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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.


Duplicated TaIAA genes of wheat homologous groups and the collinearity among TaIAAs, TuIAAs, and AetIAAs. Seven homologous groups of wheat chromosomes are displayed in different colors. Duplicated genes of each homo-group are linked using lines with corresponding color. The gray annulus on the periphery represents chromosomes of T. urartu and A. tauschii. The collinearity among TaIAAs, TuIAAs, and AetIAAs were signified by the lines between the orthologous gene-pairs.
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Figure 3: Duplicated TaIAA genes of wheat homologous groups and the collinearity among TaIAAs, TuIAAs, and AetIAAs. Seven homologous groups of wheat chromosomes are displayed in different colors. Duplicated genes of each homo-group are linked using lines with corresponding color. The gray annulus on the periphery represents chromosomes of T. urartu and A. tauschii. The collinearity among TaIAAs, TuIAAs, and AetIAAs were signified by the lines between the orthologous gene-pairs.

Mentions: There is a high homology among the scaffolds of one TaIAA member which belongs to the A, B or D sub-genome (Figure 3), proving that the TaIAA genes experienced two segmental replication events in wheat except for the four single-copy TaIAA genes. However, it could also be the case that the segmental replication genes of the four TaIAAs were lost after the expansion event. Furthermore, three genomic loci containing two TaIAA genes each were defined in the A sub-genome, and the B or D sub-genomes have four such loci (Supplementary Table 1), implying that tandem duplication is also an expansion pattern of the TaIAA gene family.


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)

Duplicated TaIAA genes of wheat homologous groups and the collinearity among TaIAAs, TuIAAs, and AetIAAs. Seven homologous groups of wheat chromosomes are displayed in different colors. Duplicated genes of each homo-group are linked using lines with corresponding color. The gray annulus on the periphery represents chromosomes of T. urartu and A. tauschii. The collinearity among TaIAAs, TuIAAs, and AetIAAs were signified by the lines between the orthologous gene-pairs.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 3: Duplicated TaIAA genes of wheat homologous groups and the collinearity among TaIAAs, TuIAAs, and AetIAAs. Seven homologous groups of wheat chromosomes are displayed in different colors. Duplicated genes of each homo-group are linked using lines with corresponding color. The gray annulus on the periphery represents chromosomes of T. urartu and A. tauschii. The collinearity among TaIAAs, TuIAAs, and AetIAAs were signified by the lines between the orthologous gene-pairs.
Mentions: There is a high homology among the scaffolds of one TaIAA member which belongs to the A, B or D sub-genome (Figure 3), proving that the TaIAA genes experienced two segmental replication events in wheat except for the four single-copy TaIAA genes. However, it could also be the case that the segmental replication genes of the four TaIAAs were lost after the expansion event. Furthermore, three genomic loci containing two TaIAA genes each were defined in the A sub-genome, and the B or D sub-genomes have four such loci (Supplementary Table 1), implying that tandem duplication is also an expansion pattern of the TaIAA gene family.

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.