-8.
43. Monforte AJ, Friedman E, Zamir D, Tanksley SD. Comparison of a set of allelic QTL-NILs for chromosome 4 of tomato: Deductions about natural variation and implications for germplasm utilization. Theor Appl Genet. 2001;102:572-90.
44. Muños S, Ranc N, Botton E, Bérard A, Rolland S, Duffé 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):2244-54.
45. Stevens MA, Kader AA, Albright M. Potential for increasing tomato flavor via increased sugar and acid content. J Am Soc Hortic Sci. 1979;104:40-2.
46. He X, Zhang J. Toward a molecular understanding of pleiotropy. Genetics. 2006;173(4):1885-91.