A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits

Zhao, Guangwei; Lian, Qiang; Zhang, Zhonghua; Fu, Qihua; He, Yue; Shuang-wu, MA; Ruggieri, Valentino; Monforte, Antonio J.; Wang, Pingyong; Julca, Irene; Wang, Huaisong; Liu, Junpu; Xu, Yong; Wang, Runze; Ji, Jiabing; Xu, Zhigao; Kong, Weihu; Zhong, Yang; Shang, Jianli; Pereira, Lara; Argyris, Jason; Zhang, Jian; Mayobre, Carlos; Pujol, Marta; Oren, Elad; Ou, Diandian; Wang, Jiming; Sun, Dan; Zhao, Shanjiang; Zhu, Y.; Li, Na; Katzir, Nurit; Gur, Amit; Dogimont, Catherine; Schaefer, Hanno; Fan, Wei; Bendahmane, Abdelhafid; Fei, Zhangjun; Pitrat, Michel; Gabaldón, Toni; Lin, Tao; García-Más, Jordi; Xu, Yong; Huang, Sanwen

doi:10.1038/s41588-019-0522-8

Cited by 177 publications

(215 citation statements)

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“…The Duda'im and Momordica accessions that were included in our study are allied with subsp. melo but form an outlying cluster within that subspecies, as recently suggested [8,17,19]. However, with respect to the comparison of phylogenetic and the combined metabolomics-based classification (Figures 2 and 3), the agrestis subspecies does not behave as a single Group.…”

Section: Phylogenomic and Phytochemical Relationships Partly Coincidementioning

confidence: 71%

“…Rapid development of new technologies has allowed for successively and increasingly more comprehensive and precise identification and analyses of genetic variability. Most recently, high throughput sequencing and massive GBS strategies have been applied to melon variability in representative GWAS populations [8,37], yielding 17,000 and 22,000 genetic polymorphisms, respectively. Such large-scale genotyping allows for a more precise assessment of genetic relationships within species.…”

Section: Phylogenomic and Phytochemical Relationships Partly Coincidementioning

confidence: 99%

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Comparative Metabolomics and Molecular Phylogenetics of Melon (Cucumis melo, Cucurbitaceae) Biodiversity

et al. 2020

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The broad variability of Cucumis melo (melon, Cucurbitaceae) presents a challenge to conventional classification and organization within the species. To shed further light on the infraspecific relationships within C. melo, we compared genotypic and metabolomic similarities among 44 accessions representative of most of the cultivar-groups. Genotyping-by-sequencing (GBS) provided over 20,000 single-nucleotide polymorphisms (SNPs). Metabolomics data of the mature fruit flesh and rind provided over 80,000 metabolomic and elemental features via an orchestra of six complementary metabolomic platforms. These technologies probed polar, semi-polar, and non-polar metabolite fractions as well as a set of mineral elements and included both flavor- and taste-relevant volatile and non-volatile metabolites. Together these results enabled an estimate of “metabolomic/elemental distance” and its correlation with the genetic GBS distance of melon accessions. This study indicates that extensive and non-targeted metabolomics/elemental characterization produced classifications that strongly, but not completely, reflect the current and extensive genetic classification. Certain melon Groups, such as Inodorous, clustered in parallel with the genetic classifications while other genome to metabolome/element associations proved less clear. We suggest that the combined genomic, metabolic, and element data reflect the extensive sexual compatibility among melon accessions and the breeding history that has, for example, targeted metabolic quality traits, such as taste and flavor.

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Section: Phylogenomic and Phytochemical Relationships Partly Coincidementioning

confidence: 71%

Section: Phylogenomic and Phytochemical Relationships Partly Coincidementioning

confidence: 99%

Comparative Metabolomics and Molecular Phylogenetics of Melon (Cucumis melo, Cucurbitaceae) Biodiversity

et al. 2020

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“…We performed an association study for aroma production (assessed subjectively by smelling the fruit) in a subset of 211 melon accessions corresponding to the ssp. melo (Supplementary Table 4 ) 30 . We identified two close association signals in the top of chromosome 8 (−log10[P] = 7.0 and (−log10[ P ] = 6.0, respectively; Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Melon accessions for genome-wide associacion studies (GWAS) were obtained from the National Mid-term Genebank for Watermelon and Melon (Zhengzhou, China), the Zhengzhou Fruit Research Institute (Chinese Academy of Agricultural Sciences) and the US Department of Agriculture. Plants were grown in Zhengzhou (Henan province), Sanya (Hainan province) and Changji (Xinjiang province) in 2015 and 2016 and were previously described 30 . Because of poor adaptation, some accessions were evaluated in one or two locations, and three replicates were evaluated at each location.…”

