High-quality genome and variation map reveal valuable loci and the genetic basis of trait divergence driven by geographic dispersal in Crotalaria pallida

Abstract

Crotalaria is a genus of the Fabaceae family with agricultural and medicinal value, but to date the genome has not been fully sequenced. Although Crotalaria pallida is widely distributed in tropical and subtropical regions, the degree of genetic diversity and the specific traits influenced by geographic dispersal remain unknown. We here report a high-quality genome assembly of C. pallida with 98.52% coverage which is assembled into 8 chromosomes. C. pallida is closely related to Lupinus angustifolius , with genetic divergence occurring ∼42.5–57.4 million years ago (MYA). Re-sequencing of 236 C. pallida accessions revealed a genetic diversity decrease as C. pallida spread from Africa to America and Asia, and from Asia to China and finally to Hainan. Significant divergence was observed in seven traits between non-Hainan and Hainan accessions. Genome-wide association studies identified 73 loci for 18 agronomic traits, 25 of which overlapped with divergent sweeps between non-Hainan accessions and Hainan accessions. Furthermore, the dispersal of C. pallida in Hainan reduced genetic diversity, leading to a divergence in allelic frequencies at four candidate genes ( CpPTR , CpMYB , CpRLPK , and CpNADK ) associated with plant height. This study reveals the genetic basis of trait divergence driven by geographic dispersal and offers valuable resources for the strategic development of C. pallida breeding.

Acknowledgements

We thank Drs Y.P. Zhou and C.H. Hocart for proofreading the manuscript. This work was supported by Chinese Academy of Tropical Agricultural Sciences for Science and Technology Innovation Team of National Tropical Agricultural Science Center (no.CATASCXTD202503), the China Agriculture Research System of MOF and MARA (no. CARS-34) and the National Science and Technology Basic Resources Investigation (no. 2017FY100600).

Author contributions

Z.N. and G.L. conceived the project. H.Y. and W.H. organized and coordinated the project. W.H., X.Y., Y.W., C.J., Y.W., Z.D. W.T., X.D., L.K., M.Z., and H.L conducted bioinformatics analyses. H.Y., F.Y., W.Y., Z.H., Q.L., and Z.Z., performed the experiments and were involved in field management. H.Y. and W.H. drafted the manuscript. X.Y., Y.W., and G.L. revised the manuscript. All authors approved the final version of the manuscript before submission.

Data availability

All sequencing data of genome and transcriptome are available at the National Genomics Data Center (NGDC, https://ngdc.cncb.ac.cn) database under BioProject number PRJCA009683.

Conflicts of interest statement

The authors declare that they have no conflicts of interest associated with this work.

Supplementary material

Supplementary material is available at Horticulture Research online.

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