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Ascorbic acid (AsA) is an important nutrient component contributing to major flavor value of tomato fruit and human health. Although transcription regulation of AsA biosynthetic genes have been well demonstrated, epigenetic modification underlying AsA accumulation remains unclear. In this study, we exposed immature tomato fruits to a methyltransferase inhibitor (5-azacytidine) and detected the impacts on AsA accumulation. Inhibition of DNA methylation enhanced AsA accumulation in tomato leaves and fruits. We further isolated a AsA biosynthetic gene, SlGalUR5, which encodes a D-galacturonic acid reductase. SlGalUR5 showed reduced DNA methylation levels and higher transcription levels in Slmet1 mutant while have converse pattern in Sldml2 mutant. 5-azacytidine treatment significantly decreased DNA methylation levels of SlGalUR5 in fruits. Conversely, transcription profiles of SlGalUR5 and enzyme activity of GalUR were enhanced in 5-azacytidine–treated fruits. Our finding revealed a new insight into epigenome modification of SlGalUR5 involved in ascorbic acid accumulation and provide a potential means of increasing AsA levels for tomato breeding.

Malic acid (MA) is an important flavor acid in fruits and acts as a mediator in a series of metabolic pathways. It is important to understand the factors affecting MA metabolism for fruit flavor improvement and to understand MA-mediated biological processes. However, the metabolic accumulation of MA is controlled by complex heredity and environmental factors, making it difficult to predict and regulate the metabolism of MA. In this study, we carried out a genome-wide association study (GWAS) on MA using eight milestone models with two-environment repeats. A series of associated SNP variations were identified from the GWAS, and 15 high-confidence annotated genes were further predicted based on linkage disequilibrium and lead SNPs. The transcriptome data of candidate genes were explored within different tomato organs as well as various fruit tissues, and suggested specific expression patterns in fruit pericarp. Based on the genetic parameters of population differentiation and SNP distribution, tomato MA content has been more influenced by domestication sweeps and less affected by improvement sweeps in the long-term history of tomato breeding. In addition, genotype × environment interaction might contribute to the difference in domestication phenotypic data under different environments. This study provides new genetic insights into how tomato changed its MA content during breeding and makes available function-based markers for breeding by marker-assisted selection.

Domestication and improvement are important processes that generate the variation in genome and phonotypes underlying crop improvement. Unfortunately, during selection for certain attributes, other valuable traits may be inadvertently discarded. One example is the decline in fruit soluble solids content (SSC) during tomato breeding. Several genetic loci for SSC have been identified, but few reports on the underlying mechanisms are available. In this study we performed a genome-wide association study (GWAS) for SSC of the red-ripe fruits in a population consisting of 481 tomato accessions with large natural variations and found a new quantitative trait locus, STP1, encoding a sugar transporter protein. The causal variation of STP1, a 21-bp InDel located in the promoter region 1124 bp upstream of the start codon, alters its expression. STP1Insertion accessions with an 21-bp insertion have higher SSC than STP1Deletion accessions with the 21-bp deletion. Knockout of STP1 in TS-23 with high SSC using CRISPR/Cas9 greatly decreased SSC in fruits. In vivo and in vitro assays demonstrated that ZAT10-LIKE, a zinc finger protein transcription factor (ZFP TF), can specifically bind to the promoter of STP1Insertion to enhance STP1 expression, but not to the promoter of STP1Deletion, leading to lower fruit SSC in modern tomatoes. Diversity analysis revealed that STP1 was selected during tomato improvement. Taking these results together, we identified a naturally occurring causal variation underlying SSC in tomato, and a new role for ZFP TFs in regulating sugar transporters. The findings enrich our understanding of tomato evolution and domestication, and provide a genetic basis for genome design for improving fruit taste.

Ascorbic acid (AsA), an important antioxidant and growth regulator, and it is essential for plant development and human health. Specifically, humans have to acquire AsA from dietary sources due to their inability to synthesize it. The AsA biosynthesis pathway in plants has been elucidated, but its regulatory mechanism remains largely unknown. In this report, we biochemically identified a CCAAT-box transcription factor (SlNFYA10) that can bind to the promoter of SlGME1, which encodes GDP-Man-3’,5’-epimerase, a pivotal enzyme in the d-mannose/l-galactose pathway. Importantly, SlNFYA10 simultaneously binds to the promoter of SlGGP1, a downstream gene of SlGME1 in the d-mannose/l-galactose pathway. Binding assays in yeast and functional analyses in plants have confirmed that SlNFYA10 exerts a negative effect on the expression of both SlGME1 and SlGGP1. Transgenic tomato lines overexpressing SlNFYA10 show decreased levels of SlGME1 and SlGGP1 abundance and AsA concentration in their leaves and fruits, accompanied by enhanced sensitivity to oxidative stress. Overall, SlNFYA10 is the first CCAAT-binding factor identified to date to negatively regulate the AsA biosynthetic pathway at multiple sites and modulate plant responses to oxidative stress.

Fruit color and pigment content are two important traits that largely determine the quality of tomato fruits. In this study, six genetic populations, namely, P1, P2, F1, BC1, BC2 and F2, were generated using tomato plants with green and purple fruits as female and male parents, respectively. The genetic developments of fruit color and pigment content were investigated through multigenerational joint analysis of quantitative traits. Results demonstrated that the optimal genetic model of fruit color between green and purple fruits was MX1-AD-ADI. The major gene heritabilities of shade values in BC1, BC2 and F2 generations were 88%, 63% and 82%, and their polygene heritabilities were 9%, 11% and 14%, respectively. The heredity of lycopene content conformed to MX2-ADI-AD model. The heritabilities of major genes in BC1, BC2 and F2 were 67%, 78% and 97%, while those of polygenes were 21%, 0% and 0%, respectively. The genetic model of chlorophyll was MX1-AD-ADI. The heritabilities of major genes in BC1, BC2 and F2 were 62%, 77% and 62%, respectively, and those of polygenes were all 0%. The inheritance of carotene was in accordance with MX2-ADI-ADI model. The heritabilities of major genes in BC1, BC2 and F2 were 80%, 47% and 57%, while those of polygenes were 0.01%, 0.02% and 14%, respectively. This study provides valuable information for fruit quality improvement in tomato breeding.