Pan‐genome and multi‐parental framework for high‐resolution trait dissection in melon (Cucumis melo)

Abstract

SUMMARY Linking genotype with phenotype is a fundamental goal in biology and requires robust data for both. Recent advances in plant‐genome sequencing have expedited comparisons among multiple‐related individuals. The abundance of structural genomic within‐species variation that has been discovered indicates that a single reference genome cannot represent the complete sequence diversity of a species, leading to the expansion of the pan‐genome concept. For high‐resolution forward genetics, this unprecedented access to genomic variation should be paralleled and integrated with phenotypic characterization of genetic diversity. We developed a multi‐parental framework for trait dissection in melon (Cucumis melo), leveraging a novel pan‐genome constructed for this highly variable cucurbit crop. A core subset of 25 diverse founders (MelonCore25), consisting of 24 accessions from the two widely cultivated subspecies of C. melo, encompassing 12 horticultural groups, and 1 feral accession was sequenced using a combination of short‐ and long‐read technologies, and their genomes were assembled de novo. The construction of this melon pan‐genome exposed substantial variation in genome size and structure, including detection of ~300 000 structural variants and ~9 million SNPs. A half‐diallel derived set of 300 F2 populations, representing all possible MelonCore25 parental combinations, was constructed as a framework for trait dissection through integration with the pan‐genome. We demonstrate the potential of this unified framework for genetic analysis of various melon traits, including rind color intensity and pattern, fruit sugar content, and resistance to fungal diseases. We anticipate that utilization of this integrated resource will enhance genetic dissection of important traits and accelerate melon breeding.

Nanopore adaptive sampling to identify the NLR-gene family in melon (Cucumis meloL.)

“…Due to the high degree of fragmentation of the Illumina-based published assembly, we could not conclude after contig alignment. As Chang-Bougi belongs to the makuwa botanical group, we mapped the two contigs to the publicly available genomes from this group: Early Silver Line, Ohgon and Sakata’s Sweet (Oren et al, 2022). We identified a very large and size-conserved insertion (ranging from 862 to 871 kb) at the breakpoint between the two contigs obtained for Chang-Bougi (Figure 8A).…”

From Sequencing to Genome Editing in Cucurbitaceae: Application of Modern Genomic Techniques to Enhance Plant Traits

“…Interestingly, melon (Cucumis melo) was the most frequently studied species within this plant family in terms of genome sequencing. Over the years, ten papers [67,[70][71][72][73][74][75][76][77][78] have described the sequences of different melon subspecies, varieties and cultivars. The first genome sequence of C. melo was revealed in 2012, as the second species after the cucumber genome in the Cucurbitaceae family.…”

“…An important work contributing greatly to the discovery of melon genomes was published in 2022 by the team of Oren et al [73]. The authors sequenced the genomes of 25 different melons, i.e., they provided 17 accessions of "melo" subspecies (in detail: 5x inodorus, 4x cantalupensis, 2x reticulatus, 2x khandalak, 1x duda'im, 1x flexuosus, 1x ameri and 1x adzhur cultivars), 7 for "agrestis" subspecies (2x chinensis, 1x conomon, 3x makuwa and 1x momordica), and 1 for C. collosus var.…”

“…The authors sequenced the genomes of 25 different melons, i.e., they provided 17 accessions of "melo" subspecies (in detail: 5x inodorus, 4x cantalupensis, 2x reticulatus, 2x khandalak, 1x duda'im, 1x flexuosus, 1x ameri and 1x adzhur cultivars), 7 for "agrestis" subspecies (2x chinensis, 1x conomon, 3x makuwa and 1x momordica), and 1 for C. collosus var. feral, an under-exploited wild melon fruit traditionally used in folk remedies [73]. Among all the sequenced melon genomes, their size ranged from 357.6 to 438.3 Mb, and predicted genes from 22,924 to 38,173 (Table 1).…”

Alternative flours from pulp melons (Cucumis melo L.): Seasonality influence on physical, chemical, technological parameters, and utilization in bakery product

“…Melons ( Cucumis melo L., Cucurbitaceae) are cultivated in almost all tropical regions of the planet, thus generating a wide diversity of phenotypic characteristics, especially size, shape, skin color and texture, pulp color, sugar content, acidity, flavor, and aroma. Melon is among the most consumed fruits in the world, among those with a large amount of pulp [ 1 ]. Some studies have demonstrated consumer preference for orange-fleshed melons [ [2] , [3] , [4] ].…”