Alternative splicing analysis provides insight into the domestication and improvement of pear (Pyrus pyrifolia) fruit

Abstract

Alternative splicing (AS) plays a vital role in response to environmental stress. However, the functional impacts of AS on fruit quality in domestication and improvement remain unknown. In this study, we analyzed AS in fruit using RNA-seq of wild, landrace, and improved pear accessions. A total of new 237,085 transcripts were mapped to 29,254 genes. Based on these assembled transcripts, 191,060 AS events for 15,324 genes were identified, of which retained intron (RI) was the most frequent AS type, accounting for approximately 46.96% of AS events. Furthermore, 847 and 841 differential AS genes (DASGs) were identified during domestication and improvement, respectively. According to gene ontology (GO) enrichment analysis, the DASGs exclusively during domestication affected glycosylation and carbohydrate metabolism, while the DASGs exclusively during improvement were enriched in response to chemical stimulus. We found little overlap between DASGs and differentially expressed genes (DEGs) in both the domestication and improvement processes, which indicated that AS was another gene regulatory mechanism for fruit development. Eight serine/arginine-rich (SR) genes related to AS regulation were differentially alternatively spliced during domestication or improvement, which indicated that SR genes might play regulatory roles in AS during the two processes in pear. Combined with gene annotation and previously identified quantitative trait loci (QTLs), 91 candidate DASGs related to fruit traits, including genes involved in sugar metabolism, acid metabolism, stone cell formation, and fruit firmness, were screened out during the investigation of domestication and improvement. Among them, Pectin acetylesterase 8 (PbrPAE8) produced PbrPAE8_1 and PbrPAE8_2 transcripts through AS, which was validated by qRT-PCR. The significant difference of AS ratio between landrace and improved groups were correlated with fruit firmness variability in these two populations. Our analysis is the first to reveal that AS variation is related to fruit quality during domestication and improvement of pear. Taken together, our study enriches the understanding of AS and its potential role in pear fruit improvement, thus providing useful references for other fruit tree crops.