A transposable element insertion in the susceptibility gene CsaMLO8 results in hypocotyl resistance to powdery mildew in cucumber

N6-Methyladenosine (m6A) Sequencing Reveals Heterodera glycines-Induced Dynamic Methylation Promoting Soybean Defense

Unraveling the intricacies of soybean cyst nematode (Heterodera glycines) race 4 resistance and susceptibility in soybean breeding lines-11-452 (highly resistant) and Dongsheng1 (DS1, highly susceptible)-was the focal point of this study. Employing cutting-edge N6-methyladenosine (m6A) and RNA sequencing techniques, we delved into the impact of m6A modification on gene expression and plant defense responses. Through the evaluation of nematode development in both resistant and susceptible roots, a pivotal time point (3 days postinoculation) for m6A methylation sequencing was identified. Our sequencing data exhibited robust statistics, successful soybean genome mapping, and prevalent m6A peak distributions, primarily in the 3' untranslated region and stop codon regions. Analysis of differential methylation peaks and differentially expressed genes revealed distinctive patterns between resistant and susceptible genotypes. In the highly resistant line (11-452), key resistance and defense-associated genes displayed increased expression coupled with inhibited methylation, encompassing crucial players such as R genes, receptor kinases, and transcription factors. Conversely, the highly susceptible DS1 line exhibited heightened expression correlated with decreased methylation in genes linked to susceptibility pathways, including Mildew Locus O-like proteins and regulatory elements affecting defense mechanisms. Genome-wide assessments, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, and differential methylation peak/differentially expressed gene overlap emphasized the intricate interplay of m6A modifications, alternative splicing, microRNA, and gene regulation in plant defense. Protein-protein interaction networks illuminated defense-pivotal genes, delineating divergent mechanisms in resistant and susceptible responses. This study sheds light on the dynamic correlation between methylation, splicing, and gene expression, providing profound insights into plant responses to nematode infection.

Fine mapping and analysis of a candidate gene controlling Phytophthora blight resistance in cucumber

Cucumber blight is a destructive disease. The best way to control this disease is resistance breeding. This study focuses on disease resistance gene mapping and molecular marker development. We used the resistant cucumber, JSH, and susceptible cucumber, B80, as parents to construct F2 populations. Bulked segregant analysis (BSA) combined with specific length amplified fragment sequencing (SLAF-seq) were used, from which we developed cleaved amplified polymorphic sequence (CAPs) markers to map the resistance gene. Resistance in F2 individuals showed a segregation ratio of resistance:susceptibility close to 3:1. The gene in JSH resistant cucumber was mapped to an interval of 9.25 kb, and sequencing results for the three genes in the mapped region revealed three mutations at base sites 225, 302, and 591 in the coding region of Csa5G139130 between JSH and B80, but no mutations in coding regions of Csa5G139140 and Csa5G139150. The mutations caused changes in amino acids 75 and 101 of the protein encoded by Csa5G139130, suggesting that Csa5G139130 is the most likely resistance candidate gene. We developed a molecular marker, CAPs-4, as a closely linked marker for the cucumber blight resistance gene. This is the first report on mapping of a cucumber blight resistance gene and will provideg a useful marker for molecular breeding of cucumber resistance to Phytophthora blight.

Multiplex gene editing reveals cucumber MILDEW RESISTANCE LOCUS O family roles in powdery mildew resistance

Powdery mildew (PM) is one of the most widespread and prevalent diseases that affects a wide range of crops. In cucumber (Cucumis sativus L.), previous forward genetic studies have identified MILDEW RESISTANCE LOCUS O 8 (CsMLO8) as necessary but alone insufficient for cucumber PM resistance (PMR) and suggested the involvement of other members of the CsMLO family. However, the function of other CsMLO family members in cucumber remains largely unknown. Here, we developed a highly efficient multiplex gene editing system in cucumber to generate a series of Csmlo mutants from all the 13 family members. Systematic analysis of these mutants revealed growth effects of these CsMLO family members on development and PMR. Importantly, we obtained the Csmlo1/8/11 triple mutant with complete resistance to PM. Transcriptome and proteome analysis of PM-resistant Csmlo mutants suggested that the kinesin-like calmodulin-binding protein (KCBP)-interacting Ca2+-binding protein (CsKIC), calmodulin-like protein 28 (CsCML28), and Ca2+-dependent protein kinase 11 (CsCPK11)-mediated calcium signaling pathway is involved in PMR. CsMLO8 interacted directly with CsKIC, and the simultaneous silencing of both genes resulted in a phenotype that resembled the silencing of CsKIC alone. Silencing CsCML28 and CsCPK11 increased susceptibility to PM, whereas overexpressing CsCPK11 through genetic transformation enhanced cucumber's PMR, demonstrating their positive regulatory roles in PMR. Given the importance of PMR for cucurbit crops, this research provides unprecedented insights into the function of the proteins encoded by the CsMLO gene family as well as the plant defense response to PM pathogen.

Different control of resistance to two Colletotrichum orbiculare pathogenic races 0 and 1 in cucumber (Cucumis sativus L.)

KEY MESSAGE

Quantitative trait locus analysis identified independent novel loci in cucumbers responsible for resistance to races 0 and 1 of the anthracnose fungal pathogen Colletotrichum orbiculare. Cucumbers have been reported to be vulnerable to Colletotrichum orbiculare, causing anthracnose disease with significant yield loss under favorable conditions. The deployment of a single recessive Cssgr gene in cucumber breeding for anthracnose resistance was effective until a recent report on high-virulent strains infecting cucumbers in Japan conquering the resistance. QTL mapping was conducted to identify the resistance loci in the cucumber accession Ban Kyuri (G100) against C. orbiculare strains 104-T and CcM-1 of pathogenic races 0 and 1, respectively. A single dominant locus An5 was detected in the disease resistance hotspot on chromosome 5 for resistance to 104-T. Resistance to CcM-1 was governed by three loci with additive effects located on chromosomes 2 (An2) and 1 (An1.1 and An1.2). Molecular markers were developed based on variant calling between the corresponding QTL regions in the de novo assembly of the G100 genome and the publicly available cucumber genomes. Multiple backcrossed populations were deployed to fine-map An5 locus and narrow the region to approximately 222 kbp. Accumulation of An2 and An1.1 alleles displayed an adequate resistance to CcM-1 strain. This study provides functional molecular markers for pyramiding resistance loci that confer sufficient resistance against anthracnose in cucumbers.

CsMLO8/11 are required for full susceptibility of cucumber stem to powdery mildew and interact with CsCRK2 and CsRbohD

Powdery mildew (PM) is one of the most destructive diseases that threaten cucumber production globally. Efficient breeding of novel PM-resistant cultivars will require a robust understanding of the molecular mechanisms of cucumber resistance against PM. Using a genome-wide association study, we detected a locus significantly correlated with PM resistance in cucumber stem, pm-s5.1. A 1449-bp insertion in the CsMLO8 coding region at the pm-s5.1 locus resulted in enhanced stem PM resistance. Knockout mutants of CsMLO8 and CsMLO11 generated by CRISPR/Cas9 both showed improved PM resistance in the stem, hypocotyl, and leaves, and the double mutant mlo8mlo11 displayed even stronger resistance. We found that reactive oxygen species (ROS) accumulation was higher in the stem of these mutants. Protein interaction assays suggested that CsMLO8 and CsMLO11 could physically interact with CsRbohD and CsCRK2, respectively. Further, we showed that CsMLO8 and CsCRK2 competitively interact with the C-terminus of CsRbohD to affect CsCRK2-CsRbohD module-mediated ROS production during PM defense. These findings provide new insights into the understanding of CsMLO proteins during PM defense responses.

