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A wild melon reference genome provides novel insights into the domestication of a key gene responsible for melon fruit acidity
Saturday, 2024/06/08 | 05:41:40

Xinxiu Chen, Hongbo Li, Yuanhua Dong, Yuanchao Xu, Kuipeng Xu, Qiqi Zhang, Zhiwang Yao, Qing Yu, Huimin Zhang & Zhonghua Zhang

Theoretical and Applied Genetics; June 2024; vol. 137, article  144.


Figure: Watermelon Acidic or Alkaline: Juicy Facts Uncovered (https://www.etprotein.com/watermelon).


Key message


A wild melon reference genome elucidates the genomic basis of fruit acidity domestication.


Structural variants (SVs) have been reported to impose major effects on agronomic traits, representing a significant contributor to crop domestication. However, the landscape of SVs between wild and cultivated melons is elusive and how SVs have contributed to melon domestication remains largely unexplored. Here, we report a 379-Mb chromosome-scale genome of a wild progenitor melon accession “P84”, with a contig N50 of 14.9 Mb. Genome comparison identifies 10,589 SVs between P84 and four cultivated melons with 6937 not characterized in previously analysis of 25 melon genome sequences. Furthermore, the population-scale genotyping of these SVs was determined in 1175 accessions, and 18 GWAS signals including fruit acidity, fruit length, fruit weight, fruit color and sex determination were detected. Based on these genotyped SVs, we identified 3317 highly diverged SVs between wild and cultivated melons, which could be the potential SVs associated with domestication-related traits. Furthermore, we identify novel SVs affecting fruit acidity and proposed the diverged evolutionary trajectories of CmPH, a key regulator of melon fruit acidity, during domestication and selection of different populations. These results will offer valuable resources for genomic studies and genetic improvement in melon.


Fig. 3: Chromosomal positions of genomic regions associated with seven seed traits identified by GWAS (green boxes). * Regions colocated with previously reported QTL for seed traits. Genes differentially expressed during seed development underlying those genomic regions revealed by RNA-seq analysis are shown at the right of each chromosome.

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