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TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
May 29, 2024;137 (6): 144.

A wild melon reference genome provides novel insights into the domestication of a key gene responsible for melon fruit acidity.

Xinxiu Chen, Hongbo Li, Yuanhua Dong, Yuanchao Xu, Kuipeng Xu, Qiqi Zhang, Zhiwang Yao, Qing Yu, Huimin Zhang, Zhonghua Zhang
Author Information
  1. Xinxiu Chen: Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
  2. Hongbo Li: Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Shenzhen Branch, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, Guangdong, China.
  3. Yuanhua Dong: College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
  4. Yuanchao Xu: Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Shenzhen Branch, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, Guangdong, China.
  5. Kuipeng Xu: Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
  6. Qiqi Zhang: College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
  7. Zhiwang Yao: Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
  8. Qing Yu: Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
  9. Huimin Zhang: Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China. Zhanghm@qau.edu.cn.
  10. Zhonghua Zhang: Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China. zhangzhonghua@caas.cn. ORCID
PMID: 38809285 DOI: 10.1007/s00122-024-04647-4

Abstract

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.

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Grants

  1. 32225044/National Natural Science Foundation of China
  2. 32130093/National Natural Science Foundation of China
  3. No.ts20190947/Taishan Scholar Foundation of Shandong Province

MeSH Term

Cucurbitaceae
Fruit
Domestication
Genome, Plant
Phenotype
Genotype
Quantitative Trait Loci
Genomic Structural Variation
Genes, Plant
Journal Article

Links to CNCB-NGDC Resources

GWH: GWHDTVT00000000 (Cucumis melo)

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