title: Transcriptome analysis reveals metabolic alteration due to consecutive monoculture and abiotic stress stimuli in Rehamannia glutinosa Libosch.
abstract: We deeply investigated the mechanism underlying metabolic regulation in response to consecutive monoculture (replanting disease) and different abiotic stresses that unfolded the response mechanism to consecutive monoculture problem through RNA-seq analysis. The consecutive monoculture problem (CMP) resulted of complex environmental stresses mediated by multiple factors. Previous studies have noted that multiple stress factors in consecutive monoculture soils or plants severely limited the interpretation of the critical molecular mechanism, and made a predict that the specifically responding factor was autotoxic allelochemicals. To identify the specifically responding genes, we compared transcriptome changes in roots of Rehamannia glutinosa Libosch using consecutive monoculture, salt, drought, and ferulic acid as stress factors. Comparing with normal growth, 2502, 2672, 2485, and 1956 genes were differentially expressed in R. glutinosa under consecutive monoculture practice, salt, drought, and ferulic acid stress, respectively. In addition, 510 genes were specifically expressed under consecutive monoculture, which were not present under the other stress conditions. Integrating the biological and enrichment analyses of the differentially expressed genes, the result demonstrated that the plants could alter enzyme genes expression to reconstruct the complicated metabolic pathways, which used to tolerate the CMP and abiotic stresses. Furthermore, most of the affected pathway genes were closely related to secondary metabolic processes, and the influence of consecutive monoculture practice on the transcriptome genes expression profile was very similar to the profile under salt stress and then to the profile under drought stress. The outlined schematic diagram unfolded the putative signal regulation mechanism in response to the CMP. Genes that differentially up- or down-regulated under consecutive monoculture practice may play important roles in the CMP or replanting disease in R. glutinosa.
authors.affiliation: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
authors.forename: Yunhe
authors.initials: Y
authors.lastname: Tian
authors.affiliation: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
authors.forename: Fajie
authors.initials: F
authors.lastname: Feng
authors.affiliation: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
authors.forename: Bao
authors.initials: B
authors.lastname: Zhang
authors.affiliation: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
authors.forename: Mingjie
authors.initials: M
authors.lastname: Li
authors.affiliation: Henan Agricultural University, Zhengzhou, 450002, China.
authors.forename: Fengqing
authors.initials: F
authors.lastname: Wang
authors.affiliation: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
authors.forename: Li
authors.initials: L
authors.lastname: Gu
authors.affiliation: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
authors.forename: Aiguo
authors.initials: A
authors.lastname: Chen
authors.affiliation: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
authors.forename: Zhanjie
authors.initials: Z
authors.lastname: Li
authors.affiliation: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
authors.forename: Wenbo
authors.initials: W
authors.lastname: Shan
authors.affiliation: Henan Agricultural University, Zhengzhou, 450002, China.
authors.forename: Xiaoran
authors.initials: X
authors.lastname: Wang
authors.affiliation: Henan Agricultural University, Zhengzhou, 450002, China.
authors.forename: Xinjian
authors.initials: X
authors.lastname: Chen
authors.affiliation: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. zyzhang@fafu.edu.cn.|Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 350002, China. zyzhang@fafu.edu.cn.
authors.forename: Zhongyi
authors.identifier: http://orcid.org/0000-0002-6375-2969
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D055864:Droughts; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant / Q000187:drug effects / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D010944:Plants / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism*; D012965:Sodium Chloride / Q000494:pharmacology; D059467:Transcriptome / Q000235:genetics
chemical_list: D010940:Plant Proteins; D012965:Sodium Chloride
keywords: Consecutive monoculture problem; Differentially expressed genes; R. glutinosa; Root transcriptome; Secondary metabolism