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Genome-wide analysis and expression profiling under heat and drought treatments of HSP70 gene family in soybean (Glycine max L.).

Zhang L, Zhao HK, Dong QL, Zhang YY, Wang YM, Li HY, Xing GJ, Li QY, Dong YS - Front Plant Sci (2015)

Bottom Line: Furthermore, the expression of some of the duplicate genes was partially redundant, while others showed functional diversity.The quantitative real-time PCR (qRT-PCR) analysis of the 61 soybean HSP70 genes confirmed their stress-inducible expression patterns under both drought and heat stress.These findings provide a thorough overview of the evolution and modification of the GmHSP70 gene family, which will help to determine the functional characteristics of the HSP70 genes in soybean growth and development.

View Article: PubMed Central - PubMed

Affiliation: Agro-Biotechnology Research Institute, Jilin Academy of Agricultural Sciences Changchun, China.

ABSTRACT
Heat shock proteins (HSPs) perform a fundamental role in protecting plants against abiotic stresses. Previous studies have made great efforts in the functional analysis of individual family members, but there has not yet been an overall analysis or expression profiling of the HSP70 gene family in soybeans (Glycine max L.). In this study, an investigation of the soybean genome revealed 61 putative HSP70 genes, which were evaluated. These genes were classified into eight sub-families, denoted I-VIII, based on a phylogenetic analysis. In each sub-family, the constituent parts of the gene structure and motif were relatively conserved. These GmHSP70 genes were distributed unequally on 17 of the 20 chromosomes. The analysis of the expression profiles showed that 53 of the 61 GmHSP70 genes were differentially expressed across the 14 tissues. However, most of the GmHSP70s were differentially expressed in a tissue-specific expression pattern. Furthermore, the expression of some of the duplicate genes was partially redundant, while others showed functional diversity. The quantitative real-time PCR (qRT-PCR) analysis of the 61 soybean HSP70 genes confirmed their stress-inducible expression patterns under both drought and heat stress. These findings provide a thorough overview of the evolution and modification of the GmHSP70 gene family, which will help to determine the functional characteristics of the HSP70 genes in soybean growth and development.

No MeSH data available.


Related in: MedlinePlus

Heat map of the expression profiles of GmHSP70 candidate genes in 14 tissues. RNA-seq relative expression data from 14 tissues were used to reconstruct the expression patterns of soybean genes. Genes were clustered into three groups (A–C). The raw data was normalized and retrieved from the online database http://soybase.org/soyseq/. The normal relative expression levels of 53 GmHSP70 genes are shown in Additional File 12.
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Figure 5: Heat map of the expression profiles of GmHSP70 candidate genes in 14 tissues. RNA-seq relative expression data from 14 tissues were used to reconstruct the expression patterns of soybean genes. Genes were clustered into three groups (A–C). The raw data was normalized and retrieved from the online database http://soybase.org/soyseq/. The normal relative expression levels of 53 GmHSP70 genes are shown in Additional File 12.

Mentions: In order to obtain more insight into the temporal and spatial expression patterns of the soybean HSP70 genes during soybean development, the RNA-Seq Atlas of the Glycine max was searched, and the RNA-Seq atlas data of the soybean HSP70 genes (Additional File 12) were downloaded from the Soybase (http://soybase.org/soyseq/). Due to the fact that the expression profiles of eight GmHSP70 genes (Glyma02g10195, Glyma02g10261, Glyma07g32921, Glyma11g31673, Glyma13g19331, Glyma13g29591, Glyma18g13077, and Glyma18g52471) were not obtained in the soybean database, only the expression patterns of 53/61 GmHSP70 genes were examined. The data analysis revealed that most soybean HSP70 genes exhibit broad expression patterns (Figure 5). With the exception of the six GmHSP70 genes (Glyma06g00310, Glyma07g02450, Glyma11g31670, Glyma15g10280, Glyma18g05610, and Glyma18g52760), which were not expressed in any tissues, the other 47 GmHSP70 genes were expressed in at least one of the seven tissues (young leaves, flowers, 1cm pod, pod-shell, roots, nodules, and seed). This particularly applied to five genes, Glyma05g36620, Glyma13g19330, Glyma03g32850, and Glyma19g35560, which were highly expressed in all types of tissues. These findings indicate that the GmHSP70 genes were involved in multiple processes during the development of the soybean. The heat map also revealed that the majority of the GmHSP70s showed preferential expressions. Based on a hierarchical clustering analysis, the 53 HSP70 genes were mainly clustered into three groups (A, B, and C), as shown in Figure 5. In Group A, with the exception of the six un-expressed genes (Glyma06g00310, Glyma07g02450, Glyma11g31670, Glyma15g10280, Glyma18g05610, and Glyma18g52760), the genes showed partial expressions in the seed (from 10 to 42 DAF). The other two groups (B and C) were the opposite, with most of the genes showing down-expression in the seeds compared with the other tissues. Four GmHSP70 genes (Glyma15g09420, Glyma18g52470, Glyma18g52650, and Glyma11g14960) showed markedly high transcript abundance profiles in only a single tissue type.


