DISCOVERY AND EXPLOITATION OF GENES CONDITIONING QUALITY AND RESISTANCE TRAITS IN MELONS, PEPPERS AND TOMATOES

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1016350
• Project Start Date: Jun 25, 2018
• Project End Date: Jun 7, 2023
• Program Code: [(N/A)]- (N/A)

Recipient Organization
TEXAS A&M UNIVERSITY
750 AGRONOMY RD STE 2701
COLLEGE STATION,TX 77843-0001

Performing Department
Horticultural Science

Non Technical Summary
New genetic lines of melon, tomato and pepper will be developed by traditional breeding techniques to improved flavor, stress resistance and post-harvest characteristics. These will be tested in multiple locations with collaborating growers, in addition to other regions of the US. Cultivars will be released for the seed industry to address regional adaptation issues. Genes for quality and stress resistance will be mapped with DNA markers to expedite the selection process for all breeders working on these three crops. Scientific publications as well as extension bulletins will be produced and outreach through field days will be conducted. Students in horticulture and plant breeding will be trained to provide industry and academia with more qualified candidates for future jobs.

Animal Health Component

40%

Research Effort Categories

Basic

40%

Applied

40%

Developmental

20%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
201	1420	1081	40%
201	1461	1081	30%
201	1460	1081	30%

Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1460 - Tomato; 1461 - Peppers; 1420 - Melons;

Field Of Science
1081 - Breeding;

Keywords

melons

peppers

tomatoes

plant breeding

quality

stress resistance

adaptation

Goals / Objectives
Breeding-Improve fruit quality of our vine decline (M. cannonballus, D. bryoniae) Improve fruit quality and disease resistance of TAMU tomato linesIncrease powdery and downy mildew resistance in TAMU melonsImprove fruit quality & nutritional value of TAMU virus resistant linesCombine horizontal bacterial leaf spot and Phytophthora resistance genes with potyvirus resistance in TAMU pepper linesCreate breeding lines with improved root systems and leaf cover for enhanced drought stress and sugar production.Increase resistance to aphids, mites and leafminers in TAMU pepper lines through inter-specific crossesImprove TAMU breeding lines for firmness, appearance, sugar accumulation, flavor and content of beneficial phytochemicals.Genetics-Develop inbred lines and heterozygous populations, segregating for genetic traits of interest, for inheritance and gene function studies.Evaluate genotype by environment interaction for important traitsStudy inheritance of sugar, ascorbic acid, flavonoid and carotenoid production and accumulation in melons and peppers.Continue to map genes of interest with molecular markers to assist selection of superior phenotypes.Utilize our genetic transformation system to create melons with enhanced carotenoid levels and virus resistance

Project Methods
In order to combine disease resistance, excellent fruit quality and improved stress tolerance, several breeding schemes will be used. A combination of backcrossing and mass selection will be used to combine multiple gene traits such as M. cannonballus resistance with important single genes such as virus resistance. A recurrent selection scheme will be implemented to develop improved populations with multiple desirable traits. These populations will then be intercrossed to develop superior lines, which can be inbred and selected to fix important gene blocks. These inbred lines will be tested as parents for hybrid development and also as open-pollinated varieties. A pedigree system will be used to introgress major genes into elite inbred lines by backcrossing, and to test elite lines as parents in hybrid combinations. To ensure the presence of disease resistance and fruit quality genes, all breeding lines will be screened in multiple environments in Texas. Field selections will be made and cuttings taken from superior lines for self-pollinations in the greenhouse. Fruit will be harvested from replicated trials to measure yield, sugar content, flavor, nutrient content and other quality attributes. All disease resistance genes will be screened under controlled conditions in a greenhouse or growth chamber with severe isolates of the pathogen. These isolates will be maintained on plants or culture plates in contamination-free chambers. This screening will be repeated each generation in the development process. Field disease screening plots will not be treated with chemical pesticides against the fungal or bacterial pathogen of interest. Field samples will be cultured in the lab to confirm presence of the disease. Viral pathogens will be confirmed by appropriate assay (ELISA, PCR, etc). New germplasm will be screened for important genes and adaptation to South Texas. Sources of important genes will be included in the breeding program. Insect-resistant lines will be screened in cages and observed in field plots as well. Root systems will be evaluated in greenhouse experiments in large pots with sterile or disease infested sand. Cleaned roots will be scanned into a computer for morphological analysis. Root systems will also be excavated from the field to evaluate the impact of the soil and environment on development. In order to evaluate the genetic components of complex traits such as M. cannonballus resistance, root development, and flavonoid synthesis, distinct populations will be created with extreme disease reaction, chemical content or root morphology phenotypes. The most resistant and most susceptible families will be compared for root development, chemical constituents of the roots, genotypic differences at the nucleic acid level and statistical differences in genetic variation. Chemical and physiological differences will be mapped in the populations in an attempt to elucidate linkage to important genes, and facilitate selection. Genotyping by sequencing along with association mapping will be utilized to create SNP markers for use in marker-assisted selection. These same families can be used to verify the inheritance and map important single genes such as resistance to CYSDV, gummy stem blight and PepMoV. In addition, recombinant inbred lines which segregate for these important genes will be developed for use in gene mapping and isolation experiments.

