Rewiring of the Fruit Metabolome in Tomato Breeding.

Breeding of crops over millennia for yield and productivity has led to reduced genetic diversity. As a result, beneficial traits of wild species, such as disease resistance and stress tolerance, have been lost. We devised a CRISPR-Cas9 genome engineering strategy to combine agronomically desirable traits with useful traits present in wild lines. We report that editing of six loci that are important for yield and productivity in present-day tomato crop lines enabled de novo domestication of wild Solanum pimpinellifolium. Engineered S. pimpinellifolium morphology was altered, together with the size, number and nutritional value of the fruits. Compared with the wild parent, our engineered lines have a threefold increase in fruit size and a tenfold increase in fruit number. Notably, fruit lycopene accumulation is improved by 500% compared with the widely cultivated S. lycopersicum. Our results pave the way for molecular breeding programs to exploit the genetic diversity present in wild plants.

/pdf/de-novo-domestication-of-wild-tomato-using-genome-editing-3bh1f0o08m.pdf

De novo domestication of wild tomato using genome editing

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato.

Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically representative accessions, revealing 4,873 genes absent from the reference genome. Presence/absence variation analyses reveal substantial gene loss and intense negative selection of genes and promoters during tomato domestication and improvement. Lost or negatively selected genes are enriched for important traits, especially disease resistance. We identify a rare allele in the TomLoxC promoter selected against during domestication. Quantitative trait locus mapping and analysis of transgenic plants reveal a role for TomLoxC in apocarotenoid production, which contributes to desirable tomato flavor. In orange-stage fruit, accessions harboring both the rare and common TomLoxC alleles (heterozygotes) have higher TomLoxC expression than those homozygous for either and are resurgent in modern tomatoes. The tomato pan-genome adds depth and completeness to the reference genome, and is useful for future biological discovery and breeding.

https://www.nature.com/articles/s41588-019-0410-2.pdf?proof=t

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor.

Tomato (Solanum lycopersicum L.) belongs to the Solanaceae family and is the second most important fruit or vegetable crop next to potato (Solanum tuberosum L.). It is cultivated for fresh fruit and processed products. Tomatoes contain many health-promoting compounds including vitamins, carotenoids, and phenolic compounds. In addition to its economic and nutritional importance, tomatoes have become the model for the study of fleshy fruit development. Tomato is a climacteric fruit and dramatic metabolic changes occur during its fruit development. In this review, we provide an overview of our current understanding of tomato fruit metabolism. We begin by detailing the genetic and hormonal control of fruit development and ripening, after which we document the primary metabolism of tomato fruits, with a special focus on sugar, organic acid, and amino acid metabolism. Links between primary and secondary metabolic pathways are further highlighted by the importance of pigments, flavonoids, and volatiles for tomato fruit quality. Finally, as tomato plants are sensitive to several abiotic stresses, we briefly summarize the effects of adverse environmental conditions on tomato fruit metabolism and quality.

/pdf/tomato-fruit-development-and-metabolism-1lcfalmbtz.pdf

Tomato Fruit Development and Metabolism

Modern commercial tomato varieties are substantially less flavorful than heirloom varieties. To understand and ultimately correct this deficiency, we quantified flavor-associated chemicals in 398 modern, heirloom, and wild accessions. A subset of these accessions was evaluated in consumer panels, identifying the chemicals that made the most important contributions to flavor and consumer liking. We found that modern commercial varieties contain significantly lower amounts of many of these important flavor chemicals than older varieties. Whole-genome sequencing and a genome-wide association study permitted identification of genetic loci that affect most of the target flavor chemicals, including sugars, acids, and volatiles. Together, these results provide an understanding of the flavor deficiencies in modern commercial varieties and the information necessary for the recovery of good flavor through molecular breeding.

http://science.sciencemag.org/content/sci/355/6323/391.full.pdf

A chemical genetic roadmap to improved tomato flavor

Modern commercial tomato varieties are substantially less flavorful than heirloom varieties. To understand and ultimately correct this deficiency, we quantified flavorassociated chemicals in 398 modern, heirloom, and wild accessions. A subset of these accessions was evaluated in consumer panels, ide

