Source: WEST VIRGINIA STATE UNIVERSITY submitted to NRP
BREEDING HIGH VALUE SQUASH FOR ENHANCED FLAVOR, NUTRACEUTICALS AND DISEASE RESISTANCE BY USING AN INTERSPECIFIC CROSS OF CUCURBITA MAXIMA AND CUCURBITA MOSCHATA
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
1030416
Grant No.
2023-38821-39806
Cumulative Award Amt.
$299,988.00
Proposal No.
2022-10140
Multistate No.
(N/A)
Project Start Date
Jun 1, 2023
Project End Date
May 31, 2026
Grant Year
2023
Program Code
[EQ]- Research Project
Recipient Organization
WEST VIRGINIA STATE UNIVERSITY
PO BOX 1000
INSTITUTE,WV 25112
Performing Department
(N/A)
Non Technical Summary
This proposal aims to develop specialty winter squashes by performing marker assisted selection for enhanced flavor and nutraceuticals involving C. maxima diverse horticulture groups to cater to the demand of consumers looking for new and interesting variations. Winter squash fruit shapes vary from banana to drum-shaped, top-shaped, fusiform, and oblate, with rind colors ranging from red-orange to pink-orange, nearly white, bluish-gray, intense green, and black-green. Our main goal is to develop prebreeding lines that are nutraceutically enriched and enhanced for flavor compounds. We aim to characterize C. maxima germplasm pools and advance interspecific cross derivatives of C. moschata X C. maxima to identify novel squash cultivars enhanced for flavor, resistance, and other nutraceutical traits.
Animal Health Component
50%
Research Effort Categories
Basic
50%
Applied
50%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011429108150%
2021429108050%
Knowledge Area
202 - Plant Genetic Resources; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1429 - Cucurbits, other;

Field Of Science
1081 - Breeding; 1080 - Genetics;
Goals / Objectives
The main goal of this project is to develop prebreeding lines that are nutraceutically enriched and enhanced for flavor compounds. We aim to characterize C. maxima germplasm pools and advance interspecific cross derivatives of C. moschata Var- Chirimen X C. maxima var. Blue Hubbard to identify novel squash cultivars enhanced for flavor, resistance and other nutraceutical traits. We will explore our collections for natural variation for fruit size, flavor metabolites and disease resistance to identify underlying candidate genes and convert them into easy-to-use KASP markers, a high throughput allele mining technique. In the current project, we expand our deliverables by developing interspecific hybrids of C. maximaandC. moschatafor use as rootstocks for grafting watermelon. This proposal will facilitate the development of improved open-pollinated varieties and prebreeding lines for on-farm trials and additional participatory selection and strategies coupled with QTLseq to result in improved varieties. These activities, which will be supported by intensive education and outreach to flow existing varieties and those bred using genomic tools and other consumer-assisted approaches to pumpkin and squash farming communities in the United States. Given the importance of pumpkin and squash in fundamental US foods and feasibility of Cucurbita spp. for high-throughput analysis and manipulation owing to their smaller genome sizes, the public investment in pumpkin and squash genomic research is highly justified. Squash programs need to improve multiple characteristics simultaneously, including fruit yield, disease resistance, flavor and quality. However, when traits manifest complex gene interactions, selection of one trait would epistatically alter the other traits or could be in linkage drag with undesirable features. In this proposal, we will use classic quantitative genetics theory that provides a solution to break such undesirable linkages, by defining theoretically optimum weights of various traits for simultaneous improvement and minimize linkage drag of deleterious alleles.The current proposal will address the need to integrate modern technologies that can create a set of common tools for marker-assisted breeding with the specific objectives mentioned below.Evaluation of a GWAS panel for flavor, carotenoid metabolites, field performance and resistant traits to identify favorable alleles and superior accessionsDevelop a recombinant inbred line (RIL) mapping population by advancing interspecific cross derivatives of C. moschata X C. maxima.Participatory breeding-based selections
Project Methods
Objective 1: Evaluation of a GWAS panel for flavor, carotenoid metabolites, field performance and resistant traits to identify favorable alleles and superior accessionsWe will conduct phenotypic evaluations of a GWAS panel for C. maxima cultivars with three replications for a number of traits associated with flavor, carotenoids, field performance, and fruit quality. Cultivars will be direct seeded, then thinned to 60 cm within rows with 3 m between rows. Fruit parameters will be evaluated at harvest, and separate subsamples will be saved for processing and storage evaluation. Field, laboratory, and storage data will be compiled and combined with genotypic data for association mapping. We will estimate VOCs in squash by using the method of Zhang and Ku, 2019. For estimating carotenoids, using HPLC, individual carotenoid compound contents will be determined by a previously described method (Chebrolu et al. 2012).Objective 2: Develop a recombinant inbred line (RIL) mapping population by advancing interspecific cross derivatives of C. moschata X C. maxima Currently, the SSD of F3 generation of the cross C. moschata X C. maxima is available for the project. Individual progeny will be forwarded (starting from summer 2023 at three generations per year) by growing a single seed (using SSD) collected by rapid cycling. The NGS-based QTL-seq approach is a cost-effective and powerful tool to identify targeted QTL regions. This approach avoids tedious genotyping and can be used to identify shorter genomic regions associated with flavor. QTL-seq can identify candidate genes underlying QTL for fine mapping and cloning. These markers will be converted into KASPar markers for a further genomic-assisted breeding program.Objective 3: Participatory selection Our project activities will include demonstrations of the fruit quality traits, taste and flavor of the new introgressed morphotypes to the growers and consumers. We hope to involve them in satisfying their requirements for good flavor, fruit quality, and high market value and address any concerns related to production. We will identify superior pumpkin and squash cultivars with favorable quantitative trait loci with enhanced nutraceutical traits and resistance to FW and CPM and make selections from the early segregating generations, accessions identified via interspecific hybridization and advance them to the F8 generation. As part of this effort, we will conduct on-farm trials for public participation in comparing superior pumpkin and squash types to local cultivars.