Progress 10/01/19 to 09/30/20

Outputs
Target Audience:These included local melon, tomato and pepper producers in south, central and west Texas, as well as New Mexico. Also, we assisted several commercial seed companies with disease screening, DNA marker analyses and field trials. Dr. Crosby served as chair or member for 6 PhD and 4 M.S. students. We presented our research results to small growers, international research faculty, TAMU administration and visiting scientists. We also provided seed for extension trials and home gardeners throughout Texas Changes/Problems:COVID19 severely impacted our ability to attend sceintific conferences and hold field days. It also prevented some travel which interfered with field trials and data collection. What opportunities for training and professional development has the project provided?Four graduate students and 3 undergraduate students were trained in plant breeding, virology and horticulture. Three graduate students and the PI attended the Texas A&M Plant Breeding Symposium. How have the results been disseminated to communities of interest?The PI participated in two video conferences for the SCRI melon project meetings in Texas and delivered a departmental seminar. What do you plan to do during the next reporting period to accomplish the goals?Screen advanced selections and new families for the quality and stress resistance traits important to Texas growers. Investigate genetic control of novel traits and attempt to map relevant genes and QTL with genotyping by sequencing approach. Release new melon and tomato germplasm to the seed industry for dissemination to growers. Publish research results in refereed journals and conference proceedings. Present research results at a national conference, the American Society for Horticultural Sciences.

Impacts
What was accomplished under these goals? Screened 50 melon inbred lines and 14 hybrids for fuit quality and disease resistance at 6 locations. Screened 30 experimental tomato hybrids and inbred lines in four field and tunnel locations. Analyzed volatile compounds, sugars, carotenoids and fruit firmness. Screened for powdery mildew and pepper mottle virus resistance in 120 pepper breeding lines. Conducted more than 300 controlled pollinations of melons, peppers and tomatoes to combine resistance and quality genes and create new populations. Screened pepper breeding lines for bacterial leaf spot and tomato spotted wilt resistance in three field trials with commercial growers. Evaluated root health of melon breeding lines inoculated with Monosporascus cannonballus at Weslaco field trial and in greenhouse pots. Selected for fruit firmness and suagr content in more than 50 melon breeding lines and hybrids. Advanced interspecific pepper families and screened for resistance to two viruses. Detected QTL linked to both pepper mottle virus and powdery mildew resistance in a single pepper population. Investigated the environment effect on tomato fruit volatiles and flavor in open field and tunnel production. Devised a tissue culture regeneration system for two species of peppers- Capsicum, so that gene editing can be attempted.

