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New insights into the cold tolerance of upland switchgrass by integrating a haplotype-resolved genome and multi-omics analysis

文献类型： 外文期刊

作者： Wu, Bingchao 1 ; Luo, Dan 1 ; Yue, Yuesen 2 ; Yan, Haidong 1 ; He, Min 3 ; Ma, Xixi 1 ; Zhao, Bingyu 4 ; Xu, Bin 5 ; Zhu, Jie 1 ; Wang, Jing 6 ; Jia, Jiyuan 1 ; Sun, Min 1 ; Xie, Zheni 1 ; Wang, Xiaoshan 1 ; Huang, Linkai 1 ;

作者机构： 1.Sichuan Agr Univ, Coll Grassland Sci & Technol, Chengdu 611130, Peoples R China

2.Beijing Acad Agr & Forestry Sci, Inst Grassland Flower & Ecol, Beijing 100097, Peoples R China

3.Sichuan Agr Univ, State Key Lab Crop Gene Explorat & Utilizat Southw, Chengdu 611130, Peoples R China

4.Virginia Tech, Coll Agr & Life Sci, Blacksburg, VA 24061 USA

5.Nanjing Agr Univ, Coll Grassland Sci, Nanjing 210095, Peoples R China

6.Sichuan Univ, Minist Educ, Coll Life Sci, Key Lab Bioresources & Ecoenvironm, Chengdu 610061, Peoples R China

7.Chengdu Univ, Inst Adv Study, Chengdu 610106, Peoples R China

关键词： Upland switchgrass; Haplotype-resolved genomes; Allele-specific expression genes; Cold tolerance

期刊名称：GENOME BIOLOGY （ 影响因子：9.4； 五年影响因子：16.3 ）

ISSN： 1474-760X

年卷期： 2025 年 26 卷 1 期

页码：

收录情况： SCI

摘要： BackgroundSwitchgrass (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.ResultsHere, 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.ConclusionsBased 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.

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