Transcriptome analysis of genes related to resistance against powdery mildew in wheat-Thinopyrum alien addition disomic line germplasm SN6306

Wheat powdery mildew resistance gene Pm13 encodes a mixed lineage kinase domain-like protein

Wheat powdery mildew is one of the most destructive diseases threatening global wheat production. The wild relatives of wheat constitute rich sources of diversity for powdery mildew resistance. Here, we report the map-based cloning of the powdery mildew resistance gene Pm13 from the wild wheat species Aegilops longissima. Pm13 encodes a mixed lineage kinase domain-like (MLKL) protein that contains an N-terminal-domain of MLKL (MLKL_NTD) domain in its N-terminus and a C-terminal serine/threonine kinase (STK) domain. The resistance function of Pm13 is validated by mutagenesis, gene silencing, transgenic assay, and allelic association analyses. The development of introgression lines with significantly reduced chromosome segments of Ae. longissima encompassing Pm13 enables widespread deployment of this gene into wheat cultivars. The cloning of Pm13 may provide valuable insights into the molecular mechanisms underlying Pm13-mediated powdery mildew resistance and highlight the important roles of kinase fusion proteins (KFPs) in wheat immunity.

Comparative transcriptome profiling reveals the role of phytohormones and phenylpropanoid pathway in early-stage resistance against powdery mildew in watermelon (Citrullus lanatus L.)

Yield and fruit quality loss by powdery mildew (PM) fungus is a major concern in cucurbits, but early-stage resistance mechanisms remain elusive in the majority of cucurbits. Here, we explored the comparative transcriptomic dynamics profiling of resistant line ZXG1755 (R) and susceptible line ZXG1996 (S) 48 h post-inoculation in watermelon seedlings to check precise expression changes induced by Podosphaera. xanthii race '2F'. Phenotypic responses were confirmed by microscopy and endogenous levels of defense and signaling related phytochromes were detected higher in resistant lines. In total, 7642 differently expressed genes (DEGs) were detected, and 57.27% of genes were upregulated in four combinations. DEGs were predominantly abundant in the KEGG pathway linked with phenylpropanoid biosynthesis, plant hormone and transduction, and phenylalanine metabolism, whereas GO terms of defense response, response to fungus, and chitin response were predominant in resistant lines, evidencing significant defense mechanisms and differences in the basal gene expression levels between these contrasting lines. The expression of selected DEGs from major pathways (hormonal, lignin, peroxidase, sugar) were validated via qRT-PCR. Detailed analysis of DEGs evidenced that along with other DEGs, genes including PR1 (Cla97C02G034020) and PRX (Cla97C11G207220/30, Cla97C02G045100 and Cla97C02G049950) should be studied for their potential role. In short, our study portrayed strong evidence indicating the important role of a complex network associated with lignin biosynthesis and phytohormone related downstream mechanisms that are responsible for incompatible interaction between PM and watermelon resistance line.

Thinopyrum intermedium TiAP1 interacts with a chitin deacetylase from Blumeria graminis f. sp. tritici and increases the resistance to Bgt in wheat

The biotrophic fungal pathogen Blumeria graminis f. sp. tritici (Bgt) is a crucial factor causing reduction in global wheat production. Wild wheat relatives, for example Thinopyrum intermedium, is one of the wild-used parents in wheat disease-resistant breeding. From T. intermedium line, we identified the aspartic protease gene, TiAP1, which is involved in resistance against Bgt. TiAP1 is a secreted protein that accumulates in large amounts at the infection sites of Bgt and extends to the intercellular space. Yeast two-hybrid, luciferase complementation imaging and bimolecular florescent complimentary analysis showed that TiAP1 interacted with the chitin deacetylase (BgtCDA1) of Bgt. The yeast expression, purification and in vitro test confirmed the chitin deacetylase activity of BgtCDA1. The bombardment and VIGS-mediated host-induced gene silencing showed that BgtCDA1 promotes the invasion of Bgt. Transcriptome analysis showed the cell wall xylan metabolism, lignin biosynthesis-related and defence genes involved in the signal transduction were up-regulated in the transgenic TiAP1 wheat induced by Bgt. The TiAP1 in wheat may inactivate the deacetylation function of BgtCDA1, cause chitin oligomers expose to wheat chitin receptor, then trigger the wheat immune response to inhibit the growth and penetration of Bgt, and thereby enhance the resistance of wheat to pathogens.

