Identification of Candidate Genes Involved in Fruit Ripening and Crispness Retention Through Transcriptome Analyses of a ‘Honeycrisp’ Population

Abstract

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.

Unraveling the pathways influencing the berry color and firmness of grapevine cv. Flame Seedless treated with bioregulators using biochemical and RNA-Seq analysis under semi-arid subtropics

“…This means plant bioregulators stimulate these processes, improving berry color, phenolics, flavonoids, and antioxidant contents. Similar findings were also reported in a few other transcriptomics studies ( Chang and Tong, 2020 , Jiang et al, 2019 ).…”

Cell Wall Calcium and Hemicellulose Have a Role in the Fruit Firmness during Storage of Blueberry (Vaccinium spp.)

“…These researchers determined that during refrigerated storage genes associated with both cell wall synthesis and remodeling were actively transcribed and found marked differences between firm versus soft firmness genotypes. Similarly, a study conducted to understand the changes of Honeycrisp apples, which is characteristic to present a significant firmness postharvest, found that this could be explained in part by the ability to continue cell wall synthesis in cold storage [ 64 ]. In addition, these authors determined that genes associated with hemicellulose metabolism, such as xyloglucan endotransglycosylase/Hydrolase (XTH), may be particularly involved in maintaining apple firmness after harvest.…”

A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica)

“…To supplement ab initio gene predictions, extensive extrinsic gene annotation homology evidence is needed. Thus, we downloaded existing RNA-seq data for 'Honeycrisp' apples from NCBI using SRA toolkit v2.9.6-1 (SRX3408575, SRX5369275, SRX5369276, SRX5369290, SRX5369299, SRX5369300, SRX5369302, SRX8712695 and SRX8712718) [44][45][46], and combined with the RNA-seq data generated for this project (described above). We de novo assembled these two sets of RNA transcripts separately using Trinity v2.13.2 [47], where we used the flag --trimmomatic to filter the reads for quality.…”