Genetic and epigenetic signatures for improved breeding of cultivated blueberry

Abstract

Blueberry belongs to the Vaccinium genus and is a highly popular fruit crop with significant economic importance. It was not until the early twentieth century that they began to be domesticated through extensive interspecific hybridization. Here, we collected 220 Vaccinium accessions from various geographical locations, including 154 from the United States, 14 from China, eight from Australia, and 29 from Europe and other countries, comprising 164 Vaccinium corymbosum, 15 Vaccinium ashei, 10 lowbush blueberries, seven half-high blueberries, and others. We present the whole-genome variation map of 220 accessions and reconstructed the hundred-year molecular history of interspecific hybridization of blueberry. We focused on the two major blueberry subgroups, the northern highbush blueberry (NHB) and southern highbush blueberry (SHB) and identified candidate genes that contribute to their distinct traits in climate adaptability and fruit quality. Our analysis unveiled the role of gene introgression from Vaccinium darrowii and V. ashei into SHB in driving the differentiation between SHB and NHB, potentially facilitating SHB’s adaptation to subtropical environments. Assisted by genome-wide association studies, our analysis suggested VcTBL44 as a pivotal gene regulator governing fruit firmness in SHB. Additionally, we conducted whole-genome bisulfite sequencing on nine NHB and 12 SHB cultivars, and characterized regions that are differentially methylated between the two subgroups. In particular, we discovered that the β -alanine metabolic pathway genes were enriched for DNA methylation changes. Our study provides high-quality genetic and epigenetic variation maps for blueberry, which offer valuable insights and resources for future blueberry breeding.

Acknowledgements

This work was supported by funds from the State Key Laboratory of Protein and Plant Gene Research, the Project of Science and Technology Development of Jilin Province, China (20220508099RC), the Project of Development and Reform Commission of Jilin Province, China (2023C035-4) and startup funds from the School of Advanced Agricultural Sciences at Peking University. We express our gratitude for the computational resources provided by the High-performance Computing Platform of Peking University. We are grateful to Dr Massimo Iorizzo at North Carolina State University for his generous help with curating the classification of blueberry accessions. Additionally, we extend our thanks to Xiaowen Wang, Yilin Zhang, Han Zhou, Yi Liu, and Minghan Huang for their valuable discussion and input on data analysis. We are also thankful to Xinyue Lu, Xuanzhi Cheng, and Cuimei Zhang for their technical support.

Author Contributions

Q.L., H.S., and H.H. designed the research. H.S., W.Z., Y.L., H.Y., and G.X. collected the samples. Z.W., Z.G., and Y.S. analysed the high-throughput sequencing data. Y.Z., Q.Z., Y.T., and M.D. coordinated the genome resequencing and bisulfite sequencing. W.Z. measured the fruit traits. Z.W. and Q.L. wrote the manuscript. Q.L., H.S., H.H., and Z.W. revised the manuscript. K.P.K. and K.M. curated the classification of blueberry accessions. All authors approved the final version of the manuscript.

Supplementary data

Supplementary data is available at Horticulture Research online.

Data availability

Whole-genome resequencing data of 220 blueberry accessions has been deposited into the Sequence Read Archive (SRA) database under accession number PRJNA948809. The whole-genome methylation data of 21 cultivars (including 11SHB and 10 NHB), as well as the whole-genome methylation and transcriptome data of ‘Draper’, ‘sharpblue’, and V. darrowii, have been deposited into the Gene Expression Omnibus (GEO) database under SuperSeries GSE228041 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE228041). RNA-seq data of five developmental stages of blueberry have been deposited into the Gene Expression Omnibus (GEO) database under SuperSeries GSE229139. SNPs and indels in Variant Call Format (VCF) have been deposited into the Figshare database (https://doi.org/10.6084/m9.figshare.22699810).

Conflict of interests

The authors declare that they have no competing interests.

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