Rong Liu, Chaoqin Hu, Dan Gao, Mengwei Li, Xingxing Yuan, Liyang Chen, Qin Shu, Zonghe Wang, Xin Yang, Zhengming Dai, Haitian Yu, Feng Yang, Aiqing Zheng, Meiyuan Lv, Vanika Garg, Chengzhi Jiao, Hongyan Zhang, Wanwei Hou, Changcai Teng, Xianli Zhou, Chengzhang Du, Chao Xiang, Dongxu Xu, Yongsheng Tang, Annapurna Chitikineni, Yinmei Duan, Fouad Maalouf, Shiv Kumar Agrawal, Libin Wei, Na Zhao, Rutwik Barmukh, Xiang Li, Dong Wang, Hanfeng Ding, Yujiao Liu, Xin Chen, Rajeev K. Varshney, Yuhua He, Xuxiao Zong, Tao Yang

Genome Biology; 2025; IF:10.1

DOI: 10.1186/s13059-025-03532-7

Abstract

Background: A comprehensive study of the genome and genetics of superior germplasms is fundamental for crop improvement. As a widely adapted protein crop with high yield potential, the improvement in breeding and development of seeds industry of faba bean have been greatly hindered by its giant genome size and high outcrossing rate.

Results: To fully explore the genomic diversity and genetic basis of important agronomic traits, we first generate a de novo genome assembly and perform annotation of a special short-wing petal faba bean germplasm (VF8137) exhibiting a low outcrossing rate. Comparative genome and pan-genome analyses reveal the genome evolution characteristics and unique pan-genes among the three different faba bean genomes. In addition, the genome diversity of 558 accessions of faba bean germplasm reveals three distinct genetic groups and remarkable genetic differences between the southern and northern germplasms. Genome wide association analysis identifies several candidate genes associated with adaptation- and yield-related traits. We also identify one candidate gene related to short-wing petals by combined quantitative trait locus mapping and bulked segregant analysis. We further elucidate its function through multiple lines of evidence from functional annotation, sequence variation, expression differences and protein structure variation.

Conclusions: Our study provides new insights into the genome evolution of Leguminosae and the genomic diversity of faba bean. It offers valuable genomic and genetic resources for breeding and improvement of faba bean.