Tomato is the most valuable horticultural crop worldwide (FAO, 2016), providing micronutrients to the human diet. Fresh-market and processing tomatoes are the two most commonly consumed types of tomatoes and account for more than $2.6 billion in annual farm cash receipts in the United States alone [U.S. Department of Agriculture (USDA), 2016].
Unlike processing tomatoes, which have been successfully adapted for farm machinery for nearly all aspects of production, field production of fresh-market tomatoes continues to heavily rely on manual labor for harvesting, as well as for staking and tying in many areas of production (Davis and Estes, 1993; USDA, 2016; VanSickle et al., 2009). But rapidly growing labor costs and recent trends in uncertainty about trained laborers (California Tomato Growers Association, 2015; Florida Tomato Committee, 2018; USDA, 2016) force the fresh-market tomato industry to seek a mechanical harvesting system to reduce dependence on farm labor.
Most of the U.S. field-grown, fresh-market tomato crop is grown on plastic-covered beds. Most of these varieties have determinate vines, but their vines generally would grow off the beds, subjecting the fruit or vegetative tissue to soil. Because of their heavy large fruit and the higher quality requirement of exterior standards, displacement of those plants, especially fruit laying on the soil, significantly reduce yield and quality by damages from human activities, machineries, and soilborne pathogens (Adelana, 1980). Thus, staking and tying are required to sustain the current production of marketable fresh-market tomatoes, particularly under the highly humid conditions in the southeastern United States.
Given the aforementioned, manipulating phenotypes to hold fruit up off the ground (e.g., fruit remain on the raised plastic beds) without the support of stakes is expected to directly contribute to tomato industries. To address this, the stem length should be reduced without negatively affecting fruit yield. Investigation of feasible traits to develop the ideal fresh-market tomato architecture for mechanical harvest has already revealed a tomato growth habit, named as compact growth habit (CGH), and shorter stem is a key component for CGH (Frasca et al., 2014; Gardner and Davis, 1991; Kemble et al., 1994a, 1994b). Moreover, the combination of CGH with jointless pedicel trait (Scott et al., 2013) could make it economical to do harvesting with mechanical harvesters. Thus, this habit has received attention from tomato communities as a means to reduce the industry’s dependence on manual labor. Presently, there are no commercial large-fruited, jointless fresh-market tomatoes that show CGH.
Short stem driven by shortened internodes is a typical characteristic of plants deficient in endogenous gibberellin (GA) biosynthesis or defective in the perception of GA, and multiple genes essential for its synthesis have been functionally validated [galbina loci (Koornneef et al., 1990) and SIDREB (Li et al., 2012)]. Similarly, the characteristic can be observed in tomatoes with different biosynthetic enzymes, such as brassinosteroid (BR); for example, the dwarf (d) gene is involved in BR synthesis in tomato (Bishop et al., 1999; Li et al., 2016; Martí et al., 2006). However, such mutant-derived phenotype(s) have not been used commercially, often because of extreme reductions in fruit size and in marketable yield (typical marketable fruit size of 5.72 cm diameter or larger), which were found for experimental tomato lines with those mutants (Scott and Harbaugh, 1989; J.W. Scott and R.G. Gardner, personal communications).
Plant br locus influences stem growth in grain/fruit crops, contributing to shorter plant architecture (Hollender et al., 2016; Knöller et al., 2010; Xing et al., 2015) and suggesting that utilization of this locus may have benefits for crop production (Salamini, 2003). Introduction of the tomato br into normal phenotype tomatoes has shorter internodes that inevitably reduced stem length (Balint-Kurti et al., 1995; Barton et al., 1955; MacArthur, 1931). The locus has been shown to be the primary source of the shortened internode phenotype in fresh-market tomato breeding programs (Frasca et al., 2014; Scott et al., 2010; Tigchelaar, 1986). Furthermore, the locus was chosen for the source of shorter architecture in indeterminate tomato lines, giving relative ease of horticultural practices (Panthee and Gardner, 2013). It is notable that no evidence for a significant negative correlation was observed between marketable fruit harvests, and the br has been reported in a peer-reviewed forum (Frasca et al., 2014; Gardner and Davis, 1991), which at least partially suggests different mechanisms/genetic loci affecting internode elongation. The br locus was mapped onto tomato chromosome 1 through classical genetic experiments (Balint-Kurti et al., 1995; MacArthur, 1931), but the molecular basis of this locus has remained unclear.
