Table 1.
GATA gene family in soybean.
Fig 1.
Phylogenetic analysis and gene structure of soybean GATA factors.
(a) Phylogenetic tree construction of soybean GATA factors based on the full-length deduced amino acid sequences using MEGA 5.0 by the neighbor-joining method with 1000 bootstrap replicates. Bootstrap values are shown as percentages (>50%) on the branches. GmGATA48 was not presented in this tree because its sequence is partial. The tree showed four major phylogenetic subfamilies (subfamilies I to IV) indicated with different colored backgrounds.(b) Exon/intron structures of GmGATA genes. Green boxes represent exons, and black lines indicate introns. GmGATA48 was not displayed in this figure because its sequence is partial. The 7 kb length base pair was represented with slash–slash. The sizes of exons and introns can be estimated using the scale at the bottom.
Fig 2.
Chromosomal location and region duplication of soybean GATA factor genes.
The schematic diagram of genome-wide chromosome organization and segmental duplication was made from the CViT genome search and synteny viewer at the Legume Information System (http://comparative-legumes.org). Colored blocks to the left of each chromosome show duplications with chromosomes of the same color. For example, the black blocks at the bottom of Gm03 correspond with regions on the black Gm19, and vice versa. Locations of centromeric repeats are shown as black rectangles over the chromosomes. The scale on the left represents the length of the chromosome.
Fig 3.
Schematic distribution of the conserved motifs in soybean GATA factors by MEME.
Each numbered box represents a conserved motif in the protein. Motifs 1 and 4 represent the conserved GATA zinc finger motifs CX2CX18CX2 and CX2CX20CX2, respectively. Multilevel consensus sequences for the MEME-defined motifs are listed in S5 Table. The length of the protein can be estimated using the scale at the bottom.
Fig 4.
Phylogenetic tree of the amino acid sequences of zinc finger domains from soybean, Arabidopsis, and rice.
The tree was conducted based on the zinc finger amino acid sequences using MEGA 5.0 by the neighbor-joining method with 1000 bootstrap replicates. The tree shows four major phylogenetic classes (Classes A to D) indicated with different colors.
Fig 5.
Relative expression profiles of soybean GATA genes in various organs.
Data were obtained by real-time PCR normalized against the reference gene ACT11 and shown as a percentage of expression in leaf. Numbers on the x-axis indicate various tissues: 1 (young leaf), 2 (root), 3 (stem), 4 (flower), and 5 (immature seed).
Fig 6.
Expression of soybean GATA genes in leaves in response to low nitrogen stress.
Data were obtained by real-time PCR normalized against the reference gene ACT11 and shown as a percentage of expression in control leaves at 4 h. White column represents the expression under normal nitrogen condition, and black column represents the expression under limited nitrogen condition. Eight genes (GmGATA17/18/29/32/40/48/50/53) not expressed in soybean leaf under normal condition were not induced under low nitrogen stress and not present in this figure.
Fig 7.
Expression of soybean GATA genes in roots in response to low nitrogen stress.
Data were obtained by real-time PCR normalized against the reference gene ACT11 and shown as a percentage of expression in control roots at 4 h. White column represents the expression under normal nitrogen condition, and black column represents the expression under limited nitrogen condition. Fourteen genes (GmGATA12/17/18/28/29/32/33/40/44/46/48/51/53/58) not expressed in soybean root under normal condition were not induced under low nitrogen stress and not present in this figure.
Fig 8.
Expression of soybean nodulation and nitrogen metabolism-related genes in roots in response to low nitrogen stress.
Data were obtained by real-time PCR normalized against the reference gene ACT11 and shown as a percentage of expression in control roots at 4 h. White column represents the expression under normal nitrogen condition, and black column represents the expression under limited nitrogen condition.
Fig 9.
GmGATA44 modulates chlorophyll content.
(a) Expression levels of GmGATA44 and AtGNC in the wild-type Arabidopsis (wt), the gnc mutant and two GmGATA44 overexpressing transgenic lines (OX31 and OX43) using semi-quantitative RT-PCR from 3 week old rosette leaf tissue.(b) Images of the wild-type plant, the gnc mutant and GmGATA44 overexpressing transgenic plants at one week (upper panel), 3 weeks (middle panel) and 5 weeks (bottom panel) post germination. Bars = 1 cm.(c) Chlorophyll content of the wild-type plants, the gnc mutant and two GmGATA44 overexpressing transgenic lines at 3 weeks post germination. Data are presented as mean ± SD (N = 10) from triplicate independent measurements. Data analysis was performed using SAS software, and significant differences were calculated using the Student’s t-test at 95% confidence limit. Asterisk indicates significant differences from the wild-type plant.(d) Relative expression levels of AtPORA, AtPORB and AtPORC in the wild-type plant, the gnc mutant and two GmGATA44 overexpressing transgenic lines by real-time PCR from 3 week old rosette leaf tissue. Data were obtained by real-time PCR normalized against the reference gene GAPDH and shown as a percentage of expression in the wild-type plant.