GWAS resolves molecular mechanisms underlying natural variation for carotenoids in Cucurbita maxima Duchesne

Authors: REDDY, UMESH - West Virginia State University; GUADALUPE TALAVERA C, ALICIA - West Virginia State University; NATARAJAN, SURESH - West Virginia State University; ALAPARTHI, SURESH - West Virginia State University; Levi, Amnon; NIMMAKAYALA, PADMA - West Virginia State University

Submitted to: HortScience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/2/2023
Publication Date: 3/1/2023
Citation: Reddy, U.K., Guadalupe Talavera C, A.A., Natarajan, S., Alaparthi, S., Levi, A., Nimmakayala, P. 2023. GWAS resolves molecular mechanisms underlying natural variation for carotenoids in Cucurbita maxima Duchesne. HortScience. 312. https://doi.org/10.1016/j.scienta.2023.111881.
DOI: https://doi.org/10.1016/j.scienta.2023.111881

Interpretive Summary: Cucurbita maxima is one of four known species representing cultivated squash. Cucurbita maxima originated in South America over 4000 years ago and is considered to be among the most diverse domesticated plant species. The Cucurbita maxima fruits contain a diverse panel of naturally occurring pigments "carotenoides" which impart vibrant colors, including bright yellow, red, and orange colors with antioxidant properties, beneficial for human health. Seed companies and breeders have great interest in identifying the gene loci controlling carotenoid production and in developing molecular (DNA) markers useful in breeding programs aiming to develop squash varieties with high carotenoid concentrations. To date, there is no sufficient knowledge about the genes that control carotenoids in squash. In these study, ARS scientists collaborated with scientists at West Virginia State University on evaluating carotenoid presence in a collection of Cucucrbita maxima accessions and in using advance genomic technology, known as "Genome Wide Association Study (GWAS)". Using this technology the researchers were able to pinpoint the gene loci controlling carotenoid production in sqush. The results of this study should be useful for researchers and plant breeders interested in utilizing molecular (DNA) markers to advance genes controlling carotenoid production into elite squash cultivars.

Technical Abstract: A diversity panel consisting classical horticulture groups of Cucurbita maxima was profiled 11 for natural variation for various carotenoids for use in genome-wide association study (GWAS) us-12 ing genome-wide single nucleotide polymorphisms (SNPs). Principal component analysis with a 13 total of 12,996 SNPs (minor allele frequency [MAF] = 0.05) was used as a covariate to control con-14 founding effects of population structure in this study. The highest content of these carotenoids was 15 found in the horticultural group buttercup (a-carotene 200 µg/g, ß-carotene 1423 µg/g, cryptoxan-16 thin 57µg/g, lutein 2038 µg/g, and zeaxanthin 738 µg/g); in the hubbard group (a-carotene 159 µg/g, 17 ß-carotene 635 µg/g, cryptoxanthin 28 µg/g, lutein 3180 µg/g and zeaxanthin 1327 µg/g); in the Aus-18 tralian group (a-carotene 162 µg/g, ß-carotene 956 µg/g, cryptoxanthin 40 µg/g, lutein 3296 µg/g 19 and zeaxanthin 1563 µg/g); and in the mammoth group (a-carotene 193 µg/g, ß-carotene 680 µg/g, 20 cryptoxanthin 28µg/g, lutein 3704 µg/g and zeaxanthin 794 µg/g). Mr Fagli, Boston Marrow, Baby 21 green hubbard, Chicago Warted Hubbard, Golden hubbard and Bush buttercup of USA; Australian 22 Butter (Australia); Marmellata and Marina di Chioggia of Italy were recorded the highest carotenoid 23 content. GWAS revealed several SNPs related to 289 genes underlying the regulation of carotenoids 24 and methylerythritol 4-phosphate (MEP) pathways. In this study, SNPs located on homologues of 25 the ankyrin repeat family protein, calcium-binding EF-hand family protein, E3 ubiquitin-protein 26 ligase, ethylene-responsive transcription factor, F-box domain-containing proteins, kinesin-like pro-27 tein, ubiquitinyl hydrolase 1, violaxanthin de-epoxidase, and Zinc finger CCCH domain-containing 28 protein have shown significant association with multiple carotenoid compounds in this study.