NLR- and mlo-Based Resistance Mechanisms against Powdery Mildew in Cannabis sativa

Powdery mildew (PM) is one of the most common Cannabis sativa diseases. In spite of this, very few documented studies have characterized the resistance genes involved in PM defense mechanisms, or sources of natural genetic resistance in cannabis. The focus of the present work is on the two primary mechanisms for qualitative resistance against PM. The first is based on resistance (R) genes characterized by conserved nucleotide-binding site and/or leucine-rich repeat domains (NLRs). The second one involves susceptibility (S) genes, and particularly mildew resistance locus o (MLO) genes, whose loss-of-function mutations seem to be a reliable way to protect plants from PM infection. Cannabis defenses against PM are thus discussed, mainly detailing the strategies based on these two mechanisms. Emerging studies about this research topic are also reported and, based on the most significant results, a potential PM resistance model in cannabis plant-pathogen interactions is proposed. Finally, innovative approaches, based on the pyramiding of multiple R genes, as well as on genetic engineering and genome editing methods knocking out S genes, are discussed, to obtain durable PM-resistant cannabis cultivars with a broad-spectrum resistance range.

Haplotype-resolved genome assembly provides insights into the evolution of S-locus supergene in distylous Nymphoides indica

Distyly has evolved independently in numerous animal-pollinated angiosperm lineages. Understanding of its molecular basis has been restricted to a few species, primarily Primula. Here, we investigate the genetic architecture of the single diallelic locus (S-locus) supergene, a linkage group of functionally associated genes, and explore how it may have evolved in distylous Nymphoides indica, a lineage of flowering plants not previously investigated. We assembled haplotype-resolved genomes, used read-coverage-based genome-wide association study (rb-GWAS) to locate the S-locus supergene, co-expression network analysis to explore gene networks underpinning the development of distyly, and comparative genomic analyses to investigate the origins of the S-locus supergene. We identified three linked candidate S-locus genes - NinBAS1, NinKHZ2, and NinS1 - that were only evident in the short-styled morph and were hemizygous. Co-expression network analysis suggested that brassinosteroids contribute to dimorphic sex organs in the short-styled morph. Comparative genomic analyses indicated that the S-locus supergene likely evolved via stepwise duplications and has been affected by transposable element activities. Our study provides novel insight into the structure, regulation, and evolution of the supergene governing distyly in N. indica. It also provides high-quality genomic resources for future research on the molecular mechanisms underlying the striking evolutionary convergence in form and function across heterostylous taxa.

The COPII subunit CsSEC23 mediates fruit glossiness in cucumber

To improve our understanding of the mechanism underlying cucumber glossiness regulation, a novel cucumber mutant with a glossy peel (Csgp) was identified. MutMap, genotyping, and gene editing results demonstrated that CsSEC23, which is the core component of COPII vesicles, mediates the glossiness of cucumber fruit peel. CsSEC23 is functionally conserved and located in the Golgi and endoplasmic reticulum. CsSEC23 could interact with CsSEC31, but this interaction was absent in the Csgp mutant, which decreased the efficiency of COPII vesicle transportation. Genes related to wax and cutin transport were upregulated in the Csgp mutant, and the cuticle structure of the Csgp-mutant peel became thinner. Moreover, the wax and cutin contents were also changed due to CsSEC23 mutation. Taken together, the results obtained from this study revealed that CsSEC23 mediates cucumber glossiness, and this mediating might be affected by COPII vesicle transportation.

Genome-wide characterization and expression analysis of the MLO gene family sheds light on powdery mildew resistance in Lagenaria siceraria

MLO (mildew locus O) genes play a vital role in plant disease defense system, especially powdery mildew (PM). Lagenaria siceraria is a distinct Cucurbitaceae crop, and PM is one of the most serious diseases threatening crop production and quality. Although MLOs have been exploited in many Cucurbitaceae species, genome-wide mining of MLO gene family in bottle gourd has not been surveyed yet. Here we identified 16 MLO genes in our recently assembled L. siceraria genome. A total of 343 unique MLO protein sequences from 20 species were characterized and compared to deduce a generally high level of purifying selection and the occurrence of regions related to candidate susceptibility factors in the evolutional divergence. LsMLOs were clustered in six clades containing seven conserved transmembrane domains and 10 clade-specific motifs along with deletion and variation. Three genes (LsMLO3, LsMLO6, and LsMLO13) in clade V showed high sequence identity with orthologues involved in PM susceptibility. The expression pattern of LsMLOs was tissue-specific but not cultivar-specific. Furthermore, it was indicated by qRT-PCR and RNA-seq that LsMLO3 and LsMLO13 were highly upregulated in response to PM stress. Subsequent sequence analysis revealed the structural deletion of LsMLO13 and a single nonsynonymous substitution of LsMLO3 in the PM-resistant genotype. Taken all together, it is speculated that LsMLO13 is likely a major PM susceptibility factor. The results of this study provide new insights into MLO family genes in bottle gourd and find a potential candidate S gene for PM tolerance breeding.

CRISPR/Cas9 based mlo-mediated resistance against Podosphaera xanthii in cucumber (Cucumis sativus L.)

Powdery mildews (PM) are common and severe pathogen groups that threaten plants, and PM resistance is complex and polygenic in cucumbers. Previously mlo-based resistance was reported in various plants, including cucumber, with generated loss-of CsaMLO function mutants. However, mlo-based resistance in cucumber is also complex and involves additional mechanisms such as hypersensitive response (HR) and papillae formation. For this reason, we focused on determining the mlo-based powdery mildew resistance mechanism in cucumber. CRISPR/Cas9 was used in the present study to generate loss-of-function mutants for CsaMLO1, CsaMLO8, and CsaMLO11 of PM susceptible ADR27 cucumber inbred lines and CsaMLO mutants were obtained and validated. Trypan Blue and DAB staining were performed to detect Podosphaera xanthii germination/penetration rates and accumulation of Reactive Oxygen Species (ROS). Our results indicate that PM-susceptibility associated CsaMLOs in cucumber are negative regulators in different defense mechanisms against powdery mildew at early and late stages of infection. Further, the experiment results indicated that CsaMLO8 mutation-based resistance was associated with the pre-invasive response, while CsaMLO1 and CsaMLO11 could be negative regulators in the post-invasive defense response in cucumber against P. xanthii. Although the loss-of CsaMLO8 function confers the highest penetration resistance, CsaMLO1 and CsaMLO11 double mutations could be potential candidates for HR-based resistance against PM pathogen in cucumber. These results highlighted the crucial role of CRISPR/Cas9 to develop PM resistant cucumber cultivars, possessing strong pre-invasive defense with CsaMLO8 or post-invasive with CsaMLO1/CsaMLO11 mutations.

Impact of LTR-Retrotransposons on Genome Structure, Evolution, and Function in Curcurbitaceae Species

Long terminal repeat (LTR)-retrotransposons (LTR-RTs) comprise a major portion of many plant genomes and may exert a profound impact on genome structure, function, and evolution. Although many studies have focused on these elements in an individual species, their dynamics on a family level remains elusive. Here, we investigated the abundance, evolutionary dynamics, and impact on associated genes of LTR-RTs in 16 species in an economically important plant family, Cucurbitaceae. Results showed that full-length LTR-RT numbers and LTR-RT content varied greatly among different species, and they were highly correlated with genome size. Most of the full-length LTR-RTs were amplified after the speciation event, reflecting the ongoing rapid evolution of these genomes. LTR-RTs highly contributed to genome size variation via species-specific distinct proliferations. The Angela and Tekay lineages with a greater evolutionary age were amplified in Trichosanthes anguina, whereas a recent activity burst of Reina and another ancient round of Tekay activity burst were examined in Sechium edule. In addition, Tekay and Retand lineages belonging to the Gypsy superfamily underwent a recent burst in Gynostemma pentaphyllum. Detailed investigation of genes with intronic and promoter LTR-RT insertion showed diverse functions, but the term of metabolism was enriched in most species. Further gene expression analysis in G.pentaphyllum revealed that the LTR-RTs within introns suppress the corresponding gene expression, whereas the LTR-RTs within promoters exert a complex influence on the downstream gene expression, with the main function of promoting gene expression. This study provides novel insights into the organization, evolution, and function of LTR-RTs in Cucurbitaceae genomes.