Publications

• Type: Journal Articles Status: Published Year Published: 2020 Citation: Lee, J.H.J., Jayaprakasha, G.K., Avila, C.A., Crosby, K., Patil, B.S. 2020. Effects of genotype and production system on quality of tomato fruits and in vitro bile acids binding capacity. Journal of Food Science. 85(11): 3806-3814. DOI: 10.1111/1750-3841.15495
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Kandel, D.R., Marconi, T.G., Badillo-Vargas, I.E., Enciso, J., Zapata, S.D., Lazcano, C.A., Crosby, K., and Avila, C.A. Yield and fruit quality of high-tunnel tomato cultivars produced during the o?-season in South Texas. Scientia Hort 272 (2020) 109582
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Singh, J., Metrani, R., Jayaprakasha, G.K., Crosby, K.M., Ravishankar, S., Patil, B.S. 2020. Multivariate Analysis of Amino Acids and Health Bene?cial Properties of Cantaloupe Varieties Grown in Six Locations in the United States. Plants 9: 1058.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Lee, J.H.J., Awika, H., Jayaprakasha, G.K., Avila, C.A., Crosby, K., Patil, B.S. 2020. Tomato Metabolic Changes in Response to Tomato-Potato Psyllid (Bactericera cockerelli) and Its Vectored Pathogen Candidatus Liberibacter solanacearum. Plants 2020, 9, 1154. DOI: 10.3390/plants9091154
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Acharya, P., Jayaprakasha, Crosby, K., Jifon, J.L., Patil, B.S. 2020 Nanoparticle-Mediated Seed Priming Improves Germination, Growth, Yield, and Quality of Watermelons (Citrullus lanatus) at multi-locations in Texas. Scientific Reports 10(1): 5037. DOI: 10.1038/s41598-020-61696-7
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Djidonou, D., Leskovar, D.I., Joshi, M., Jifon, J., Avila, C.A., Masabni, J., Wallace, R.W., and K. Crosby. 2020. Stability of yield and its components in grafted tomato tested across multiple environments in Texas. Scientific Reports (2020) 10: 13535
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Sharma, S.P., Leskovar, D.I., Crosby, K., Ibrahim, A.M.H., 2020. GGE Biplot Analysis of Genotype-by-environment Interactions for Melon Fruit Yield and Quality Traits. HortScience 55(4) 533-542. DOI: 10.21273/HORTSCI14760-19
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Chaudhary, S., Laughlin, D., Setamou, M., daGraca, J., Kunta, M., Alabi, O.J., Crosby, K., Ong, K.L., Ancona, V. 2020. Incidence, Severity, and Characterization of Phytophthora Foot Rot of Citrus in Texas and Implications for Disease Management. Plant Disease 104(9): 2455-2461. DOI: 10.1094/PDIS-07-19-1493-RE
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Lee, J.H.J., Kasote, D.M., Jayaprakasha, G.K., Avila, C.A., Crosby, K., Patil, B.S. 2020. Effect of Production System and Inhibitory Potential of Aroma Volatiles on Polyphenol Oxidase and Peroxidase Activities of Tomatoes. Journal of the Science of Food and Agriculture. DOI: 10.1002/jsfa.10644

Progress 10/01/18 to 09/30/19

Outputs
Target Audience: These included local melon, onion, tomato and pepper producers in south and west Texas, as well as New Mexico. Also, we assisted several commercial seed companies with disease screening, DNA marker analyses and field trials. Dr. Crosby served as chair or member for 5 graduating PhD and M.S. students. We presented our research results to visiting student groups, master gardeners, TAMU administration and visiting scientists. We also provided seed for extension trials and home gardeners throughout Texas. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Trained 5 graduate students and two undergraduate students in plant breeding, genetics and disease resistance screening. Held a symposium for tomato growers at the Texas A&M Horticulture research greenhouses. How have the results been disseminated to communities of interest?Held a symposium on tomato culture. PI delivered two talks at field days to growers and one talk to master gardeners about tomato. We published 4 journal articles, and presented 8 talks at scientific conferences. We hosted two seed companies to field trials in south Texas. The PI visited 6 vegetable farms in Texas, New Mexico and Arizona to provide expert advice to growers. What do you plan to do during the next reporting period to accomplish the goals?Continue projects with 4 graduate students to identify genes and develop germplasm with improved quality and stress resistance traits. Develope saturated linkage maos of two pepper poulations and SNP markers linked to virus and powdery mildew resistance genes. Release several hybrid melon and pepper cultivars to the seed industry.

Impacts
What was accomplished under these goals? Evaluated 39 melon hybrids for disease resistance and quality at Uvalde, Weslaco, Arizona, California, North Carolina, Georgia and Indiana. Six were identified for further trialing. Evaluated more than 500 pepper breeding lines at Weslaco, Uvalde and College Station, selecting about 300 inbreds and 16 hybrids to advance. Evaluated 70 tomato breeding lines and 30 hybrids at Edinburg, College Station, Waller and Uvalde. Selected about 50 inbred lines to advance and 10 hybrids for additional commercial trials. More than 50 pepper breeding lines and two F2 populations were screened by 2 graduate students for resistance to TSWV and PepMoV in a greenhouse. 150 F2 progeny from the pepper family segregating for PepMoV resistance were sequenced to be used for SNP development. An interspecific pepper family was screened for resistance to Tobacco Etch Virus through controlled inoculations in a greenhouse. Inheritance of a novel resistance gene was estimated. Tomato quality analyses by HPLC and Mass-spectrometry were carried out by a PhD student to identify breeding lines with high levels of lycopene and volatile compounds associated with flavor. One MS student created and screened 34 experimental muskmelon hybrids for fruit quality and determined heritabilities for important traits. Thre outstanding hybrids were identified. One PhD student screened a melon population for resistance to Monosporascus cannonballus root rot. We conducted more than 500 controlled pollinations of peppers, melons and tomatoes in the greenhouse to create new families, F1 hybrids and backcross generations. We conducted commercial trials of pepper, onion and tomato hybrids with 10 growers in four states. Twelve pepper hybrids, three melon hybrids and one tomato hybrid were selected for potential commercialization.

