Abstract
The domestication process of tomato (Solanum lycopersium L.) resulted in very low variability for most agronomic interesting traits. In this work we explore the variability present in an unusual segregating population obtained by selfing a second cycle hybrid to identify and mapping novel Quantitative Trait Loci (QTL) for fruit quality traits. With this aim, a molecular characterization of the population by 130 single nucleotide polymorphism designed from genome sequencing of the parental lines was performed, which resulted in a genetic map and the location of seven novel QTL associated with the inheritance of the fruit quality traits: fruit diameter (R2 ranging from 0.179 to 0.207), fruit weight (R2 = 0.171) and fruit shape index (R2 ranging from 0.179 to 0.341). The analysis through the G-statistic allowed to define the consistence of the novel QTL identified, especially those associated to fruit shape index and fruit diameter. This approach has also led to the identification of new codominant molecular markers flanking the QTL which will be useful in future genetic breeding programs.
Similar content being viewed by others
References
Blanca J, Cañizares J, Cordero L, Pascual L, Díez MJ, Nuez F (2012) Variation revealed by SNP genotyping and morphology provides insight into the origin of the tomato. PLoS ONE 7:e48198. https://doi.org/10.1371/journal.pone.0048198
Brewer MT, Moyseenko JB, Monforte AJ, van der Knaap E (2007) Morphological variation in tomato: a comprehensive study of quantitative trait loci controlling fruit shape and development. J Exp Bot 58(6):1339–1349. https://doi.org/10.1093/jxb/erl301
Cabodevila VG, Picardi LA, Pratta GR (2017) A multivariate approach to explore the genetic variability in the F2 segregating population of a tomato second cycle hybrid. J Basic Appl Genet 28(1):7–17
Cambiaso V, Pratta GR, Pereira da Costa JH, Zorzoli R, Francis DM, Rodríguez GR (2019a) Whole genome re-sequencing analysis of two tomato genotypes for polymorphism insight in cloned genes and a genetic map construction. Sci Hortic 247:58–66. https://doi.org/10.1016/j.scienta.2018.12.001
Cambiaso V, Gimenez MD, Pereira da Costa JH, Vazquez DV, Picardi LA, Pratta GR, Rodríguez GR (2019b) Selected genome regions for fruit weight and shelf life in tomato RILs discernible by markers based on genomic sequence information. Breed Sci 69(3):447–454. https://doi.org/10.1270/jsbbs.19015
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 (2015) 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 128(10):2019–2035. https://doi.org/10.1007/s00122-015-2563-4
Capel C, Yuste-Lisbona FJ, López-Casado G, Angosto T, Cuartero J, Lozano R, Capel J (2017a) Multi-environment QTL mapping reveals genetic architecture of fruit cracking in a tomato RIL Solanum lycopersicum × S. pimpinellifolium population. Theor Appl Genet 130(1):213–222. https://doi.org/10.1007/s00122-016-2809-9
Capel C, Yuste-Lisbona FJ, López-Casado G, Angosto T, Heredia A, Cuartero J, Fernández-Muñoz R, Lozano R, Capel J (2017b) QTL mapping of fruit mineral contents provides new chances for molecular breeding of tomato nutritional traits. Theor Appl Genet 130(5):903–913. https://doi.org/10.1007/s00122-017-2859-7
Celik I, Gurbuz N, Uncu AT, Frary A, Doganlar S (2017) Genome-wide SNP discovery and QTL mapping for fruit quality traits in inbred backcross lines (IBLs) of Solanum pimpinellifolium using genotyping by sequencing. BMC Genom 18(1):1–10. https://doi.org/10.1186/s12864-016-3406-7
Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 142:169–196. https://doi.org/10.1007/s10681-005-1681-5
Del Medico AP, Cabodevila VG, Vitelleschi MS, Pratta GR (2019) Multivariate estimate of heritability for quality traits in tomatoes by the multiple factor analysis. Pesq Agropec Bras 54:e00064
Di Giacomo M, Luciani MD, Cambiaso V, Zorzoli R, Rodríguez GR, Pereira da Costa JH (2020) Tomato near isogenic lines to unravel the genetic diversity of S. pimpinellifolium LA0722 for fruit quality and shelf life breeding. Euphytica 216:126. https://doi.org/10.1007/s10681-020-02649-z
Fernandez-Pozo N, Menda N, Edwards JD, Saha S, Tecle IY, Strickler SR, Bombarely A, Fisher-York T, Pujar A, Foerster H, Yan A, Mueller LA (2015) The sol genomics network (SGN)—from genotype to phenotype to breeding. Nucleic Acids Res 43:D1036–D1041. https://doi.org/10.1093/nar/gku1195
Figueiredo AST, de Resende JTV, Faria MV, de Paula JT, Schwarz K, Zanin DS (2015) Combining ability and heterosis of relevant fruit traits of tomato genotypes for industrial processing. Crop Breed Appl Biotechnol 15(3):154–161. https://doi.org/10.1590/1984-70332015v15n3a27
