Genome-Wide Analysis of Serine Hydroxymethyltransferase Genes in Triticeae Species Reveals That TaSHMT3A-1 Regulates Fusarium Head Blight Resistance in Wheat

Abstract

Serine hydroxymethyltransferase (SHMT) plays a pivotal role in cellular one-carbon, photorespiration pathways and it influences the resistance to biotic and abiotic stresses. However, the function of SHMT proteins in wheat remains largely unexplored. In the present study, SHMT genes in five Triticeae species, Oryza sativa, and four dicotyledon species were identified based on whole genome information. The origin history of the target gene was traced by micro-collinearity analysis. Gene expression patterns of TaSHMTs in different tissues, various biotic stresses, exogenous hormones, and two biotic stresses were determined by Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). The function of the selected TaSHMT3A-1 was studied by barley stripe mosaic virus-induced gene silencing in common wheat Bainong207. A total of 64 SHMT members were identified and further classified into two main classes based on the structure of SHMT proteins. The gene structure and motif composition analyses revealed that SHMTs kept relatively conserved within the same subclasses. Interestingly, there was a gene, TdSHMT7B-1, on chromosome 7B of Triticum dicoccoides, but there was no SHMT gene on chromosome 7 of other analyzed Triticeae species; TdSHMT7B-1 had fewer exons and conserved motifs than the genes in the same subclass, suggesting that the gene of TdSHMT7B-1 has a notable evolutionary progress. The micro-collinearity relationship showed that no homologs of TaSHMT3A-1 and its two neighboring genes were found in the collinearity region of Triticum urartu, and there were 27 genes inserted into the collinearity region of T. urartu. Furthermore, qRT-PCR results showed that TaSHMT3A-1 was responsive to abiotic stresses (NaCl and cold), abscisic acid, methyl jasmonate, and hydrogen peroxide. Significantly, upon Fusarium graminearum infection, the expression of TaSHMT3A-1 was highly upregulated in resistant cultivar Sumai3. More importantly, silencing of TaSHMT3A-1 compromises Fusarium head blight resistance in common wheat Bainong207. Our new findings suggest that the TaSHMT3A-1 gene in wheat plays an important role in resistance to Fusarium head blight. This provides a valuable reference for further study on the function of this gene family.

Keywords: Fusarium head blight; SHMT gene family; evolutionary progress; expression pattern; genome-wide analysis; virus-induced gene silencing.

FIGURE 1

Phylogenetic relationship analysis of 64 SHMT proteins from T. aestivum, T. urartu, Ae. Tauschii, T. dicoccoides, H. vulgare, O. sativa, Arabidopsis, S. lycopersicum, C. sativus, and V. vinifera. The phylogenetic tree was built using the Maximum likelihood method (ML) with 1000 bootstrap replicates by MEGA X. The diverse subgroups of SHMT proteins were marked with different colors. The SHMT proteins of T. aestivum, T. urartu, Ae. Tauschii, T. dicoccoides, H. vulgare, O. sativa, Arabidopsis, S. lycopersicum, C. sativus, and V. vinifera were represented by red triangles, green squares, purple circles, blue circles, green triangles, red stars, purple checkmarks, blue checkmarks, green checkmarks, and red checkmarks, respectively. Gene IDs of the analyzed genes can be found in Supplementary Table 2.

FIGURE 2

Phylogenetic relationships, conserved motifs, and gene structure of SHMT genes in Triticeae species. (A) The phylogenetic tree was constructed using the neighbor-joining method with 1,000 bootstrap replicates by MEGA X. (B) The motif composition of SHMT proteins. The motif compositions of SHMT proteins. The 20 motifs were indicated by colored boxes and numbered 1–20. (C) Exon–intron structure of SHMTs. Yellow boxes indicated exons; black lines indicated introns.

FIGURE 3

Micro-collinearity analysis by TGT to track the evolutionary history of TaSHMT3A-1 gene homologs. (A,B) TaSHMT3A-1 was used as the query gene. The micro-collinearity relationship showed that no homolog of TaSHMT3A-1 and its two neighboring genes was found in the collinearity region of T. urartu, but other genes were relatively conserved across other investigated genomes and there were 27 genes inserted into the collinearity region of T. urartu. The red arrow indicates TaSHMT3A-1 (A). In the micro-collinearity relationship analyze the genome of T. urartu was deleted. The neighboring genes of TaSHMT3A-1 were conserved across investigated genomes and homologs of TaSHMT3A-1 were found in all investigated genomes (B). Blackline, 1-to-1-mutual-best. Greenline, 1-to-its-best. Yellowline, 1-to-many. RBH, “reciprocal best hits”; SBH “single-side best hits”.

FIGURE 4

Relative expressions of three TaSHMT genes in different tissues, under different abiotic stresses and response to ABA and H₂O₂ treatment by qRT-PCR. Expression profiling of TaSHMT genes. Tissues were sampled from Sumai3 at the adult stage (A). Fourteen -day -old seedling leaves were sampled after 1, 12, and 24 h under stress conditions comprising 20% PEG6000 (B), 200 mM NaCl (C), cold (4°C) (D), 100 μmol H₂O₂ (E) and 100 μmol ABA (F). Asterisks indicate significant differences (assessed using Duncan’s honestly significant difference test), *P < 0.05, **P < 0.01. All the raw data for qRT-PCR are listed in Supplementary Table 3.

FIGURE 5

Relative expressions of three TaSHMT genes after Bgt inoculation and F. graminearum by qRT-PCR. Expression profiling of three TaSHMT genes in response to Bgt (A) and F. graminearum (B–C). Data were normalized to the TaTubulin gene. The values are the means of three technical replicates of one biological experiment. Error bars indicate the standard error. Asterisks indicate significant differences (assessed using Duncan’s honestly significant difference test), **P < 0.01. Bgt, Blumeria graminis f. sp. tritici; Fg, Fusarium graminearum.

FIGURE 6

Functional analysis of TaSHMT3A-1 by Barley stripe mosaic virus-based virus-induced gene silencing (BSMV-VIGS) in Bainong207. (A) BSMV: TaSHMT3A-1 infected individual plants were inoculated with F. graminearum, and their leaves were photographed at 3 and 5 days post-inoculation (dpi). BSMV:γ were performed as a control. The experiment was repeated independently three times and the same results were obtained. Scale bar, 5 mm. (B) Expression of TaSHMT3A-1 at 14 days in BSMV: TaSHMT3A-1-infected leaves was compared with that in BSMV:γ-infected controls of Bainong207. CK represents plants inoculated with BSMV:γ, and 1-3 represents plants inoculated with BSMV: TaSHMT3A-1. Asterisks show significant differences compared with the control (Duncan’s honestly significant difference test), **P < 0.01.