Identification of candidate genes associated with slow-melting flesh trait in peach using bulked segregant analysis and RNA-seq

Flesh texture is an important characteristic that breeders used to select preferred cultivars. The slow-melting flesh (SMF) trait could both increase fruit harvest-time and shelf life. However, the mechanism underlying slow-melting flesh still remains unknown. In this study, a combination of bulked segregant analysis (BSA) and RNA-seq was used to identify candidate genes involved in slow-melting trait. Two adjacent major QTLs were identified on chromosome 4 from BSA result. In RNA-seq analysis, 2194 differentially expressed genes (DEGs) were detected by comparing RNA-seq data between non-slow melting flesh (NSMF) and SMF peach individuals at three different fruit developmental stages. Functional enrichment analysis revealed that DEGs of response to auxin were significantly enriched. Considerable DEGs associated with fruit softening process were identified, such as cellulose, pectate lyase and polygalacturonase. By integrating BSA and RNA-seq results, a total of 29 candidate genes located in the mapping site were discovered. These results would provide great help in casual gene identification for SMF trait and facilitate peach genomic study.