Progress 06/01/23 to 05/31/24

Outputs
Target Audience:Cucurbit breeders, geneticists, Molecular Biologists Graduate and Undergraduate students of WVSU and Local Farmers Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The project has significantly advanced training and professional development opportunities through a multifaceted approach. It has organized six workshops tailored for local graduate students, undergraduate students, postdoctoral associates, and faculty, focusing on bioinformatics pipelines such as machine learning, transcriptomics, and genomics. These workshops have enhanced participants' technical skills and provided practical insights into cutting-edge methodologies crucial for modern genetic research and breeding programs. Additionally, the project has offered training in marker-assisted selection (MAS) techniques and genotyping by sequencing (GBS) analysis, equipping participants with hands-on experience in advanced breeding strategies and genomic data analysis. Managing ongoing field trials with segregating populations has provided valuable practical experience in agricultural research and experimental design. Through collaborative research efforts with diverse horticultural groups and international partners, the project has fostered interdisciplinary collaboration and networking opportunities, enriching the professional development of participants across various stages of their academic and research careers. How have the results been disseminated to communities of interest?The project has disseminated its results effectively to communities of interest through multiple channels. Hands-on training sessions have been conducted to educate stakeholders on advanced breeding techniques and genomic analysis, fostering practical implementation of research findings. Information has also been disseminated via email, ensuring timely updates and direct engagement with interested parties. Moreover, the project has showcased its findings through presentations at both national and international conferences, reaching a broader audience of researchers, industry professionals, and policymakers. A notable dissemination effort includes developing and public availability of PCR allele competitive extension (PACE) assays specifically designed to distinguish pumpkins with higher nutraceutical content. These assays have been detailed in publications, ensuring accessibility and utilization by interested stakeholders. This comprehensive approach to dissemination ensures that the project's innovative findings and methodologies are accessible and impactful across relevant communities, advancing knowledge and practical applications in plant genetics and nutritional enhancement. What do you plan to do during the next reporting period to accomplish the goals?Our efforts will center on several strategic initiatives to advance our goals during the upcoming reporting period. We will intensify our transcriptome analysis, delineating comprehensive gene expression profiles in pumpkins with high nutraceutical compounds compared to those with lower levels. Concurrently, we plan to implement Marker-Assisted Selection (MAS) methodologies to breed segregating populations that emphasize enhanced nutraceutical content. This approach will utilize molecular markers linked to desired traits identified through transcriptome studies, refining our breeding strategies. Additionally, we will conduct rigorous field trials to assess the performance and stability of selected populations under varying environmental conditions, which is crucial for validating the efficacy of MAS in pumpkin breeding. Data derived from these trials and transcriptome analyses will inform scholarly publications aimed at disseminating our findings and contributing to the broader scientific community's knowledge base. Furthermore, we remain committed to engaging with stakeholders through workshops, seminars, and conferences to foster collaboration, exchange insights, and ensure the practical applicability of our research in addressing nutritional and agricultural challenges.

Impacts
What was accomplished under these goals? This proposal achieved significant milestones in developing specialty winter squashes by employing marker-assisted selection to enhance flavor and nutraceutical properties, focusing on C. maxima and diverse horticultural groups. Characterization of C. maxima germplasm identified varieties with high carotenoid content essential for flavor and health benefits. Interspecific crosses, particularly C. moschata X C. maxima, yielded novel squash cultivars enriched for flavor, resistance, and nutraceutical traits. Carotenoid profiling highlighted specific varieties with notable α-carotene, β-carotene, and lutein levels. A comprehensive genome-wide association study using EMMAX identified SNPs linked to genes influencing carotenoid biosynthesis, fruit ripening, and transport. Additionally, genotyping by sequencing facilitated population structure analysis, revealing three primary clusters and their admixed genotypes. Ongoing field trials with segregating populations further support future breeding efforts to enhance carotenoid levels in winter squashes.

Publications

  • Type: Journal Articles Status: Published Year Published: 2024 Citation: Reddy CS, Ramireddy S, Reddy UK. Widening Genetic Diversity Using Embryo Rescue in Cucurbit Crops: A Review. Plants (Basel). 2024 May 10;13(10):1320. doi: 10.3390/plants13101320. PMID: 38794391; PMCID: PMC11124774.
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Flores-Iga G, Lopez-Ortiz C, Gracia-Rodriguez C, Almeida A, Nimmakayala P, Reddy UK, Balagurusamy N. A Genome-Wide Identification and Comparative Analysis of the Heavy-Metal-Associated Gene Family in Cucurbitaceae Species and Their Role in Cucurbita pepo under Arsenic Stress. Genes. 2023; 14(10):1877. https://doi.org/10.3390/genes14101877
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Reddy, U.K.; Lopez-Ortiz, C.; Talavera-Caro, A.G.; Natarajan, P.; Tomason, Y.; Alaparthi, S.; Levi, A.; Nimmakayala, P. GWAS Resolves Molecular Mechanisms Underlying Natural Variation for Carotenoids in Cucurbita Maxima Duchesne. Sci. Hortic. 2023, 312, 111881