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Article|28 Sep 2023|OPEN
Telomere-to-telomere genome assembly of melon (Cucumis melo L. var. inodorus) provides a high-quality reference for meta-QTL analysis of important traits
Minghua Wei1 , Ying Huang1 , Changjuan Mo1 , Haiyan Wang1 , Qingguo Zeng1 , Wenli Yang2 , Jihao Chen3 , Xuejun Zhang2,3 , , Qiusheng Kong,1 ,
1National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
2Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
3Hainan Sanya Experimental Center for Crop Breeding, Xinjiang Academy of Agricultural Sciences, Sanya 572014, China
*Corresponding author. E-mail:,

Horticulture Research 10,
Article number: uhad189 (2023)
Views: 270

Received: 25 Jun 2023
Accepted: 12 Sep 2023
Published online: 28 Sep 2023


Melon is an important horticultural crop with extensive diversity in many horticultural groups. To explore its genomic diversity, it is necessary to assemble more high-quality complete genomes from different melon accessions. Meanwhile, a large number of QTLs have been mapped in several studies. Integration of the published QTLs onto a complete genome can provide more accurate information for candidate gene cloning. To address these problems, a telomere-to-telomere (T2T) genome of the elite melon landrace Kuizilikjiz (Cucumis melo L. var. inodorus) was de novo assembled and all the published QTLs were projected onto it in this study. The results showed that a high-quality Kuizilikjiz genome with the size of 379.2 Mb and N50 of 31.7 Mb was de novo assembled using the combination of short reads, PacBio high-fidelity long reads, Hi-C data, and a high-density genetic map. Each chromosome contained the centromere and telomeres at both ends. A large number of structural variations were observed between Kuizilikjiz and the other published genomes. A total of 1294 QTLs published in 67 studies were collected and projected onto the T2T genome. Several clustered, co-localized, and overlapped QTLs were determined. Furthermore, 20 stable meta-QTLs were identified, which significantly reduced the mapping intervals of the initial QTLs and greatly facilitated identification of the candidate genes. Collectively, the T2T genome assembly together with the numerous projected QTLs will not only broaden the high-quality genome resources but also provide valuable and abundant QTL information for cloning the genes controlling important traits in melon.