Genome-wide presence/absence variation discovery and its application in Peach (Prunus persica)

Gene presence/absence variation (PAV) is an important contributor to the studies of genetic diversity, gene identification, and molecular marker development in plants. In the present study, 100 peach (Prunus persica) accessions were used for genome resequencing to identify PAVs. Alignmentwith a reference genome yielded a total of 2.52 Mb non-reference sequences and 923 novel genes were identified. The dispensable PAVs were enriched in resistance, perhaps reflecting their roles in plant adaptation to various environments. Furthermore, selection sweeps associated with peach domestication and improvement were identified based on PAV data. Only 4.3% and 13.4% of domestication and improvement sweeps, respectively, were identified simultaneously using single nucleotide polymorphism (SNP) data, suggesting flexible identification between the different methods. To further verify the applicability of PAV identification, a genome-wide association study was conducted using 21 agronomic traits. Some of the identified loci were consistent with those reported in previous studies, while some were mapped for the first time; the latter included petiole length, petiole gland shape, and petiole gland number. Through tissue-specific expression analysis and gene transformation experiments, a novel gene, evm.model.Contig322_A94.1, was identified and found to be involved in chilling requirements. We speculated that this novel gene might regulate the trait by participating in the ABA signaling pathway. The PAVs identified in P. persica provide valuable resources for mapping the entire gene set and identifying optional markers for molecular selection in future studies. •Genome-wide PAVs analyses of P. persica yielded a total of 2.52 Mb non-reference sequences and 923 novel genes.•4.3% and 13.4% of domestication and improvement sweeps, respectively, were identified simultaneously using PAV and SNP data.•PAV-GWAS for traits including petiole length, petiole gland shape, and petiole gland number, were reported firstly.•A novel gene, evm.model.Contig322_A94.1, was identified and found to be involved in chilling requirements.•PAVs in P. persica provide valuable resources for mapping the entire gene set and optional markers for molecular selection.