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A genome-wide analysis of the LBD (LATERAL ORGAN BOUNDARIES domain) gene family in Malus domestica with a functional characterization of MdLBD11.

Wang X, Zhang S, Su L, Liu X, Hao Y - PLoS ONE (2013)

Bottom Line: At the same time, the expression analysis implied that members of this apple gene family were responsive to hormones and stress and that they may participate in hormone-mediated plant organogenesis, which was demonstrated with the overexpression of the apple LBD gene MdLBD11, resulting in an abnormal phenotype.This phenotype included upward curling leaves, delayed flowering, downward-pointing flowers, siliques and other abnormal traits.Based on these data, we concluded that the MdLBD genes may play an important role in apple growth and development as in Arabidopsis and other species.

View Article: PubMed Central - PubMed

Affiliation: National Key laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong, China.

ABSTRACT
The plant-specific LBD (LATERAL ORGAN BOUNDARIES domain) genes belong to a major family of transcription factor that encode a zinc finger-like domain. It has been shown that LBD genes play crucial roles in the growth and development of Arabidopsis and other plant species. However, no detailed information concerning this family is available for apple. In the present study, we analyzed the apple (Malus domestica) genome and identified 58 LBD genes. This gene family was tested for its phylogenetic relationships with homologous genes in the Arabidopsis genome, as well as its location in the genome, structure and expression. We also transformed one MdLBD gene into Arabidopsis to evaluate its function. Like Arabidopsis, apple LBD genes also have a conserved CX2CX6CX3C zinc finger-like domain in the N terminus and can be divided into two classes. The expression profile indicated that apple LBD genes exhibited a variety of expression patterns, suggesting that they have diverse functions. At the same time, the expression analysis implied that members of this apple gene family were responsive to hormones and stress and that they may participate in hormone-mediated plant organogenesis, which was demonstrated with the overexpression of the apple LBD gene MdLBD11, resulting in an abnormal phenotype. This phenotype included upward curling leaves, delayed flowering, downward-pointing flowers, siliques and other abnormal traits. Based on these data, we concluded that the MdLBD genes may play an important role in apple growth and development as in Arabidopsis and other species.

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The chromosomal mapping analysis of the LBD gene family in apple.The scale bar represents a 10.0 Mb chromosomal distance. The chromosome number (Chr01-Chr17) is indicated at the top of each chromosome. To simplify the presentation, we named the putative LBD genes from MdLBD1 to MdLBD58 on the basis of the LBD family and gene order on the chromosomes from Chr01 to Chr17, respectively. Segmented duplicate homologous blocks are indicated with a blue shadow. Sister paralogous pairs are indicated by a red line.
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pone-0057044-g003: The chromosomal mapping analysis of the LBD gene family in apple.The scale bar represents a 10.0 Mb chromosomal distance. The chromosome number (Chr01-Chr17) is indicated at the top of each chromosome. To simplify the presentation, we named the putative LBD genes from MdLBD1 to MdLBD58 on the basis of the LBD family and gene order on the chromosomes from Chr01 to Chr17, respectively. Segmented duplicate homologous blocks are indicated with a blue shadow. Sister paralogous pairs are indicated by a red line.

Mentions: Fifty-five genes were located in 15 out of 17 chromosomes, and 3 MdLBD genes (MdLBD56, MdLBD57 and MdLBD58) were localized to unassembled genomic sequence scaffolds and thus were not mapped to any particular chromosome (Fig. 3). Chromosome 01 encompassed the largest number with 9 MdLBD genes, followed by Chr02 and Chr05 (6 genes per chromosome). Five MdLBD genes were distributed in Chr15, four genes were distributed in Chr04, 7 genes were distributed in Chr03, 10 genes were distributed in Chr06, and three genes were distributed in Chr08. Two LBD genes were identified in Chr12, while only one gene was located on Chr11, 14 and 17. In addition, further investigation showed that the distribution of each type of LBD genes was significantly irregular (Fig. 3), while no MdLBD genes were located on Chr13 or Chr16. Among them, a total of 21 genes were found in the segmental duplication blocks (Fig. 3), and five homologous pairs (MdLBD17/18, MdLBD24/25, MdLBD23/45, MdLBD32/33 and MdLBD30/49) were definitely located on the duplicated blocks.


