Fig 1.
Maximum likelihood phylogeny of MADS-box proteins from wild emmer wheat (Triticum dicoccoides), rice (Oryza sativa), and Arabidopsis.
A phylogenetic unrooted tree of MADS-box proteins from T. dicoccoides, rice, and Arabidopsis was inferred using MAFFT-aligned sequences and IQ-Tree [51, 52]. T. dicoccoides genes are colored black, whereas rice and Arabidopsis genes are in green and red, respectively. Subfamilies are indicated outside the tree. Dots next to T. dicoccoides gene names indicate the presence of MADS-box (red), K-box (blue), or both (green) within the coding region of the gene as detected by CDD. Yellow circles: none was detected. Accession numbers of T. dicoccoides genes are available in S1 Table.
Fig 2.
Chromosomal location of MADS-box genes on T. dicoccoides genome.
The genes were mapped to 14 T. dicoccoides chromosomes on which the overall gene density heatmap is presented as well. Chromosome numbers are indicated outside the outer circle. Homoeologous genes are connected using central links. Chromosomes are banded according to pTa535-1 (red bands) and (GAA)10 (blue bands) FISH patterns. M-type MADS-box genes are highlighted with green color.
Fig 3.
The structure of MADS-box genes in T. dicoccoides.
A) Comparison of exon-intron structures between type I and a representative sample of type II genes. Exons are in blue; 3’ and 5’ untranslated regions (UTRs) are shown in white and introns are represented by black lines. B) The mean number of exons and the mean length of MADS-box genes (± standard errors). The number of genes in each group is also indicated. Almost all type I MADS-box genes were single exon genes.
Fig 4.
Potential cis-acting elements in promoter region of TdMADS-box genes of T. dicoccoides.
The number of potential cis-acting elements in 2-kb upstream promoter region of TdMADS-box genes were predicted using the PlantCARE database [67]. The number of each cis-acting element (shown on the right side) identified for each gene is presented inside the cells.
Table 1.
Cis-acting elements on the promoter region of MADS-box genes in T. dicoccoides.
Overall cis-acting elements on the 2kb upstream of MADS-box genes related to different stimuli are presented.
Fig 5.
Expression analysis of the T. dicoccoides MADS-box genes as reveled by RNA-seq data.
A) A heat map of mean expression of type-II MADS-box genes in different tissues and developmental stages of T. dicoccoides. Numbers followed by the developing stages are days from sowing (d) or spike length (cm). B) Co-expression clustering of the T. dicoccoides MADS-box genes based on their expression values from different tissues and developmental stages. Colors indicate the different modules. Note that M-type MADS-box genes were not presented in ’A’ but they were included in co-expression pattern analysis in ’B’.
Fig 6.
Expression of MADS-box genes of wild emmer wheat under drought stress.
Mean expression (± standard error) of MADS-box genes of wild emmer wheat which differentially responded to drought stress conditions as revealed by microarray data (GEO accession: GSE31762). The microarray data belongs to the flag leaf of two wild emmer wheat genotypes contrasting in their productivity and yield stability under terminal drought stress.