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.
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