Increasing the activities of protective enzymes is an important strategy to improve resistance in cucumber to powdery mildew disease and melon aphid under different infection/infestation patterns

Powdery mildew, caused by Sphaerotheca fuliginea (Schlecht.) Poll., and melon aphids (Aphis gossypii Glover) are a typical disease and insect pest, respectively, that affect cucumber production. Powdery mildew and melon aphid often occur together in greenhouse production, resulting in a reduction in cucumber yield. At present there are no reports on the physiological and biochemical effects of the combined disease and pest infection/infestation on cucumber. This study explored how cucumbers can regulate photosynthesis, protective enzyme activity, and basic metabolism to resist the fungal disease and aphids. After powdery mildew infection, the chlorophyll and free proline contents in cucumber leaves decreased, while the activities of POD (peroxidase) and SOD (superoxide dismutase) and the soluble protein and MDA (malondialdehyde) contents increased. Cucumber plants resist aphid attack by increasing the rates of photosynthesis and basal metabolism, and also by increasing the activities of protective enzymes. The combination of powdery mildew infection and aphid infestation reduced photosynthesis and basal metabolism in cucumber plants, although the activities of several protective enzymes increased. Aphid attack after powdery mildew infection or powdery mildew infection after aphid attack had the opposite effect on photosynthesis, protective enzyme activity, and basal metabolism regulation. Azoxystrobin and imidacloprid increased the contents of chlorophyll, free proline, and soluble protein, increased SOD activity, and decreased the MDA content in cucumber leaves. However, these compounds had the opposite effect on the soluble sugar content and POD and CAT (catalase) activities. The mixed ratio of the two single agents could improve the resistance of cucumber to the combined infection of powdery mildew and aphids. These results show that cucumber can enhance its pest/pathogen resistance by changing physiological metabolism when exposed to a complex infection system of pathogenic microorganisms and insect pests.

Genome-Wide Identification of Powdery Mildew Responsive Long Non-Coding RNAs in Cucurbita pepo

Cucurbita pepo L. is an essential economic vegetable crop worldwide, and its production is severely affected by powdery mildew (PM). However, our understanding of the molecular mechanism of PM resistance in C. pepo is very limited. Long non-coding RNAs (lncRNAs) play an important role in regulating plant responses to biotic stress. Here, we systematically identified 2,363 reliably expressed lncRNAs from the leaves of PM-susceptible (PS) and PM-resistant (PR) C. pepo. The C. pepo lncRNAs are shorter in length and expressed at a lower level than the protein-coding transcripts. Among the 2,363 lncRNAs, a total of 113 and 146 PM-responsive lncRNAs were identified in PS and PR, respectively. Six PM-responsive lncRNAs were predicted as potential precursors of microRNAs (miRNAs). In addition, 58 PM-responsive lncRNAs were predicted as targets of miRNAs and one PM-responsive lncRNA was predicted as an endogenous target mimic (eTM). Furthermore, a total of 5,200 potential cis target genes and 5,625 potential trans target genes were predicted for PM-responsive lncRNAs. Functional enrichment analysis showed that these potential target genes are involved in different biological processes, such as the plant-pathogen interaction pathway, MAPK signaling pathway, and plant hormone signal transduction pathway. Taken together, this study provides a comprehensive view of C. pepo lncRNAs and explores the putative functions of PM-responsive lncRNAs, thus laying the foundation for further study of the regulatory mechanisms of lncRNAs responding to PM.

Morphological Characterization and Integrated Transcriptome and Proteome Analysis of Organ Development Defective 1 (odd1) Mutant in Cucumis sativus L

Cucumber (Cucumis sativus L.) is an economically important vegetable crop with the unique growth habit and typical trailing shoot architecture of Cucurbitaceae. Elucidating the regulatory mechanisms of growth and development is significant for improving quality and productivity in cucumber. Here we isolated a spontaneous cucumber mutant organ development defective 1 (odd1) with multiple morphological changes including root, plant stature, stem, leaf, male and female flowers, as well as fruit. Anatomical and cytological analyses demonstrated that both cell size and number decreased, and the shoot apical meristem (SAM) was smaller in odd1 compared with WT. Pollen vigor and germination assays and cross tests revealed that odd1 is female sterile, which may be caused by the absence of ovules. Genetic analysis showed that odd1 is a recessive single gene mutant. Using the MutMap strategy, the odd1 gene was found to be located on chromosome 5. Integrated profiling of transcriptome and proteome indicated that the different expression genes related to hormones and SAM maintenance might be the reason for the phenotypic changes of odd1. These results expanded the insight into the molecular regulation of organ growth and development and provided a comprehensive reference map for further studies in cucumber.

CmPMRl and CmPMrs are responsible for resistance to powdery mildew caused by Podosphaera xanthii race 1 in Melon

Two genes for resistance to Podosphaera xanthii race 1 in melon were identified on chromosomes 10 and 12 of the Cucumis melo cultivar MR-1. Cucumis melo L. is an economically important crop, the production of which is threatened by the prevalence of melon powdery mildew (PM) infections. We herein utilized the MR-1 (P₁; resistant to PM) and M4-7 (P₂; susceptible to PM) accessions to assess the heritability of PM (race 1) resistance in these melon plants. PM resistance in MR-1 leaves was linked to a dominant gene (CmPMRl), whereas stem resistance was under the control of a recessive gene (CmPMrs), with the dominant gene having an epistatic effect on the recessive gene. The CmPMRl gene was mapped to a 50 Kb interval on chromosome 12, while CmPMrs was mapped to an 89 Kb interval on chromosome 10. The CmPMRl candidate gene MELO3C002441 and the CmPMrs candidate gene MELO3C012438 were identified through sequence alignment, functional annotation, and expression pattern analyzes of all genes within these respective intervals. MELO3C002441 and MELO3C012438 were both localized to the cellular membrane and were contained conserved NPR gene-like and MLO domains, respectively, which were linked to PM resistance. In summary, we identified patterns of PM resistance in the disease-resistant MR-1 melon cultivar and identified two putative genes linked to resistance. Our results offer new genetic resources and markers to guide future marker-assisted breeding for PM resistance in melon.

Identification of Susceptibility Genes for Fusarium oxysporum in Cucumber via Comparative Proteomic Analysis

Fusarium wilt (FW) in cucumber (Cucumis sativus L.), caused by Fusarium oxysporum f. sp. cucumerinum (Foc), poses a major threat to cucumber growth and productivity. However, lack of available natural resistance resources for FW restricts the breeding of resistant cultivars via conventional approaches. Susceptibility (S) genes in susceptible host plants facilitate infection by the pathogen and contribute to susceptibility. Loss of function of these S genes might provide broad-spectrum and durable disease resistance. Here, we screened S genes via comparative proteomic analysis between cucumber cultivars Rijiecheng and Superina, which exhibited resistance and high -susceptibility to FW, respectively. We identified 210 and 243 differentially regulated proteins (DRPs) in the Rijiecheng and Superina, respectively, and further found that 32 DRPs were predominantly expressed in Superina and significantly up-regulated after Foc inoculation. Expression verification found that TMEM115 (CsaV3_5G025750), encoding a transmembrane protein, TET8 (CsaV3_2G007840), encoding function as a tetraspanin, TPS10 (CsaV3_2G017980) encoding a terpene synthase, and MGT2 (CsaV3_7G006660), encoding a glycosyltransferase, were significantly induced in both cultivars after Foc infection but were induced to a higher expression level in Superina. These candidate genes might act as negative regulators of FW resistance in cucumber and provide effective FW-susceptibility gene resources for improving cucumber FW resistance through breeding programs.