Efficient expression and function of a receptor-like kinase in wheat powdery mildew defence require an intron-located MYB binding site

The LRK10-like receptor kinases (LRK10L-RLKs) are ubiquitously present in higher plants, but knowledge of their expression and function is still limited. Here, we report expression and functional analysis of TtdLRK10L-1, a typical LRK10L-RLK in durum wheat (Triticum turgidum L. ssp. durum). The introns of TtdLRK10L-1 contained multiple kinds of predicted cis-elements. To investigate the potential effect of these cis-elements on TtdLRK10L-1 expression and function, two types of transgenic wheat lines were prepared, which expressed a GFP-tagged TtdLRK10L-1 protein (TtdLRK10L-1:GFP) from the cDNA or genomic DNA (gDNA) sequence of TtdLRK10L-1 under the native promoter. TtdLRK10L-1:GFP expression was up-regulated by the powdery mildew pathogen Blumeria graminis f. sp. tritici (Bgt) in both types of transgenic plants, with the scale of the elevation being much stronger in the gDNA lines. Both types of transgenic plants exhibited enhanced resistance to Bgt infection relative to wild type control. Notably, the Bgt defence activated in the gDNA lines was significantly stronger than that in the cDNA lines. Further analysis revealed that a putative MYB transcription factor binding site (MYB-BS, CAGTTA) located in TtdLRK10L-1 intron I was critical for the efficient expression and function of TtdLRK10L-1 in Bgt defence. This MYB-BS could also increase the activity of a superpromoter widely used in ectopic gene expression studies in plants. Together, our results deepen the understanding of the expression and functional characteristics of LRK10L-RLKs. TtdLRK10L-1 is likely useful for further dissecting the molecular processes underlying wheat defence against Bgt and for developing Bgt resistant wheat crops.

Transcriptome profiling analysis reveals distinct resistance response of cucumber leaves infected with powdery mildew

Powdery mildew is the main disease affecting cucumber cultivation and causes severe economic loss. So far, research on cucumber resistance to powdery mildew has not yielded feasible solutions. This study selected two inbred cucumber lines, XY09-118 (resistant) and Q10 (susceptible) and investigated their responses to powdery mildew infection (harvested 24 and 48 h after inoculation) using RNA sequencing. More than 20,000 genes were detected in cucumber leaves both with and without powdery mildew infection at the above two time points. Among these, 5478 genes were identified as differently expressed genes (DEGs) between XY09-118 and Q10. Based on the databases GO and KEGG, the functions of DEGs were analysed. Moreover, the complex regulatory network for powdery mildew resistance was assessed, which involves plant hormone signal transduction, phenylpropanoid biosynthesis, plant-pathogen interaction and the MAPK signalling pathway. In particular, genes encoding WRKY, NAC and TCP were highlighted. In addition, genes involved in plant hormone biosynthesis, metabolism and signal transduction, pathogen resistance and abiotic stress response were analysed. Co-expression analysis indicated that the transcription factors correlated with plant hormone signal pathway and metabolism, defence and abiotic response. The expression of several genes was validated by qRT-PCR. The pathogen resistance regulatory network was identified by comparing resistant and susceptible inbred lines infected with powdery mildew. The transcriptome data provide novel insights into cucumber response to powdery mildew infection and the identified pathogen resistance genes will be highly useful for breeding efforts to enhance the resistance of cucumber to powdery mildew.

