Population genomics reveals demographic history and selection signatures of hazelnut (Corylus)

Abstract

Hazelnut (Corylus spp.) is known as one of the four famous tree nuts in the world due to its pleasant taste and nutritional benefits. However, hazelnut promotion worldwide is increasingly challenged by global climate change, limiting its production to a few regions. Focusing on the eurytopic Section Phyllochlamys, we conducted whole-genome resequencing of 125 diverse accessions from five geo-ecological zones in Eurasia to elucidate the genomic basis of adaptation and improvement. Population structure inference outlined five distinct genetic lineages corresponding to climate conditions and breeding background, and highlighted the differentiation between European and Asian lineages. Demographic dynamics and ecological niche modeling revealed that Pleistocene climatic oscillations dominantly shaped the extant genetic patterns, and multiple environmental factors have contributed to the lineage divergence. Whole-genome scans identified 279, 111, and 164 selective sweeps that underlie local adaptation in Corylus heterophylla, Corylus kweichowensis, and Corylus yunnanensis, respectively. Relevant positively selected genes were mainly involved in regulating signaling pathways, growth and development, and stress resistance. The improvement signatures of hybrid hazelnut were concentrated in 312 and 316 selected genes, when compared to C. heterophylla and Corylus avellana, respectively, including those that regulate protein polymerization, photosynthesis, and response to water deprivation. Among these loci, 22 candidate genes were highly associated with the regulation of biological quality. Our study provides insights into evolutionary processes and the molecular basis of how sibling species adapt to contrasting environments, and offers valuable resources for future climate-resilient breeding.

Acknowledgements

This work was supported by the National Natural Science Foundation of China (32101541) and the Key Research and Development Program of Hebei Province (21326804D).

Author contributions

Z.Y. and Q.M. conceived the study; Z.Y. and W.M. performed molecular experiments and analyzed the data; X.Y., L.W., T.Z., and G.W. collected materials; L.L. contributed to data analysis; Z.Y. and Q.M. wrote the paper. All authors contributed to revisions and gave final approval for publication.

Data availability

The raw sequencing data of 125 accessions have been submitted to the NCBI BioProject database under accession number PRJNA899594. The unfiltered variant call format (VCF) file relative to the resequencing experiment is publicly available at the Figshare repository (10.6084/m9.figshare.22306681).

Conflict of interest

The authors declare no conflict of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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