Analysis of allelic variants of RhMLO genes in rose and functional studies on susceptibility to powdery mildew related to clade V homologs

Rose has 19 MLO genes. Of these, RhMLO1 and RhMLO2 were shown to be required for powdery mildew infection, which suggests their potential as susceptibility targets towards disease resistance. Powdery mildew, caused by Podosphaera pannosa, is one of the most serious and widespread fungal diseases for roses, especially in greenhouse-grown cut roses. It has been shown that certain MLO genes are involved in powdery mildew susceptibility and that loss of function in these genes in various crops leads to broad-spectrum, long-lasting resistance against this fungal disease. For this reason, these MLO genes are called susceptibility genes. We carried out a genome-wide identification of the MLO gene family in the Rosa chinensis genome, and screened for allelic variants among 22 accessions from seven different Rosa species using re-sequencing and transcriptome data. We identified 19 MLO genes in rose, of which four are candidate genes for functional homologs in clade V, which is the clade containing all dicot MLO susceptibility genes. We detected a total of 198 different allelic variants in the set of Rosa species and accessions, corresponding to 5-15 different alleles for each of the genes. Some diploid Rosa species shared alleles with tetraploid rose cultivars, consistent with the notion that diploid species have contributed to the formation of tetraploid roses. Among the four RhMLO genes in clade V, we demonstrated using expression study, virus-induced gene silencing as well as transient RNAi silencing that two of them, RhMLO1 and RhMLO2, are required for infection by P. pannosa and suggest their potential as susceptibility targets for powdery mildew resistance breeding in rose.

Identification of quantitative trait loci for powdery mildew resistance in highly resistant cucumber (Cucumis sativus L.) using ddRAD-seq analysis

Powdery mildew, caused by Podosphaera xanthii (syn. Sphaerotheca fuliginea ex Fr. Poll.), is one of the most economically important foliar diseases in cucumber (Cucumis sativus L.). Cucumber parental line 'Kyuri Chukanbohon Nou 5 Go', developed from weedy cucumber line CS-PMR1, is highly resistant to powdery mildew and is promising breeding material. We performed quantitative trait locus (QTL) analysis using double-digest restriction-site-associated DNA sequencing (ddRAD-Seq) in a population from a cross between 'Kyuri Chukanbohon Nou 5 Go' and the Japanese native cultivar 'Kaga-aonaga-fushinari', which is susceptible to powdery mildew. The resistance of the population and its parents was evaluated using leaf disc assays and image analysis. We detected one major QTL on Chr. 5 that was effective at both 20°C and 25°C and one minor QTL on Chr. 1 effective at 20°C. We detected two additional QTLs in subpopulation: one on Chr. 3 effective at 20°C and one on Chr. 5 effective at both 20°C and 25°C in a position different from the major QTL. The resistance alleles at all four QTLs were contributed by 'Kyuri Chukanbohon Nou 5 Go'. The results of this study can be used to develop practical DNA markers tightly linked to genes for powdery mildew resistance.

The amino acid permease (AAP) genes CsAAP2A and SlAAP5A/B are required for oomycete susceptibility in cucumber and tomato

Cucurbit downy mildew (DM), caused by the obligate biotroph Pseudoperonospora cubensis, is a destructive disease in cucumber. A valuable source of DM resistance is the Indian cucumber accession PI 197088, which harbours several quantitative trait loci (QTLs) contributing to quantitatively inherited DM resistance. With a combination of fine-mapping and transcriptomics, we identified Amino Acid Permease 2A (CsAAP2A) as a candidate gene for QTL DM4.1.3. Whole-genome and Sanger sequencing revealed the insertion of a Cucumis Mu-like element (CUMULE) transposon in the allele of the resistant near-isogenic line DM4.1.3. To confirm whether loss of CsAAP2A contributes to partial DM resistance, we performed targeting induced local lesions in genomes on a DM-susceptible cucumber genotype to identify an additional csaap2a mutant, which indeed was partially DM resistant. In view of the loss of the putative function as amino acid transporter, we measured amino acids in leaves. We found that DM-inoculated leaves of line DM4.1.3 (with the csaap2a mutation) contained significantly fewer amino acids than wild-type cucumber. The decreased flow of amino acids towards infected leaves in csaap2a plants compared to the wild type might explain the resistant phenotype of the mutant, as this would limit the available nutrients for the pathogen and thereby its fitness. To examine whether AAP genes play a conserved role as susceptibility factors in plant-oomycete interactions, we made targeted mutations in two AAP genes from tomato and studied the effect on susceptibility to Phytophthora infestans. We conclude that not only CsAAP2A but also SlAAP5A/SlAAP5B are susceptibility genes for oomycete pathogens.

Discovery and Characterization of a Novel Tomato mlo Mutant from an EMS Mutagenized Micro-Tom Population

In tomato (Solanum lycopersicum), there are at least three SlMLO (Mildew resistance Locus O) genes acting as susceptibility genes for the powdery mildew disease caused by Oidium neolycopersici, namely SlMLO1, SlMLO5 and SlMLO8. Of the three homologs, the SlMLO1 gene plays a major role since a natural mutant allele called ol-2 can almost completely prevent fungal penetration by formation of papillae. The ol-2 allele contains a 19-bp deletion in the coding sequence of the SlMLO1 gene, resulting in a premature stop codon within the second cytoplasmic loop of the predicted protein. In this study, we have developed a new genetic resource (M200) in the tomato cv. Micro-Tom genetic background by means of ethyl methane sulfonate (EMS) mutagenesis. The mutant M200 containing a novel allele (the m200 allele) of the tomato SlMLO1 gene showed profound resistance against powdery mildew with no fungal sporulation. Compared to the coding sequence of the SlMLO1 gene, the m200 allele carries a point mutation at T65A. The SNP results in a premature stop codon L22* located in the first transmembrane domain of the complete SlMLO1 protein. The length of the predicted protein is 21 amino acids, while the SlMLO1 full-length protein is 513 amino acids. A high-resolution melting (HRM) marker was developed to distinguish the mutated m200 allele from the SlMLO1 allele in backcross populations. The mutant allele conferred recessive resistance that was associated with papillae formation at fungal penetration sites of plant epidermal cells. A comprehensive list of known mlo mutations found in natural and artificial mutants is presented, which serves as a particularly valuable resource for powdery mildew resistance breeding.

