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A transcriptomic analysis of bermudagrass (Cynodon dactylon) provides novel insights into the basis of low temperature tolerance.

Chen L, Fan J, Hu L, Hu Z, Xie Y, Zhang Y, Lou Y, Nevo E, Fu J - BMC Plant Biol. (2015)

Bottom Line: The objective of this study was to characterize the transcriptomic response to low temperature in bermudagrass by using RNA-Seq platform.KEGG pathway enrichment analysis for DEGs revealed that photosynthesis, nitrogen metabolism and carbon fixation pathways play key roles in bermudagrass response to cold stress.The results of this study may contribute to our understanding the molecular mechanism underlying the responses of bermudagrass to cold stress, and also provide important clues for further study and in-depth characterization of cold-resistance breeding candidate genes in bermudagrass.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture and Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China. chenliang888@wbgcas.cn.

ABSTRACT

Background: Cold stress is regarded as a key factor limiting widespread use for bermudagrass (Cynodon dactylon). Therefore, to improve cold tolerance for bermudagrass, it is urgent to understand molecular mechanisms of bermudagrass response to cold stress. However, our knowledge about the molecular responses of this species to cold stress is largely unknown. The objective of this study was to characterize the transcriptomic response to low temperature in bermudagrass by using RNA-Seq platform.

Results: Ten cDNA libraries were generated from RNA samples of leaves from five different treatments in the cold-resistant (R) and the cold-sensitive (S) genotypes, including 4 °C cold acclimation (CA) for 24 h and 48 h, freezing (-5 °C) treatments for 4 h with or without prior CA, and controls. When subjected to cold acclimation, global gene expressions were initiated more quickly in the R genotype than those in the S genotype. The R genotype activated gene expression more effectively in response to freezing temperature after 48 h CA than the S genotype. The differentially expressed genes were identified as low temperature sensing and signaling-related genes, functional proteins and transcription factors, many of which were specifically or predominantly expressed in the R genotype under cold treatments, implying that these genes play important roles in the enhanced cold hardiness of bermudagrass. KEGG pathway enrichment analysis for DEGs revealed that photosynthesis, nitrogen metabolism and carbon fixation pathways play key roles in bermudagrass response to cold stress.

Conclusions: The results of this study may contribute to our understanding the molecular mechanism underlying the responses of bermudagrass to cold stress, and also provide important clues for further study and in-depth characterization of cold-resistance breeding candidate genes in bermudagrass.

No MeSH data available.


KOG annotation of putative proteins. In total, there were 10,709 unigenes assigned to KOG classification and divided into 25 specific categories. The x-axis indicates 25 groups of KOG. The y-axis indicates the percentage of the number of genes annotation under the group in the total number of genes annotation
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Fig3: KOG annotation of putative proteins. In total, there were 10,709 unigenes assigned to KOG classification and divided into 25 specific categories. The x-axis indicates 25 groups of KOG. The y-axis indicates the percentage of the number of genes annotation under the group in the total number of genes annotation

Mentions: The KEGG database is supposed to provide a systematic analysis of metabolic pathways and functions of gene products. To further identify the biological pathways that are active in bermudagrass, the 8067 unigenes annotated by blast analysis against KAAS (KEGG Automatic Annotation Server) were classified into five main biochemical pathways: ‘cellular processes’, ‘environmental information processing’, ‘genetic information processing’, ‘metabolism’ and ‘organismal systems’. The most represented pathways were ‘metabolism’ (3887 unigenes, 48.18 %) (Fig. 3). Among the 3887 unigenes in ‘metabolism’ pathway, ‘Carbohydrate metabolism’ (698), ‘Amino acid metabolism’ (534) ‘Energy metabolism’ (452) ‘Lipid metabolism’ (402) were highly represented (Fig. 3). The pathways related to ‘environmental information processing’ with the most representation were ‘signal transduction’ (571). These annotations provided a valuable resource for investigating the processes, functions, and pathways involved in cold response.Fig. 3


A transcriptomic analysis of bermudagrass (Cynodon dactylon) provides novel insights into the basis of low temperature tolerance.

