Sl-ALMT9, directly regulated by Sl-WRKY42, contributes to fruit malate accumulation both in fruit and root and enhances aluminum tolerance of tomato.

Tomato (Solanum lycopersicum) is one of the highest-value vegetable crops worldwide. Understanding the genetic regulation of primary metabolite levels can inform efforts aimed toward improving the nutrition of commercial tomato cultivars, while maintaining key traits such as yield and stress tolerance. We identified 388 suggestive association loci (including 126 significant loci) for 92 metabolic traits including nutrition and flavor-related loci by genome-wide association study from 302 accessions in two different environments. Among them, an ascorbate quantitative trait locus TFA9 (TOMATO FRUIT ASCORBATEON CHROMOSOME 9) co-localized with SlbHLH59, which promotes high ascorbate accumulation by directly binding to the promoter of structural genes involved in the D-mannose/L-galactose pathway. The causal mutation of TFA9 is an 8-bp InDel, named InDel_8, located in the promoter region of SlbHLH59 and spanned a 5’UTR Py-rich stretch motif affecting its expression. Phylogenetic analysis revealed that differentially expressed SlbHLH59 alleles were selected during tomato domestication. Our results provide a dramatic illustration of how ascorbate biosynthesis can be regulated and was selected during the domestication of tomato. Furthermore, the findings provide novel genetic insights into natural variation of metabolites in tomato fruit, and will promote efficient utilization of metabolite traits in tomato improvement. Deciphering the diverse, interconnected plant metabolome can facilitate crop improvement. In this study, the use of a combination of multiple technologies has allowed us to obtain novel functional and genetic insights into our GWAS investigating variation in ascorbate accumulation in tomato. The InDel_8 in the promoter of SlbHLH59 was selected during tomato domestication and determines fruit ascorbate content by directly regulating the expression of structural genes involved in ascorbate biosynthesis in tomato fruit. The genes and polymorphisms responsible for the variations identified in this study lay the foundation for further comparative genomic studies and for improving nutrition quality in tomato and other fruit crops.

Ascorbic acid (AsA) has high antioxidant activities, and its biosynthesis has been well studied by engineering of a single structural gene (SG) in staple crops, such as tomato (Solanum lycopersicum). However, engineering the AsA metabolic pathway by multi-SG for biofortification remains unclear. In this study, pyramiding transgenic lines including GDP-Mannose 3′,5′-epimerase (GME) × GDP-d-mannose pyrophosphorylase (GMP), GDP-l-Gal phosphorylase (GGP) × l-Gal-1-P phosphatase (GPP) and GME × GMP × GGP × GPP, were obtained by hybridization of four key genes to get over-expression transgenic plants (GME, GMP, GGP, and GPP) in tomato. Pyramiding lines exhibited a significant increase in total ascorbate in leaves and red fruits except for GGP × GPP. Expression analysis indicated that increased accumulation of AsA in pyramiding transgenic lines is due to multigene regulation in AsA biosynthesis. Substrate feeding in leaf and fruit suggested that AsA biosynthesis was mainly contributed by the d-Man/l-Gal pathway in leaves, while alternative pathways may contribute to AsA accumulation in tomato fruit. Pyramiding lines showed an enhanced light response, stress tolerance, and AsA transport capacity. Also, fruit shape, fruit size, and soluble solids were slightly affected by pyramiding. This study provides the first comprehensive analysis of gene pyramiding for ascorbate biosynthesis in tomato. SGs pyramiding promotes AsA biosynthesis, which in turn enhances light response and oxidative stress tolerance. Also, the data revealed an alternative ascorbate biosynthesis pathway between leaves and fruit of tomato.

Addressing the global malnutrition crisis requires precise and timely diagnostics of plant stresses to enhance the quality and yield of nutrient-rich crops, such as tomatoes. Soft wearable sensors offer a promising approach by continuously monitoring plant physiology. However, challenges remain in identifying direct physiological indicators of plant stresses, hindering the development of accurate diagnostic models for predicting symptom progression. Here, we introduce a machine-learning-powered spectral-dominant multimodal soft wearable system (MapS-Wear) for precise, long-term, and early-stage diagnosis of stresses in tomatoes. MapS-Wear continuously tracks leaf surrounding temperature, humidity, and unique in-situ transmission spectra, which are critical stress-related indicators. The machine learning framework processes these multimodal data to predict gradual stress progression and diagnose nutrient deficiencies in plants over 10 days earlier than conventional computer vision methods. Moreover, MapS-Wears enables portable and large-scale screening of grafted tomato varieties in greenhouses, accelerating the identification of compatible grafting combinations. This demonstration highlights the potential for high-throughput plant phenotyping and yield improvement.

In plants, chloroplasts are the sites at which photosynthesis occurs, and an increased abundance of chloroplasts increases the nutritional quality of plants and the resultant color of fruits. However, the molecular mechanisms underlying chlorophyll synthesis and chloroplast development in tomato fruits remain unknown. In this study, we isolated a chlorophyll-deficient mutant, reduced chlorophyll mutant 1 (rcm1), by ethylmethanesulfonate mutagenesis; this mutant produced yellowish fruits with altered chloroplast development. MutMap revealed that Solyc08g005010 is the causal gene underlying the rcm1 mutant phenotype. A single-nucleotide base substitution in the second exon of SlRCM1 results in premature termination of its translated protein. SlRCM1 encodes a chloroplast-targeted metalloendopeptidase that is orthologous to the BCM1 protein of Arabidopsis and the stay-green G protein of soybean (Glycine max L. Merr.). Notably, the yellowish phenotype of the lutescent1 mutant can be restored with the allele of SlRCM1 from wild-type tomato. In contrast, knockout of SlRCM1 by the CRISPR/Cas9 system in Alisa Craig yielded yellowish fruits at the mature green stage, as was the case for lutescent1. Amino acid sequence alignment and functional complementation assays showed that SlRCM1 is indeed Lutescent1. These findings provide new insights into the regulation of chloroplast development in tomato fruits.

The domestication of tomato has led to striking variations in fruit morphology. Here, we show a genome-wide association study (GWAS) to understand the development of the fruit tip and describe aPOINTED TIP(PT) gene that encodes a C2H2-type zinc finger transcription factor. A single nucleotide polymorphism is found to change a histidine (H) to an arginine (R) in the C2H2 domain of PT and the two alleles are referred to asPT^HandPT^R. Knocking outPT^Hleads to development of pointed tip fruit.PT^Hfunctions to suppress pointed tip formation by downregulating the transcription ofFRUTFULL 2(FUL2), which alters the auxin transport. Our evolutionary analysis and previous studies by others suggest that thePT^Rallele likely hitch-hiked along with other selected loci during the domestication process. This study uncovers variation inPTand molecular mechanism underlying fruit tip development in tomato.