Identification of Novel Loci and Candidate Genes for Resistance to Powdery Mildew in a Resequenced Cucumber Germplasm

Powdery mildew (PM) is one of the most serious diseases in cucumber and causes huge yield loss. Multiple quantitative trait loci (QTLs) for PM resistance have been reported in previous studies using a limited number of cucumber accessions. In this study, a cucumber core germplasm (CG) consisting of 94 resequenced lines was evaluated for PM resistance in four trials across three years (2013, 2014, and 2016). These trials were performed on adult plants in the field with natural infection. Using genome-wide association study (GWAS), 13 loci (pmG1.1, pmG1.2, pmG2.1, pmG2.2, pmG3.1, pmG4.1, pmG4.2, pmG5.1, pmG5.2, pmG5.3, pmG5.4, pmG6.1, and pmG6.2) associated with PM resistance were detected on all chromosomes except for Chr.7. Among these loci, ten were mapped to chromosomal intervals where QTLs had been reported in previous studies, while, three (pmG2.1, pmG3.1, and pmG4.1) were novel. The loci of pmG2.1, pmG5.2, pmG5.3 showed stronger signal in four trials. Based on the annotation of homologous genes in Arabidopsis and pairwise LD correlation analysis, candidate genes located in the QTL intervals were predicted. SNPs in these candidate genes were analyzed between haplotypes of highly resistant (HR) and susceptible (HS) CG lines, which were defined based on combing disease index data of all trials. Furthermore, candidate genes (Csa5G622830 and CsGy5G015660) reported in previous studies for PM resistance and cucumber orthologues of several PM susceptibility (S) genes (PMR5, PMR-6, and MLO) that are colocalized with certain QTLs, were analyzed for their potential contribution to the QTL effect on both PM and DM in the CG population. This study shows that the CG germplasm is a very valuable resource carrying known and novel QTLs for both PM and DM resistance, which can be exploited in cucumber breeding.

A chromosome-scale genome assembly of European hazel (Corylus avellana L.) reveals targets for crop improvement

The European hazelnut (Corylus avellana L.) is a tree crop of economic importance worldwide, but especially for northern Turkey, where the majority of production takes place. Hazelnut production is currently challenged by environmental stresses, such as a recent outbreak of severe powdery mildew disease; furthermore, allergy to hazelnuts is an increasing health concern in some regions. In order to provide a foundation for using the available hazelnut genetic resources for crop improvement, we produced a fully assembled genome sequence and annotation for a hazelnut species, from C. avellana cv. 'Tombul', one of the most important Turkish varieties. A hybrid sequencing strategy, combining short reads, long reads and proximity ligation methods, enabled us to resolve heterozygous regions and produce a high-quality 370-Mb assembly that agrees closely with cytogenetic studies and genetic maps of the 11 C. avellana chromosomes, and covers 97.8% of the estimated genome size. The genome includes 27 270 high-confidence protein-coding genes, over 20 000 of which were functionally annotated based on homology with known plant proteins. We focused particularly on gene families encoding hazelnut allergens, and the Mildew resistance Locus O (MLO) proteins that are an important susceptibility factor for powdery mildew. The complete assembly enabled us to differentiate between members of these families and to identify homologues that may be important in mildew disease and hazelnut allergy. These findings provide examples of how the genome can be used to guide research and to develop effective strategies for crop improvement in C. avellana.

QTL-seq analysis of powdery mildew resistance in a Korean cucumber inbred line

QTL mapping and RT-PCR analyses identified the CsGy5G015660 as a strong powdery mildew resistance candidate gene and natural variation of CsGy5G015660 allele was observed using 115 core germplasm. Powdery mildew (PM) is among the most serious fungal diseases encountered in the cultivation of cucurbits. The development of PM-resistant inbred lines is thus of considerable significance for cucumber breeding programs. In this study, we applied bulked segregant analysis combined with QTL-seq to identify PM resistance loci using F₂ population derived from a cross between two Korean cucumber inbred lines, PM-R (resistant) and PM-S (susceptible). Genome-wide SNP profiling using bulks of the two extreme phenotypes identified two QTLs on chromosomes 5 and 6, designated pm5.2 and pm6.1, respectively. The two PM resistance loci were validated using molecular marker-based classical QTL analysis: pm5.2 (30% R² at LOD 11) and pm6.1 (11% R² at LOD 3.2). Furthermore, reverse transcriptase-PCR analyses, using genes found to be polymorphic between PM-R and PM-S, were conducted to identify the candidate gene(s) responsible for PM resistance. We found that transcripts of the gene CsGy5G015660, encoding a putative leucine-rich repeat receptor-like serine/threonine-protein kinase (RPK2), showed specific accumulation in PM-R prior to the appearance of disease symptoms, and was accordingly considered a strong candidate gene for PM resistance. In addition, cleaved amplified polymorphic sequence markers from CsGy5G015660 were developed and used to screen 35 inbred lines. Natural variation in the CsGy5G015660 allele was also observed based on analysis of a core collection of 115 cucumber accessions. Our results provide new genetic insights for gaining a better understanding of the genetic basis of PM resistance in cucumber, and pave the way for further utilization in cucumber PM resistance breeding programs.

Comparative analysis of powdery mildew resistant and susceptible cultivated cucumber (Cucumis sativus L.) varieties to reveal the metabolic responses to Sphaerotheca fuliginea infection

BACKGROUND

Cucumber (Cucumis sativus L.) is a widely planted vegetable crop that suffers from various pathogen infections. Powdery mildew (PM) is typical disease caused by Sphaerotheca fuliginea infection and destroys the production of cucumber. However, the metabolic responses to S. fuliginea infection are largely unknown.

RESULTS

In our study, a PM resistant variety 'BK2' and a susceptible variety 'H136' were used to screen differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs) under S. fuliginea infection. Most of DEGs and DAMs were enriched in several primary and secondary metabolic pathways, including flavonoid, hormone, fatty acid and diterpenoid metabolisms. Our data showed that many flavonoid-related metabolites were significantly accumulated in BK2 rather than H136, suggesting an essential role of flavonoids in formation of resistant quality. Changes in expression of CYP73A, CYP81E1, CHS, F3H, HCT and F3'M genes provided a probable explanation for the differential accumulation of flavonoid-related metabolites. Interestingly, more hormone-related DEGs were detected in BK2 compared to H136, suggesting a violent response of hormone signaling pathways in the PM-resistant variety. The number of fatty acid metabolism-related DAMs in H136 was larger than that in BK2, indicating an active fatty acid metabolism in the PM-susceptible variety.

CONCLUSIONS

Many differentially expressed transcription factor genes were identified under S. fuliginea infection, providing some potential regulators for the improvement of PM resistance. PM resistance of cucumber was controlled by a complex network consisting of various hormonal and metabolic pathways.

Pepper CaMLO6 Negatively Regulates Ralstonia solanacearum Resistance and Positively Regulates High Temperature and High Humidity Responses

Plant mildew-resistance locus O (MLO) proteins influence susceptibility to powdery mildew. However, their roles in plant responses to other pathogens and heat stress remain unclear. Here, we showed that CaMLO6, a pepper (Capsicum annuum) member of MLO clade V, is a protein targeted to plasma membrane and probably endoplasmic reticulum. The transcript expression level of CaMLO6 was upregulated in the roots and leaves of pepper plants challenged with high temperature and high humidity (HTHH) and was upregulated in leaves but downregulated in roots of plants infected with the bacterial pathogen Ralstonia solanacearum. CaMLO6 was also directly upregulated by CaWRKY40 upon HTHH but downregulated by CaWRKY40 upon R. solanacearum infection. Virus-induced gene silencing of CaMLO6 significantly decreased pepper HTHH tolerance and R. solanacearum susceptibility. Moreover, CaMLO6 overexpression enhanced the susceptibility of Nicotiana benthamiana and pepper plants to R. solanacearum and their tolerance to HTHH, effects that were associated with the expression of immunity- and thermotolerance-associated marker genes, respectively. These results suggest that CaMLO6 acts as a positive regulator in response to HTHH but a negative regulator in response to R. solanacearum. Moreover, CaMLO6 is transcriptionally affected by R. solanacearum and HTHH; these transcriptional responses are at least partially regulated by CaWRKY40.

