Structural variation drives rhizome innovation and adaptive divergence in sister <i>Medicago</i> species
Wild perennial sister species Medicago archiducis-nicolai (rhizomatous/alpine) and M. ruthenica (non-rhizomatous/xeric) constitute vital genetic resources for forage improvement. To decode the genomic basis of their contrasting trait and habitat adaptation, we generated chromosome-scale genome assemblies, resequenced 128 individuals, profiled transcriptomes under cold/heat stress, and functionally validated causal alleles. We demonstrate that structural variations (SVs)-particularly gene duplications-are primary drivers of rhizome formation and alpine/xeric adaptation. Further, pervasive presence-absence SVs (PAVs) in noncoding regulatory regions underpin divergent allele-specific expression governing rhizome development and stress responses. Crucially, these regulatory PAVs induce contrasting expression patterns during trait development and stress adaptation. Our findings reveal a dual mechanism whereby coding and regulatory SVs convergently orchestrate phenotypic innovation and ecological specialization in sister species, offering valuable genomic resources for legume evolution studies and alfalfa breeding.
Authors
- Kunjing Qu (ORCID: https://orcid.org/0009-0009-2945-7155)
- Chenxiang Jiang (ORCID: https://orcid.org/0009-0006-3488-3034)
- Jianquan Liu (ORCID: https://orcid.org/0000-0002-4237-7418)
- Shuang Wu (ORCID: https://orcid.org/0009-0001-8107-0144)
- Zhipeng Liu (ORCID: https://orcid.org/0000-0001-7687-8256)
- Yudan Zheng (ORCID: https://orcid.org/0009-0007-5173-7642)
- Guangpeng Ren (ORCID: https://orcid.org/0000-0002-4052-9115)
- Ao Li (ORCID: https://orcid.org/0000-0002-4989-8136)
- Haiqing Wang (ORCID: https://orcid.org/0000-0002-2859-5136)
- Zhao-Ming Wang (ORCID: https://orcid.org/0000-0002-8976-9515)
- Hongyin Hu (ORCID: https://orcid.org/0000-0002-3318-7794)
- Na Wang (ORCID: https://orcid.org/0009-0005-9865-3265)
- Xue Yang (ORCID: https://orcid.org/0009-0005-9262-9846)
- Yi Wan (ORCID: https://orcid.org/0009-0002-0756-1778)
- Ying Yang (ORCID: https://orcid.org/0000-0002-8208-3625)
Institutions
- Chinese Academy of Sciences (CN)
- Ministry of Agriculture (EE)
- Xinjiang Institute of Ecology and Geography (CN)
- Shandong Academy of Agricultural Sciences (CN)
- Propagation Research Associates (United States) (US)
- Lanzhou University (CN)
Publication Details
- Journal
- Journal of Integrative Plant Biology
- Published
- 2025-11-26
- DOI
- https://doi.org/10.1111/jipb.70098
- Primary Topic
- Plant Molecular Biology Research
- Type
- article
- Field-Weighted Citation Impact
- 0.00