Performing Department
(N/A)
Non Technical Summary
Tomato is one of the most widely cultivated, extensively consumed, and economically important horticultural crops in the US. However, the US tomato industry is facing certain major challenges, such as sustaining the competitiveness of domestic production, resilience to the increased frequency and severity of biotic and abiotic stresses driven by climate change, and meeting consumer demands for high-quality fresh and processed tomato products. Hence, the project will focus on developing tomato lines with high water use efficiency (WUE) and heat tolerance (HT) to mitigate the impacts of biotic and abiotic stresses compounded by a dynamic and changing climate. It is anticipated that this stakeholder-driven approach will lead to the development of n regionally adapted, disease-resistant, high-quality WUE and HT advanced breeding lines that support breeding flavorful, high-quality, healthy tomatoes, thus adding value for tomato breeders, seed companies, producers, distributors, processors, and retailers via increased consumer demand (SCRI focus areas 1, 3, and 5). Moreover, the high WUE and HT tomatoes will reduce the cost of tomato production while enhancing economic opportunities in agricultural areas and supporting rural living. The project focuses on field-grown tomatoes, but the identified traits and advanced breeding lines will be useful for tomatoes grown in other production systems. The project will yield vital data, advanced breeding lines, molecular breeding tools, elite inbred lines for fresh, mature green, and processing tomato types, and novel genetic diversity that breeders can use to improve future varieties.
Animal Health Component
50%
Research Effort Categories
Basic
30%
Applied
50%
Developmental
20%
Goals / Objectives
The long-term goal of this multidisciplinary project is to commercialize high water use efficiency (WUE) and heat tolerance (HT) tomato varieties with high-quality fruit, reduced foodborne pathogens (FBP) contamination, and improved postharvest shelf-life. In the timeframe of the project, we will focus on developing advanced breeding lines and molecular breeding tools (e.g., markers) that will be useful to both public breeders and seed companies for the further development of elite varieties with enhanced WUE, HT, and fruit quality targeted to specific growing regions and production systems (field, greenhouse, and Controlled Environment Agriculture). By combining traits that benefit producers (WUE, HT, shelf-life, and regional adaptation) and consumers (quality and decreased FBP susceptibility) with a robust evaluation of key marketing factors, our project activities will also support the eventual adoption of the resulting improved varieties across the supply chain to consumers.The project goal will accomplish the five stakeholder-driven objectives:Objective 1. Identify novel tomato genotypes with improved WUE, HT, disease resistance, and high nutritional and fruit quality. We believe that a broad panel of germplasm from across the U.S. will provide sufficient diversity for identifying loci/alleles and markers associated with key traits to improve abiotic/biotic stress tolerance and tomato fruit quality/nutrition, broadening trait improvement opportunities for all breeding programs.Objective 2. Develop and share advanced germplasm with the traits in Objective 1 and regional adaptation. The selected accessions from Obj 1 will have regional-specific adaptability, allowing us to develop germplasm specific to various geographic regions with unique climatic conditions.Objective 3. Produce advanced breeding lines and test their economic feasibility. A deep reservoir of germplasm diversity will enable the development of high-WUE and HT tomato accessions with high quality, shelf-life, texture, and nutrient traits. Informing consumers about the enhanced quality, health benefits, and climate resilience will support acceptance.
Project Methods
The following methods will be employed to achieve planned objectives.Activity 1.1: Screening and breeding for high WUE and HT tomatoes.Method 1. Screening of fresh market and processing tomato types for WUE and HT: Each breeding program will contribute 100 inbred lines and a core panel of 200 sequenced tomato accessions. WUE and HT traits will be field-evaluated to link them with genomic loci through GWAS and develop genomic selection models.Method 2. Morpho-physiological evaluations: Yield and quality will be assessed through leaf-level measurements of flower number, pollen and stigma health, fruit set, and size, damage from heat or sun, acidity, firmness, harvest index, ripening patterns, retail/eating quality, and disorders such as blossom-end rot and sunburn.Method 3. Root architecture analysis: High and low WUE genotypes will be evaluated for root architecture using high-resolution digital scans analyzed with WinRHIZO Pro software, crucial for understanding plant responses to soil, water, and nitrogen availability.Activity 1.2: Breeding for combined WUE and HT tomatoes: Each breeding program will focus on regional adaptability. OSU will develop WUE processing tomatoes for dry farm production. UF will breed for Florida and the Southeast, combining HT with resistance to multiple viruses and diseases using marker-assisted selection (MAS).Activity 1.3: Genomic and genetic studies to understand genes and markers associated with high-WUE and HTMethod 1. Marker development: Strong QTLs identified by GWAS will be validated using linkage analysis with four mapping populations of 200 F2 plants, phenotyped under water or heat stress. Genotyping will utilize the TAMU AgSeq platform, traditional GBS, or the Commercial Fresh Market Tomato PlexSeq SNP Panel.Method 2. QTL mapping: We'll map the chromosome 12 HT QTL using flanking markers in a backcross to pinpoint recombination. Progeny will be field-tested for fruit set and yield traits. Candidate genes