QTL for horticulturally important traits associated with pleiotropic andromonoecy and carpel number loci, and a paracentric inversion in cucumber

The legendary cucumber inbred line WI2757 possesses a rare combination of resistances against nine pathogens, which is an important germplasm for cucumber breeding. However, WI2757 flowers late and does not perform well under field conditions. The genetic basis for horticulturally important traits other than disease resistances in WI2757 is largely unknown. In this study, we conducted QTL mapping using F₂ and recombinant inbred line (RIL) populations from the WI2757 × True Lemon cross that were segregating for multiple traits. Phenotypic data were collected in replicated field trials across multiple years for seven traits including fruit carpel number (CN) and sex expression. A high-density SNP-based genetic map was developed with genotyping by sequencing of the RIL population, which revealed a region on chromosome 1 with strong recombination suppression. The reduced recombination in this region was due to a ~ 10-Mbp paracentric inversion in WI2757 that was confirmed with additional segregation and cytological (FISH) analyses. Thirty-six QTL were detected for flowering time, fruit length (FL), fruit diameter (FD), fruit shape (LD), fruit number (FN), CN, and powdery mildew resistance. Five moderate- or major-effect QTL for FL, FD, LD, and FN inside the inversion are likely the pleiotropic effects of the andromonoecy (m), or the cn locus. The major-effect flowering time QTL ft1.1 was also mapped inside the inversion, which seems to be different from the previously assigned delayed flowering in WI2757. Implications of these findings on the use of WI2757 in cucumber breeding are discussed.

Identification of MicroRNAs and Their Targets That Respond to Powdery Mildew Infection in Cucumber by Small RNA and Degradome Sequencing

Powdery mildew (PM) is a prevalent disease known to limit cucumber production worldwide. MicroRNAs (miRNAs) are single-stranded molecules that regulate host defense responses through posttranscriptional gene regulation. However, which specific miRNAs are involved and how they regulate cucumber PM resistance remain elusive. A PM-resistant single-segment substitution line, SSSL508-28, was developed previously using marker-assisted backcrossing of the PM-susceptible cucumber inbred D8 line. In this study, we applied small RNA and degradome sequencing to identify PM-responsive miRNAs and their target genes in the D8 and SSSL508-28 lines. The deep sequencing resulted in the identification of 156 known and 147 novel miRNAs. Among them, 32 and six differentially expressed miRNAs (DEMs) were detected in D8 and SSSL508-28, respectively. The positive correlation between DEMs measured by small RNA sequencing and stem-loop quantitative real-time reverse transcription-polymerase chain reaction confirmed the accuracy of the observed miRNA abundances. The 32 DEMs identified in the PM-susceptible D8 were all upregulated, whereas four of the six DEMs identified in the PM-resistant SSSL508-28 were downregulated. Using in silico and degradome sequencing approaches, 517 and 20 target genes were predicted for the D8 and SSSL508-28 DEMs, respectively. Comparison of the DEM expression profiles with the corresponding mRNA expression profiles obtained in a previous study with the same experimental design identified 60 and three target genes in D8 and SSSL508-28, respectively, which exhibited inverse expression patterns with their respective miRNAs. In particular, five DEMs were located in the substituted segment that contained two upregulated DEMs, Csa-miR172c-3p and Csa-miR395a-3p, in D8 and two downregulated DEMs, Csa-miR395d-3p and Csa-miR398b-3p, in SSSL508-28. One gene encoding L-aspartate oxidase, which was targeted by Csa-miR162a, was also located on the same segment and was specifically downregulated in PM-inoculated D8 leaves. Our results will facilitate the future use of miRNAs in breeding cucumber varieties with enhanced resistance to PM.

Molecularly tagged genes and quantitative trait loci in cucumber with recommendations for QTL nomenclature

Cucumber, Cucumis sativus L. (2n = 2x = 14), is an important vegetable crop worldwide. It was the first specialty crop with a publicly available draft genome. Its relatively small, diploid genome, short life cycle, and self-compatible mating system offers advantages for genetic studies. In recent years, significant progress has been made in molecular mapping, and identification of genes and QTL responsible for key phenotypic traits, but a systematic review of the work is lacking. Here, we conducted an extensive literature review on mutants, genes and QTL that have been molecularly mapped or characterized in cucumber. We documented 81 simply inherited trait genes or major-effect QTL that have been cloned or fine mapped. For each gene, detailed information was compiled including chromosome locations, allelic variants and associated polymorphisms, predicted functions, and diagnostic markers that could be used for marker-assisted selection in cucumber breeding. We also documented 322 QTL for 42 quantitative traits, including 109 for disease resistances against seven pathogens. By alignment of these QTL on the latest version of cucumber draft genomes, consensus QTL across multiple studies were inferred, which provided insights into heritable correlations among different traits. Through collaborative efforts among public and private cucumber researchers, we identified 130 quantitative traits and developed a set of recommendations for QTL nomenclature in cucumber. This is the first attempt to systematically summarize, analyze and inventory cucumber mutants, cloned or mapped genes and QTL, which should be a useful resource for the cucurbit research community.

Sequence Composition of Bacterial Chromosome Clones in a Transgressive Root-Knot Nematode Resistance Chromosome Region in Tetraploid Cotton

Plants evolve innate immunity including resistance genes to defend against pest and pathogen attack. Our previous studies in cotton (Gossypium spp.) revealed that one telomeric segment on chromosome (Chr) 11 in G. hirsutum cv. Acala NemX (rkn1 locus) contributed to transgressive resistance to the plant parasitic nematode Meloidogyne incognita, but the highly homologous segment on homoeologous Chr 21 had no resistance contribution. To better understand the resistance mechanism, a bacterial chromosome (BAC) library of Acala N901 (Acala NemX resistance source) was used to select, sequence, and analyze BAC clones associated with SSR markers in the complex rkn1 resistance region. Sequence alignment with the susceptible G. hirsutum cv. TM-1 genome indicated that 23 BACs mapped to TM-1-Chr11 and 18 BACs mapped to TM-1-Chr 21. Genetic and physical mapping confirmed less BAC sequence (53-84%) mapped with the TM-1 genome in the rkn1 region on Chr 11 than to the homologous region (>89%) on Chr 21. A 3.1-cM genetic distance between the rkn1 flanking markers CIR316 and CIR069 was mapped in a Pima S-7 × Acala NemX RIL population with a physical distance ∼1 Mbp in TM-1. NCBI Blast and Gene annotation indicated that both Chr 11 and Chr 21 harbor resistance gene-rich cluster regions, but more multiple homologous copies of Resistance (R) proteins and of adjacent transposable elements (TE) are present within Chr 11 than within Chr 21. (CC)-NB-LRR type R proteins were found in the rkn1 region close to CIR316, and (TIR)-NB-LRR type R proteins were identified in another resistance rich region 10 cM from CIR 316 (∼3.1 Mbp in the TM-1 genome). The identified unique insertion/deletion in NB-ARC domain, different copies of LRR domain, multiple copies or duplication of R proteins, adjacent protein kinases, or TE in the rkn1 region on Chr 11 might be major factors contributing to complex recombination and transgressive resistance.

Intraspecific Diversity in the Cold Stress Response of Transposable Elements in the Diatom Leptocylindrus aporus

Transposable elements (TEs), activated as a response to unfavorable conditions, have been proposed to contribute to the generation of genetic and phenotypic diversity in diatoms. Here we explore the transcriptome of three warm water strains of the diatom Leptocylindrus aporus, and the possible involvement of TEs in their response to changing temperature conditions. At low temperature (13 °C) several stress response proteins were overexpressed, confirming low temperature to be unfavorable for L. aporus, while TE-related transcripts of the LTR retrotransposon superfamily were the most enriched transcripts. Their expression levels, as well as most of the stress-related proteins, were found to vary significantly among strains, and even within the same strains analysed at different times. The lack of overexpression after many months of culturing suggests a possible role of physiological plasticity in response to growth under controlled laboratory conditions. While further investigation on the possible central role of TEs in the diatom stress response is warranted, the strain-specific responses and possible role of in-culture evolution draw attention to the interplay between the high intraspecific variability and the physiological plasticity of diatoms, which can both contribute to the adaptation of a species to a wide range of conditions in the marine environment.

