Genomic and transcriptomic analyses provide new insights into the complex impacts of bud mutation in peach

Abstract Bud mutation is an important solution in fruit breeding, but the mechanism of bud mutation remains largely unknown. Here, we present the phenotypic, genomic, and transcriptomic analyses of a peach hairless bud mutation. Phenotypic analyses found an increase in the soluble solid content (SSC), fructose, and glucose, as well as a decrease in fruit weight, sucrose, and sorbitol in hairless bud mutation. Genomic analyses showed a higher number of SNPs, indels, SVs, and TEs in the hairless bud mutation than the wild type. Moreover, most of the variations were heterozygous. An LTR transpose element in the third exon of PpMYB25 was identified in the hairless mutation, but was absent in the wild type, underlying the hairless phenotype. A total of 660 differentially expressed genes were identified in mutation, including 254 were upregulated and 406 were downregulated. The functional annotation of differentially expressed genes revealed two sucrose synthase gene PpSUS3 and PpSUS4, as well as two nitrate transporter gene PpNRT2.5 and PpNRT1, implying the candidates underlying the increase in the SSC and decrease in the fruit weight in mutation. Our results elucidated the complicated impacts of bud mutation on the genome and transcriptome provide new insights into, providing new insights into the molecular mechanism of somatic mutation in plants.