Impact of Allele-Specific Expression on Ripening and Quality Characteristics of ABB Banana Fruit

Allele-specific expression (ASE) is a phenomenon in which the expression level of an allele from both parents is inconsistent, which is considered to play a key role in the differences between hybrids. As a typical climacteric fruit, banana undergoes a ripening process that affects the quality of the fruit. BaXi (<i>Musa</i>, AAA group) and Fen Jiao (<i>Musa</i>, ABB group) banana fruits show different traits during postharvest ripening, and their high-quality reference genomic sequences have been published. In this work, we analyzed differentially expressed genes (DEGs) in these two banana cultivars based on the transcriptomes during the postharvest stages. Additionally, the imbalance expression of alleles of DEGs in Fen Jiao banana fruit was analyzed, revealing that 27.2% (3 d) and 22.2% (6 d) of the 15,415 DEGs showed ASE. Then, the ASE profiles related to the post-ripening of banana fruit were built, focusing on ripening-related pathways, such as ethylene biosynthesis (62.5-83.3%), starch degradation (0-75%) and cell wall material degradation (34.6-90.9%). The ASE genes involved in ripening were more frequent than those associated with general gene expression. In addition, the candidate key genes of ASE alleles involved in ethylene synthesis and starch degradation were identified, including the alleles of <i>MaACS7</i>/<i>MbACS7</i>, <i>MaACO2</i>/<i>MbACO6</i>, <i>MaACO3</i>/<i>MbACO7</i>, <i>MaACO8</i>/<i>MbACO13</i> and <i>MaACO6</i>/<i>MbACO17</i> involved in ethylene biosynthesis, and those of <i>MaAMY1</i>/<i>MbAMY3</i>, <i>MaBMY1</i>/<i>MbBMY2</i>, <i>MaBMY7</i>/<i>MbBMY8</i> and <i>MaDPE2</i>/<i>MbDPE2</i> involved in starch degradation. The expression of the B genes of these key enzyme genes (<i>ACS</i>/<i>ACO</i>/<i>AMY</i>) is more active than that of the A genes in Fen Jiao bananas.