The first semi-wild-type melon T2T genome assembled by Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, and China Agricultural University

Peer-Reviewed Publication

NANJING AGRICULTURAL UNIVERSITY THE ACADEMY OF SCIENCE

 

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PHENOTYPE, HI-C MAP AND GENOMIC LANDSCAPE OF 821

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CREDIT: HORTICULTURAL RESEARCH

Melon (Cucumis melo L.) is an important vegetable crop that has an extensive history of cultivation, and has been classified into two subspecies, C. melo ssp. agrestis and C. melo ssp. melo. Previous study suggested that the two subspecies were domesticated independently [1], which may have generated different genetic mechanisms for the same trait between the two subspecies. Furthermore, the difference in their geographical distribution resulted in diverse characteristics between the two subspecies, shaping genomic imprinting in their genomes. Wild germplasm is an important genetic resource in crop breeding because of its high genetic diversity and resistance against diseases. However, all of the previous reported genomes were assembled based on the cultivated melon[2-7], the genome of wild and semi-wild melon types is not yet available. Therefore, assembling high-quality wild/semi-wild melon genome will provide an unprecedented opportunity for gene discovery and resistance breeding in melon.

Recently, the study of ‘The haplotype resolved T2T reference genome highlights structural variation underlying agronomic traits of melon’ was published on Horticulture Research by Yongyang Xu, from Melon Genetic Breeding Team of Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, cooperated with professor Tao Lin from China Agricultural University.

PI 313970 is an accession derived from C. melo ssp. agrestis var. acidulus native to India, which possess high resistance to powdery mildew and a variety of viral diseases (ToLCNDV, CYSDV, CABYV, WmCSV and CuLCrV). The ‘821’ accession was self-fertilized from PI 313970 for several generations. Here we reported 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 (Fig.1).

Comparative genome analysis discovered a significant number of structural variants (SVs) between melo and agrestis genomes, including a copy number variation located in the ToLCNDV resistance locus on chromosome 11, of which a candidate gene was identified for ToLCNDV resistance (Fig. 2). Additionally, melon is a unique model species for studying fruit ripening because of presenting both climacteric and non-climacteric types. 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 resistance breeding in melon.

References

1. Zhao, G. et al. (2019) A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits. Nat Genet 51, 1607-1615.
2. Garcia-Mas J et al. (2012) The genome of melon (Cucumis melo L.). PNAS 109, 11872-11877.
3. Yang, J.H. et al. (2020) The chromosome-scale genome of melon dissects genetic architecture of important agronomic traits. iScience 23, 101422.
4. Zhang, H. et al. (2019) A high-quality melon genome assembly provides insights into genetic basis of fruit trait improvement. iScience 22, 16-27.
5. Pichot, C. et al. (2022) Cantaloupe melon genome reveals 3D chromatin features and structural relationship with the ancestral cucurbitaceae karyotype. iScience 25, 103696.
6. Ling, J. et al. (2021) High-quality chromosome-level genomes of Cucumis metuliferus and Cucumis melo provide insight into Cucumis genome evolution. Plant J 107, 136-148.  
7. Castanera, R. et al. (2019) An improved melon reference genome with Single-Molecule Sequencing Uncovers a recent burst of transposable elements with potential impact on genes. Front Plant Sci 10, 1815.

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Authors

Guoli Li1,2#, Lingli Tang1,3,4#, Yuhua He1,3, Yongyang Xu1,3, Abdelhafid Bendahmane5, Jordi Garcia-Mas6,7, Tao Lin2*, Guangwei Zhao1,3,4*

Affiliations

1. National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, 450009, China.

2. China Agricultural University, College of Horticulture, Beijing 100193, China.

3. National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya Hainan, 572024, China

4. Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Xinxiang 453400, China.

5. Institute of Plant Sciences Paris-Saclay (IPS2), INRAE, CNRS, University of Paris-Saclay, University of Evry, University of Paris-Diderot, Gif sur Yvette 91192, France.

6. Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain.

7. Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain.

About Guangwei Zhao

Guangwei Zhao, Doctor, doctoral supervisor, engaged in melon genetic breeding, E-mail: zhaoguangwei@caas.cn

Structural variations between melo and agrestis

CREDIT

Horticultural Research

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JOURNAL

Horticulture Research

DOI

10.1093/hr/uhad182 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

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