Foolad MR (2007) Genome mapping and molecular breeding of tomato. Int J Plant Genomics 2007:64358. https://doi.org/10.1155/2007/64358
Foolad MR, Zhang L (2015) A recombinant inbred line population of tomato and its genetic map constructed based on a Solanum lycopersicum × S. pimpinellifolium cross. Adv Stud Biol 7(11):441–471. https://doi.org/10.12988/asb.2015.5527
Francaviglia R, Di Bene C (2019) Deficit drip irrigation in processing tomato production in the Mediterranean Basin. A data analysis for Italy. Agriculture 9(4):79. https://doi.org/10.3390/agriculture9040079
Frary A, Nesbitt TC, Frary A, Grandillo S, van der Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanksley SD (2000) fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289(5476):85–88. https://doi.org/10.1126/science.289.5476.85
Gerszberg A, Hnatuszko-Konka K (2017) Tomato tolerance to abiotic stress: a review of most often engineered target sequences. Plant Growth Regul 83(2):175–198. https://doi.org/10.1007/s10725-017-0251-x
Giovannoni JJ (2004) Genetic regulation of fruit development and ripening. Plant Cell 16(Supplement 2004):S170–S180. https://doi.org/10.1105/tpc.019158
Gonzalo MJ, van der Knaap E (2008) A comparative analysis into the genetic bases of morphology in tomato varieties exhibiting elongated fruit shape. Theor Appl Genet 116(5):647–656. https://doi.org/10.1007/s00122-007-0698-7
Grandillo S, Ku HM, Tanksley SD (1999) Identifying the loci responsible for natural variation in fruit size and shape in tomato. Theor Appl Genet 99(6):978–987. https://doi.org/10.1007/s001220051405
Green GY, Pereira da Costa JH, Cambiaso V, Pratta GR, Zorzoli R, Rodríguez GR (2016) Single and joint effect of the basal region of chromosome 2 and centromeric region of chromosome 8 on morphological and fruit quality traits in tomato. Euphytica 210(3):327–339. https://doi.org/10.1007/s10681-016-1689-z
Ipsilandis CG, Tokatlidis IS, Vafias B, Stefanis D (2006) Criteria for developing second-cycle hybrids in maize. Asian J Plant Sci 5(4):680–685. https://doi.org/10.3923/ajps.2006.680.685
Joehanes R, Nelson JC (2008) QGene 4.0, an extensible Java QTL-analysis platform. Bioinformatics 24(23):2788–2789. https://doi.org/10.1093/bioinformatics/btn523
Kosambi DD (1943) The estimation of map distances from recombination values. Ann Eugen 12(1):172–175. https://doi.org/10.1111/j.1469-1809.1943.tb02321.x
Liberatti DR, Rodríguez GR, Zorzoli R, Pratta GR (2013) Tomato second cycle hybrids differ from parents at three levels of genetic variation. Int J Plant Breed 7(1):1–6
Lin T, Zhu G, Zhang J, Xu X, Yu Q, Zheng Z, Zhang Z, Lun Y, Li S, Wang X, Huang Z, Li J, Zhang C, Wang T, Zhang Y, Wang A, Zhang Y, Lin K, Li C, Xiong G, Xue Y, Mazzucato A, Causse M, Fei Z, Giovannoni JJ, Chetelat RT, Zamir D, Städler T, Li J, Ye Z, Du Y, Huang S (2014) Genomic analyses provide insights into the history of tomato breeding. Nat Genet 46:1220–1226. https://doi.org/10.1038/ng.3117
Lippman Z, Tanksley SD (2001) 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 158(1):413–422
Marchionni Basté E, Liberatti DR, Mahuad SL, Rodriguez GR, Pratta GR, Zorzoli R, Picardi LA (2010) Diallel analysis for fruit traits among tomato recombinant inbred lines derived from an interspecific cross Solanum lycopersicum × S. pimpinellifolium. J Appl Hortic 12(1):21–25
Montgomery J, Wittwer CT, Palais R, Zhou L (2007) Simultaneous mutation scanning and genotyping by high-resolution DNA melting analysis. Nat Protoc 2:59–66. https://doi.org/10.1038/nprot.2007.10
Ohyama A, Shirasawa K, Matsunaga H, Negoro S, Miyatake K, Yamaguchi H, Nunome T, Iwata H, Fukuoka H, Hayashi T (2017) Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial F1 hybrids of tomato. Theor Appl Genet 130(8):1601–1616. https://doi.org/10.1007/s00122-017-2913-5
Pereira da Costa JH, Rodríguez GR, Pratta GR, Picardi LA, Zorzoli R (2013) QTL detection for fruit shelf life and quality traits across segregating populations of tomato. Sci Hortic 156:47–53. https://doi.org/10.1016/j.scienta.2013.03.015
Pereira da Costa JH, Rodríguez GR, Liberatti DR, Mahuad SL, Marchionni Basté E, Picardi LA, Zorzoli R, Pratta GR (2016) Tomato second cycle hybrids as a source of genetic variability for fruit quality traits. Crop Breed Appl Biotechnol 16(4):289–297. https://doi.org/10.1590/1984-70332016v16n4a44
