Quantitative Trait Loci (QTL) Analysis of Fruit and Agronomic Traits of Tropical Pumpkin (Cucurbita moschata) in an Organic Production System

Abstract

Interest in the development of organically grown vegetable crops has risen over the past decades due to consumer preferences. However, most crops that have desirable consumer traits have been bred in conventional growing conditions, and their transfer to an organic setting is challenging. Here, the organically grown Hawaiian pumpkin (Cucurbita moschata) accession ‘Shima’ was crossed with the conventionally grown Puerto Rican variety ‘Taina Dorada’ to develop a backcross (BC1) population, where ‘Shima’ was the recurrent parent. A total of 202 BC1 (‘Shima’ X F1) progenies were planted in a certified organic field, and twelve traits were evaluated. We used genotype-by-sequencing (GBS) to identify the Quantitative Trait Loci (QTL) associated with insect tolerance along with commercially desirable traits. A total of 1582 single nucleotide polymorphisms (SNPs) were identified, from which 711 SNPs were used to develop a genetic map and perform QTL mapping. Reads associated with significant QTLs were aligned to the publicly available Cucurbita moschata genome and identified several markers linked to genes that have been previously reported to be associated with that trait in other crop systems, such as melon (Cucumis melo L.). This research provides a resource for marker-assisted selection (MAS) efforts in Cucurbita moschata, as well as serving as a model study to improve cultivars that are transitioning from a conventional to an organic setting.

Identification of Fruit-Associated QTLs in Winter Squash (Cucurbita maxima Duchesne) Using Recombinant Inbred Lines

“…Zhong et al [15] constructed a high-density SNP-based linkage map using an F 2 population of C. moschata and identified 29 QTLs associated with 12 fruit traits for this species. Echevarria et al [28] using a BC 1 population identified several QTLs for fruit and agronomic traits in tropical pumpkin C. moschata. For C. maxima, the genetic bases of fruit-associated traits are largely unknown [4].…”

QTL Mapping for Pumpkin Fruit Traits Using a GBS-based High-density Genetic Map

“…A genetic map spanning a total genetic distance of 3087.03 cM on 20 LGs with an average genetic distance of 0.89 cM was constructed to map QTLs for fruit-related traits in pumpkin (Zhong et al 2017). Moreover, using the GBS approach, a genetic map consisting of 24 LGs with an overall genetic length of 2665.0 cM and an average spacing of 3.7 cM was constructed for a pumpkin BC1 population (Echevarria et al 2020). These genetic maps were constructed without using the information of reference genome, which hampered their comparisons with the other genetic maps.…”

“…Using a pyriform-shaped maternal parent and a dumbbell-shaped paternal parent, a moderate-effect QTL was detected for pumpkin fruit length (FL) and FW in the F2 population, respectively (Hashimoto et al 2020). Using the pumpkin parents with attened shape and spheroid shape, respectively, a signi cant QTL underlying SCS was detected in the BC1 population (Echevarria et al 2020). These works have provided necessary information to understand the genetic control of fruit traits in pumpkin.…”

“…A saturated genetic map with an average spacing of 0.4 cM was established for QTL analysis of fruit-related traits in Zucchini (C. pepo) using GBS approach. In pumpkin, a GBS-based genetic map with an average of 3.7 cM was constructed to detect the QTLs underlying fruit and agronomic traits (Echevarria et al 2020). The comparatively low density of genetic map decreased the resolution of QTL mapping in pumpkin.…”

Quantitative Trait Locus Analysis in Squash (Cucurbita moschata) Based on Simple Sequence Repeat Markers and Restriction Site-Associated DNA Sequencing Analysis

“…C. moschata, the next most variable species in this genus, is distributed to tropical, subtropical, and temperate regions, and has adapted to a humid tropical climate. Genetic loci for fruit traits have been mapped in C. moschata [7][8][9][10], but only limited information is available. Since the introduction of C. moschata to Japan in the 16th century, multiple local cultivars and landraces have been differentiated there, rendering it one of the centers of C. moschata diversity [11].…”