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A genome-wide analysis of the auxin/indole-3-acetic acid gene family in hexaploid bread wheat (Triticum aestivum L.).

Qiao L, Zhang X, Han X, Zhang L, Li X, Zhan H, Ma J, Luo P, Zhang W, Cui L, Li X, Chang Z - Front Plant Sci (2015)

Bottom Line: The duplicated genes have undergone an evolutionary process of purifying selection, resulting in the high conservation of copy genes among sub-genomes and functional redundancy among several members of the TaIAA family.However, functional divergence probably existed in most TaIAA members due to the diversity of the functional domain and expression pattern.Our research provides useful information for further research into the function of Aux/IAA genes in wheat.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, College of Life Science, Shanxi University Taiyuan, China ; Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Institute of Crop Science, Shanxi Academy of Agricultural Sciences Taiyuan, China.

ABSTRACT
The Auxin/indole-3-acetic acid (Aux/IAA) gene family plays key roles in the primary auxin-response process and controls a number of important traits in plants. However, the characteristics of the Aux/IAA gene family in hexaploid bread wheat (Triticum aestivum L.) have long been unknown. In this study, a comprehensive identification of the Aux/IAA gene family was performed using the latest draft genome sequence of the bread wheat "Chinese Spring." Thirty-four Aux/IAA genes were identified, 30 of which have duplicated genes on the A, B or D sub-genome, with a total of 84 Aux/IAA sequences. These predicted Aux/IAA genes were non-randomly distributed in all the wheat chromosomes except for chromosome 2D. The information of wheat Aux/IAA proteins is also described. Based on an analysis of phylogeny, expression and adaptive evolution, we prove that the Aux/IAA family in wheat has been replicated twice in the two allopolyploidization events of bread wheat, when the tandem duplication also occurred. The duplicated genes have undergone an evolutionary process of purifying selection, resulting in the high conservation of copy genes among sub-genomes and functional redundancy among several members of the TaIAA family. However, functional divergence probably existed in most TaIAA members due to the diversity of the functional domain and expression pattern. Our research provides useful information for further research into the function of Aux/IAA genes in wheat.

No MeSH data available.


Related in: MedlinePlus

Heatmap of expression profiles for TaIAA genes across different organs of seedling and adult stages. The expression data were generated from GeneVestigator database and viewed in MeV software. The relative expression level of a particular gene in each row was normalized against the mean value by log2 transformation. The color scale below represents expression values, green indicating low levels and red indicating high levels of transcript abundance.
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Figure 6: Heatmap of expression profiles for TaIAA genes across different organs of seedling and adult stages. The expression data were generated from GeneVestigator database and viewed in MeV software. The relative expression level of a particular gene in each row was normalized against the mean value by log2 transformation. The color scale below represents expression values, green indicating low levels and red indicating high levels of transcript abundance.

Mentions: The coding sequences of 34 TaIAAs were used to search the Plex database for corresponding probes. All gene copies of each TaIAA gene share one probe. The probes of TaIAA20 and TaIAA34 were not found. Several genes have the same probe, including TaIAA2, 9; TaIAA18, 22, 33; and TaIAA29, 30. Finally, 28 probes for 32 TaIAAs were obtained from the GeneVestigator database (Supplementary Table 4). The expression profile of 32 TaIAAs in 19 wheat organs covering the seedling to adult stage is shown as a heat map (Figure 6). TaIAAs were divided into eight classes according to the subgroups of phylogenetic analysis. In general, the majority of genes in groups A3, B1, B2, and B3 are expressed in vegetative organs of wheat, and genes in group A3 are also expressed in the pistil and embryo. Moreover, all genes in A1, A2 and TaIAA14 of B2 have high expression levels in the vast majority of wheat organs throughout the entire growing stage. In addition, TaIAA6 and TaIAA27 are specifically expressed in the roots, while TaIAA16, TaIAA28, and TaIAA31 are specifically expressed in inflorescence, flag leaf and seed, respectively. TaIAA1, 7, 10, 17, 29, and 30 showed low expression in wheat.


