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Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits

Author

Listed:
  • Ting Wang

    (China Agricultural University)

  • Shiyao Duan

    (Beijing University of Agriculture)

  • Chen Xu

    (China Agricultural University)

  • Yi Wang

    (China Agricultural University)

  • Xinzhong Zhang

    (China Agricultural University)

  • Xuefeng Xu

    (China Agricultural University)

  • Liyang Chen

    (Smartgenomics Technology Institute)

  • Zhenhai Han

    (China Agricultural University)

  • Ting Wu

    (China Agricultural University)

Abstract

Structural variations (SVs) and copy number variations (CNVs) contribute to trait variations in fleshy-fruited species. Here, we assemble 10 genomes of genetically diverse Malus accessions, including the ever-green cultivar ‘Granny Smith’ and the widely cultivated cultivar ‘Red Fuji’. Combining with three previously reported genomes, we assemble the pan-genome of Malus species and identify 20,220 CNVs and 317,393 SVs. We also observe CNVs that are positively correlated with expression levels of the genes they are associated with. Furthermore, we show that the noncoding RNA generated from a 209 bp insertion in the intron of mitogen-activated protein kinase homology encoding gene, MMK2, regulates the gene expression and affects fruit coloration. Moreover, we identify overlapping SVs associated with fruit quality and biotic resistance. This pan-genome uncovers possible contributions of CNVs to gene expression and highlights the role of SVs in apple domestication and economically important traits.

Suggested Citation

  • Ting Wang & Shiyao Duan & Chen Xu & Yi Wang & Xinzhong Zhang & Xuefeng Xu & Liyang Chen & Zhenhai Han & Ting Wu, 2023. "Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43270-7
    DOI: 10.1038/s41467-023-43270-7
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