Crotalaria pallida belongs to a legume genus widely used as green manure, cover crops, fiber sources, forage, and medicinal plants. The species can support nitrogen fixation, improve soil organic matter, suppress weeds, and produce bioactive compounds, including alkaloids and flavonoids. However, compared with major legumes such as soybean, pigeonpea, and chickpea, genomic research on Crotalaria has lagged far behind. The absence of a reference genome and large-scale variation map has limited systematic evaluation of germplasm resources and the development of molecular breeding strategies. Due to these challenges, deeper research is needed into the genome, dispersal history, and trait divergence of C. pallida.
Researchers from Lanzhou University, the Chinese Academy of Tropical Agricultural Sciences, Novogene Bioinformatics Institute, Yunnan Academy of Agricultural Sciences, Shaanxi University of Technology, Hainan University, Wenshan Academy of Agricultural Sciences, and Wuhan Healthcare Metabolic Biotechnology Co., Ltd. reported (DOI: 10.1093/hr/uhag026) the study in Horticulture Research on 29 January 2026. The article presents a chromosome-level genome assembly, a genome-wide variation map, and population analyses showing how geographic dispersal shaped genetic diversity and agronomic trait divergence in C. pallida.
The team assembled a 1,153.05-megabase genome and anchored 98.52% of the assembly onto eight chromosomes using chromosome conformation capture (Hi-C) data. They annotated 31,762 protein-coding genes and found expanded gene families related to flavonoid biosynthesis, including genes encoding 4-coumarate-CoA ligases (4CLs), offering genomic clues to the plant’s medicinal potential. Resequencing of 236 wild accessions generated 5,319,493 high-quality single-nucleotide polymorphisms (SNPs) and revealed four major genetic groups. Population analyses showed decreasing genetic diversity from Africa to the Americas and Asia, and from Asia to non-Hainan regions of China and finally Hainan. A genome-wide association study (GWAS) identified 73 marker-trait associations (MTAs) for 18 agronomic traits. Notably, 25 GWAS signals overlapped with divergent genomic regions between non-Hainan and Hainan accessions, linking geographic dispersal to trait divergence. Four plant-height-associated genes—CpPTR, CpMYB, CpRLPK, and CpNADK—showed divergent allele frequencies associated with reduced plant height in Hainan accessions.
The authors said the study turns C. pallida from a genomically underexplored legume into a species with practical genetic resources for research and breeding. They said the findings show that the plant’s spread across continents was not only a movement across geography, but also a process of genetic narrowing and trait reshaping. By connecting population history with plant architecture, the study provides a clearer path for selecting useful alleles and designing targeted breeding strategies for this valuable tropical legume.
The findings provide a foundation for genomics-assisted breeding, germplasm conservation, and functional studies in C. pallida. The reference genome and variation map can help breeders identify accessions carrying favorable alleles for plant height, branching, inflorescence length, and other architecture-related traits. The expansion of flavonoid-related genes also opens opportunities to investigate medicinal compounds with greater precision. In sustainable agriculture, improved C. pallida varieties could strengthen green manure production, soil fertility management, weed suppression, and forage use. More broadly, the study offers a model for understanding how dispersal shapes genetic diversity and trait evolution in underutilized tropical crops.
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References
DOI
10.1093/hr/uhag026
Original Source URL
https://doi.org/10.1093/hr/uhag026
Funding information
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).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.