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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.
The first consensus genetic map in fresh-market tomato (Solanum lycopersicum) was constructed, combining genetic recombination data from two biparental F2 segregating populations derived from four different fresh-market tomatoes. Each F2 population was nominated by different academic tomato breeding programs located in major fresh-market tomato-producing areas of the United States, and chromosome-wide variation in recombination rates was observed between tomato populations based on the origin of their breeding programs. A consensus map constructed using 335 common single nucleotide polymorphism (SNP) sites found in both populations spanned 737.3 cM across 12 tomato chromosomes, with chromosome 2 containing more than 40% of the total SNPs and chromosomes 4, 5, 7, and 10 together representing less than 10% of the SNPs. There was a high degree of collinearity between the genetic and physical positions of those 335 SNP markers. The integration of 6553 SNP sites that were detected in either of the two populations with 335 common sites resulted in an extended consensus genetic map. The total length of the extended map was estimated to be 1997.9 cM, which was compatible with a previous estimate for large-fruited fresh-market tomato. A linkage panel for fresh-market tomato was also established using the combined dataset of the consensus map of 335 SNP loci and 73 SNP-genotyped core fresh-market tomatoes. An empirical genetic mapping study of the tomato brachytic trait using the linkage panel demonstrated the value of the consensus map and linkage panel for tomato research. The allelic information in the linkage panel will serve as a basis for SNP marker implementation, such as genotyping platforms and genomic association map, in tomato.
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.
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.
Fusarium wilt of tomato (Solanum lycopersicum), caused by fungal pathogen Fusarium oxysporum f. sp. lycopersici (Fol), is one of the most important diseases in tomato production. Three races of the pathogen are described, and race-specific resistance genes have been applied in commercial tomato cultivars for controlling the disease. Race 3 (Fol3) threatens tomato production in many regions around the world, and novel resistance resources could expand the diversity and durability of Fol resistance. The wild tomato species, Solanum pennellii, is reported to harbor broad resistance to Fol and was the source of two known Fol3 resistance genes. In this study, we evaluated 42 S. pennellii accessions for resistance to each fusarium wilt race. F1 plants, developed from crossing each accession with the Fol3 susceptible line ‘Suncoast’, were evaluated for Fol3 resistance, and BC1F1 plants were screened to determine the likelihood that Fol3 resistance was based on a novel locus (loci). Nearly all accessions showed resistance to Fol3, and many accessions were resistant to all races. Evaluation of F1 plants indicated a dominant resistance effect to Fol3 from most accessions. Genetic analysis indicated 24 accessions are expected to contain one or more novel Fol3 resistance loci other than an allele near the I-3 locus. To investigate genetic structure of the S. pennellii accessions used in this study, we genotyped all 42 accessions using genotyping by sequencing. Approximately 20% of the single nucleotide polymorphism (SNP) loci were heterozygous across accessions, likely due to the outcrossing nature of the species. Genetic structure analysis at 49,120 unique SNP loci across accessions identified small but obvious genetic differentiations.