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

Ting Wang, Shiyao Duan, Chen Xu, Yi Wang, Xinzhong Zhang, Xuefeng Xu, Liyang Chen, Zhenhai Han () and Ting Wu ()
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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

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-43270-7

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