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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.


Phylogenetic relationship of Aux/IAA proteins among wheat and another species. The full-length amino-acid sequences of 85 wheat, 31 rice, 29 Arabidopsis, 7 tomato, 2 maize, 2 grape, 1 sorghum, and 1 pear genes were aligned by Clustal W and the phylogenetic tree was constructed using MEGA 6.0 by the neighbor-joining method with 1000 bootstrap replicates. Each TaIAA protein is indicated by a black dot. Two major groups, group A and B, are represented by the red and blue. The functions of some clades were annotated.
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Figure 5: Phylogenetic relationship of Aux/IAA proteins among wheat and another species. The full-length amino-acid sequences of 85 wheat, 31 rice, 29 Arabidopsis, 7 tomato, 2 maize, 2 grape, 1 sorghum, and 1 pear genes were aligned by Clustal W and the phylogenetic tree was constructed using MEGA 6.0 by the neighbor-joining method with 1000 bootstrap replicates. Each TaIAA protein is indicated by a black dot. Two major groups, group A and B, are represented by the red and blue. The functions of some clades were annotated.

Mentions: The phylogenetic tree shows that TaIAA proteins can be classified into two major groups: A and B (Figure 5). Based on the clustering tree of OsIAAs (Jain et al., 2006), groups A and B can be further separated into several subgroups: A1, A3, and A4 contain monocotyledon IAA proteins; A5 contains dicotyledon proteins; and A2, B1, B2, B3, and B4 are all types of IAA protein. Moreover, monocot and dicot IAA proteins are not gathered for one class in every subgroup, while the paralogous proteins of each TaIAA are clustered to the same branch, similar to the clustering result in Figure 1A. Orthologous genes usually have similar biological functions (Li et al., 2005). In group A1, OsIAA5 was induced by drought (Peleg et al., 2011), suggesting that TaIAA12 may be related to drought resistance. In addition, OsIAA2 and OsIAA6 in group B1 were induced by pathogens (Chen et al., 2009), OsIAA1 in group A2 regulates plant type (Song et al., 2009), SbIAA1 in group A3 may be related to stress response (Wang et al., 2010a), and OsIAA4 in group B2 regulates plant tiller (Song and Xu, 2013), implying that their orthologs, such as TaIAA1, 9, 10, 13, and 24, may have similar functions 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)

Phylogenetic relationship of Aux/IAA proteins among wheat and another species. The full-length amino-acid sequences of 85 wheat, 31 rice, 29 Arabidopsis, 7 tomato, 2 maize, 2 grape, 1 sorghum, and 1 pear genes were aligned by Clustal W and the phylogenetic tree was constructed using MEGA 6.0 by the neighbor-joining method with 1000 bootstrap replicates. Each TaIAA protein is indicated by a black dot. Two major groups, group A and B, are represented by the red and blue. The functions of some clades were annotated.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 5: Phylogenetic relationship of Aux/IAA proteins among wheat and another species. The full-length amino-acid sequences of 85 wheat, 31 rice, 29 Arabidopsis, 7 tomato, 2 maize, 2 grape, 1 sorghum, and 1 pear genes were aligned by Clustal W and the phylogenetic tree was constructed using MEGA 6.0 by the neighbor-joining method with 1000 bootstrap replicates. Each TaIAA protein is indicated by a black dot. Two major groups, group A and B, are represented by the red and blue. The functions of some clades were annotated.
Mentions: The phylogenetic tree shows that TaIAA proteins can be classified into two major groups: A and B (Figure 5). Based on the clustering tree of OsIAAs (Jain et al., 2006), groups A and B can be further separated into several subgroups: A1, A3, and A4 contain monocotyledon IAA proteins; A5 contains dicotyledon proteins; and A2, B1, B2, B3, and B4 are all types of IAA protein. Moreover, monocot and dicot IAA proteins are not gathered for one class in every subgroup, while the paralogous proteins of each TaIAA are clustered to the same branch, similar to the clustering result in Figure 1A. Orthologous genes usually have similar biological functions (Li et al., 2005). In group A1, OsIAA5 was induced by drought (Peleg et al., 2011), suggesting that TaIAA12 may be related to drought resistance. In addition, OsIAA2 and OsIAA6 in group B1 were induced by pathogens (Chen et al., 2009), OsIAA1 in group A2 regulates plant type (Song et al., 2009), SbIAA1 in group A3 may be related to stress response (Wang et al., 2010a), and OsIAA4 in group B2 regulates plant tiller (Song and Xu, 2013), implying that their orthologs, such as TaIAA1, 9, 10, 13, and 24, may have similar functions 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.