Mildew Resistance Locus O Genes CsMLO1 and CsMLO2 Are Negative Modulators of the Cucumis sativus Defense Response to Corynespora cassiicola

Corynespora leaf spot caused by Corynespora cassiicola is one of the major diseases in cucumber (Cucumis sativus L.). However, the resistance mechanisms and signals of cucumber to C. cassiicola are unclear. Here, we report that the mildew resistance locus O (MLO) genes, CsMLO1 and CsMLO2, are both negative modulators of the cucumber defense response to C. cassiicola. Subcellular localization analysis showed that CsMLO1 and CsMLO2 are localized in the plasma membrane. Expression analysis indicated that the transcript levels of CsMLO1 and CsMLO2 are linked to the defense response to C. cassiicola. Transient overexpression of either CsMLO1 or CsMLO2 in cucumber cotyledons reduced resistance to C. cassiicola, whereas silencing of either CsMLO1 or CsMLO2 enhanced resistance to C. cassiicola. The relationships of pathogenesis-related proteins, reactive oxygen species (ROS)-associated genes, and abscisic acid (ABA)-related genes to the overexpression and silencing of CsMLO1/CsMLO2 in non-infested cucumber plants were investigated. The results indicated that CsMLO1 mediated resistance against C. cassiicola by regulating the expression of pathogenesis-related proteins and ROS-associated genes, as well as through ABA signaling pathway-associated genes. The CsMLO2-mediated resistance against C. cassiicola primarily involves regulation of the expression of pathogenesis-related proteins. Our findings will guide strategies to enhance the resistance of cucumber to corynespora leaf spot.

The rhg1-a (Rhg1 low-copy) nematode resistance source harbors a copia-family retrotransposon within the Rhg1-encoded α-SNAP gene

Soybean growers widely use the Resistance to Heterodera glycines 1 (Rhg1) locus to reduce yield losses caused by soybean cyst nematode (SCN). Rhg1 is a tandemly repeated four gene block. Two classes of SCN resistance-conferring Rhg1 haplotypes are recognized: rhg1-a ("Peking-type," low-copy number, three or fewer Rhg1 repeats) and rhg1-b ("PI 88788-type," high-copy number, four or more Rhg1 repeats). The rhg1-a and rhg1-b haplotypes encode α-SNAP (alpha-Soluble NSF Attachment Protein) variants α-SNAP Rhg1 LC and α-SNAP Rhg1 HC, respectively, with differing atypical C-terminal domains, that contribute to SCN resistance. Here we report that rhg1-a soybean accessions harbor a copia retrotransposon within their Rhg1 Glyma.18G022500 (α-SNAP-encoding) gene. We termed this retrotransposon "RAC," for Rhg1 alpha-SNAP copia. Soybean carries multiple RAC-like retrotransposon sequences. The Rhg1 RAC insertion is in the Glyma.18G022500 genes of all true rhg1-a haplotypes we tested and was not detected in any examined rhg1-b or Rhg1WT (single-copy) soybeans. RAC is an intact element residing within intron 1, anti-sense to the rhg1-a α-SNAP open reading frame. RAC has intrinsic promoter activities, but overt impacts of RAC on transgenic α-SNAP Rhg1 LC mRNA and protein abundance were not detected. From the native rhg1-a RAC+ genomic context, elevated α-SNAP Rhg1 LC protein abundance was observed in syncytium cells, as was previously observed for α-SNAP Rhg1 HC (whose rhg1-b does not carry RAC). Using a SoySNP50K SNP corresponding with RAC presence, just ~42% of USDA accessions bearing previously identified rhg1-a SoySNP50K SNP signatures harbor the RAC insertion. Subsequent analysis of several of these putative rhg1-a accessions lacking RAC revealed that none encoded α-SNAPRhg1LC, and thus, they are not rhg1-a. rhg1-a haplotypes are of rising interest, with Rhg4, for combating SCN populations that exhibit increased virulence against the widely used rhg1-b resistance. The present study reveals another unexpected structural feature of many Rhg1 loci, and a selectable feature that is predictive of rhg1-a haplotypes.

Identification and Characterization of a Potential Candidate Mlo Gene Conferring Susceptibility to Powdery Mildew in Rubber Tree

Mildew resistance locus O (Mlo) gene was first found in barley as a powdery mildew susceptibility gene, and recessive mlo alleles confer durable resistance to barley powdery mildew. To identify candidate Mlo susceptibility genes in rubber tree, HbMlo12 was cloned from rubber tree clone CATAS7-33-97, which is susceptible to powdery mildew. Protein architecture analysis showed that HbMlo12 was a typical Mlo protein with seven transmembrane domains. Protein blast search in the Arabidopsis thaliana proteome database showed that HbMlo12 shared the highest similarity with AtMlo12, with 63% sequence identity. Furthermore, HbMlo12 together with the dicot powdery mildew susceptible Mlo proteins (including AtMlo2, AtMlo6, AtMlo12, tomato SlMlo1, pepper CaMlo2, pea PsMlo1, etc.) were grouped into clade V. Subcellular localization analysis in tobacco epidermal cells revealed that HbMlo12 was localized to the endoplasmic reticulum membrane. HbMlo12 was preferentially expressed in the flower and leaf of rubber tree. Moreover, its expression was significantly upregulated in response to powdery mildew inoculation. Application of exogenous ethephon caused a distinct increase in HbMlo12 expression. Additionally, HbMlo12 transcript was quickly induced by spraying salicylic acid and gibberellic acid and reached the maximum at 0.5 h after treatments. By contrast, HbMlo12 expression was downregulated by methyl jasmonate, abscisic acid, and drought stress treatments. There was no significant change in HbMlo12 expression after indole-3-acetic acid, H₂O₂, and wounding stimuli. Taken together, these results suggested that HbMlo12 might be a candidate Mlo gene conferring susceptibility to powdery mildew in rubber tree. The results of this study are vital in understanding Mlo gene evolution and developing new rubber tree varieties with powdery mildew resistance using reverse genetics.

Non-coding RNAs and transposable elements in plant genomes: emergence, regulatory mechanisms and roles in plant development and stress responses

This review will provide evidence for the indispensable function of these elements in regulating plant development and resistance to biotic and abiotic stresses, as well as their evolutionary role in facilitating plant adaptation. Over millions of years of evolution, plant genomes have acquired a complex constitution. Plant genomes consist not only of protein coding sequences, but also contain large proportions of non-coding sequences. These include introns of protein-coding genes, and intergenic sequences such as non-coding RNA, repeat sequences and transposable elements. These non-coding sequences help to regulate gene expression, and are increasingly being recognized as playing an important role in genome organization and function. In this review, we summarize the known molecular mechanisms by which gene expression is regulated by several species of non-coding RNAs (microRNAs, long non-coding RNAs, and circular RNAs) and by transposable elements. We further discuss how these non-coding RNAs and transposable elements evolve and emerge in the genome, and the potential influence and importance of these non-coding RNAs and transposable elements in plant development and in stress responses.