Publications

• Type: Journal Articles Status: Published Year Published: 2019 Citation: Xie, L., Klein, P., Crosby, K. and J. Jifon. 2019. A genotyping-by-sequencing single nucleotide polymorphism-based map and genetic analysis of root traits in an interspecific tomato population. J. Amer. Soc. Hort Sci. 144: 1-11.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Lee, J.H.J., Jayaprakasha, G.K., Avila, C.A., Crosby, K.M., and B.S. Patil. 2019. Metabolomic studies of volatiles from tomatoes grown in net-house and open-field conditions. Food Chemistry 275: 282-291.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Lee, J.H.J., Jayaprakasha, G.K., Rush, C.M., Crosby, K.M., and B.S. Patil. 2018. Production system influences volatile biomarkers in tomato. Metabolomics 14:99.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Perez, J.L., Jayaprakasha, G.K., Crosby, K., and B.S. Patil. 2018. Evaluation of bitter melon (Momordica charantia) cultivars grown in Texas and levels of various phytonutrients. J. Sci. Food. Agric. 99:379-390.

Progress 06/25/18 to 09/30/18

Outputs
Target Audience:These included local melon, tomato and pepper producers in south and west Texas, as well as New Mexico. Also, we assisted several commercial seed companies with disease screening, DNA marker analyses and field trials. Dr. Crosby served as chair or member for4 PhD and 4 M.S. students. We presented our research results to small growers, international research faculty, TAES administration and visiting scientists. We also provided seed for extension trials and home gardeners throughout Texas. Changes/Problems:The development of transgenic melons will not be pursued further. Funding and industry demand is limited. What opportunities for training and professional development has the project provided?Three graduate students were trained in plant breeding, virology and horticulture. The Project investigator and one graduate student attended international conferences to present results of the melon breeding program for quality and stress tolerance. How have the results been disseminated to communities of interest?The PI participated in two field days andtwo annual meetings in Texas to present results to growers and public attendees. Power point presentations and field talks were delivered. What do you plan to do during the next reporting period to accomplish the goals?Screen advanced selections and new families for the quality and stress resistance traits important to Texas growers. Investigate genetic control of novel traits and attempt to map relevant genes and QTL with genotyping by sequencing approach. Release new onion and tomato germplaswm to the seed industry for dissemination to growers. Publish research results in refereed journals and conference proceedings. Present research results at a national conference, the American Society for Horticultural Sciences.

Impacts
What was accomplished under these goals? Screened 90 melon inbred lines and hybrids for fuit quality and disease resistance at two locations. Screened three experimental tomato hybrids in three field locations and two tunnel systems. Analyzed volatile compounds, sugars, lycopene and fruit firmness. Selected powdery mildew resistance in melon brreding lines. Conducted controlled pollinations of melons, peppers and tomatoes to combine resistance and quality genes and create new populations. Screened pepper breeding lines for bacterial leaf spot resistance in three field trials with commercial growers. Evaluated root health of melons breeding lines at Weslaco field trial. Selected for fruit firmness and suagr content in more than 90 melon breeding lines and hybrids. Advanced interspecific pepper families and screened for resistance to two viruses. Investigated the environment effect on tomato fruit volatiles and flavor in open field and tunnel production.

Publications

• Type: Journal Articles Status: Published Year Published: 2018 Citation: Lee, J.H.J., Jayaprakasha, G.K., Rush, C.M., Crosby, K.M., and B.S. Patil. 2018. Production system influences volatile biomarkers in tomato. Metabolomics (2018) 14:99.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Perez, J.L., Jayaprakasha, G.K., Crosby, K., and B.S. Patil. 2018. Evaluation of bitter melon (Momordica charantia) cultivars grown in Texas and levels of various phytonutrients. J. Sci. Food. Agric. 99:379-390.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Sharma, S.P., Leskovar, D.I., Volder, A., Crosby, K.M., and A.M.H. Ibrahim. 2018. Root distribution patterns of reticulatus and inodorus melon (Cucumis melo L.) under subsurface deficit irrigation. Irrig. Sci. https://doi.org/10.1007/s00271-018-0587-7
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Leskovar, D.I., Agehara, S., Crosby, K. and D. Holcroft. 2018. Optimizing 1-methylcyclopropene concentration and immersion time to extend shelf life of muskmelon (Cucumis melo L. var. reticulatus) fruit. Sci. Hort 230: 117-125.