Identification of candidate genes involved in fruit ripening and crispness retention through transcriptome analyses of a ‘Honeycrisp’ population

Hsueh Yuan Chang, Cindy B.S. Tong

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


Crispness retention is a postharvest trait that fruit of the ’Honeycrisp’ apple and some of its progeny possess. To investigate the molecular mechanisms of crispness retention, progeny individuals derived from a ’Honeycrisp’ × MN1764 population with fruit that either retain crispness (named “Retain”), lose crispness (named “Lose”), or that are not crisp at harvest (named “Non-crisp”) were selected for transcriptomic comparisons. Differentially expressed genes (DEGs) were identified using RNA-Seq, and the expression levels of the DEGs were validated using nCounter®. Functional annotation of the DEGs revealed distinct ripening behaviors between fruit of the “Retain” and “Non-crisp” individuals, characterized by opposing expression patterns of auxin-and ethylene-related genes. However, both types of genes were highly expressed in the fruit of “Lose” individuals and ’Honeycrisp’, which led to the potential involvements of genes encoding auxin-conjugating enzyme (GH3), ubiquitin ligase (ETO), and jasmonate O-methyltransferase (JMT) in regulating fruit ripening. Cell wall-related genes also differentiated the phenotypic groups; greater numbers of cell wall synthesis genes were highly expressed in fruit of the “Retain” individuals and ’Honeycrisp’ when compared with “Non-crisp” individuals and MN1764. On the other hand, the phenotypic differences between fruit of the “Retain” and “Lose” individuals could be attributed to the functioning of fewer cell wall-modifying genes. A cell wall-modifying gene, MdXTH, was consistently identified as differentially expressed in those fruit over two years in this study, so is a major candidate for crispness retention.

Original languageEnglish (US)
Article number1335
Pages (from-to)1-26
Number of pages26
Issue number10
StatePublished - Oct 2020

Bibliographical note

Funding Information:
Funding: This research was funded by the Minnesota Experiment Station for project MN 21-028.

Publisher Copyright:
© 2020 by the authors. Licensee MDPI, Basel, Switzerland.


  • Cell wall
  • Fruit ripening
  • NCounter®
  • RNA-Seq
  • Xyloglucan endotransglucosylase/hydrolase (MdXTH)


Dive into the research topics of 'Identification of candidate genes involved in fruit ripening and crispness retention through transcriptome analyses of a ‘Honeycrisp’ population'. Together they form a unique fingerprint.

Cite this