Tomato (Solanum lycopersicum L.) is the most valuable horticultural crop worldwide (Food and Agriculture Organization of the United Nations; http://www.fao.org/faostat/en/#data/QC/metadata). Fresh-market and processing tomatoes, the two most commonly consumed types of tomatoes, are economically important in many countries, including the United States [United States Department of Agriculture Economic Research Service (USDA ERS); www.ers.usda.gov/topics/crops/vegetables-pulses/tomatoes]. Nonetheless, further improvement in horticultural performance is necessary to achieve future productivity gains, especially given the rapidly growing labor costs and recent trends in uncertainty about trained labors (California Tomato Growers Association; www.ctga.org, Florida Tomato Committee; www.floridatomatoes.org, USDA ERS).
A major change among agricultural industries has been a shift toward farm machinery to achieve higher levels of productivity and market value (Pardey et al., 2016; Zahara and Johnson, 1981). Unlike processing tomatoes that have been successfully adapted for mechanized harvest, production of fresh-market tomatoes continues to rely on manual labor for harvesting and other common cultural practices (such as staking, tying, and pruning), which can account for as much as a half of the total production cost (Davis and Estes, 1993; USDA ERS). Thus, there is a significant need to research traits which will facilitate a transition to broader mechanization in fresh-market tomato production.
Tomato inflorescences typically have an abscission zone (joint) in the pedicel of each flower. Detachment of the fruit at this joint at harvest results in the calyx and stem remaining attached to the fruit, which can in turn puncture or otherwise damage neighboring fruit. The jointless pedicel trait was first reported by Butler (1936). Because jointless tomatoes lack an abscission zone in the pedicel, the calyx and stem remain attached to the plant, enabling of stem-free harvest of fruit. Hand harvesting of jointed pedicel tomatoes involves the manual removal of any attached stems from fruit, but jointless pedicels are an essential component for maintaining fruit quality and marketability in cultivars intended for mechanical harvest (Scott et al., 2013; Zahara and Scheuerman, 1988).
Two recessive genes known to mediate the jointless pedicels in tomato have been identified. The first gene, jointless (j), is located on chromosome 11 and was identified from S. lycopersicum accession LA624 (Rick, 1980; Wing et al., 1994). Mao et al. (2000) determined that j was a MADS-box gene controlling tomato flower abscission zone development. Later, an alternative allele, jointless-2 (j-2; Rick, 1956) was identified in S. cheesmanii accession LA166 and also as a spontaneous mutation in cultivated tomato (Reynard, 1961). j-2 was mapped to an ≈6-Mbp interval in the centromeric region on chromosome 12 (Budiman et al., 2004; Yang et al., 2005; Zhang et al., 2000). Recent progress in understanding the molecular characteristics of the jointless trait has revealed the underlying gene, a MADS-box transcription factor 11 gene (Solyc12g038510) of S. lycopersicum (the jointed pedicel trait-derived allele) (Soyk et al., 2017), and determined that loss of function mutations in this gene resulted in the jointless inflorescence. Hence, mutated versions of Solyc12g038510 are referred to as j-2 in the present study.
j-2 has been broadly used by tomato breeding programs in the United States and around the world. However, current selection methods rely predominantly on phenotypic expression at flowering or thereafter. Marker resources to aid in selection efforts are limited. In the late 1990s, Zhang et al. (2000) developed a random amplified polymorphic DNA (RAPD) marker for j-2 which has been used in independent research efforts (Budiman et al., 2004; Yang et al., 2005). However, the marker system is not fully feasible because of the cumbersome process of the RAPD system and difficulty in its reproduction. The CAPS marker tagging j-2 alleles (Soyk et al., 2017) is detected via a gel-based polymerase chain reaction (PCR) image and is not immediately useful for high-throughput genotyping. Thus, a practical means to select for this trait could be very helpful for introducing and selecting the jointless trait in tomato germplasm, especially for fresh-market backgrounds which are predominantly jointed.
