Genome sequencing revealed the red-flower trait candidate gene of a peach landrace
Background: Peach (Prunus persica) is an economically vital fruit crop with diverse ecotypes, yet the genetic basis of certain unique traits in landraces, such as the red-flowering phenotype, has remained poorly understood. While red petal coloration is highly valued for its ornamental appeal, the specific molecular mechanisms driving intensified red pigmentation versus the common pink flowers were previously unclear. This study aimed to bridge this knowledge gap by assembling a high-quality genome for the red-flowered landrace 'Yingzui' ('RedY') and identifying the critical determinants of flower color through multi-omics and functional analyses.
Results: The research team generated a high-quality, chromosome-level, and haplotype-resolved diploid genome for 'RedY' using PacBio HiFi and Hi-C sequencing, resulting in two haploid assemblies of 242.77 Mb and 247.40 Mb anchored into eight chromosomes. Metabolomic profiling revealed that the intensified red color in 'RedY' petals is caused by a 4-fold increase in anthocyanin accumulation (specifically Cy-3-Glu) alongside a concurrent decline in flavonols. Genome-wide association studies (GWAS) and sequence alignment identified a natural variant of Flavonol Synthase (FLS)—harboring a 9-bp exonic insertion that results in a Gly-Leu-Gln (GLQ) amino acid duplicate—as the best candidate gene for this trait. Prokaryotic expression and enzymatic assays confirmed that this FLS variant has significantly diminished catalytic activity (reduced by 78.66%), which channels substrates away from flavonol synthesis and toward the anthocyanin pathway, thereby determining the red-flower characteristic.
Conclusions: The pioneering assembly of the red-flowered peach genome and the identification of the FLS natural variant provide a definitive molecular and biochemical explanation for the monogenic inheritance of the red-flower trait in peach. By demonstrating how a structural variation in a fundamental catalytic enzyme dictates the metabolic flux between competing flavonoid branches, this study expands the understanding of petal coloration mechanisms in perennials. These findings offer a valuable genetic resource and reference for target loci selection in future peach breeding efforts aimed at developing new cultivars that integrate both high-quality fruit and ornamental traits.
https://pubmed.ncbi.nlm.nih.gov/38023475/
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