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.
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