Genome-wide identification of the aspartic protease gene family and their response under powdery mildew stress in wheat

Aspartic proteases (APs) are one of the four main protease super families. In plants, they are involved in many biological processes, such as biotic and abiotic stress resistance, protein processing and degradation, senescence, and programmed cell death. By performing a database (TGACv1) search and domain prediction, we identified 263 wheat AP (TaAP) proteins and observed 38 TaAP genes exhibiting alternative splicing. Moreover, by constructing a phylogenetic tree, we found that the TaAP proteins can be divided into three families and have a certain close evolutionary relationship to Arabidopsis thaliana and rice AP proteins. Transcriptome analysis showed that 29 genes in the TaAP family were up-regulated after being induced by powdery mildew. The expression of TaAP224 showed the most significant difference in transcriptome and qRT-PCR analyses. Subsequently, the promoters of these 29 genes were analysed, and we found that they contained multiple disease resistance and hormone elements, such as WRKY71OS, a common disease resistance element that is also involved in the GA signalling pathway and inhibits starch hydrolysis. The comprehensive annotation and expression profiling performed in this study increased our understanding of the TaAP family genes in wheat growth and development, and the results can be used as a basis for further study of candidate TaAP genes involved in powdery mildew resistance mechanisms.

A spontaneous wheat-Aegilops longissima translocation carrying Pm66 confers resistance to powdery mildew

A spontaneous Robertsonian T4S^lS·4BL translocation chromosome carrying Pm66 for powdery mildew resistance was discovered and confirmed by RNA-seq, molecular marker, and in situ hybridization analyses. Powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt) is a severe disease of bread wheat worldwide. Discovery and utilization of resistance genes to powdery mildew from wild relatives of wheat have played important roles in wheat improvement. Aegilops longissima, one of the S-genome diploid wild relatives of wheat, is a valuable source of disease and pest resistance for wheat. Chromosome 4S^l from Ae. longissima confers moderate resistance to powdery mildew. In this study, we conducted RNA-seq on a putative Chinese Spring (CS)-Ae. longissima 4S^l(4B) disomic substitution line (TA3465) to develop 4S^l-specific markers to assist the transfer of a Bgt resistance gene from 4S^l by induced homoeologous recombination. A pairwise comparison of genes between CS and TA3465 demonstrated that a number of genes on chromosome 4BS in CS were not expressed in TA3465. Analysis of 4B- and 4S^l-specific molecular markers showed that 4BS and 4S^lL were both missing in TA3465, whereas 4BL and 4S^lS were present. Further characterization by genomic and fluorescent in situ hybridization confirmed that TA3465 carried a spontaneous Robertsonian T4S^lS·4BL translocation. Powdery mildew tests showed that TA3465 was resistant to 10 of 16 Bgt isolates collected from different regions of China, whereas CS was susceptible to all those Bgt isolates. The powdery mildew resistance gene(s) in TA3465 was further mapped to the short arm of 4S^l and designated as Pm66.

Discovery of powdery mildew resistance gene candidates from Aegilops biuncialis chromosome 2Mb based on transcriptome sequencing