Pratta G, Zorzoli R, Picardi LA (1996) Evaluación de caracteres de interés agronómico en especies del género Lycopersicon. Horticult Argent 15(39):25–32
Pratta GR, Rodriguez GR, Zorzoli R, Valle EM, Picardi LA (2011) Phenotypic and molecular characterization of selected tomato recombinant inbred lines derived from the cross Solanum lycopersicum × S. pimpinellifolium. J Genet 90(2):229–237. https://doi.org/10.1007/s12041-011-0063-0
Rodríguez GR, Pratta GR, Zorzoli R, Picardi LA (2006) Recombinant lines obtained from an interspecific cross between Lycopersicon species selected by fruit weight and fruit shelf life. J Am Soc Hortic Sci 131(5):651–656. https://doi.org/10.21273/JASHS.131.5.651
Salinas M, Capel C, Alba JM, Mora B, Cuartero J, Fernández-Muñoz R, Lozano R, Capel J (2013) 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 126(1):83–92. https://doi.org/10.1007/s00122-012-1961-0
Sim S-C, Durstewitz G, Plieske J, Wieseke R, Ganal MW, Van Deynze A, Hamilton JP, Buell CR, Causse M, Wijeratne S, Francis DM (2012) Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS ONE 7(7):e40563. https://doi.org/10.1371/journal.pone.0040563
Tanksley SD, Rick CM (1980) Isozymic gene linkage map of the tomato: applications in genetics and breeding. Theor Appl Genet 58(2):161–170. https://doi.org/10.1007/BF00279708
The Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641. https://doi.org/10.1038/nature11119
van der Knaap E, Tanksley SD (2003) The making of a bell pepper-shaped tomato fruit: identification of loci controlling fruit morphology in Yellow Stuffer tomato. Theor Appl Genet 107(1):139–147. https://doi.org/10.1007/s00122-003-1224-1
van Ooijen JW (2006) JoinMap® 4.0: software for the calculation of genetic linkage maps in experimental populations. Kyazma B.V., Wageningen
Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93(1):77–78. https://doi.org/10.1093/jhered/93.1.77
Zhang J, Zhao J, Liang Y, Zou Z (2016) Genome-wide association-mapping for fruit quality traits in tomato. Euphytica 207(2):439–451. https://doi.org/10.1007/s10681-015-1567-0
Acknowledgements
We thank Dr. Fernando J. Yuste-Lisbona for the critical review of the manuscript. The authors thank to the BEC.AR Programme (Scholarship Programme for Overseas Training of Argentine Professionals in the Fields of Sciences, Technology and Productive Innovation) for funding the scholarship in Spain for VGC and the ANPCyT (National Agency for Scientist and Technological Promotion) for funding part of the project (PICT 2014-3181). This research was also supported by the Spanish Ministry of Science, Innovation and Universities through the grant AGL2017-88702-C2-1-R and Campus de Excelencia Internacional Agroalimentario (CeiA3).
Author information
Authors and Affiliations
Contributions
VGC performed the phenotyping, designed the markers, genotyped the molecular markers and performed the QTL analysis. VC sequenced the parental genotypes and listed the polymorphic SNPs. GRR developed the plant material and sequenced the parental genotypes. GRP developed the plant material and conceptualized the research. LAP, GRP, RL and JC devised the study. CC designed the markers and contributed to the QTL analysis. VGC, RL and JC wrote the manuscript. All the authors reviewed the manuscript.
Corresponding author
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Online Resource 1
Marker name, chromosome (CH), polymorphism and sequences for primers.
Online Resource 2
Reference genetic map and reference physical map used to select the position of the designed molecular markers. CH: chromosome; (a): reference genetic map (TraitGenetics EXPEN2012, Fernandez-Pozo et al., 2015); (b): reference physical map (Tomato - Kazusa and SolCAP markers mapped to genome, Fernandez-Pozo et al., 2015); cM: centimorgan; black spots in (a): approximate location of the marker in the genetic map; black spots in (b): represents the location of the marker in the physical map. The scale of physical map was lightly modified from original to reflect the real size of the chromosomes in Megabases (Mb). The image is an adaptation from SolGenomicsNetworks – Comparative Map Viewer (Fernandez-Pozo et al., 2015).
Rights and permissions
About this article
Cite this article
Cabodevila, V.G., Cambiaso, V., Rodríguez, G.R. et al. A segregating population from a tomato second cycle hybrid allows the identification of novel QTL for fruit quality traits. Euphytica 217, 6 (2021). https://doi.org/10.1007/s10681-020-02731-6
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s10681-020-02731-6