Section: Methodsmentioning

confidence: 99%

Genetic dissection of climacteric fruit ripening in a melon population segregating for ripening behavior

et al. 2020

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Melon is as an alternative model to understand fruit ripening due to the coexistence of climacteric and non-climacteric varieties within the same species, allowing the study of the processes that regulate this complex trait with genetic approaches. We phenotyped a population of recombinant inbred lines (RILs), obtained by crossing a climacteric (Védrantais, cantalupensis type) and a non-climcteric variety (Piel de Sapo T111, inodorus type), for traits related to climacteric maturation and ethylene production. Individuals in the RIL population exhibited various combinations of phenotypes that differed in the amount of ethylene produced, the early onset of ethylene production, and other phenotypes associated with ripening. We characterized a major QTL on chromosome 8, ETHQV8.1, which is sufficient to activate climacteric ripening, and other minor QTLs that may modulate the climacteric response. The ETHQV8.1 allele was validated by using two reciprocal introgression line populations generated by crossing Védrantais and Piel de Sapo and analyzing the ETHQV8.1 region in each of the genetic backgrounds. A Genome-wide association study (GWAS) using 211 accessions of the ssp. melo further identified two regions on chromosome 8 associated with the production of aromas, one of these regions overlapping with the 154.1 kb interval containing ETHQV8.1. The ETHQV8.1 region contains several candidate genes that may be related to fruit ripening. This work sheds light into the regulation mechanisms of a complex trait such as fruit ripening.

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“…One of these young Gypsy LTR-transposons is inserted into the promoter of the AGAMOUS MADS box transcription factor MELO3C019694, which was missannotated in assembly v3.6.1 (Supplementary Figure S6). Recently, MELO3C019694 has been suggested as the candidate gene for the presence of sutures trait after performing GWAS and bi-parental mapping experiments (Zhao et al, 2019), and the orthologous SHP1 and SHP2 in Arabidopsis regulates pod dehiscence in this plant (Liljegren et al, 2000). The insertion of a Gypsy element in the promoter of MELO3C019694 will have to be tested in a wide collection of non-and sutured accessions.…”

Section: Impact Of Young Ltr-retrotransposons On Genesmentioning

confidence: 99%

An Improved Melon Reference Genome With Single-Molecule Sequencing Uncovers a Recent Burst of Transposable Elements With Potential Impact on Genes

et al. 2020

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The published melon (Cucumis melo L.) reference genome assembly (v3.6.1) has still 41.6 Mb (Megabases) of sequences unassigned to pseudo-chromosomes and about 57 Mb of gaps. Although different approaches have been undertaken to improve the melon genome assembly in recent years, the high percentage of repeats (~40%) and limitations due to read length have made it difficult to resolve gaps and scaffold's misassignments to pseudomolecules, especially in the heterochromatic regions. Taking advantage of the PacBio single-molecule real-time (SMRT) sequencing technology, an improvement of the melon genome was achieved. About 90% of the gaps were filled and the unassigned sequences were drastically reduced. A lift-over of the latest annotation v4.0 allowed to re-collocate protein-coding genes belonging to the unassigned sequences to the pseudomolecules. A direct proof of the improvement reached in the new melon assembly was highlighted looking at the improved annotation of the transposable element fraction. By screening the new assembly, we discovered many young (inserted less than 2Mya), polymorphic LTR-retrotransposons that were not captured in the previous reference genome. These elements sit mostly in the pericentromeric regions, but some of them are inserted in the upstream region of genes suggesting that they can have regulatory potential. This improved reference genome will provide an invaluable tool for identifying new gene or transposon variants associated with important phenotypes.

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A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits

Abstract: S. 2019. "A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits". Nature Genetics.

Cited by 177 publications

References 66 publications

Comparative Metabolomics and Molecular Phylogenetics of Melon (Cucumis melo, Cucurbitaceae) Biodiversity

Comparative Metabolomics and Molecular Phylogenetics of Melon (Cucumis melo, Cucurbitaceae) Biodiversity

Genetic dissection of climacteric fruit ripening in a melon population segregating for ripening behavior

An Improved Melon Reference Genome With Single-Molecule Sequencing Uncovers a Recent Burst of Transposable Elements With Potential Impact on Genes

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