will undergo functional analysis, and enhanced molecular markers linked to the QTL will be developed for MAS or genomic selection in breeding.Method 3. Genome and transcriptome profiling: Tomato pangenome will be integrated into transcriptome mapping to identify novel and variant transcripts. Trait-linked genomic regions will be analyzed for sequence and expression changes associated with traits of interest. Candidate genes linked to WUE, HT, disease resistance, and quality traits will undergo functional analysis using gene editing techniques.Method 4. Genomic selection: GS methods (GBLUP, RRBLUP, and LASSO) will be evaluated for prediction accuracy, with the best selected. The TAMU AgSeq platform or Agriplex PlexSeq SNP Panel will provide informative SNPs. Prediction accuracy will be the mean Pearson correlation between predicted GEBVs and phenotypic BLUPs.Method 5. Marker-assisted selection for disease resistance: Breeding will use marker-assisted selection for key disease resistance genes (Ty-1, Ty-2, Ty-3, Ty-6, Sw-5, Sw-7, Tm-2, I-2, I-3, Frl, Ve, Mi) each cycle. Advanced HT and WUE lines and hybrids will be evaluated using seedling disease screens and natural field disease pressures and then tested at multiple locations.Activity 1.4: Evaluating fruit quality: Physico-chemical, sensory, and metabolomic analyses will be conducted annually on top-performing fresh market and processing tomato lines, using tomato juice processed via the hot break method to assess attributes.Method 1. Physicochemical evaluation: Internal and external fruit color (Chroma Meter), titratable acidity (DL 22 Food and beverage analyzer), texture, firmness (digital penetrometer), and total soluble solids (TSS, digital refractometer) will be evaluated for all the selected breeding lines.Method 2. Sensory evaluation: Sensory quality, including color, flavor, and texture, of tomato cultivars will be evaluated using affective scaling instruments like the 9-point Hedonic scale, 5-point Just-About-Right scale, and Check-All-That-Apply scale to assess overall acceptability and specific attributes.Method 3. Metabolomic analysis by GC-MS, GC - olfactory detector, and UHPLC-MS: We will evaluate improved HT and WUE lines for consumer-preferred nutritional and phytochemical compositions, including vitamins, carotenoids, polyphenols, amino acids, GABA, fatty acids (FAs), and green leaf volatiles (GLVs). Volatiles will be analyzed by GC-MS with olfactory detection, and non-volatile flavor compounds by LC. Metabolites will be identified and quantified using UHPLC-HR-ESI-QTOF-MS and GC-MS.Activity 2.1: Impact of genotype x environment on selected WUE and HT tomato lines: The team will analyze GxE interactions, collect yield data, assess disease resistance, and evaluate regional adaptability across multiple states. They'll also test promising germplasm for yield, size, health, and fruit quality.Activity 2.2: Development of CRISPR higher-order knockout WUE and HT lines for reduced decay and higher juice viscosity: Gene-edited knockouts of PG, PL, PME, and LOB1 will be created using Golden Gate technology with Cas9 plasmids. Transformants will be assessed for enzyme activity reduction in ripe fruit and monitored for fruit traits and juice consistency.Activity 2.3: Stress management of WUE and HT tomatoes by using growth regulators: Transient growth attenuation induced by plant hormones is integral to stress tolerance. As a complementary, non-GMO approach, we will use commercial plant growth regulators, such as paclobutrazol (antagonist of gibberellin) and abscisic acid, to optimize growth and stress tolerance.Activity 2.4: Flavor, aroma, and quality profiling of selected lines: As per Activity 1.4, the quality, sensory, and metabolomic analysis of the selected advanced breeding lines will be performed on both fresh market and processing tomato types.Activity 3.1: Assessment of microbial load, pathogen attachment, and surface decontamination of various tomato advanced breeding linesMethod 1. Efficacy of HT and high WUE tomatoes in deterring FBP attachment & internalization.HT and high WUE tomato lines will undergo field assessment for microbiological quality and pathogen prevalence. Lines will be categorized based on microbial attachment strength and correlated with intrinsic antimicrobials.Method 2. Evaluation of postharvest sanitation treatments of selected HT and high WUE tomato lines for FBP decontamination. We will test gaseous ozone, plant-based antimicrobials via low-water fogging, and a commercial sanitizer to evaluate bacterial populations at different concentrations and contact times.Activity 3.2: Evaluation of postharvest fruit rotting: To evaluate fruit susceptibility to fungal decay in the selected advanced breeding lines with high WUE and HT, two common postharvest pathogens (Rhizopus stolonifera and Botrytis cinerea) will be used for fruit inoculations.Activity 3.3: Mining for potential metabolite markers linked to disease resistance and microbial control in high WUE and HT tomatoes: Metabolomic analysis will be performed on the high and low fruit surface attachment lines for FBP. GLVs and FA levels will be measured, and their correlation with disease resistance and microbial control will be evaluated.Activity 3.4: Economic feasibility study of developed advanced breeding lines and consumer neuro-economics analysis: Consumer attention, evaluated through sensory evaluation and neuroscience techniques, will predict willingness to pay (WTP) for new food products, shaping marketing strategies and policies. Promising WUE and HT tomato lines will be screened based on consumer willingness-to-accept (WTA) and WTP for sensory and nutritional qualities.Activity 3.5: Dissemination of information to key stakeholders: To efficiently disseminate information, bilingual fact sheets will be created for producers, processors, retailers, seed companies, extension agents, dietitians, and the public.