High-quality genome and variation map reveal valuable loci and the genetic basis of trait divergence driven by geographic dispersal in Crotalaria pallida
1College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China 2National Key Laboratory for Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Institute of Tropical Bioscience and Biotechnology,Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China 3Hainan KeyLaboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China 4Hainan KeyLaboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China 5Novogene Bioinformatics Institute, Beijing 100000, China 6Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan 678000, China 7Shaanxi Provincial Bioresource Key Laboratory, College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723000, China 8Mountains Bioresources Comprehensive Development C.I.C., Hanzhong 723001, China 9College of Tropical Crops, Hainan University, Hainan 570228, China 10Wenshan Academy of Agricultural Sciences, Yunnan 663000, China 11Wuhan Healthcare Metabolic Biotechnology Co., Ltd, Hubei 430000, China *Corresponding author. E-mail: huwei2010916@126.com,liuguodao2008@163.com,zhibiao@lzu.edu.cn †Hubiao Yang,Xiaoxue Ye,Yiming Wang,Wei Yan contributed equally to the study.
Received: 23 May 2025 Accepted: 20 Jan 2026 Published online: 29 Jan 2026
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.
, Guodao Liu2 ,