The objective of this project was to develop molecular markers linked to the j-2 locus that can be useful for marker-assisted selection (MAS). We used whole-genome sequencing of jointless and jointed tomato lines to identify SNPs proximal to the locus.
Budiman, M.A., Chang, S.B., Lee, S., Yang, T.J., Zhang, H.B., de Jong, H. & Wing, R.A. 2004 Localization of jointless-2 gene in the centromeric region of tomato chromosome 12 based on high resolution genetic and physical mapping Theor. Appl. Genet. 108 190 196
Davis, J.M. & Estes, E.A. 1993 Spacing and pruning affect growth, yield, and economic returns of staked fresh-market tomatoes J. Amer. Soc. Hort. Sci. 118 719 725
Garrison, E. & Marth, G. 2012 Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907
Li, J., Chitwood, J., Menda, N., Mueller, L. & Hutton, S.F. 2018 Linkage between the I-3 gene for resistance to Fusarium wilt race 3 and increased sensitivity to bacterial spot in tomato Theor. Appl. Genet. 131 145 155
Mao, L., Begum, D., Chuang, H.W., Budiman, M.A., Szymkowiak, E.J., Irish, E.E. & Wing, R.A. 2000 JOINTLESS is a MADS-box gene controlling tomato flower abscission zone development Nature 406 910 913
McAvoy, E. & Ozores-Hampton, M. 2011 Unique challenges for Florida growers in tomato and pepper Production. Univ. Florida, Inst. Food Agr. Sci., Electronic Data Info. Source, IPM-201. 4 Oct. 2017. <http://edis.ifas.ufl.edu/in733>.
Scott, J.W., Hutton, S.F. & Strobel, J. 2010 Some highlights from the University of Florida tomato breeding program Proc. Florida Tomato Inst. 53 9 10
Scott, J.W., Myers, J.R., Boches, P.S., Nichols, C.G. & Angell, F.F. 2013 Classical genetics and traditional breeding, p. 60–61. In: B.E. Liedl, J.A. Labate, J.R. Stommel, A. Slade, and C. Kole (eds.). Genetics, Genomics, and Breeding of Tomato. CRC Press, NW
Soyk, S., Lemmon, Z.H., Oved, M., Fisher, J., Liberatore, K.L., Park, S.J., Goren, A., Jiang, K., Ramos, A., van der Knaap, E., Van Eck, J., Zamir, D., Eshed, Y. & Lippman, Z.B. 2017 Bypassing negative epistasis on yield in tomato imposed by a domestication gene Cell 169 1142 1155.e12
Wing, R.A., Zhang, H.B. & Tanksley, S.D. 1994 Map-based cloning in crop plants. Tomato as a model system: I. Genetic and physical mapping of jointless Mol. Gen. Genet. 242 681 688
Yang, T.J., Lee, S., Chang, S.B., Yu, Y., de Jong, H. & Wing, R.A. 2005 In-depth sequence analysis of the tomato chromosome 12 centromeric region: Identification of a large CAA block and characterization of pericentromere retrotranposons Chromosoma 114 103 117
Ye, J., Coulouris, G., Zaretskaya, I., Cutcutache, I., Rozen, S. & Madden, T.L. 2012 Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction BMC Bioinformatics 13 134
Zahara, M.B. & Johnson, S.S. 1981 Cost comparison of hand harvest and mechanical harvest of mature green tomatoes. Univ. California, Veg. Res. and Info. Ctr. 4 Oct. 2017. <https://ucanr.edu/repositoryfiles/ca3507p7-61772.pdf>.
Zahara, M.B. & Scheuerman, R.W. 1988 Hand-harvesting jointless vs. jointed-stem tomatoes: Jointless-stem fresh-market varieties take much less time to pick than jointed types. Univ. California, Veg. Res. and Info. Ctr. 4 Oct. 2017. <http://ucce.ucdavis.edu/files/repositoryfiles/ca4203p14-68779.pdf>.
Zhang, H.B., Budiman, M.A. & Wing, R.A. 2000 Genetic mapping of jointless-2 to tomato chromosome 12 using RFLP and RAPD markers Theor. Appl. Genet. 100 1183 1189