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

<i>Crotalaria</i> is a genus of the Fabaceae family with agricultural and medicinal value, but to date the genome has not been fully sequenced. Although <i>Crotalaria pallida</i> 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 <i>C. pallida</i> with 98.52% coverage which is assembled into 8 chromosomes. <i>C. pallida</i> is closely related to <i>Lupinus angustifolius</i>, with genetic divergence occurring ~42.5-57.4 million years ago (MYA). Re-sequencing of 236 <i>C. pallida</i> accessions revealed a genetic diversity decrease as <i>C. pallida</i> 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 <i>C. pallida</i> in Hainan reduced genetic diversity, leading to a divergence in allelic frequencies at four candidate genes (<i>CpPTR</i>, <i>CpMYB</i>, <i>CpRLPK</i>, and <i>CpNADK</i>) 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 <i>C. pallida</i> breeding.