Chen L, Fan J, Hu L, Hu Z, Xie Y, Zhang Y, Lou Y, Nevo E, Fu J - BMC Plant Biol. (2015)

KOG annotation of putative proteins. In total, there were 10,709 unigenes assigned to KOG classification and divided into 25 specific categories. The x-axis indicates 25 groups of KOG. The y-axis indicates the percentage of the number of genes annotation under the group in the total number of genes annotation
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4566850&req=5

Fig3: KOG annotation of putative proteins. In total, there were 10,709 unigenes assigned to KOG classification and divided into 25 specific categories. The x-axis indicates 25 groups of KOG. The y-axis indicates the percentage of the number of genes annotation under the group in the total number of genes annotation
Mentions: The KEGG database is supposed to provide a systematic analysis of metabolic pathways and functions of gene products. To further identify the biological pathways that are active in bermudagrass, the 8067 unigenes annotated by blast analysis against KAAS (KEGG Automatic Annotation Server) were classified into five main biochemical pathways: ‘cellular processes’, ‘environmental information processing’, ‘genetic information processing’, ‘metabolism’ and ‘organismal systems’. The most represented pathways were ‘metabolism’ (3887 unigenes, 48.18 %) (Fig. 3). Among the 3887 unigenes in ‘metabolism’ pathway, ‘Carbohydrate metabolism’ (698), ‘Amino acid metabolism’ (534) ‘Energy metabolism’ (452) ‘Lipid metabolism’ (402) were highly represented (Fig. 3). The pathways related to ‘environmental information processing’ with the most representation were ‘signal transduction’ (571). These annotations provided a valuable resource for investigating the processes, functions, and pathways involved in cold response.Fig. 3

Bottom Line: The objective of this study was to characterize the transcriptomic response to low temperature in bermudagrass by using RNA-Seq platform.KEGG pathway enrichment analysis for DEGs revealed that photosynthesis, nitrogen metabolism and carbon fixation pathways play key roles in bermudagrass response to cold stress.The results of this study may contribute to our understanding the molecular mechanism underlying the responses of bermudagrass to cold stress, and also provide important clues for further study and in-depth characterization of cold-resistance breeding candidate genes in bermudagrass.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture and Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China. chenliang888@wbgcas.cn.

ABSTRACT

Background: Cold stress is regarded as a key factor limiting widespread use for bermudagrass (Cynodon dactylon). Therefore, to improve cold tolerance for bermudagrass, it is urgent to understand molecular mechanisms of bermudagrass response to cold stress. However, our knowledge about the molecular responses of this species to cold stress is largely unknown. The objective of this study was to characterize the transcriptomic response to low temperature in bermudagrass by using RNA-Seq platform.

Results: Ten cDNA libraries were generated from RNA samples of leaves from five different treatments in the cold-resistant (R) and the cold-sensitive (S) genotypes, including 4 °C cold acclimation (CA) for 24 h and 48 h, freezing (-5 °C) treatments for 4 h with or without prior CA, and controls. When subjected to cold acclimation, global gene expressions were initiated more quickly in the R genotype than those in the S genotype. The R genotype activated gene expression more effectively in response to freezing temperature after 48 h CA than the S genotype. The differentially expressed genes were identified as low temperature sensing and signaling-related genes, functional proteins and transcription factors, many of which were specifically or predominantly expressed in the R genotype under cold treatments, implying that these genes play important roles in the enhanced cold hardiness of bermudagrass. KEGG pathway enrichment analysis for DEGs revealed that photosynthesis, nitrogen metabolism and carbon fixation pathways play key roles in bermudagrass response to cold stress.

Conclusions: The results of this study may contribute to our understanding the molecular mechanism underlying the responses of bermudagrass to cold stress, and also provide important clues for further study and in-depth characterization of cold-resistance breeding candidate genes in bermudagrass.

No MeSH data available.