Analyzing genomic variation in cultivated pumpkins and identification of candidate genes controlling seed traits

Pumpkins are important vegetable crops widely grown worldwide, and seeds are considered a popular nutraceutical food and an excellent source of protein, oil, and vitamins. Seed size is one of the most important targets for commercial breeding in Cucurbita species; studies have shown that pumpkin seed size variation has a similar trend with fruit size, shape, and seed yield. However, few studies have been conducted to identify genetic loci controlling seed-related traits in cultivated pumpkins. This study analyzed the genomic characteristics of pumpkin breeding materials of 321 Cucurbita accessions collected worldwide, including Cucurbita moschata, Cucurbita maxima, and Cucurbita pepo, using extensive single nucleotide polymorphisms obtained from the genotyping-by-sequencing method, significant genetic variations were identified within and between Cucurbita species. Four major cultivar fruit types were further revealed in C. moschata species, and significant differentiation patterns were detected in several chromosomal regions. A total of 15 significant loci associated with pumpkin seed traits were mapped through a genome-wide association approach; 32 genes previously reported to be associated with seed size regulation in Arabidopsis and Oryza sativa were located in the intervals defined by linkage disequilibrium. Through this study, we gained a deep understanding of the genomic variation distribution across Cucurbita species. The available genetic resources and the associated genetic contents could be used in commercial pumpkin breeding and will facilitate molecular marker-assisted selection in pumpkin seed trait improvement.

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

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.

Morphological and molecular characterization of some pumpkin (Cucurbita pepo L.) genotypes collected from Erzincan province of Turkey

Plant genetic resources constitute the most valuable assets of countries. It is of great importance to determine the genetic variation among these resources and to use the data in breeding studies. To determine the genetic diversity among genotypes of Cucurbita pepo L. species of pumpkin, which is widely grown in Erzincan, 29 different pumpkin genotypes collected were examined based on the morphological parameters and molecular characteristics. SSR (Simple Sequence Repeat) markers were used to determine genetic diversity at the molecular level. The analysis of morphological characterization within genotypes showed a wide variability in morphological traits of plant, flower, fruit, and leaf. In the evaluation performed using SSR markers, all primers exhibited polymorphism rate of %100. Seven SSR markers yielded a total of 15 polymorphic bands, the number of alleles per marker ranged from 2 to 3, and the mean number of alleles was 2.14. Polymorphic information content (PIC) ranged from 0.06 (GMT-M61) to 0.247 (GMT-P41), and the mean PIC value per marker was 0.152. Cluster analysis using Nei's genetic distance determined that 29 genotypes were divided into 4 major groups. The present findings have revealed the genetic diversity among pumpkin genotypes collected from Erzincan province and may form the basis for further breeding studies in pumpkin.