To better use the br, the tomato breeding community needs genetic markers closely linked to the locus to improve selection efficiency. In addition, to understand the molecular mechanisms of the br gene, it needs to be cloned and this effort would benefit from narrowing the genetic intervals where the gene maps.
The objective of this study was to fine-map the br locus in the tomato genome. Nucleotide sequence polymorphisms obtained from the tomato Illumina Infinium array SNP chip and the alignment of whole-genome shotgun sequencing (WGS) reads of tomato lines with and without br provided resources to saturate near the br region in recombinant populations with different genetic backgrounds.
Balint-Kurti, P.J., Jones, D.A. & Jones, J.D. 1995 Integration of the classical and RFLP linkage maps of the short arm of tomato chromosome 1 Theor. Appl. Genet. 90 17 26
Barton, D.W., Butler, L., Jenkins, J.A., Rick, C.M. & Young, P.A. 1955 Rules for nomenclature in tomato genetics (includes a list of known genes) J. Hered. 46 22 76
Bishop, G.J., Nomura, T., Yokota, T., Harrison, K., Noguchi, T., Fujioka, S., Takatsuto, S., Jones, J.D.G. & Kamiya, Y. 1999 The tomato DWARF enzyme catalyses C-6 oxidation in brassinosteroid biosynthesis Proc. Natl. Acad. Sci. USA 96 1761 1766
California Tomato Growers Association 2015 California tomato growers association. 16 May 2018. <http://www.ctga.org>
Crill, P., Strobel, J.W., Burgis, D.S., Bryan, H.H., John, C.A., Everett, P.H., Bartz, J.A., Hayslip, N.C. & Dean, W.W. 1971 Florida MH-1, Florida’s first machine harvest fresh market tomato. Florida Agr. Expt. Sta. Circ. S-212
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
FAO 2016 Value of agricultural production. 16 May 2018. <http://www.fao.org/faostat/en/#data/QC/metadata>
Fernandez-Pozo, N., Menda, N., Edwards, J.D., Saha, S., Tecle, I.Y., Strickler, S.R., Bombarely, A., Fisher-York, T., Pujar, A., Foerster, H., Yan, A. & Mueller, L.A. 2015 The Sol Genomics Network (SGN) - From genotype to phenotype to breeding Nucl. Acids Res. 43 D1036 D1041
Florida Tomato Committee 2018 Florida tomato committee. 16 May 2018. <https://www.floridatomatoes.org>
Frasca, A.C., Ozores-Hampton, M., Scott, J. & McAvoy, E. 2014 Effect of plant population and breeding lines on fresh-market, compact growth habit tomatoes growth, flowering pattern, yield, and postharvest quality HortScience 49 1529 1536
Freeman, J.H., McAvoy, E.J., Boyd, N.S., Dittmar, P.J., Ozores-Hampton, M., Smith, H.A., Vallad, G.E. & Webb, S.E. 2015 Tomato production, p. 211–234. In: J.H. Freeman, P.J. Dittmar, and G.E. Vallad (eds.). Vegetable production handbook of Florida 2015–16. Univ. Florida, Inst. Food Agr. Sci., Gainesville, FL
Gardner, R.G. & Davis, J.M. 1991 Evaluation of a fresh-market tomato breeding line with brachytic and prostrate growth habits HortScience 26 713 (abstr.)
