Decoding wild melon genomes: A groundbreaking study on disease resistance and fruit ripening
image: Phenotype, Hi-C map and Genomic landscape of 821.
Credit: Horticulture Research
Melon (Cucumis melo L.), a globally cultivated important vegetable crop, boasts a rich history of domestication, leading to its classification into 16 varieties within two subspecies. However, while high-quality genomes of cultivated melons exist, the genetic resources of wild and semi-wild melons remain underexplored, with existing genomes having significant gaps. This genome gap is particularly relevant considering the distinct fruit quality and disease resistance traits between wild and cultivated melons. The semi-wild melon accession PI 313970, known for its resistance to various diseases and non-climacteric fruit with an extended shelf life, highlights the potential for studying fruit ripening and disease resistance. Therefore, exploring the genomes of wild and semi-wild melon types represents a crucial area of research to understand agronomic traits and improve melon breeding.
In August 2023, Horticulture Research published a research entitled by “The haplotype-resolved T2T reference genome highlights structural variation underlying agronomic traits of melon”.
In this study, researchers presented a genome assembly of a semi-wild melon accession, 821 (C. melo ssp. agrestis var. acidulus), known for its disease resistance and long shelf life. They utilized an array of sequencing technologies—PacBio HiFi, Hi-C, and Illumina—to achieve a T2T assembly, covering approximately 882.10 Mb genome assembly across 24 chromosomes. This assembly process identified a large number of structural variations (SVs) and several resistance genes, enhancing our understanding of the genetic diversity between the melo and agrestis subspecies of melon.
The results showcased the assembly of two haplotypes with an impressive contig N50 size and a comprehensive annotation, revealing over 27,000 protein-coding genes in each haplotype. The quality of the assembly was further validated by identifying syntenic blocks, and heterozygous variants, and confirming a near-complete assembly with identified telomeres and centromeres. Comparative analysis with other melon genomes illuminated the SVs and their distribution across chromosomes, highlighting the impact of these SVs on resistance genes and underscoring the genetic divergences between the melo and agrestis genomes. Additionally, the study pinpointed a copy number variation (CNV) that strongly correlates with resistance to the ToLCNDV virus, alongside identifying significant single nucleotide polymorphisms (SNPs) associated with climacteric fruit ripening. The genome-wide association study (GWAS) identified a gene related to ABA biosynthesis, suggesting its crucial role in the ripening process of non-climacteric fruits.
Through meticulous genome sequencing, assembly, and annotation, this research has not only advanced our understanding of the genetic makeup of the semi-wild melon accession 821 but also provided invaluable insights into disease resistance, fruit ripening mechanisms, and the impact of SVs on these traits. Overall, this study offers an unprecedented opportunity for gene discovery and melon breeding, marking a significant contribution to genomics and agricultural science.
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References
Authors
Guoli Li1,2,†, Lingli Tang1,3,4,†, Yuhua He1,3, Yongyang Xu1,3, Abdelhafid Bendahmane5, Jordi Garcia-Mas6,7, Tao Lin2*, and Guangwei Zhao1,3,4,*
†These authors contributed equally to this work.
Affiliations
1National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan 450009, China
2China Agricultural University, College of Horticulture, Beijing 100193, China
3National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
4Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Xinxiang 453400, China
5Institute of Plant Sciences Paris-Saclay (IPS2), INRAE, CNRS, University of Paris-Saclay, University of Evry, University of Paris-Diderot, Gif sur Yvette 91192, France
6Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain
7Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain
About Guangwei Zhao
Professor, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences. His research interests include plant genetics, plant breeding, and population genetics.