A genome-wide analysis of the auxin/indole-3-acetic acid gene family in hexaploid bread wheat (Triticum aestivum L.).

Qiao L, Zhang X, Han X, Zhang L, Li X, Zhan H, Ma J, Luo P, Zhang W, Cui L, Li X, Chang Z - Front Plant Sci (2015)

Heatmap of expression profiles for TaIAA genes across different organs of seedling and adult stages. The expression data were generated from GeneVestigator database and viewed in MeV software. The relative expression level of a particular gene in each row was normalized against the mean value by log2 transformation. The color scale below represents expression values, green indicating low levels and red indicating high levels of transcript abundance.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4588698&req=5

Figure 6: Heatmap of expression profiles for TaIAA genes across different organs of seedling and adult stages. The expression data were generated from GeneVestigator database and viewed in MeV software. The relative expression level of a particular gene in each row was normalized against the mean value by log2 transformation. The color scale below represents expression values, green indicating low levels and red indicating high levels of transcript abundance.
Mentions: The coding sequences of 34 TaIAAs were used to search the Plex database for corresponding probes. All gene copies of each TaIAA gene share one probe. The probes of TaIAA20 and TaIAA34 were not found. Several genes have the same probe, including TaIAA2, 9; TaIAA18, 22, 33; and TaIAA29, 30. Finally, 28 probes for 32 TaIAAs were obtained from the GeneVestigator database (Supplementary Table 4). The expression profile of 32 TaIAAs in 19 wheat organs covering the seedling to adult stage is shown as a heat map (Figure 6). TaIAAs were divided into eight classes according to the subgroups of phylogenetic analysis. In general, the majority of genes in groups A3, B1, B2, and B3 are expressed in vegetative organs of wheat, and genes in group A3 are also expressed in the pistil and embryo. Moreover, all genes in A1, A2 and TaIAA14 of B2 have high expression levels in the vast majority of wheat organs throughout the entire growing stage. In addition, TaIAA6 and TaIAA27 are specifically expressed in the roots, while TaIAA16, TaIAA28, and TaIAA31 are specifically expressed in inflorescence, flag leaf and seed, respectively. TaIAA1, 7, 10, 17, 29, and 30 showed low expression in wheat.

Bottom Line: The duplicated genes have undergone an evolutionary process of purifying selection, resulting in the high conservation of copy genes among sub-genomes and functional redundancy among several members of the TaIAA family.However, functional divergence probably existed in most TaIAA members due to the diversity of the functional domain and expression pattern.Our research provides useful information for further research into the function of Aux/IAA genes in wheat.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, College of Life Science, Shanxi University Taiyuan, China ; Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Institute of Crop Science, Shanxi Academy of Agricultural Sciences Taiyuan, China.

ABSTRACT
The Auxin/indole-3-acetic acid (Aux/IAA) gene family plays key roles in the primary auxin-response process and controls a number of important traits in plants. However, the characteristics of the Aux/IAA gene family in hexaploid bread wheat (Triticum aestivum L.) have long been unknown. In this study, a comprehensive identification of the Aux/IAA gene family was performed using the latest draft genome sequence of the bread wheat "Chinese Spring." Thirty-four Aux/IAA genes were identified, 30 of which have duplicated genes on the A, B or D sub-genome, with a total of 84 Aux/IAA sequences. These predicted Aux/IAA genes were non-randomly distributed in all the wheat chromosomes except for chromosome 2D. The information of wheat Aux/IAA proteins is also described. Based on an analysis of phylogeny, expression and adaptive evolution, we prove that the Aux/IAA family in wheat has been replicated twice in the two allopolyploidization events of bread wheat, when the tandem duplication also occurred. The duplicated genes have undergone an evolutionary process of purifying selection, resulting in the high conservation of copy genes among sub-genomes and functional redundancy among several members of the TaIAA family. However, functional divergence probably existed in most TaIAA members due to the diversity of the functional domain and expression pattern. Our research provides useful information for further research into the function of Aux/IAA genes in wheat.

No MeSH data available.


Related in: MedlinePlus