PLANT SCIENCE: A chemical genetic roadmap to improved tomato flavor

Fruit mass is an important factor for determining the yield of tomatoes ( Solanum lycopersicum ), with higher mass being an important objective. Most fruit traits, including fruit mass, are quantitative, and numerous quantitative trait loci (QTL) control these traits. Previous studies investigating tomato introgression lines (ILs) revealed several QTLs for fruit yield, and suggested that IL12-1 is a potential line to increase fruit mass. Our aim was to facilitate genetic studies of the diverse characteristics of wild relatives of tomato. Therefore, tomato ILs from a cross between Solanum pennellii and the cultivar S. lycopersicum ‘M82’ were used. ILs that carry a S. pennellii chromosome segment on chromosome 12 of ‘M82’ were evaluated further for fruit mass expansion and regulation. IL12-1-1, a subline of IL12-1, was found to produce large ripening fruits compared with ‘M82’, a phenotype that resulted in increased pericarp thicknesses. To investigate the physiological mechanisms contributing to the increased fruit mass of IL12-1-1, the cell counts of fruit pericarp tissues during fruit development were evaluated. Cell numbers of IL12-1-1 fruit pericarp at 20 days after flowering were higher than those of ‘M82’, a difference that most likely occurred during the cell division phase. In addition, the levels of the phytohormones auxin and cytokinin, which are known to be related to cell division of the fruit tissue, were higher in IL12-1-1 compared with ‘M82’. Therefore, differences in these phytohormones between ‘M82’ and IL12-1-1 may be affected by the number of cells in the pericarp tissues. Expression analysis of Solyc12g005250 ( SlKLP ) and Solyc12g005310 ( SlGH3-15 ), which are located in the IL12-1-1 region of the S. pennellii chromosome, showed significant differences between ‘M82’ and IL12-1-1 during the cell division phase; a better understanding of IL12-1-1 cellular and molecular features can contribute to the breeding and increased production of tomato crops.

https://www.jstage.jst.go.jp/article/hortj/advpub/0/advpub_UTD-356/_pdf

Physiological Investigation of Quantitative Traits for Fruit Mass Assessment Using a Tomato Introgression Line

Onion ( Allium cepa L.) is one of the most important vegetable crops in the world, and its cultivation is roughly divided into two types: autumn- (overwinter) and spring-sowing. In this study, we compared the changes in plant growth and bulb development of four short-day and intermediate-day onion cultivars under two years of varying environmental conditions to understand autumn-sowing cultivation and growth characteristics. A comparison of the growth parameters of the four cultivars throughout the growth period revealed that the increase in total leaf number and area, and plant height were almost completely inhibited in winter. In spring, these growth parameters increased rapidly in the early maturing cultivars and reached a plateau depending on the cultivar’s maturity type, as previously shown in spring-sowing cultivation. It is known that AcFT1 and AcFT4 play a key role in the bulb development of cultivated onions. Therefore, we conducted expression analysis of these genes for the four cultivars grown in the field and confirmed that AcFT1 was expressed following the maturity, irrespective of cultivation methods. We also analyzed AcGI expression in leaf blades, and a certain relationship between changes in bulb development and AcGI expression was observed. Correlation analysis of AcFT1 expression and total leaf number and area was conducted, and strong positive correlations were observed. In conclusion, our study demonstrated genetically that leaf number and area are important for inducing onion bulb development.

Growth and Gene Expression Related to Bulb Development and Day-length Responses in Onion Cultivars During Overwinter Cultivation

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A chemical genetic roadmap to improved tomato flavor

PLANT SCIENCE: A chemical genetic roadmap to improved tomato flavor

Physiological Investigation of Quantitative Traits for Fruit Mass Assessment Using a Tomato Introgression Line

Growth and Gene Expression Related to Bulb Development and Day-length Responses in Onion Cultivars During Overwinter Cultivation