What makes a giant fruit? Assembling a genomic toolkit underlying various fruit traits of the mammoth group of Cucurbita maxima

Abstract

Since their introduction in Europe, pumpkins (Cucurbita maxima Duch.) have rapidly dispersed throughout the world. This is mainly because of their wide genetic diversity and Plasticity to thrive in a wide range of geographical regions across the world, their high nutritional value and suitability to integrate with local cuisines, and their long shelf life. Competition for growing the showy type or mammoth-sized pumpkins that produce the largest fruit of the entire plant kingdom has drawn attention. In this study, we used genome-wide single nucleotide polymorphisms to resolve admixture among different pumpkin groups. Also, to resolve population differentiation, genome-wide divergence and evolutionary forces underlying the evolution of mammoth-sized pumpkin. The admixture analysis indicates that the mammoth group (also called Display or Giant) evolved from the hubbard group with genome-wide introgressions from the buttercup group. We archived a set of private alleles underlying fruit development in mammoth group, and resolved haplotype level divergence involved in the evolutionary mechanisms. Our genome-wide association study identified three major allelic effects underlying various fruit-size genes in this study. For fruit weight, a missense variant in the homeobox-leucine zipper protein ATHB-20-like (S04_18528409) was significantly associated (false discovery rate = 0.000004) with fruit weight, while high allelic effect was consistent across the 3 years of the study. A cofactor (S08_217549) on chromosome 8 is strongly associated with fruit length, having superior allelic effect across the 3 years of this study. A missense variant (S10_4639871) on translocation protein SEC62 is a cofactor for fruit diameter. Several known molecular mechanisms are likely controlling giant fruit size, including endoreduplication, hormonal regulation, CLV-WUS signaling pathway, MADS-box family, and ubiquitin-proteasome pathway. This study provides a general framework for the evolutionary relationship among horticulture groups of C. maxima and elucidates the origins of rare variants contributing to the giant pumpkin fruit size.

Multi-Omics Analysis Reveals the Distinct Features of Metabolism Pathways Supporting the Fruit Size and Color Variation of Giant Pumpkin

“…Fruit size and color are important quality and yield traits of pumpkins [20]. The giant pumpkin (AG) produces the largest fruit in the world and holds great ornamental and economic value [21]. The AG cultivar is a modern cultivated pumpkin likely derived from…”

“…Fruit size and color are important quality and yield traits of pumpkins [20]. The giant pumpkin (AG) produces the largest fruit in the world and holds great ornamental and economic value [21]. The AG cultivar is a modern cultivated pumpkin likely derived from its small-fruited ancestor (Hubbard), though its fruit present different colors and have expanded significantly in terms of size in contrast to the fruit of the Hubbard cultivar.…”

Metabolomics and Transcription Profiling of Pumpkin Fruit Reveals Enhanced Bioactive Flavonoids and Coumarins in Giant Pumpkin (Cucurbita maxima)

“…Edible pumpkin with small fruit is favored by consumers due to its abundant nutrients, such as carotenoids, starch, and polysaccharides. ,, The giant pumpkin AG is often used for viewing due to its attractive appearance quality. Currently, the main focus has been on fruit enlargement in giant pumpkins. , Thus far, the accumulated bioactive metabolites, including flavonoids, coumarins and others, in giant pumpkin fruit have not been thoroughly studied. Here, we found a great deal of metabolites that belong to different categories using LC–MS/MS-based widely non-targeted metabolomics.…”

“…Currently, the main focus has been on fruit enlargement in giant pumpkins. 20,35 Thus far, the accumulated bioactive metabolites, including flavonoids, coumarins and others, in giant pumpkin fruit have not been thoroughly studied. Here, we found a great deal of metabolites that belong to different categories using LC−MS/MS-based widely non-targeted metabolomics.…”

Genome-wide analysis of genetic diversity in a germplasm collection including wild relatives and interspecific clones of garden asparagus

“…Also present near this SNP is a gene with a myb-related protein 305-like function ( AsparagusV1_10.1876 ). These myb-related genes are usually involved in response to abiotic stresses, as in Vigna unguiculata , where a myb-related protein 305-like gene has been found to be upregulated after exposure to salt stress ( Zhang et al., 2022 ); however, they can also be associated with fruit production, as in Vigna mungo , where a myb-related protein 305-like gene has been found to be associated with a quantitative trait locus (QTL) for yield ( Singh et al., 2022 ), or with the ability to produce giant (mammoth) fruits, as in Cucurbita maxima ( Reddy et al., 2022 ). Therefore, it could be reasonable to assume that they may also be involved in determining flowering time and not solely in fruit characteristics.…”