A metabolic perspective of selection for fruit quality related to apple domestication and improvement

Qiong Lin, Jing Chen, Xuan Liu, Bin Wang, Yaoyao Zhao, Liao Liao, Andrew C. Allan, Chongde Sun, Yuquan Duan, Xuan Li, Donald Grierson, Julian C. Verdonk, Kunsong Chen, Yuepeng Han, Jinfeng Bi*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

8 Citations (Scopus)


Background: Apple is an economically important fruit crop. Changes in metabolism accompanying human-guided evolution can be revealed using a multiomics approach. We perform genome-wide metabolic analysis of apple fruits collected from 292 wild and cultivated accessions representing various consumption types. Results: We find decreased amounts of certain metabolites, including tannins, organic acids, phenolic acids, and flavonoids as the wild accessions transition to cultivated apples, while lysolipids increase in the “Golden Delicious” to “Ralls Janet” pedigree, suggesting better storage. We identify a total of 222,877 significant single-nucleotide polymorphisms that are associated with 2205 apple metabolites. Investigation of a region from 2.84 to 5.01 Mb on chromosome 16 containing co-mapping regions for tannins, organic acids, phenolic acids, and flavonoids indicates the importance of these metabolites for fruit quality and nutrition during breeding. The tannin and acidity-related genes Myb9-like and PH4 are mapped closely to fruit weight locus fw1 from 3.41 to 3.76 Mb on chromosome 15, a region under selection during domestication. Lysophosphatidylethanolamine (LPE) 18:1, which is suppressed by fatty acid desaturase-2 (FAD2), is positively correlated to fruit firmness. We find the fruit weight is negatively correlated with salicylic acid and abscisic acid levels. Further functional assays demonstrate regulation of these hormone levels by NAC-like activated by Apetala3/Pistillata (NAP) and ATP binding cassette G25 (ABCG25), respectively. Conclusions: This study provides a metabolic perspective for selection on fruit quality during domestication and improvement, which is a valuable resource for investigating mechanisms controlling apple metabolite content and quality.

Original languageEnglish
Article number95
JournalGenome Biology
Issue number1
Publication statusPublished - 26 Apr 2023


  • Apple
  • Fruit weight
  • Metabolome
  • mGWAS
  • Quality
  • Storage
  • Taste


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