Wu Bingchao, Luo Dan, Yue Yuesen, Yan Haidong, He Min, Ma Xixi, Zhao Bingyu, Xu Bin, Zhu Jie, Wang Jing, Jia Jiyuan, Sun Min, Xie Zheni, Wang Xiaoshan, Huang Linkai
College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
Institute of Grassland, Flower and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
Genome Biol. 2025 May 14;26(1):128. doi: 10.1186/s13059-025-03604-8.
Switchgrass (Panicum virgatum L.) is a bioenergy and forage crop. Upland switchgrass exhibits superior cold tolerance compared to the lowland ecotype, but the underlying molecular mechanisms remain unclear.
Here, we present a high-quality haplotype-resolved genome of the upland ecotype "Jingji31." We then conduct multi-omics analysis to explore the mechanism underlying its cold tolerance. By comparative transcriptome analysis of the upland and lowland ecotypes, we identify many genes with ecotype-specific differential expression, particularly members of the cold-responsive (COR) gene family, under cold stress. Notably, AFB1, ATL80, HOS10, and STRS2 gene families show opposite expression changes between the two ecotypes. Based on the haplotype-resolved genome of "Jingji31," we detect more cold-induced allele-specific expression genes in the upland ecotype than in the lowland ecotype, and these genes are significantly enriched in the COR gene family. By genome-wide association study, we detect an association signal related to the overwintering rate, which overlaps with a selective sweep region containing a cytochrome P450 gene highly expressed under cold stress. Heterologous overexpression of this gene in rice alleviates leaf chlorosis and wilting under cold stress. We also verify that expression of this gene is suppressed by a structural variation in the promoter region.
Based on the high-quality haplotype-resolved genome and multi-omics analysis of upland switchgrass, we characterize candidate genes responsible for cold tolerance. This study advances our understanding of plant cold tolerance, which provides crop breeding for improved cold tolerance.
柳枝稷（Panicum virgatum L.）是一种生物能源和饲料作物。与低地生态型相比，高地柳枝稷表现出更强的耐寒性，但其潜在的分子机制尚不清楚。
在此，我们展示了高地生态型“京稷31”的高质量单倍型解析基因组。然后，我们进行多组学分析以探索其耐寒性的潜在机制。通过对高地和低地生态型的比较转录组分析，我们鉴定出许多在冷胁迫下具有生态型特异性差异表达的基因，特别是冷响应（COR）基因家族的成员。值得注意的是，AFB1、ATL80、HOS10和STRS2基因家族在两种生态型之间表现出相反的表达变化。基于“京稷31”的单倍型解析基因组，我们在高地生态型中检测到比低地生态型更多的冷诱导等位基因特异性表达基因，并且这些基因在COR基因家族中显著富集。通过全基因组关联研究，我们检测到一个与越冬率相关的关联信号，该信号与一个包含在冷胁迫下高表达的细胞色素P450基因的选择性清除区域重叠。该基因在水稻中的异源过表达减轻了冷胁迫下的叶片黄化和萎蔫。我们还验证了该基因的表达受到启动子区域结构变异的抑制。
基于高质量的单倍型解析基因组和高地柳枝稷的多组学分析，我们鉴定了负责耐寒性的候选基因。本研究推进了我们对植物耐寒性的理解，为提高耐寒性的作物育种提供了依据。