Powdery mildew is one of the most widespread diseases of wheat. The development and deployment of resistant varieties are one of the most economical and effective methods to manage this disease. Our previous study showed that the gene(s) at 2Mb in Chinese Spring (CS)-Aegilops biuncialis 2Mb disomic addition line TA7733 conferred a high level of resistance to powdery mildew of wheat. In this study, resistance spectrum of TA7733 was assayed by using 15 Blumeria graminis f. sp. tritici (Bgt) isolates prevalent in different regions of China. The result indicated that TA7733 was highly resistant to all tested Bgt isolates and the gene(s) on chromosome 2Mb conferred broad-spectrum resistance to powdery mildew. In order to characterize mechanism of powdery mildew resistance by identifying candidates R-genes derived from Ae. biuncialis chromosome 2Mb and develop 2Mb-specific molecular markers, we performed RNA-seq analysis on TA7733 and CS. In total we identified 7,278 unigenes that showed specific expression in TA7733 pre and post Bgt-infection when compared to CS. Of these 7,278 unigenes, 295 were annotated as putative resistance (R) genes. Comparatively analysis of R-gene sequences from TA7733 and CS and integration CS Ref Seq v1.0 were used to develop R-gene specific primers. Of 295 R-genes we identified 53 R-genes were specific to 2Mb and could be involved in powdery mildew resistance. Functional annotation of majority of the 53 R-genes encoded nucleotide binding leucine rich repeat (NLR) protein. The broad-spectrum resistance to powdery mildew in TA7733 and availability of 2Mb-derived putative candidate R-gene specific molecular markers identified in this study will lay foundations for transferring powdery mildew resistance from 2Mb to common wheat by inducing CS-Ae. biuncialis homoeologous recombination. Our study also provides useful candidates for further isolation and cloning of powdery mildew resistance gene(s) from Ae. biuncialis chromosome 2Mb.

The genome-wide transcriptional consequences of the nullisomic-tetrasomic stocks for homoeologous group 7 in bread wheat

Background

Hexaploid bread wheat (Triticum aestivum L) arose by two polyploidisation events from three diploid species with homoeologous genomes. Nullisomic-tetrasomic (nulli-tetra or NT) lines are aneuploid wheat plants lacking two and adding two of six homoeologous chromosomes. These plants can grow normally, but with significantly morphological variations because the adding two chromosomes or the remaining four chromosomes compensate for those absent. Despite these interesting phenomena, detailed molecular mechanisms underlying dosage deletion and compensation in these useful genetic materials have not been determined.

Results

By sequencing the transcriptomes of leaves in two-week-old seedlings, we showed that the profiles of differentially expressed genes between NT stocks for homoeologous group 7 and the parent hexaploid Chinese Spring (CS) occurred throughout the whole genome with a subgenome and chromosome preference. The deletion effect of nulli-chromosomes was compensated partly by the tetra-chromosomes via the dose level of expressed genes, according to the types of homoeologous genes. The functions of differentially regulated genes primarily focused on carbon metabolic process, photosynthesis process, hormone metabolism, and responding to stimulus, and etc., which might be related to the defective phenotypes that included reductions in plant height, flag leaf length, spikelet number, and kernels per spike.

Conclusions

The perturbation of the expression levels of transcriptional genes among the NT stocks for homoeologous group 7 demonstrated the gene dosage effect of the subgenome at the genome-wide level. The gene dosage deletion and compensation can be used as a model to elucidate the functions of the subgenomes in modern polyploid plants.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5421-3) contains supplementary material, which is available to authorized users.

Comparative Digital Gene Expression Analysis of Tissue-Cultured Plantlets of Highly Resistant and Susceptible Banana Cultivarsin Response to Fusarium oxysporum

Banana Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc) is one of the most destructive soil-borne diseases. In this study, young tissue-cultured plantlets of banana (Musa spp. AAA) cultivars differing in Foc susceptibility were used to reveal their differential responses to this pathogen using digital gene expression (DGE). Data were evaluated by various bioinformatic tools (Venn diagrams, gene ontology (GO) annotation and Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses) and immunofluorescence labelling method to support the identification of gene candidates determining the resistance of banana against Foc. Interestingly, we have identified MaWRKY50 as an important gene involved in both constitutive and induced resistance. We also identified new genes involved in the resistance of banana to Foc, including several other transcription factors (TFs), pathogenesis-related (PR) genes and some genes related to the plant cell wall biosynthesis or degradation (e.g., pectinesterases, β-glucosidases, xyloglucan endotransglucosylase/hydrolase and endoglucanase). The resistant banana cultivar shows activation of PR-3 and PR-4 genes as well as formation of different constitutive cell barriers to restrict spreading of the pathogen. These data suggest new mechanisms of banana resistance to Foc.