Genome-wide analysis and expression profiling under heat and drought treatments of HSP70 gene family in soybean (Glycine max L.).

Zhang L, Zhao HK, Dong QL, Zhang YY, Wang YM, Li HY, Xing GJ, Li QY, Dong YS - Front Plant Sci (2015)

Heat map of the expression profiles of GmHSP70 candidate genes in 14 tissues. RNA-seq relative expression data from 14 tissues were used to reconstruct the expression patterns of soybean genes. Genes were clustered into three groups (A–C). The raw data was normalized and retrieved from the online database http://soybase.org/soyseq/. The normal relative expression levels of 53 GmHSP70 genes are shown in Additional File 12.
© Copyright Policy
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4585176&req=5

Figure 5: Heat map of the expression profiles of GmHSP70 candidate genes in 14 tissues. RNA-seq relative expression data from 14 tissues were used to reconstruct the expression patterns of soybean genes. Genes were clustered into three groups (A–C). The raw data was normalized and retrieved from the online database http://soybase.org/soyseq/. The normal relative expression levels of 53 GmHSP70 genes are shown in Additional File 12.
Mentions: In order to obtain more insight into the temporal and spatial expression patterns of the soybean HSP70 genes during soybean development, the RNA-Seq Atlas of the Glycine max was searched, and the RNA-Seq atlas data of the soybean HSP70 genes (Additional File 12) were downloaded from the Soybase (http://soybase.org/soyseq/). Due to the fact that the expression profiles of eight GmHSP70 genes (Glyma02g10195, Glyma02g10261, Glyma07g32921, Glyma11g31673, Glyma13g19331, Glyma13g29591, Glyma18g13077, and Glyma18g52471) were not obtained in the soybean database, only the expression patterns of 53/61 GmHSP70 genes were examined. The data analysis revealed that most soybean HSP70 genes exhibit broad expression patterns (Figure 5). With the exception of the six GmHSP70 genes (Glyma06g00310, Glyma07g02450, Glyma11g31670, Glyma15g10280, Glyma18g05610, and Glyma18g52760), which were not expressed in any tissues, the other 47 GmHSP70 genes were expressed in at least one of the seven tissues (young leaves, flowers, 1cm pod, pod-shell, roots, nodules, and seed). This particularly applied to five genes, Glyma05g36620, Glyma13g19330, Glyma03g32850, and Glyma19g35560, which were highly expressed in all types of tissues. These findings indicate that the GmHSP70 genes were involved in multiple processes during the development of the soybean. The heat map also revealed that the majority of the GmHSP70s showed preferential expressions. Based on a hierarchical clustering analysis, the 53 HSP70 genes were mainly clustered into three groups (A, B, and C), as shown in Figure 5. In Group A, with the exception of the six un-expressed genes (Glyma06g00310, Glyma07g02450, Glyma11g31670, Glyma15g10280, Glyma18g05610, and Glyma18g52760), the genes showed partial expressions in the seed (from 10 to 42 DAF). The other two groups (B and C) were the opposite, with most of the genes showing down-expression in the seeds compared with the other tissues. Four GmHSP70 genes (Glyma15g09420, Glyma18g52470, Glyma18g52650, and Glyma11g14960) showed markedly high transcript abundance profiles in only a single tissue type.

Bottom Line: Furthermore, the expression of some of the duplicate genes was partially redundant, while others showed functional diversity.The quantitative real-time PCR (qRT-PCR) analysis of the 61 soybean HSP70 genes confirmed their stress-inducible expression patterns under both drought and heat stress.These findings provide a thorough overview of the evolution and modification of the GmHSP70 gene family, which will help to determine the functional characteristics of the HSP70 genes in soybean growth and development.

View Article: PubMed Central - PubMed

Affiliation: Agro-Biotechnology Research Institute, Jilin Academy of Agricultural Sciences Changchun, China.

ABSTRACT
Heat shock proteins (HSPs) perform a fundamental role in protecting plants against abiotic stresses. Previous studies have made great efforts in the functional analysis of individual family members, but there has not yet been an overall analysis or expression profiling of the HSP70 gene family in soybeans (Glycine max L.). In this study, an investigation of the soybean genome revealed 61 putative HSP70 genes, which were evaluated. These genes were classified into eight sub-families, denoted I-VIII, based on a phylogenetic analysis. In each sub-family, the constituent parts of the gene structure and motif were relatively conserved. These GmHSP70 genes were distributed unequally on 17 of the 20 chromosomes. The analysis of the expression profiles showed that 53 of the 61 GmHSP70 genes were differentially expressed across the 14 tissues. However, most of the GmHSP70s were differentially expressed in a tissue-specific expression pattern. Furthermore, the expression of some of the duplicate genes was partially redundant, while others showed functional diversity. The quantitative real-time PCR (qRT-PCR) analysis of the 61 soybean HSP70 genes confirmed their stress-inducible expression patterns under both drought and heat stress. These findings provide a thorough overview of the evolution and modification of the GmHSP70 gene family, which will help to determine the functional characteristics of the HSP70 genes in soybean growth and development.

No MeSH data available.


Related in: MedlinePlus