Comprehensive analysis of GASA family members in the Malus domestica genome: identification, characterization, and their expressions in response to apple flower induction

Abstract

Background: The plant-specific gibberellic acid stimulated Arabidopsis (GASA) gene family is critical for plant development. However, little is known about these genes, particularly in fruit tree species.

Results: We identified 15 putative Arabidopsis thaliana GASA (AtGASA) and 26 apple GASA (MdGASA) genes. The identified genes were then characterized (e.g., chromosomal location, structure, and evolutionary relationships). All of the identified A. thaliana and apple GASA proteins included a conserved GASA domain and exhibited similar characteristics. Specifically, the MdGASA expression levels in various tissues and organs were analyzed based on an online gene expression profile and by qRT-PCR. These genes were more highly expressed in the leaves, buds, and fruits compared with the seeds, roots, and seedlings. MdGASA genes were also responsive to gibberellic acid (GA₃) and abscisic acid treatments. Additionally, transcriptome sequencing results revealed seven potential flowering-related MdGASA genes. We analyzed the expression levels of these genes in response to flowering-related treatments (GA₃, 6-benzylaminopurine, and sugar) and in apple varieties that differed in terms of flowering ('Nagafu No. 2' and 'Yanfu No. 6') during the flower induction period. These candidate MdGASA genes exhibited diverse expression patterns. The expression levels of six MdGASA genes were inhibited by GA₃, while the expression of one gene was up-regulated. Additionally, there were expression-level differences induced by the 6-benzylaminopurine and sugar treatments during the flower induction stage, as well as in the different flowering varieties.

Conclusion: This study represents the first comprehensive investigation of the A. thaliana and apple GASA gene families. Our data may provide useful clues for future studies and may support the hypotheses regarding the role of GASA proteins during the flower induction stage in fruit tree species.

Keywords: Apple; Characterization; Expression profile; Flower induction; GASA gene.

Fig. 1

Locations of MdGASA genes on each apple chromosome

Fig. 2

Alignment of the GASA domain from MdGASA proteins. a Analysis of GASA protein structures, red column represented their conserved twelve cysteines. b Multiple alignments of the MdGASA protein sequences. Their conserved GASA domains were indicated. c Sequence logo analysis of the conserved GASA domains. Each stack represented their amino acids

Fig. 3

Predicted dimensional structures of MdGASA proteins

Fig. 4

Analysis of MdGASA gene structures. a An unrooted phylogenetic tree constructed based on MdGASA protein sequences. b Exon-intron composition analysis, red boxes and black line were exon and intron positions, respectively. c Conserved motifs analysis, details motifs can be seen Fig. S2

Fig. 5

Phylogenetic analysis of apple and Arabidopsis thaliana GASA genes. Protein designations: Arabidopsis (At, blue triangle) and apple (Md, red circle)

Fig. 6

Analysis of evolutionary relationships among GASA gene family members. Relative positive positions were depicted according to the apple chromosomes, colored lines were syntenic regions of the apple genome. (b) Synteny analysis of GASA genes between Arabidopsis and apple, relative positive positions were depicted according to the apple and Arabidopsis chromosomes, colored lines were syntenic regions of apple and Arabidopsis genome

Fig. 7

MdGASA gene expression profiles in different tissues and in different apple varieties. Relative expression profiles are based the online database (E-GEOD-42873)

Fig. 8

Analysis of MdGASA expression levels in different ‘Nagafu No. 2’ tissues. Each value represents the mean ± standard error of three biological replicates. Means followed by small letters are significantly different at the 0.05 level

Fig. 9

Analysis of flowering-related MdGASA expression levels in response to GA₃ (a) and 6-BA (b) treatments. Samples were collected at 30, 40, 50, 60, 70, and 80 days after full bloom (DAFB), with water used as a control. Each value represents the mean ± standard error of three replicates. Means followed by small letters are significantly different at the 0.05 level

Fig. 10

Analysis of flowering-related MdGASA expression levels in response to sugar (a) and in different apple varieties (‘Nagafu No. 2’ and ‘Yanfu No. 6’) (b). Samples were collected at 30, 40, 50, 60, 70, and 80 days after full bloom (DAFB), with water used as a control. Each value represents the mean ± standard error of three replicates. Means followed by small letters are significantly different at the 0.05 level

Fig. 11

Predicted cis-elements in the MdGASA promoters. The 1.5-kb sequences of 26 MdGASA genes were analyzed with the PlantCARE program