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Global Transcriptome Profiles of 'Meyer' Zoysiagrass in Response to Cold Stress.

Wei S, Du Z, Gao F, Ke X, Li J, Liu J, Zhou Y - PLoS ONE (2015)

Bottom Line: Zoysiagrasses (Zoysia spp.In response to the stress, genes involved in proline synthesis, in starch hydrolysis, in methionine and ascorbic acid metabolism, in SOD activity, and in DREBs response pathway were up-regulated.GA metabolism, ABA and JA stimulus response were affected under cold exposure.

View Article: PubMed Central - PubMed

Affiliation: College of Life & Environmental Sciences, Minzu University of China, Beijing, PR China.

ABSTRACT
A long green period is essential for a turfgrass species with high ornamental value and a wide area of use. Zoysiagrasses (Zoysia spp. Willd.) are perennial turfgrass species popular in tropical, subtropical and temperate zones, possessing many properties necessary to be economically useful turfgrass. They do not have a long green period because of cold sensitivity. A main focus in zoysiagrass research is to develop cold tolerant cultivars. Understanding the cold response in zoysiagrass is a fundamental area of research. In the present study, 'Meyer' zoysiagrass (Zoysia japonica), a widely cultivated variety in the genus, is used. We employed RNA-Seq to investigate genome-wide gene expression profiles in leaves under cold stress (4°C). Using the Illumina sequencing platform, we obtained approximately 206 million high-quality paired-end reads from three libraries (0 h, 2 h, and 72 h cold treatment at 4°C). After de novo assembly and quantitative assessment, 46,412 unigenes were generated with an average length of 998 bp and an N50 of 1,522 bp. A total of 25,644 (55.2%) unigenes were annotated by alignment with public protein databases including NR, SwissProt, KEGG and KOG. Differentially expressed genes (DEGs) were investigated using the RPKM method. A total of 756 DEGs were identified between 0 h and 2 h-cold treatment, with 522 up-regulated and 234 down-regulated; and 5327 DEGs were identified between 0 h and 72 h-cold treatment, with 2453 up-regulated and 2874 down-regulated. The expression profile of 15 DEGs selected randomly was confirmed with qRT-PCR. The results suggest that cold stress can induce desiccation and oxidative stress, inhibit photosynthesis and substance transport. In response to the stress, genes involved in proline synthesis, in starch hydrolysis, in methionine and ascorbic acid metabolism, in SOD activity, and in DREBs response pathway were up-regulated. GA metabolism, ABA and JA stimulus response were affected under cold exposure. This is the first transcriptome sequencing of Z. japonica, providing a large set of sequence data as well as gene expression profiles under cold stress. It will improve our current understanding of the cold response of zoysiagrass and be beneficial in breeding research.

No MeSH data available.


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Number of DEGs between normal condition and cold treatments.
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pone.0131153.g007: Number of DEGs between normal condition and cold treatments.

Mentions: To identify a significant change in gene expression induced by low temperature, we used the FPKM method (Fragments per kilobase of transcript permillion fragments mapped) allowing us to calculate the expression levels of genes. Compared with CK, unigenes with absolute values of log2 (ratio) ≥ 2 and p-value ≤ 0.001 were considered as DEGs (differentially expressed genes). There were 756 DEGs between CK and CT_2h, including 522 up-regulated unigenes and 234 down-regulated ones (Fig 7, S2 Table). There were 5327 DEGs between CK and CT_72h, including 2453 up-regulated unigenes and 2874 down-regulated ones (Fig 7, S3 Table). To further validate our RNA-seq expression profile data, we performed qRT-PCR assays with primers designed according to fifteen randomly-selected unigenes (S1 Table). qRT-PCR data were normalized using the ‘housekeeping’ gene Actin-1.The results showed that gene expression profiles were consistent using either RNA-seq or qRT-PCR analysis, although the exact fold change varied between the two techniques (Table 4). The correlation coefficient between RNA-Seq data and qRT-PCR data is 0.837 (p < 0.01). In addition, PCR products of these primers showed the expected fragment size by agarose gel electrophoresis, which was consistent with the reliability of the assembled sequences.


