Cantaloupe melon genome reveals 3D chromatin features and structural relationship with the ancestral cucurbitaceae karyotype

Pichot, Clement; Djari, Anis; Tran, Joseph; Verdenaud, Marion; Marande, William; Huneau, Cécile; Gautier, Véronique; Latrasse, David; Arribat, Sandrine; Sommard, Vivien; Troadec, Christelle; Poncet, Charles; Bendahmane, Mohammed; Szécsi, Judit; Dogimont, Catherine; Salse, Jérôme; Benhamed, Moussa; Zouine, Mohamed; Boualem, Adnane

doi:10.1016/j.isci.2021.103696

Cited by 20 publications

(15 citation statements)

References 109 publications

(164 reference statements)

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“…Melon genetic and genomic research was enhanced since the release of the first melon genome 10 years ago (Garcia-Mas et al ., 2012), followed by extensive re-sequencing of hundreds of melon accessions (Zhao et al ., 2019; S., Liu et al ., 2020; Dafna et al ., 2021). Five additional high-quality melon genome assemblies that can be used as references for this species were published over the last 4 years (Zhang et al ., 2019; Yang et al ., 2020; Yano et al ., 2020; Ling et al ., 2021; Pichot et al ., 2022). However, the recent expansion of the pan-genome concept, based on the realization that multiple genomes capturing the diversity within species are required for complete representation of the genomic variation (Li et al ., 2022; Della Coletta et al ., 2021; Bayer et al ., 2020; Ho et al ., 2020), suggest that the SV layer is not fully exposed in melon.…”

Section: Resultsmentioning

confidence: 99%

“…Five additional genome assemblies were published for Cucumis melo in the last 4 years: Three ssp. melo lines; the Inodorus line Payzawat (Zhang et al ., 2019), the reticulatus line ‘Harukai’ (Yano et al ., 2020), and the cantaloupe line ‘Charmono’ (Pichot et al ., 2022), and two ssp. agrestis lines; HS (Yang et al ., 2020) and IVF77 (Ling et al ., 2021).…”

Section: Introductionmentioning

confidence: 99%

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Melon pan-genome and multi-parental framework for high-resolution trait dissection

Oren

Dafna

Tzuri

et al. 2022

Preprint

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Linking between genotype and phenotype is a fundamental goal in biology and requires robust data for both layers. The prominent increase in plant genome sequencing and comparisons of multiple related individuals, exposed the abundance of structural genomic variation and suggest that a single reference genome cannot represent the complete sequence diversity of a crop species, leading to the expansion of the pan-genome concept. For high-resolution forward genetics, this unprecedented access to genomic variation should be paralleled by availability and phenotypic characterization of genetic diversity, and effective integration between these layers. Here, we describe a multi-parental framework for trait dissection in melon, leveraging a novel pan-genome constructed for this crop. Melon (Cucumis melo L.) is an important crop from the Cucurbitaceae family, which display extensive phenotypic variation available for breeding. A diverse core set of 25 founder lines (MelonCore25) was sequenced using a combination of short and long-read technologies and their genomes were assembled de novo. The construction of a 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 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 and mottling 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.Significance statementPan-genomes aim to address the abundance of genome structural variation within species for improved genomic analyses. New pan-genome, constructed from de novo genome assemblies of 25 diverse melon (Cucumis melo L.) accessions is integrated with a half-diallel derived set of 300 F2 populations representing all possible parental combinations. The potential of this unified multi-parental trait dissection framework for melon genetics and breeding is presented.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Melon pan-genome and multi-parental framework for high-resolution trait dissection

Oren

Dafna

Tzuri

et al. 2022

Preprint

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“…Three of these were of susp. Melo : ‘Payzawat’ from the Inodorus Group (Zhang et al., 2019 ), ‘Harukei‐3’ from the Reticulatus Group (Yano et al., 2020 ), and ‘Charmono’ from the Cantalupensis Group (Pichot et al., 2022 ). The other two were of susp.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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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.

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“…Melon ( Cucumis melo ) is a eudicot diploid (2n = 24) species from the Cucurbitaceae family of economic and scientific value [ 45 ]. Like other Cucurbitaceae members, melon displays a range of sexual phenotypes, including various combinations of male, female, or bisexual flowers [ 46 ].…”

Section: Introductionmentioning

confidence: 99%

Precision Phenotyping of Nectar-Related Traits Using X-ray Micro Computed Tomography

Begot¹,

Slavković

Oger³

et al. 2022

Cells

Self Cite

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Flower morphologies shape the accessibility to nectar and pollen, two major traits that determine plant–pollinator interactions and reproductive success. Melon is an economically important crop whose reproduction is completely pollinator-dependent and, as such, is a valuable model for studying crop-ecological functions. High-resolution imaging techniques, such as micro-computed tomography (micro-CT), have recently become popular for phenotyping in plant science. Here, we implemented micro-CT to study floral morphology and honey bees in the context of nectar-related traits without a sample preparation to improve the phenotyping precision and quality. We generated high-quality 3D models of melon male and female flowers and compared the geometric measures. Micro-CT allowed for a relatively easy and rapid generation of 3D volumetric data on nectar, nectary, flower, and honey bee body sizes. A comparative analysis of male and female flowers showed a strong positive correlation between the nectar gland volume and the volume of the secreted nectar. We modeled the nectar level inside the flower and reconstructed a 3D model of the accessibility by honey bees. By combining data on flower morphology, the honey bee size and nectar volume, this protocol can be used to assess the flower accessibility to pollinators in a high resolution, and can readily carry out genotypes comparative analysis to identify nectar-pollination-related traits.

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Cantaloupe melon genome reveals 3D chromatin features and structural relationship with the ancestral cucurbitaceae karyotype

Cited by 20 publications

References 109 publications

Melon pan-genome and multi-parental framework for high-resolution trait dissection

Melon pan-genome and multi-parental framework for high-resolution trait dissection

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

Precision Phenotyping of Nectar-Related Traits Using X-ray Micro Computed Tomography

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