Background: Tomatoes (Solanum lycopersicum) are an economically and nutritionally important crop colored by carotenoids such as lycopene and β-carotene. Market diversification and interest in the health benefits of carotenoids has created the desire in plant, food, and nutritional scientists for improved extraction and quantification protocols that avoid the analytical bottlenecks caused by current methods.

Novel diversity may be mined from databases and de novo sequencing, but functional characterization remains a limiting step to identifying new alleles. Classical breeding approaches augmented by marker‐assisted selection offer a means to rapidly assess the function of new variation in coding or regulatory regions to modulate traits. We used the Cyc‐B gene (B) of tomato (Solanum lycopersicum L.) for a proof of concept because of its role in the production of β‐carotene, a provitamin A carotenoid with importance to human nutrition. We measured carotenoid content in vintage and contemporary varieties and the profiles had a range of β‐carotene from 0.2 to 4.06 mg 100 g−1 fresh weight. We characterized variation in B from 84 sequences recovered from public databases and from an additional 29 high β‐carotene tomato, S. galapagense S. C. Darwin & Peralta, and S. cheesmaniae (L. Riley) Fosberg accessions. Thirteen unique haplotypes across 1600 bp of sequence 5′ to the first ATG were identified with 11 occurring in high β‐carotene accessions we sequenced, and additional haplotypes were identified in public data. Phylogenetic analysis suggested that the alleles in high β‐carotene varieties were derived from wild species. Association analysis suggested two single nucleotide polymorphisms (SNPs) as the most likely causes of high β‐carotene, presumably through their influence on transcription of B that is elevated in ripening fruit. A marker‐assisted backcross breeding scheme leveraging SNPs for background genome selection was used to rapidly develop germplasm resources containing different alleles of B in a uniform genetic background. Evaluation demonstrated that distinct promoter haplotypes function as different alleles that can be used to modulate the levels of β‐carotene in tomato.

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Bacterial, fungal, and viral diseases of tomato (Solanum lycopersicum) are responsible for widespread yield losses, especially in humid growing environments. Chromosome 11 of tomato contains genes that modulate resistance to several prominent tomato pathogens, including bacterial spot caused by Xanthomonas spp., gray leaf spot caused by Stemphylium spp., Fusarium wilt caused by race 2 of Fusarium oxysporum f. sp. lycopersici, and tomato yellow leaf curl virus (TYLCV) caused by begomoviruses. Major resistance loci are quantitative trait locus 11 (QTL-11) and Xv3/Rx4 for bacterial spot, Sm for gray leaf spot, I2 for Fusarium wilt, and Ty-2 for TYLCV. Marker-assisted selection was used to select for rare recombination events that combined these resistance loci into a linked cassette that can be inherited together in future crosses. A pedigree breeding strategy was used with marker-assisted selection and used to identify a novel coupling of Xv3/Rx4 and Ty-2. Recombination between the two genes was estimated as 0.056 cM, demonstrating that effective combinations of resistance can be established using publicly available germplasm. Progeny from the recombinant plants were screened using inoculated seedling trials to confirm resistance. The recombinants identified maintained resistance levels similar to the resistant controls. Trial results suggest that the trait markers on chromosome 11 are tightly linked to the respective resistance loci and are effective for selecting plants with resistance to the target diseases.