Nuclear Factor Y (NF-Y) is a heterotrimeric complex composed of three unique subunits: NF-YA, NF-YB, and NF-YC. The NF-Y transcription factor complex binds to the CCAAT box of eukaryotic promoters, playing a vital role in various biological processes in plants. However, the NF-Y gene family has not yet been reported from the peach genome. The current study identified and classified candidate peach NF-Y genes for further functional analysis of this family. The current study identified 24 Nuclear Factor Y (NF-Y) transcription factor subunits (6 NF-YA, 12 NF-YB, and 6 NF-YC subunits) in peach. These NF-Y subunits were described with respect to basic physicochemical characteristics, chromosome locations, gene structures, and conserved domains. Based on an analysis of the phylogenetic relationships among peach NF-Ys, six pairs of paralogous NF-Ys were detected. The expansion of the peach NF-Y family occurred by segmental and tandem duplication. Phylogenetic gene synteny of NF-Y proteins was observed between peach and Arabidopsis, and five pairs of paralogous NF-Y proteins from peach and Arabidopsis were identified. Twenty-four peach NF-Ys displayed a diversity of tissue expression patterns. In addition, drought-responsive cis-elements were observed in peach NF-Y promoters, and 9 peach NF-Y genes were shown to distinctly increase their transcript abundances under drought stress. This study identified 24 NF-Y genes in the peach genome and analysed their properties at different levels, providing a foundation for researchers to understand this gene family in peach. The up-regulation of 9 NF-Y genes under drought stress indicates that they can serve as candidate functional genes to further study drought resistance in peach.

Peach (Prunus persica L.) generally exhibits self-pollination, however, they can also be pollinated by other varieties of pollen. Here we found two varieties that are different from other peaches: ‘Daifei’ and ‘Liuyefeitao’. ‘Daifei’ produces less pollen, which needs artificial pollination, honeybee pollination, and the fruit setting depends on other varieties of peach pollen. ‘Liuyefeitao’ exhibits strictly self-pollination, hence pollen from other species is rejected. To explore the mechanism of this phenomenon, we performed a high-throughput sequencing of the stigma (including style) of ‘Daifei’ and ‘Liuyefeitao’ to explain the rejection mechanism of other varieties of pollen of ‘Liuyefeitao’ peach. In our study, we found one S gene, and lots of non-S-locus factors such as: F-box proteins, Ub/26S, MAPKs, RLK, and transcription factor were differential expressed between ‘Daifei’ and ‘Liuyefeitao’. We supposed that the strictly self-compatible of ‘Liuyefeitao’ may result from the synthesis of these factors.

Peach (Prunus persica L. Batsch) is one of the most popular fruits worldwide. Although the reference genome of ‘Lovell’ peach has been released, the diversity of genome-level variations cannot be explored with one genome. To detect these variations, it is necessary to assemble more genomes. We sequenced and de novo assembled the genome of ‘Feichenghongli’ (FCHL), a representative landrace with strict self-pollination, which maintained the homozygosity of the genome as much as possible. The chromosome-level genome of FCHL was 239.06 Mb in size with a contig N50 of 26.93 Mb and only 4 gaps at the scaffold level. The alignment of the FCHL genome with the reference ‘Lovell’ genome enabled the identification of 432535 SNPs, 101244 insertions and deletions, and 7299 structural variants. Gene family analysis showed that the expanded genes in FCHL were enriched in sesquiterpenoids and triterpenoid biosynthesis. RNA-seq analyses were carried out to investigate the two distinct traits of late florescence and narrow leaves. Two key genes, PpDAM4 and PpAGL31, were identified candidates for the control of flower bud dormancy, and an F-box gene, PpFBX92, was identified as a good candidate gene in the regulation of leaf size. The assembled high-quality genome could deepen our understanding of variations among diverse genomes and provide valuable information for identifying functional genes and improving the molecular breeding process.