BL-Hi-C reveals the 3D genome structure of Brassica crops with high sensitivity

Abstract

High-throughput Chromatin Conformation Capture (Hi-C) technologies can be used to investigate the three-dimensional genomic structure of plants. However, the practical utility of these technologies is impeded by significant background noise, hindering their capability in detecting fine 3D genomic structures. In this study, we optimized the Bridge Linker Hi-C technology (BL-Hi-C) to comprehensively investigate the 3D chromatin landscape of Brassica rapa and Brassica oleracea. The Bouquet configuration of both B. rapa and B. oleracea was elucidated through the construction of a 3D genome simulation. The optimized BL-Hi-C exhibited lower background noise compared to conventional Hi-C methods. Taking this advantage, we used BL-Hi-C to identify FLC gene loops in Arabidopsis, B. rapa, and B. oleracea. We observed that gene loops of FLC2 exhibited conservation across Arabidopsis, B. rapa, and B. oleracea. While gene loops of syntenic FLCs exhibited conservation across B. rapa and B. oleracea, variations in gene loops were evident among multiple paralogs FLCs within the same species. Collectively, our findings highlight the high sensitivity of optimized BL-Hi-C as a powerful tool for investigating the fine 3D genomic organization.

Acknowledgements

This work was funded by the National Key Research and Development Program of China (2021YFF1000101) and the Agricultural Science and Technology Innovation Program (ASTIP). The research was conducted in the State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, P.R. China, and the Sino-Dutch Joint Lab of Horticultural Genomics Technology, Beijing.

Authors’ contributions

X.W. and J.W. designed the project; Lu.Z., R.Z., and Le.Z. prepared materials and performed the experiments; Lu.Z., H.G., and Z.Z. performed the data analysis; Lu.Z., X.W., and J.W. wrote the manuscript; J.W., J.L., and X.C. revised the manuscript. All authors read and approved the final manuscript.

Data availability

All sequencing data generated for this study have been submitted to the NCBI Sequence Read Archive under accession number PRJNA945226. Previously published Hi-C data analysed in this study can be obtained from GEO via accession code (SRR8633037, SRR8633038).

Conflict of interest

The authors declare no competing interests.

Supplementary data

Supplementary data is available at Horticulture Research online.

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