Low-temperature is one of the important factors which limit the production and expansion of cassava (Manihot esculenta Grantz). As a tropical crop, cultivated cassava has specific tolerance to intermittent drought, but is hypersensitive to cold. The molecular mechanism of cassava cold-sensitive is remaining unknown. It is on this context that Professor Ming Peng’s team applied for a joint research project and was accepted by The National Natural Science Foundation of China and CGIAR (NSFC-CGIAR, grant no. 31561143012) with the project title “The molecular basis of cassava (Manihot esculenta Crantz) cold-sensitive and molecular breeding for cold tolerance” (Project period: 2016/01-2020/12). According to the project design, those cold-tolerant cassava germplasms from high altitude area of South America, cold-sensitive cultivated cassava and several transgenic cassava lines will be used in the study to unravel the mechanism by which cassava response to cold. The omics approaches, such as genomics, transcriptomics, proteomics and metabolomics are used to analyze the molecular basis of cassava cold-sensitive. Based on the omics analysis results, those genes that play key roles in cassava cold response signal transduction pathways will be selected as candidates. Then the function and regulation of these genes will be analyzed in transgenic cassava. Different transgenic strategies of these genes will be proofed in cassava to find out the magnificent method to create cold-tolerant cassava. The achievements of this project help to understanding the cassava cold-sensitive mechanisms, and expanding of cassava cultivated area.
With the initiation of the project, some progress has already been made. Plants respond and adapt to cold and/or drought stresses through complex physiological and biochemical processes that include altered gene expression levels, signal transition pathways, and cellular metabolic rate, thus acquiring resistance. Under drought and cold stresses, manyMeMYBs exhibited different expression patterns in cassava leaves, indicating that these genes might play a role in abiotic stress responses. We found that several stress-responsiveMeMYBswere responded to abscisic acid (ABA) in cassava leaves. Peng’s team characterized four MeMYBs, i.e., MeMYB1, MeMYB2, MeMYB4, and MeMYB9,as R2R3-MYB transcription factors. Furthermore, RNAi-driven repression ofMeMYB2resulted in drought and cold tolerance in transgenic cassava. Gene expression assays in wild type andMeMYB2-RNAicassava plants revealed thatMeMYB2may affect other MeMYBs as well as MeWRKYs under drought and cold stress, suggesting the crosstalk between MYB and WRKY family genes under stress conditions in cassava.
Long noncoding RNAs (lncRNAs) are generally defined as RNA transcripts with length more than 200 nucleotide (nt) but lacking a coding sequence (CDS) or open reading frame (ORF). Peng’s group has presented the first reference catalog of 682 high-confidence lncRNAs based on analysis of strand-specific RNA-seq data from cassava shoot apices and young leaves under cold, drought stress and control conditions. Among them, 16 lncRNAs were identified as putative target mimics of cassava known miRNAs. Additionally, by comparing with small RNA-seq data, they found 42 lncNATs and sense gene pairs could generate nat-siRNAs. They also identified 318 lncRNAs responsive to cold and/or drought stress, which were typically co-expressed concordantly or discordantly with their neighboring genes. Trans-regulatory network analysis suggested that many lncRNAs were associated with hormone signal transduction, secondary metabolites biosynthesis, and sucrose metabolism pathway. The study provides an opportunity for future computational and experimental studies to uncover the functions of lncRNAs in cassava. Two papers reported some progress they made have been published in different journals as showed below.
Li, S., X. Yu, N. Lei, Z. Cheng, P. Zhao, Y. He, W. Wang and M. Peng. 2017. Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava.Scientific Reports7, 45981 .Meng-Bin Ruan, Xin Guo, Bin Wang, Yi-Ling Yang, Wen-Qi Li, Xiao-Ling Yu, Peng Zhang, Ming Peng. Genome-wide characterization and expression analysis enables identification of abiotic stress-responsive MYB transcription factor in cassava (Manihot esculenta).Journal of Experimental Botany, 2017, Accepted.
With the initiation of the project, some progress has already been made. Plants respond and adapt to cold and/or drought stresses through complex physiological and biochemical processes that include altered gene expression levels, signal transition pathways, and cellular metabolic rate, thus acquiring resistance. Under drought and cold stresses, manyMeMYBs exhibited different expression patterns in cassava leaves, indicating that these genes might play a role in abiotic stress responses. We found that several stress-responsiveMeMYBswere responded to abscisic acid (ABA) in cassava leaves. Peng’s team characterized four MeMYBs, i.e., MeMYB1, MeMYB2, MeMYB4, and MeMYB9,as R2R3-MYB transcription factors. Furthermore, RNAi-driven repression ofMeMYB2resulted in drought and cold tolerance in transgenic cassava. Gene expression assays in wild type andMeMYB2-RNAicassava plants revealed thatMeMYB2may affect other MeMYBs as well as MeWRKYs under drought and cold stress, suggesting the crosstalk between MYB and WRKY family genes under stress conditions in cassava.
Long noncoding RNAs (lncRNAs) are generally defined as RNA transcripts with length more than 200 nucleotide (nt) but lacking a coding sequence (CDS) or open reading frame (ORF). Peng’s group has presented the first reference catalog of 682 high-confidence lncRNAs based on analysis of strand-specific RNA-seq data from cassava shoot apices and young leaves under cold, drought stress and control conditions. Among them, 16 lncRNAs were identified as putative target mimics of cassava known miRNAs. Additionally, by comparing with small RNA-seq data, they found 42 lncNATs and sense gene pairs could generate nat-siRNAs. They also identified 318 lncRNAs responsive to cold and/or drought stress, which were typically co-expressed concordantly or discordantly with their neighboring genes. Trans-regulatory network analysis suggested that many lncRNAs were associated with hormone signal transduction, secondary metabolites biosynthesis, and sucrose metabolism pathway. The study provides an opportunity for future computational and experimental studies to uncover the functions of lncRNAs in cassava. Two papers reported some progress they made have been published in different journals as showed below.
Li, S., X. Yu, N. Lei, Z. Cheng, P. Zhao, Y. He, W. Wang and M. Peng. 2017. Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava.Scientific Reports7, 45981 .Meng-Bin Ruan, Xin Guo, Bin Wang, Yi-Ling Yang, Wen-Qi Li, Xiao-Ling Yu, Peng Zhang, Ming Peng. Genome-wide characterization and expression analysis enables identification of abiotic stress-responsive MYB transcription factor in cassava (Manihot esculenta).Journal of Experimental Botany, 2017, Accepted.
By TBBRI
