Overview
Genome Size
240 Mb
Date performed
2021
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Publication
Abstract
Background: Prunus persica is an important perennial fruit crop, but the genetic mechanisms underlying its favorable traits are poorly understood, partly due to the scarcity of high-quality genomic resources. Traditional SNP-based genome-wide association studies (GWAS) have limitations in peach, and the role of structural variations (SVs) in shaping traits remains underexplored.
Results: A high-quality de novo genome assembly for Prunus persica was generated, with a significantly improved contig N50 and reduced gap number compared to previous assemblies. Whole-genome resequencing of 417 peach accessions identified 3,749,618 high-quality SNPs, 577,154 small indels, and numerous SVs. SV-based GWAS revealed a ~1.67 Mb inversion on chromosome 6 associated with flat fruit shape, which alters the expression of the Prupe.6G290900 gene (Ovate family protein). Additionally, a complex rearrangement on chromosome 4 containing a NAC transcription factor (Prupe.4G187100) was associated with fruit development period, and transposable element insertions in the promoter of miR172d (Prupe.2G237700) were linked to double flowers.
Conclusions: The high-quality genome assembly of Prunus persica provides valuable genomic resources for functional genomics and evolutionary research. SV-based GWAS effectively identifies candidate genes for key agronomic traits, offering targets for molecular breeding. This approach highlights the importance of SVs in driving functional discoveries in Prunus persica and can be applied to other organisms.
