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1. Agrobacterium tumefaciens-Mediated Transformation of Tomato

   https://doi.org/10.1007/978-1-4939-8778-8_16  

   Van Eck, J.; Keen, P.; Tjahjadi, M. (January 2019, Methods and protocols)
2. Natural Genetic Diversity in Tomato Flavor Genes

   https://doi.org/10.3389/fpls.2021.642828  

   Pereira, Lara; Sapkota, Manoj; Alonge, Michael; Zheng, Yi; Zhang, Youjun; Razifard, Hamid; Taitano, Nathan K.; Schatz, Michael C.; Fernie, Alisdair R.; Wang, Ying; et al (June 2021, Frontiers in Plant Science)

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   Fruit flavor is defined as the perception of the food by the olfactory and gustatory systems, and is one of the main determinants of fruit quality. Tomato flavor is largely determined by the balance of sugars, acids and volatile compounds. Several genes controlling the levels of these metabolites in tomato fruit have been cloned, including LIN5 , ALMT9 , AAT1 , CXE1 , and LoxC . The aim of this study was to identify any association of these genes with trait variation and to describe the genetic diversity at these loci in the red-fruited tomato clade comprised of the wild ancestor Solanum pimpinellifolium , the semi-domesticated species Solanum lycopersicum cerasiforme and early domesticated Solanum lycopersicum . High genetic diversity was observed at these five loci, including novel haplotypes that could be incorporated into breeding programs to improve fruit quality of modern tomatoes. Using newly available high-quality genome assemblies, we assayed each gene for potential functional causative polymorphisms and resolved a duplication at the LoxC locus found in several wild and semi-domesticated accessions which caused lower accumulation of lipid derived volatiles. In addition, we explored gene expression of the five genes in nine phylogenetically diverse tomato accessions. In general, the expression patterns of these genes increased during fruit ripening but diverged between accessions without clear relationship between expression and metabolite levels. 

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3. Tomato pollen tube growth requires flavonol glycosylation

   https://doi.org/10.1093/plphys/kiaf556  

   Shin, Doosan; Zhao, Haohao; Tucker, Ethan; Cho, Keun Ho; Liu, Dake; Wang, Zhixin; Latimer, Scott; Basset, Gilles; Wang, Yu; Ding, Yousong; et al (October 2025, Plant Physiology)

   Abstract Flavonols are a subclass of flavonoids widely found in plants and typically exist in glycosylated forms, decorated with various sugars at different positions on the flavonol aglycone. The composition and abundance of flavonol glycosides vary across species and among tissues within a species. Although flavonols are collectively known for their antioxidant activity, the specific physiological functions of individual flavonol structures remain poorly understood. Here, we show that 2 flavonol glycosides, kaempferol 3-O-glucosyl(1 → 2)galactoside (K2) and quercetin 3-O-glucosyl(1 → 2)galactoside (Q2), predominantly accumulate in the pollen of Solanaceae plants. K2 is evolutionarily conserved across Solanaceae, while Q2 has been lost in species such as tomato (Solanum lycopersicum). Our transcriptome profiling and biochemical analysis revealed SlUGT78D-B (78-B) as a pollen-specific flavonol 3-O-galactosyltransferase responsible for K2 production in tomato. Disruption of 78-B abolished K2 accumulation, leading to defective pollen tube growth in our in vitro assays. Supplementation with kaempferol 3-O-galactoside (K2 precursor) restores pollen tube growth, whereas quercetin 3-O-galactoside (Q2 precursor) or flavonol aglycones do not, suggesting distinct roles for individual flavonol structures. We further show that 3 key amino acid residues of 78-B dictate its sugar specificity, favoring galactosylation over glucosylation. Substitution of any one of these residues enables 78-B to acquire glucosyltransferase activity. However, 78-B remains evolutionarily constrained from gaining this activity, suggesting selective pressure to maintain flavonol galactoside accumulation in pollen. These findings indicate that individual flavonol glycosides can have specific physiological roles beyond enhancing solubility and stability. 

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4. Functional analysis of the seven in absentia ubiquitin ligase family in tomato: Analysis of SINA ubiquitin ligases in tomato

   https://doi.org/10.1111/pce.13140  

   Wang, Wenjie; Fan, Youhong; Niu, Xiangli; Miao, Min; Kud, Joanna; Zhou, Bangjun; Zeng, Lirong; Liu, Yongsheng; Xiao, Fangming (March 2018, Plant, Cell & Environment)
5. TOMATO: A Topic-Wise Multi-Task Sparsity Model

   https://doi.org/10.1145/3340531.3411972  

   Zhang, Jason; Lee, Dongwon (October 2020, 29th ACM Int'l Conf. on Information and Knowledge Management (CIKM))

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