A genome-wide analysis of the LBD (LATERAL ORGAN BOUNDARIES domain) gene family in Malus domestica with a functional characterization of MdLBD11.

Wang X, Zhang S, Su L, Liu X, Hao Y - PLoS ONE (2013)

The chromosomal mapping analysis of the LBD gene family in apple.The scale bar represents a 10.0 Mb chromosomal distance. The chromosome number (Chr01-Chr17) is indicated at the top of each chromosome. To simplify the presentation, we named the putative LBD genes from MdLBD1 to MdLBD58 on the basis of the LBD family and gene order on the chromosomes from Chr01 to Chr17, respectively. Segmented duplicate homologous blocks are indicated with a blue shadow. Sister paralogous pairs are indicated by a red line.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3585328&req=5

pone-0057044-g003: The chromosomal mapping analysis of the LBD gene family in apple.The scale bar represents a 10.0 Mb chromosomal distance. The chromosome number (Chr01-Chr17) is indicated at the top of each chromosome. To simplify the presentation, we named the putative LBD genes from MdLBD1 to MdLBD58 on the basis of the LBD family and gene order on the chromosomes from Chr01 to Chr17, respectively. Segmented duplicate homologous blocks are indicated with a blue shadow. Sister paralogous pairs are indicated by a red line.
Mentions: Fifty-five genes were located in 15 out of 17 chromosomes, and 3 MdLBD genes (MdLBD56, MdLBD57 and MdLBD58) were localized to unassembled genomic sequence scaffolds and thus were not mapped to any particular chromosome (Fig. 3). Chromosome 01 encompassed the largest number with 9 MdLBD genes, followed by Chr02 and Chr05 (6 genes per chromosome). Five MdLBD genes were distributed in Chr15, four genes were distributed in Chr04, 7 genes were distributed in Chr03, 10 genes were distributed in Chr06, and three genes were distributed in Chr08. Two LBD genes were identified in Chr12, while only one gene was located on Chr11, 14 and 17. In addition, further investigation showed that the distribution of each type of LBD genes was significantly irregular (Fig. 3), while no MdLBD genes were located on Chr13 or Chr16. Among them, a total of 21 genes were found in the segmental duplication blocks (Fig. 3), and five homologous pairs (MdLBD17/18, MdLBD24/25, MdLBD23/45, MdLBD32/33 and MdLBD30/49) were definitely located on the duplicated blocks.

Bottom Line: At the same time, the expression analysis implied that members of this apple gene family were responsive to hormones and stress and that they may participate in hormone-mediated plant organogenesis, which was demonstrated with the overexpression of the apple LBD gene MdLBD11, resulting in an abnormal phenotype.This phenotype included upward curling leaves, delayed flowering, downward-pointing flowers, siliques and other abnormal traits.Based on these data, we concluded that the MdLBD genes may play an important role in apple growth and development as in Arabidopsis and other species.

View Article: PubMed Central - PubMed

Affiliation: National Key laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong, China.

ABSTRACT
The plant-specific LBD (LATERAL ORGAN BOUNDARIES domain) genes belong to a major family of transcription factor that encode a zinc finger-like domain. It has been shown that LBD genes play crucial roles in the growth and development of Arabidopsis and other plant species. However, no detailed information concerning this family is available for apple. In the present study, we analyzed the apple (Malus domestica) genome and identified 58 LBD genes. This gene family was tested for its phylogenetic relationships with homologous genes in the Arabidopsis genome, as well as its location in the genome, structure and expression. We also transformed one MdLBD gene into Arabidopsis to evaluate its function. Like Arabidopsis, apple LBD genes also have a conserved CX2CX6CX3C zinc finger-like domain in the N terminus and can be divided into two classes. The expression profile indicated that apple LBD genes exhibited a variety of expression patterns, suggesting that they have diverse functions. At the same time, the expression analysis implied that members of this apple gene family were responsive to hormones and stress and that they may participate in hormone-mediated plant organogenesis, which was demonstrated with the overexpression of the apple LBD gene MdLBD11, resulting in an abnormal phenotype. This phenotype included upward curling leaves, delayed flowering, downward-pointing flowers, siliques and other abnormal traits. Based on these data, we concluded that the MdLBD genes may play an important role in apple growth and development as in Arabidopsis and other species.

Show MeSH
Related in: MedlinePlus