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.

Tomato ripening is a highly coordinated developmental process that coincides with seed maturation. Regulated expression of thousands of genes controls fruit softening as well as accumulation of pigments, sugars, acids, and volatile compounds that increase attraction to animals. A combination of molecular tools and ripening-affected mutants has permitted researchers to establish a framework for the control of ripening. Tomato is a climacteric fruit, with an absolute requirement for the phytohormone ethylene to ripen. This dependence upon ethylene has established tomato fruit ripening as a model system for study of regulation of its synthesis and perception. In addition, several important ripening mutants, including rin, nor, and Cnr, have provided novel insights into the control of ripening processes. Here, we describe how ethylene and the transcription factors associated with the ripening process fit together into a network controlling ripening.

Humans heavily rely on dozens of domesticated plant species that have been further improved through intensive breeding. To evaluate how breeding changed the tomato fruit metabolome, we have generated and analyzed a dataset encompassing genomes, transcriptomes, and metabolomes from hundreds of tomato genotypes. The combined results illustrate how breeding globally altered fruit metabolite content. Selection for alleles of genes associated with larger fruits altered metabolite profiles as a consequence of linkage with nearby genes. Selection of five major loci reduced the accumulation of anti-nutritional steroidal glycoalkaloids in ripened fruits, rendering the fruit more edible. Breeding for pink tomatoes modified the content of over 100 metabolites. The introgression of resistance genes from wild relatives in cultivars also resulted in major and unexpected metabolic changes. The study reveals a multi-omics view of the metabolic breeding history of tomato, as well as provides insights into metabolome-assisted breeding and plant biology.

We conclude that MAX3 is required for the synthesis of a novel carotenoid-derived long-range signal that regulates shoot branching.

Highlights d Long-read sequencing of 100 tomato genomes uncovered 238,490 structural variants d Transposons underlie many SVs, and SV hotspots revealed large introgressions d SVs associated with genes are predictive of population-scale changes in expression d New genome assemblies resolved complex breeding QTLs caused by SVs

The ripening-impaired tomato mutant Never-ripe (Nr) is insensitive to the plant hormone ethylene. The gene that cosegregates with the Nr locus encodes a protein with homology to the Arabidopsis ethylene receptor ETR1 but is lacking the response regulator domain found in ETR1 and related prokaryotic two-component signal transducers. A single amino acid change in the sensor domain confers ethylene insensitivity when expressed in transgenic tomato plants. Modulation of NR gene expression during fruit ripening controls response to the hormone ethylene.

No abstract

Plants produce many volatile metabolites. A small subset of these compounds is sensed by animals and humans, and the volatile profiles are defining elements of the distinct flavors of individual foods. Flavor volatiles are derived from an array of nutrients, including amino acids, fatty acids, and carotenoids. In tomato, almost all of the important flavor-related volatiles are derived from essential nutrients. The predominance of volatiles derived from essential nutrients and health-promoting compounds suggests that these volatiles provide important information about the nutritional makeup of foods. Evidence supporting a relation between volatile perception and nutrient or health value will be reviewed.