Transcriptome Profiles Reveal That Phytohormone Signal Transduction-related Genes Involved in Regulating Xenia in Rabbiteye Blueberry

Blueberries are small perennial evergreen or deciduous shrub berries of the genus Vaccinium in Ericaceae family. Pollination with different parental genotypes has significant effects on fruit size, fruit harvest time, fruit firmness, and chemical composition, such as soluble solids, titratable acids, anthocyanins, fructose, sucrose, glucose, flavonoids, and total phenols, showing an evident xenia effect. To understand the molecular mechanism and biosynthetic pathways involved in the xenia effect in rabbiteye blueberry, we employed transcriptome profiling by RNA sequencing to identify differentially expressed genes (DEGs) during fruit development of the variety ‘Premier’ produced by self and cross-pollination with ‘Brightwell’ and ‘Powderblue’. On the basis of the transcriptomic sequences, DEGs related to plant hormone signal transduction were identified through bioinformatics analysis, screening of DEGs, and functional enrichment analysis. The results showed that the single fruit weight and the contents of anthocyanins fructose, glucose, and sucrose showed significant differences between self- and cross-pollinated fruits, demonstrating a distinct xenia effect. High-throughput sequencing was conducted on the transcriptomes of young fruits harvested at six developmental stages (at 10-day intervals from 40 to 90 days after self- and cross-pollination). After screening and identification, 16.37 million to 25.52 million raw reads were generated and 4,937,201,302 to 7,709,896,920 clean bases were obtained. The comparison group of 80-day-old fruits generated through self-pollinated ‘Premier’ and those crossed with ‘Brightwell’ (PBR-80 vs. PPR-80) showed the largest number of DEGs (6377), of which 3052 were upregulated and 3325 were downregulated. Through further screening, 174 DEGs were found related to plant hormone signal transduction, comprising 147 known genes and 27 new genes and that 76 genes were downregulated and 98 genes were upregulated. Of the eight DEGs randomly selected for quantitative real-time polymerase chain reaction verification, their expression patterns were consistent with those revealed by high-throughput sequencing. The results elucidated the underlying mechanism of xenia, thereby providing a solid theoretical foundation for the targeted breeding, quality control, and improvement of economic benefits of blueberry, which are of important theoretical value and practical significance.