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Article|18 Oct 2023|OPEN
Genome sequencing revealed the red-flower trait candidate gene of a peach landrace
Ping Zhou1,2 , ,† , Siru Lei3,4 ,† , Xiaodan Zhang5 , Yinghao Wang3,4 and Rui Guo1,2 , Shaobin Yan1,2 , Guang Jin1,2 , Xingtan Zhang,4 ,
1Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
2Research Centre for Engineering Technology of Fujian Deciduous Fruits, Fuzhou 350013, China
3College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
4Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
5Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
*Corresponding author. E-mail: zhouping@faas.cn,zhangxingtan@caas.cn
Both authors contributed equally to the study.

Horticulture Research 10,
Article number: uhad210 (2023)
doi: https://doi.org/10.1093/hr/uhad210
Views: 227

Received: 02 May 2023
Accepted: 11 Oct 2023
Published online: 18 Oct 2023

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.