Hollender, C.A., Hadiarto, T., Srinivasan, C., Scorza, R. & Dardick, C. 2016 A brachytic dwarfism trait (dw) in peach trees is caused by a nonsense mutation within the gibberellic acid receptor PpeGID1c New Phytol. 210 227 239
Kemble, J.M., Davis, J.M., Gardner, R.G. & Sanders, D.C. 1994a Root cell volume affects growth of compact-growth-habit tomato transplants HortScience 29 261 262
Kemble, J.M., Davis, J.M., Gardner, R.G. & Sanders, D.C. 1994b Spacing, root cell volume, and age affect production and economics of compact-growth-habit tomatoes HortScience 29 1460 1464
Knöller, A.S., Blakeslee, J.J., Richards, E.L., Peer, W.A. & Murphy, A.S. 2010 Brachytic2/ZmABCB1 functions in IAA export from intercalary meristems J. Expt. Bot. 61 3689 3696
Koornneef, M., Bosma, T.D., Hanhart, C.J., van der Veen, J.H. & Zeevaart, J.A. 1990 The isolation and characterization of gibberellin-deficient mutants in tomato Theor. Appl. Genet. 80 852 857
Lee, T.G., Shekasteband, R. & Hutton, S.F. 2018 Molecular markers to select for the j-2–mediated jointless pedicel in tomato HortScience 53 153 158
Li, X.J., Guo, X., Zhou, Y.H., Shi, K., Zhou, J., Yu, J.Q. & Xia, X.J. 2016 Overexpression of a brassinosteroid biosynthetic gene Dwarf enhances photosynthetic capacity through activation of Calvin cycle enzymes in tomato BMC Plant Biol. 16 33
Li, J., Sima, W., Ouyang, B., Wang, T., Ziaf, K., Luo, Z., Liu, L., Li, H., Chen, M., Huang, Y., Feng, Y., Hao, Y. & Ye, Z. 2012 Tomato SlDREB gene restricts leaf expansion and internode elongation by downregulating key genes for gibberellin biosynthesis J. Expt. Bot. 63 6407 6420
Martí, E., Gisbert, C., Bishop, G.J., Dixon, M.S. & García-Martínez, J.L. 2006 Genetic and physiological characterization of tomato cv. Micro-Tom J. Expt. Bot. 57 2037 2047
Scott, J.W. & Harbaugh, B.K. 1989 Micro-Tom. A miniature dwarf tomato. Florida Agr. Expt. Sta. Circ. S-370
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, Boca Raton, FL
Sim, S.C., Durstewitz, G., Plieske, J., Wieseke, R., Ganal, M.W., Van Deynze, A., Hamilton, J.P., Buell, C.R., Causse, M., Wijeratne, S. & Francis, D.M. 2012 Development of a large SNP genotyping array and generation of high-density genetic maps in tomato PLoS One 7 e40563
Tigchelaar, E.C. 1986 Tomato breeding, p. 135–171. In: M.J. Bassett (ed.). Breeding vegetable crops. AVI Publ., Westport, CT
U.S. Department of Agriculture 2008 Solanaceae coordinated agricultural project. 19 May 2018. <http://solcap.msu.edu/tomato_genotype_data.shtml>
U.S. Department of Agriculture 2016 Tomatoes. 19 Oct. 2016. <www.ers.usda.gov/topics/crops/vegetables-pulses/tomatoes>
VanSickle, J., Smith, S. & McAvoy, E. 2009 Production budget for tomatoes grown in Southwest Florida. Univ. Florida, Inst. Food Agr. Sci., Electronic Data Info. Source PE818. Dec. 2009
Xing, A., Gao, Y., Ye, L., Zhang, W., Cai, L., Ching, A., Llaca, V., Johnson, B., Liu, L., Yang, X., Kang, D., Yan, J. & Li, J. 2015 A rare SNP mutation in Brachytic2 moderately reduces plant height and increases yield potential in maize J. Expt. Bot. 66 3791 3802