Multiple-model GWAS identifies optimal allelic combinations of quantitative trait loci for malic acid in tomato

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,themetabolic 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 geneswere further predicted based on linkage disequilibrium and lead SNPs.The transcriptome data of candidate geneswere 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.

A 21-bp InDel in the promoter of STP1 selected during tomato improvement accounts for soluble solid content in fruits

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.STP1 Insertion 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.

Heat-inducible SlWRKY3 confers thermotolerance by activating the SlGRXS1 gene cluster in tomato

High temperature stress is one of the major environmental factors that affect the growth and development of plants. Although WRKY transcription factors play a critical role in stress responses, there are few studies on the regulation of heat stress by WRKY transcription factors,especially in tomato. Here, we identified a group I WRKY transcription factor, SlWRKY3, involved in thermotolerance in tomato. First, SlWRKY3 was induced and upregulated under heat stress. Accordingly, overexpression of SlWRKY3 led to an increase, whereas knock-out of SlWRKY3 resulted in decreased tolerance to heat stress. Overexpression of SlWRKY3 accumulated less reactive oxygen species(ROS), whereas knock-out of SlWRKY3 accumulated more ROS under heat stress. This indicated that SlWRKY3 positively regulates heat stress in tomato. In addition,SlWRKY3 activated the expression of a range of abiotic stress-responsive genes involved in ROS scavenging, such as a SlGRXS1 gene cluster.Further analysis showed that SlWRKY3 can bind to the promoters of the SlGRXS1 gene cluster and activate their expression. Collectively, these results imply that SlWRKY3 is a positive regulator of thermotolerance through direct binding to the promoters of the SlGRXS1 gene cluster and activating their expression and ROS scavenging.

A CCAAT-binding factor,SlNFYA10,negatively regulates ascorbate accumulation by modulating the D-mannose/L-galactose pathway in tomato

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 Dmannose/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.

Effect of shading on ascorbic acid accumulation and biosynthetic gene expression during tomato fruit development and ripening

The purpose of the current study was to determine the effect of leaf shading,fruit shading,and a combination of both,on the accumulation of ascorbic acid(AsA)and the expression levels of AsA biosynthetic genes at the immature green,mature green,breaker,and red ripe stages of Ailsa craig tomato during fruit development.Shading(72%reducing of light intensity)imposed on the leaves significantly reduced AsA content and AsA biosynthetic gene expression in the fruits.Leaf shading,fruit shading,and a combination of both significantly decreased the amount of total AsA and reduced AsA to a range of 18.5%−31.5%at mature green,breaker,and red ripe stages of tomato fruits,with no significant change at the immature green stage of fruits.Moreover,reducing the light intensity in tomato leaves,fruits or both resulted in reduced expression of most AsA biosynthetic genes in the fruits,except for PMM,cAPX,tAPX,and APX7 genes under leaf shading,GPI,PMI,PMM,GP1,GP2,cAPX,and tAPX genes under fruit shading,and PMM,cAPX,APX1,and APX7 genes under both shading.The expression level of GMP,GP1,and GalDH showed an upregulation at the red ripe stage in fruits with leaf shading,and also an up-regulation at the immature green and red ripe stages with both shading.Furthermore,positive correlations between expression of AsA biosynthetic genes and AsA accumulation were recorded under leaf shading,fruit shading,and both types of shading,while a negative correlation was recorded under normal conditions without shading.

Regulation of invertase and sucrose for improving tomato fruit flavor:A review

Tomato(Solanum lycopersicum L.)is a commercially farmed vegetable belonging to the Solanaceae family,the third most important vegetable after potato(Solanum tuberosum L.)and onion(Allium cepa L.).It is cultivated for its fresh fruits and processed paste,with over 153 million metric tons of global production.However,modern tomato cultivars have limited sugars,acids,and volatiles allelic diversity as flavor has generally been less prioritized in breeding programs.Invertase is an essential regulator of flavor and sugar metabolism in tomato.Genetic control of tomato flavor is still incomplete without a clear understanding of the roles of invertase and sucrose metabolism.This review provides an overview of our current understanding of the invertase mode of action in sucrose metabolism,their evolutionary and functional divergence in the tomato genome,role in stress response,genetic and hormonal control of fruit flavor and quality.We summarized the primary roles of invertase in sugar metabolism and fruit flavor.