Global Transcriptome Profiles of 'Meyer' Zoysiagrass in Response to Cold Stress.

Wei S, Du Z, Gao F, Ke X, Li J, Liu J, Zhou Y - PLoS ONE (2015)

Number of DEGs between normal condition and cold treatments.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482698&req=5

pone.0131153.g007: Number of DEGs between normal condition and cold treatments.
Mentions: To identify a significant change in gene expression induced by low temperature, we used the FPKM method (Fragments per kilobase of transcript permillion fragments mapped) allowing us to calculate the expression levels of genes. Compared with CK, unigenes with absolute values of log2 (ratio) ≥ 2 and p-value ≤ 0.001 were considered as DEGs (differentially expressed genes). There were 756 DEGs between CK and CT_2h, including 522 up-regulated unigenes and 234 down-regulated ones (Fig 7, S2 Table). There were 5327 DEGs between CK and CT_72h, including 2453 up-regulated unigenes and 2874 down-regulated ones (Fig 7, S3 Table). To further validate our RNA-seq expression profile data, we performed qRT-PCR assays with primers designed according to fifteen randomly-selected unigenes (S1 Table). qRT-PCR data were normalized using the ‘housekeeping’ gene Actin-1.The results showed that gene expression profiles were consistent using either RNA-seq or qRT-PCR analysis, although the exact fold change varied between the two techniques (Table 4). The correlation coefficient between RNA-Seq data and qRT-PCR data is 0.837 (p < 0.01). In addition, PCR products of these primers showed the expected fragment size by agarose gel electrophoresis, which was consistent with the reliability of the assembled sequences.

Bottom Line: Zoysiagrasses (Zoysia spp.In response to the stress, genes involved in proline synthesis, in starch hydrolysis, in methionine and ascorbic acid metabolism, in SOD activity, and in DREBs response pathway were up-regulated.GA metabolism, ABA and JA stimulus response were affected under cold exposure.

View Article: PubMed Central - PubMed

Affiliation: College of Life & Environmental Sciences, Minzu University of China, Beijing, PR China.

ABSTRACT
A long green period is essential for a turfgrass species with high ornamental value and a wide area of use. Zoysiagrasses (Zoysia spp. Willd.) are perennial turfgrass species popular in tropical, subtropical and temperate zones, possessing many properties necessary to be economically useful turfgrass. They do not have a long green period because of cold sensitivity. A main focus in zoysiagrass research is to develop cold tolerant cultivars. Understanding the cold response in zoysiagrass is a fundamental area of research. In the present study, 'Meyer' zoysiagrass (Zoysia japonica), a widely cultivated variety in the genus, is used. We employed RNA-Seq to investigate genome-wide gene expression profiles in leaves under cold stress (4°C). Using the Illumina sequencing platform, we obtained approximately 206 million high-quality paired-end reads from three libraries (0 h, 2 h, and 72 h cold treatment at 4°C). After de novo assembly and quantitative assessment, 46,412 unigenes were generated with an average length of 998 bp and an N50 of 1,522 bp. A total of 25,644 (55.2%) unigenes were annotated by alignment with public protein databases including NR, SwissProt, KEGG and KOG. Differentially expressed genes (DEGs) were investigated using the RPKM method. A total of 756 DEGs were identified between 0 h and 2 h-cold treatment, with 522 up-regulated and 234 down-regulated; and 5327 DEGs were identified between 0 h and 72 h-cold treatment, with 2453 up-regulated and 2874 down-regulated. The expression profile of 15 DEGs selected randomly was confirmed with qRT-PCR. The results suggest that cold stress can induce desiccation and oxidative stress, inhibit photosynthesis and substance transport. In response to the stress, genes involved in proline synthesis, in starch hydrolysis, in methionine and ascorbic acid metabolism, in SOD activity, and in DREBs response pathway were up-regulated. GA metabolism, ABA and JA stimulus response were affected under cold exposure. This is the first transcriptome sequencing of Z. japonica, providing a large set of sequence data as well as gene expression profiles under cold stress. It will improve our current understanding of the cold response of zoysiagrass and be beneficial in breeding research.

No MeSH data available.


Related in: MedlinePlus