Genomes and integrative genomic insights into the genetic architecture of main agronomic traits in the edible cherries

Abstract

Cherries are one of the economically important fruit crops in the Rosaceae family, Prunus genus. As the first fruits of the spring season in the northern hemisphere, their attractive appearance, intensely desirable tastes, high nutrients content, and consumer-friendly size captivate consumers worldwide. In the past 30 years, although cherry geneticists and breeders have greatly progressed in understanding the genetic and molecular basis underlying fruit quality, adaptation to climate change, and biotic and abiotic stress resistance, the utilization of cherry genomic data in genetics and molecular breeding has remained limited to date. Here, we thoroughly investigated recent discoveries in constructing genetic linkage maps, identifying quantitative trait loci (QTLs), genome-wide association studies (GWAS), and validating functional genes of edible cherries based on available de novo genomes and genome resequencing data of edible cherries. We further comprehensively demonstrated the genetic architecture of the main agronomic traits of edible cherries by methodically integrating QTLs, GWAS loci, and functional genes into the identical reference genome with improved annotations. These collective endeavors will offer new perspectives on the availability of sequence data and the construction of an interspecific pangenome of edible cherries, ultimately guiding cherry breeding strategies and genetic improvement programs, and facilitating the exploration of similar traits and breeding innovations across Prunus species.

Acknowledgement

This work was financially supported by Sichuan Science and Technology Program (2024YFHZ0302), Natural Science Foundation of Sichuan Province (2023NSFSC0158), Sichuan Fruit Innovation Team of National Modern Agricultural Industrial Technology System in China (SCCXTD-2024-4), the Project of Rural Revitalization Research Institute in Tianfu New Area of Sichuan Province (XZY1-04) and Cherry Resources Sharing and Service Platform of Sichuan Province.

Author contributions

Z.-S.L. collected and analyzed data and wrote the manuscript; A.B. and E.D. collected data and conceived and revised the manuscript; W.Y. revised the manuscript; and X.-R.W. supervised and revised the manuscript.

Data availability

All the data is presented in the text file.

Conflict of interest

The authors declare no conflict of interests.

Supplementary Data

Supplementary data is available at Horticulture Research online.

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