Genetic maps saturated with genetic markers are useful for genetic research and crop breeding; however, the genetic map for the large-fruited fresh-market tomato (Solanum lycopersicum) has never been constructed, and the recombination frequency between DNA fragments is only partly understood for fresh-market tomato. We constructed a novel fresh-market tomato genetic map by using 3614 single nucleotide polymorphism (SNP) markers and a 93 F2 segregating progeny derived from a cross between two United States large-fruited fresh-market tomato lines. The average distance between markers was less than 1 cM, and substantial recombination densities between markers were observed across the approximate centromere locations. A linkage panel for large-fruited fresh-market tomato was also established using the combined dataset of the genetic map and 58 SNP-genotyped core tomato lines. The allelic information in the linkage panel will be a significant resource for both tomato genetics and future breeding approaches.
Prashant Bhandari and Tong Geon Lee
Tong Geon Lee, Samuel F. Hutton, and Reza Shekasteband
Mechanization of farm work is increasingly demanded for the current system of fresh-market tomato (Solanum lycopersicum) production. One essential element for the adoption of mechanical harvest of fresh-market tomatoes is modification of plant architecture so that the crop can be grown without staking. To address this in the current production system, the stem length should be reduced. The tomato brachytic (br) locus has been shown to be a primary source of reducing stem length. To improve the effectiveness of marker-assisted selection (MAS) for the br-mediated trait and to provide resources for cloning this gene, we fine-mapped br to the tomato genome. Fine mapping of br to chromosome 1 was initiated by a survey of genome-wide single-nucleotide polymorphisms (SNPs) shown to be polymorphic between the br phenotype and normal using the tomato array, identifying the interval that harbors br. Genetic markers that flank the locus further permitted saturation of the interval. Twenty-six fixed homozygous recombinant lines were identified together in two different populations and tested with those markers. These efforts resulted in the first report that the br is fine-mapped to a 763-kb physical interval of tomato reference genome. The identified markers close to the br in the present study will be significant resources for MAS and gene cloning research.
Tong Geon Lee, Reza Shekasteband, Naama Menda, Lukas A. Mueller, and Samuel F. Hutton
The jointless pedicel trait of tomato conferred by the j-2 gene is widely used in processing markets for stem-free removal of fruit to accommodate mechanized harvest. Although current utilization of j-2 for fresh-market tomato breeding is limited, interest in this trait may increase as breeders seek to address high labor costs through the development of mechanically harvestable cultivars for the fresh market. Yet, the introduction of this trait into new market classes heavily relies on phenotypic selection because there are presently no high-throughput methods available to genotype j-2. Reliable, high-throughput molecular markers to genotype the presence/absence of j-2 for selective breeding were developed. The molecular markers described here use the high-resolution DNA melting analysis (HRM) genotyping with single-nucleotide polymorphism (SNP) and derived cleaved amplified polymorphic sequence (dCAPS)–based genotyping. Two separate HRM-based markers target the j-2 on chromosome 12 or a linked sequence region 3.5 Mbp apart from the gene, and a dCAPS marker resides on the latter. We demonstrate the association between each marker and the jointless pedicel phenotype using segregating populations of diverse filial generations in multiple genetic backgrounds. These markers provide a useful resource for marker-assisted selection of j-2 in breeding populations.