Genome-Wide Identification, Expression, and Response to Fusarium Infection of the SWEET Gene Family in Garlic (Allium sativum L.)

Abstract

Proteins of the SWEET (Sugar Will Eventually be Exported Transporters) family play an important role in plant development, adaptation, and stress response by functioning as transmembrane uniporters of soluble sugars. However, the information on the SWEET family in the plants of the Allium genus, which includes many crop species, is lacking. In this study, we performed a genome-wide analysis of garlic (Allium sativum L.) and identified 27 genes putatively encoding clade I-IV SWEET proteins. The promoters of the A. sativum (As) SWEET genes contained hormone- and stress-sensitive elements associated with plant response to phytopathogens. AsSWEET genes had distinct expression patterns in garlic organs. The expression levels and dynamics of clade III AsSWEET3, AsSWEET9, and AsSWEET11 genes significantly differed between Fusarium-resistant and -susceptible garlic cultivars subjected to F. proliferatum infection, suggesting the role of these genes in the garlic defense against the pathogen. Our results provide insights into the role of SWEET sugar uniporters in A. sativum and may be useful for breeding Fusarium-resistant Allium cultivars.

Keywords: Allium sativum L.; Fusarium; SWEET uniporters; biotic stress; garlic; gene expression; gene structure.

Figure 1

Location and structure of the identified AsSWEET genes. (a) Chromosomal distribution of the AsSWEET1–26 genes; AsSWEET27 is absent as a scaffold-localized gene. The scale on the left indicates chromosome size according to the A. sativum cv. Ershuizao genome (PRJNA606385, assembly Garlic.V2.fa) [52]; chr, chromosome; Mb, megabase. (b) Predicted exon–intron structures of the AsSWEET1–27 genes.

Figure 2

Structure of the predicted AsSWEET proteins. (a) Sequence alignment. Gray-shaded regions are 70–100% identical; red blocks on the top indicate positions of transmembrane (TM) helices 1–7. (b) Consensus sequences of TM helices 1–7.

Figure 3

Phylogenetic analysis of the AsSWEET proteins. (a) The unrooted dendrogram based on amino acid sequences was constructed using the neighbor-joining method in MEGA7.0.26 [53]. Percentages of replicate trees in which the associated sequences clustered together in the bootstrap test (1000 replicates) are shown next to the branches. (b) The distribution of conserved motifs was revealed using MEME 5.4.1. The length of each box is proportional to the size of the motif.

Figure 4

Phylogenetic relationships of SWEET proteins from A. sativum (red) and A. thaliana (black). Analysis was performed using the neighbor-joining method in MEGA7.0.26 [53]. Percentages of replicate trees in which the associated sequences clustered together in the bootstrap test (1000 replicates) are shown next to the branches. Clades I–IV refer to SWEET clades previously identified in A. thaliana [16]. The numbering of maize genes is given in accordance with [51].

Figure 5

Hormone- and stress-related cis-acting elements found in the promoter regions of AsSWEET genes. MeJA, methyl jasmonate. The color scheme (from pale to dark) corresponds to the numbers of cis˗elements (from low to high).

Figure 6

Heatmap of AsSWEET expression in A. sativum cv. Ershuizao (PRJNA607255). AsSWEET mRNA levels were analyzed in the roots, bulbs (stages 1–8 corresponding to 192-, 197-, 202-, 207-, 212-, 217-, 222-, and 227-day-old bulbs, respectively), leaves, pseudostems (ps.stem), buds, flowers, and sprouts. The color scheme indicates gene expression gradient from low (red) to high (green).

Figure 7

Transcription of the selected AsSWEET genes in A. sativum cv. Sarmat tissues. “AsSWEET18–19” means the sum expression of AsSWEET18 and AsSWEET19 genes; the high identity (over 98%) of their mRNAs forced the design of common primers. The data were normalized to glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and ubiquitin (UBQ) mRNA levels; ^a–h p < 0.01 indicates significant differences between tissues; ps.stems, pseudostems.

Figure 8

Expression of the selected AsSWEET genes in the roots of A. sativum FBR-resistant cv. Sarmat and FBR-susceptible Strelets in response to F. proliferatum infection. The plants were incubated with F. proliferatum conidia and analyzed for the transcription of the indicated genes at 24 and 96 h post-inoculation (hpi). The data were normalized to GAPDH and UBQ mRNA levels and presented as fold change (mean ± SE) of control (24 h in cv. Sarmat taken as 1); * p < 0.01 compared to uninfected control.

Figure 9

Changes in glucose, fructose, and sucrose contents in the roots of FBR-resistant cv. Sarmat and FBR-susceptible cv. Strelets in response to F. proliferatum infection. The plants were incubated with F. proliferatum conidia and analyzed for sugar contents at 24 and 96 h post-inoculation (hpi). The data are presented as fold change (mean ± SE) of control (24 h in cv. Sarmat taken as 1); * p < 0.01 compared to uninfected control.