A gap-free genome of pillar peach (Prunus persica L.) provides new insights into branch angle and double flower traits
Background: Peach (Prunus persica) is a globally cultivated deciduous fruit tree, and while the release of previous peach genomes has significantly propelled gene mapping, existing assemblies still contain multiple gaps that can lead to inaccurate gene annotation. To address these limitations, researchers utilized the 'Zhaoshouhong' (ZSH) peach—a cultivar characterized by a pillar growth habit and double flowers—to generate a high-quality reference. The aim of this work was to construct a complete, gap-free genome assembly to provide a more precise foundation for exploring the genetic mechanisms underlying key architectural and ornamental traits in peach.
Results: By combining Nanopore ultra-long and Hi-C sequencing reads, the study produced a 239.34 Mb gap-free nuclear genome anchored to eight chromosomes with a contig N50 of 29.67 Mb and high assembly accuracy (QV = 53.3). Comparative genomic analysis identified PpTAC1 as the major gene influencing branch angle, revealing that ZSH harbors a 4,422 bp exonic insertion and an 11 bp promoter deletion that distinguish pillar types from standard types. Additionally, the researchers found that the double-flower trait is co-regulated by miR172d and the APETALA2 transcription factor PpAP2; specific mutations disrupting miR172d or a single nucleotide polymorphism (SNP) preventing the degradation of PpAP2 were found to drive the development of double flowers in different peach varieties.
Conclusions: The completion of this first gap-free peach genome represents a significant advancement in Prunus genomics, offering a highly accurate resource that overcomes the limitations of previous fragmented assemblies. By clarifying the molecular variations in PpTAC1, miR172d, and PpAP2, this study provides essential insights into plant architecture and floral morphogenesis, facilitating future genetic improvements. Ultimately, this gap-free assembly serves as a valuable tool for breeders to conduct precise gene mapping and molecular breeding to enhance the ornamental and agronomic value of peach cultivars.
https://pubmed.ncbi.nlm.nih.gov/39306859/
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