Genome-wide identification of the SPL gene family in Tartary Buckwheat (Fagopyrum tataricum) and expression analysis during fruit development stages

Abstract

Background: SPL (SQUAMOSA promoter binding protein-like) is a class of plant-specific transcription factors that play important roles in many growth and developmental processes, including shoot and inflorescence branching, embryonic development, signal transduction, leaf initiation, phase transition, and flower and fruit development. The SPL gene family has been identified and characterized in many species but has not been well studied in tartary buckwheat, which is an important edible and medicinal crop.

Results: In this study, 24 Fagopyrum tataricum SPL (FtSPL) genes were identified and renamed according to the chromosomal distribution of the FtSPL genes. According to the amino acid sequence of the SBP domain and gene structure, the SPL genes were divided into eight groups (group I to group VII) by phylogenetic tree analysis. A total of 10 motifs were detected in the tartary buckwheat SPL genes. The expression patterns of 23 SPL genes in different tissues and fruits at different developmental stages (green fruit stage, discoloration stage and initial maturity stage) were determined by quantitative real-time polymerase chain reaction (qRT-PCR).

Conclusions: The tartary buckwheat genome contained 24 SPL genes, and most of the genes were expressed in different tissues. qRT-PCR showed that FtSPLs played important roles in the growth and development of tartary buckwheat, and genes that might regulate flower and fruit development were preliminarily identified. This work provides a comprehensive understanding of the SBP-box gene family in tartary buckwheat and lays a significant foundation for further studies on the functional characteristics of FtSPL genes and improvement of tartary buckwheat crops.

Keywords: Expression patterns; Fruit development; FtSPL; Genome; Tartary buckwheat.

Fig. 1

Unrooted phylogenetic tree representing the relationships among 24 SPL genes of tartary buckwheat and Arabidopsis. The genes in tartary buckwheat are marked in red, while those in Arabidopsis are marked in black.

Fig. 2

Phylogenetic relationships, gene structures and architectures of the conserved protein motifs of the SPL genes from tartary buckwheat. a The phylogenetic tree was constructed based on the full-length sequences of tartary buckwheat SPL proteins using Geneious R11 software. b Exon-intron structures of tartary buckwheat SPL genes. Yellow boxes indicate untranslated 5′- and 3′-regions; blue boxes indicate exons; and black lines indicate introns. The SBP domain is highlighted by a red box. The number indicates the phases of the corresponding introns. c The motif compositions of the tartary buckwheat SPL proteins. The motifs, numbered 1–10, are displayed in different colored boxes. The sequence information for each motif is provided in Table S2. The protein length can be estimated using the scale at the bottom.

Fig. 3

Schematic representations of the chromosomal distribution of the tartary buckwheat SPL genes. The chromosome number is indicated to the left of each chromosome.

Fig. 4

Schematic representations of the interchromosomal relationships of the tartary buckwheat SPL genes. Colored lines indicate all syntenic blocks in the tartary buckwheat genome.

Fig. 5

Phylogenetic relationships and motif compositions of the SPL proteins from seven different plant species. Outer layer: An unrooted phylogenetic tree constructed using Geneious R11 with the neighbor-joining method. Inner layer: Distribution of the conserved motifs in SPL proteins. The differently colored boxes represent different motifs and their positions in each SPL protein sequence.

Fig. 6

Synteny analyses between the SPL genes of tartary buckwheat and six representative plant species. Gray lines in the background indicate collinear blocks within tartary buckwheat and other plant genomes, while red lines highlight syntenic SPL gene pairs.

Fig. 7

Tissue-specific gene expression of 23 tartary buckwheat SPL genes and the correlation between the gene expression patterns of FtSPLs.a The expression patterns of 23 tartary buckwheat SPL genes in flower, leaf, root, stem and fruit tissues were examined by qPCR. Error bars were obtained from three measurements. Lowercase letter(s) above the bars indicate significant differences (α = 0.05, LSD) among the treatments. b Positive number: positively correlated; negative number: negatively correlated. The red numbers indicate a significant correlation at the 0.05 level.

Fig. 8

Gene expression of 21 tartary buckwheat SPL genes during fruit development and the correlation between the gene expression patterns of FtSPLs during fruit development. a The expression patterns of 21 tartary buckwheat SPL genes in the fruit development stage were examined using a qPCR assay. Error bars were obtained from three measurements. Lowercase letter(s) above the bars indicate significant differences (α = 0.05, LSD) among the treatments. b Positive number: positively correlated; negative number: negatively correlated. Red numbers indicate a significant correlation at the 0.05 level