The haplotype-resolved T2T reference genome highlights structural variation underlying agronomic traits of melon

Li, Guoli; Tang, Lingli; He, Yuhua; Xu, Yongyang; Bendahmane, Abdelhafid; García-Mas, Jordi; Lin, Tao; Zhao, Guangwei; Chinese Academy of Agricultural Sciences; Earmarked Fund for China Agriculture Research System; Hainan Province; European Research Council; Henan Province

The haplotype-resolved T2T reference genome highlights structural variation underlying agronomic traits of melon

2023

Melon (Cucumis melo L.) is an important vegetable crop that has an extensive history of cultivation. However, the genome of wild and semi-wild melon types that can be used for the analysis of agronomic traits is not yet available. Here we report a chromosome-level T2T genome assembly for 821 (C. melo ssp. agrestis var. acidulus), a semi-wild melon with two haplotypes of ~373 Mb and ~364 Mb, respectively. Comparative genome analysis discovered a significant number of structural variants (SVs) between melo (C. melo ssp. melo) and agrestis (C. melo ssp. agrestis) genomes, including a copy number variation located in the ToLCNDV resistance locus on chromosome 11. Genome-wide association studies detected a significant signal associated with climacteric ripening and identified one candidate gene CM_ac12g14720.1 (CmABA2), encoding a cytoplasmic short chain dehydrogenase/reductase, which controls the biosynthesis of abscisic acid. This study provides valuable genetic resources for future research on melon breeding.

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This work was supported by funding from the Agricultural Science and Technology Innovation Program (CAAS-ASTIP-2016-ZFRI-06), the China Agriculture Research System (CARS-25-2023-G6), the Key Research and Development Program of Hainan (ZDYF2021XDNY164), the European Research Council (ERC-NectarGland, 101095736), the 111 Project (B17043) and Henan Province Science and Technology Research Project (232102110185).

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Peer reviewed

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