Genome sequencing revealed the red-flower trait candidate gene of a peach landrace

Abstract

Peach ( Prunus persica) is an economically important fruit crop globally and an excellent material for genomic studies. While considerable progress has been made in unveiling trait-associated genes within cultivars and wild relatives, certain novel genes controlling valuable traits in peach landraces, such as the red-flowering gene, remained unclear. In this study, we sequenced and assembled the diploid genome of the red-flower landrace ‘Yingzui’ (abbreviated as ‘RedY’). Multi-omics profiling of red petals of ‘RedY’ revealed the intensified red coloration associated with anthocyanins accumulation and concurrent decline in flavonols. This phenomenon is likely attributed to a natural variant of Flavonol Synthase ( FLS) harboring a 9-bp exonic insertion. Intriguingly, the homozygous allelic configurations of this FLS variant were only observed in red-flowered peaches. Furthermore, the 9-bp sequence variation tightly associated with pink/red petal color in genome-wide association studies (GWAS) of collected peach germplasm resources. Functional analyses of the FLS variant, purified from procaryotic expression system, demonstrated its diminished enzymatic activity in flavonols biosynthesis, impeccably aligning with the cardinal trait of red flowers. Therefore, the natural FLS variant was proposed as the best candidate gene for red-flowering trait in peach. The pioneering unveiling of the red-flowered peach genome, coupled with the identification of the candidate gene, expanded the knowledge boundaries of the genetic basis of peach traits and provided valuable insights for future peach breeding efforts.

Acknowledgements

This work was supported by the project fund (YDXM2023001 and CXTD2021009-2) from Fujian Academy of Agricultural Sciences. It was also funded by the grant (2022R1028009) from the Department of Science and Technology of Fujian Province. We are grateful to CNPGRN staffs, especially for Lirong Wang and Weichao Fang (Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences) and Ruijuan Ma (Institute of Pomology, Jiangsu Academy of Agricultural Sciences) who provided the information of petal colors and valuable red-flower peach materials.

Author contributions

P.Z. and Xin.Z. designed the project. P.Z. performed the experiments. S.L. and Xin.Z. assembled and annotated the chromosome-level and haplotype-resolved peach genome. P.Z. and S.L. analysed and plotted the high-throughput sequencing and metabolic data. Xia.Z., S.Y., R.G., and G.J. collected peach germplasms and improved analysis results. Y.W. completed the GWAS analysis. P.Z., S.L., and Xia.Z. wrote the manuscript. P.Z., Xia.Z., and Xin.Z. revised the manuscript.

Data availability

The raw sequencing data of current study were deposited in the Genome Sequence Archive (GSA, https://ngdc.cncb.ac.cn/gsa/) of the National Genomics Data Center (NGDC) / China National Center for Bioinformation (CNCB) under the following accession numbers: PacBio de novo Hifi sequencing of ‘RedY’: CRA009407; Hi-C sequencing of ‘RedY’: CRA009408; Illumina RNA-Seq paired end reads of ‘RedY’ diverse tissues: CRA009422; Illumina RNA-Seq paired end reads of ‘RedY’ and ‘PinkY’ petal at four developmental stages: CRA009421. The re-sequencing data of 24 peaches were publicly accessible at NCBI Sequence Read Archive under accession PRJNA951060. P. persica RedY whole genome v1.0 assembly and annotation are available in Genome Warehouse (GWH, https://ngdc.cncb.ac.cn/gwh/) at NGDC / CNCB under accession number GWHCBHS00000000.

Conflict of interest statement

The authors declare that they have no conflict of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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