De novo transcriptome sequencing and gene expression profiling of Elymus nutans under cold stress.
Elymus nutans Griseb., is an important alpine perennial forage of Pooideae subfamily with strong inherited cold tolerance. To get a deeper insight into its molecular mechanisms of cold tolerance, we compared the transcriptome profiling by RNA-Seq in two genotypes of Elymus nutans Griseb. the tolerant Damxung (DX) and the sensitive Gannan (GN) under cold stress.



The new E. nutans transcriptomes were assembled and comprised 200,520 and 181,331 transcripts in DX and GN, respectively. Among them, 5436 and 4323 genes were differentially expressed in DX and GN, with 170 genes commonly expressed over time. Early cold responses involved numerous genes encoding transcription factors and signal transduction in both genotypes. The AP2/EREBP famliy of transcription factors was predominantly expressed in both genotypes. The most significant transcriptomic changes in the later phases of cold stress are associated with oxidative stress, primary and secondary metabolism, and photosynthesis. Higher fold expressions of fructan, trehalose, and alpha-linolenic acid metabolism-related genes were detected in DX. The DX-specific dehydrins may be promising candidates to improve cold tolerance. Twenty-six hub genes played a central role in both genotypes under cold stress. qRT-PCR analysis of 26 genes confirmed the RNA-Seq results.



The stronger transcriptional differentiation during cold stress in DX explains its better cold tolerance compared to GN. The identified fructan biosynthesis, alpha-linolenic acid metabolism, and DX-specific dehydrin-related genes may provide genetic resources for the improvement of cold-tolerant characters in DX. Our findings provide important clues for further studies of the molecular mechanisms underlying cold stress responses in plants.
Department of grassland science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
Juanjuan
J
Fu
College of Plant Science, Agriculture and Animal Husbandry College of Tibet University, Linzhi, Tibet, 860000, China.
Yanjun
Y
Miao
Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100101, China.
Linhui
L
Shao
Department of grassland science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China. hutianming@126.com.
Tianming
T
Hu
Department of grassland science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China. yangpeizhi@126.com.
Peizhi
P
Yang
D000220:Adaptation, Biological / Q000235:genetics; D016000:Cluster Analysis; D058639:Cold-Shock Response / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D031749:Elymus / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D005838:Genotype; D058977:Molecular Sequence Annotation; D010937:Plant Growth Regulators / Q000378:metabolism; D015203:Reproducibility of Results; D015398:Signal Transduction; D059467:Transcriptome
D010937:Plant Growth Regulators
Co-expression; Cold stress; Dehydrin; Species-specificity; Transcriptome