A Transcriptome Analysis Identifies Candidate Genes Related to Fruit Cracking in Pomelo Fruits

Fruit cracking is a universal physiological disorder that occurs during growth in citrus fruits. However, the molecular mechanisms that regulate cracking in citrus fruits remain unclear. The aim of this study was to screen genes that were related to resistance to fruit cracking.

Normal fruits from a pomelo (Citrus grandis (L). Osbeck) cultivar (Duxin 1) resistant to cracking, as well as normal and cracked fruits from Duwei, a cultivar sensitive to cracking, were collected on August 3, 2021 and August 20, 2021, respectively. The pericarp surrounding blossom ends of the fruits (the blossom end was considered the center, approximate 30 millimeters radius) were sampled for RNA-seq.

The differentially expressed genes (DEGs) in each stage were screened based on the comparisons of a transcriptome between cracked fruits from the cracking-sensitive cultivar and normal fruits from both cultivars. In the stage A, 1 660 DEGs were obtained, and 104 DEGs were common between the comparison. A total of 1 972 DEGs were screened in stage B, and 82 were common in the comparison. All the DEGs screened at both stages were used for a Gene Ontology enrichment analysis. In the classification of biological process, the major common sub-classifications, including ‘metabolic process’, ‘cellular process’, ‘single-organism process’, ‘biological regulation’, ‘response to stimulus’, and ‘signaling’ were identified in both stages. All the screened DEGs were also analyzed using Kyoto Encyclopedia of Genes and Genomes enrichment. Many genes were enriched in several metabolic pathways, including ‘carbon metabolism’, ‘MAPK signaling pathway-plant’, ‘plant hormone signal transduction’ and ‘protein processing in endoplasmic reticulum’. In addition, these pathways were identified in both stages. Several genes related to resistance to fruit cracking were identified in this study. The levels of transcription of Expansin-A1 were significantly higher in the pericarp of normal fruits from the two cultivars than that in the pericarp of cracked fruits from the sensitive cultivar. Calcineurin B-like protein gene was highly expressed in the pericarp of normal fruits from both cultivars when compared with the pericarp of cracked fruits from the sensitive cultivar. However, this difference disappeared at the stage B. The genes for heat stress transcription factor, serine/threonine-protein kinase, auxin-responsive protein, and dehydration-responsive element-binding protein were upregulated in the pericarp of cracked fruits from the sensitive cultivar compared with the pericarp of normal fruits from the two cultivars in both stages.

These findings suggested that the genes related to strength of pericarp, water movement, and responsing to high temperature and water deficiency stresses were critical to regulating resistance to fruit cracking.