Transcriptome Profile Analysis Reveals that CsTCP14 Induces Susceptibility to Foliage Diseases in Cucumber

Foliage diseases are prevalent in cucumber production and cause serious yield reduction across the world. Identifying resistance or susceptible genes under foliage-disease stress is essential for breeding resistant varieties, of which leaf-specific expressed susceptible genes are extremely important but rarely studied in crops. This study performed an in-depth mining of public transcriptome data both in different cucumber tissues and under downy mildew (DM) inoculation, and found that the expression of leaf-specific expressed transcription factor CsTCP14 was significantly increased after treatment with DM, as well as being upregulated under stress from another foliage disease, watermelon mosaic virus (WMV), in susceptible cucumbers. Furthermore, the Pearson correlation analysis identified genome-wide co-expressed defense genes with CsTCP14. A potential target CsNBS-LRR gene, Csa6M344280.1, was obtained as obviously reduced and was negatively correlated with the expression of the susceptible gene CsTCP14. Moreover, the interaction experiments of electrophoretic mobility shift assay (EMSA) and yeast one-hybrid assay (Y1H) were successfully executed to prove that CsTCP14 could transcriptionally repress the expression of the CsNBS-LRR gene, Csa6M344280.1, which resulted in inducing susceptibility to foliage diseases in cucumber. As such, we constructed a draft model showing that the leaf-specific expressed gene CsTCP14 was negatively regulating the defense gene Csa6M344280.1 to induce susceptibility to foliage diseases in cucumber. Therefore, this study explored key susceptible genes in response to foliage diseases based on a comprehensive analysis of public transcriptome data and provided an opportunity to breed new varieties that can resist foliage diseases in cucumber, as well as in other crops.

Selection of reference genes for quantitative real-time PCR analysis in cucumber (Cucumis sativus L.), pumpkin (Cucurbita moschata Duch.) and cucumber-pumpkin grafted plants

Background

Quantitative real-time PCR (qRT-PCR) is a commonly used high-throughput technique to measure mRNA transcript levels. The accuracy of this evaluation of gene expression depends on the use of optimal reference genes. Cucumber-pumpkin grafted plants, made by grafting a cucumber scion onto pumpkin rootstock, are superior to either parent plant, as grafting conveys many advantages. However, although many reliable reference genes have been identified in both cucumber and pumpkin, none have been obtained for cucumber-pumpkin grafted plants.

Methods

In this work, 12 candidate reference genes, including eight traditional genes and four novel genes identified from our transcriptome data, were selected to assess their expression stability. Their expression levels in 25 samples, including three cucumber and three pumpkin samples from different organs, and 19 cucumber-pumpkin grafted samples from different organs, conditions, and varieties, were analyzed by qRT-PCR, and the stability of their expression was assessed by the comparative ΔCt method, geNorm, NormFinder, BestKeeper, and RefFinder.

Results

The results showed that the most suitable reference gene varied dependent on the organs, conditions, and varieties. CACS and 40SRPS8 were the most stable reference genes for all samples in our research. TIP41 and CACS showed the most stable expression in different cucumber organs, TIP41 and PP2A were the optimal reference genes in pumpkin organs, and CACS and 40SRPS8 were the most stable genes in all grafted cucumber samples. However, the optimal reference gene varied under different conditions. CACS and 40SRPS8 were the best combination of genes in different organs of cucumber-pumpkin grafted plants, TUA and RPL36Aa were the most stable in the graft union under cold stress, LEA26 and ARF showed the most stable expression in the graft union during the healing process, and TIP41 and PP2A were the most stable across different varieties of cucumber-pumpkin grafted plants. The use of LEA26, ARF and LEA26+ARF as reference genes were further verified by analyzing the expression levels of csaCYCD3;1, csaRUL, cmoRUL, and cmoPIN in the graft union at different time points after grafting.

Discussion

This work is the first report of appropriate reference genes in grafted cucumber plants and provides useful information for the study of gene expression and molecular mechanisms in cucumber-pumpkin grafted plants.

Genome-wide association study revealed that the TaGW8 gene was associated with kernel size in Chinese bread wheat

Using Wheat 90 K SNP assay, kernel-related traits of Chinese bread wheat were used to perform association mapping in 14 environments by GWAS. Results indicated that 996 and 953 of 4417 and 3172 significant SNPs for kernel length and thousand-kernel weight were located on the chromosome 7B. Haplotype analysis of these SNPs on 7B generated the block containing the predicted TaGW8-B1 gene. TaGW8-B1 gene was further cloned by sequencing in bread wheat and a 276-bp InDel was found in the first intron. TaGW8-B1 without and with the 276-bp InDel were designated as TaGW8-B1a and TaGW8-B1b, respectively. Analysis of agronomic traits indicated that cultivars with TaGW8-B1a possessed significantly wider kernel width, significantly more kernel number per spike, longer kernel length, higher thousand-kernel weight and more spikelet number per spike than cultivars with TaGW8-B1b. Furthermore, cultivars with TaGW8-B1a possessed significantly higher yield than cultivars with TaGW8-B1b. Therefore, TaGW8-B1a was considered as a potentially superior allele. Meanwhile, TaGW8-B1a possessed a significantly higher expression level than TaGW8-B1b in mature seeds by qRT-PCR. It possibly suggested that the high expression of TaGW8-B1 was positively associated with kernel size in bread wheat. Distribution of TaGW8-B1 allele indicated that TaGW8-B1a has been positively selected in Chinese wheat.

A Single Nucleotide Deletion in an ABC Transporter Gene Leads to a Dwarf Phenotype in Watermelon

Dwarf habit is one of the most important traits in crop plant architecture, as it can increase plant density and improved land utilization, especially for protected cultivation, as well as increasing lodging resistance and economic yield. At least four dwarf genes have been identified in watermelon, but none of them has been cloned. In the current study, the Cldw-1 gene was primary-mapped onto watermelon chromosome 9 by next-generation sequencing-aided bulked-segregant analysis (BSA-seq) of F₂ plants derived from a cross between a normal-height line, WT4, and a dwarf line, WM102, in watermelon. The candidate region identified by BSA-seq was subsequently validated and confirmed by linkage analysis using 30 simple sequence repeat (SSR) markers in an F₂ population of 124 plants. The Cldw-1 gene was further fine-mapped by chromosome walking in a large F₂ population of 1,053 plants and was delimited into a candidate region of 107.00 kb. Six genes were predicted to be in the candidate region, and only one gene, Cla010337, was identified to have two single nucleotide polymorphisms (SNPs) and a single nucleotide deletion in the exons in the dwarf line, WM102. A derived cleaved amplified polymorphic sequence (dCAPS) marker was developed from the single nucleotide deletion, co-segregated with the dwarf trait in both the F₂ population and a germplasm collection of 165 accessions. Cla010337 encoded an ATP-binding cassette transporter (ABC transporter) protein, and the expression levels of Cla010337 were significantly reduced in all the tissues tested in the dwarf line, WM102. The results of this study will be useful in achieving a better understanding of the molecular mechanism of the dwarf plant trait in watermelon and for the development of marker-assisted selection (MAS) for new dwarf cultivars.

Complete resistance to powdery mildew and partial resistance to downy mildew in a Cucumis hystrix introgression line of cucumber were controlled by a co-localized locus

Key message A single recessive gene for complete resistance to powdery mildew and a major-effect QTL for partial resistance to downy mildew were co-localized in a Cucumis hystrix introgression line of cucumber. Downy mildew (DM) and powdery mildew (PM) are two major foliar diseases in cucumber. DM resistance (DMR) and PM resistance (PMR) may share common components; however, the genetic relationship between them remains unclear. IL52, a Cucumis hystrix introgression line of cucumber which has been reported to possess DMR, was recently identified to exhibit PMR as well. In this study, a single recessive gene pm for PMR was mapped to an approximately 468-kb region on chromosome 5 with 155 recombinant inbred lines (RILs) and 193 F₂ plants derived from the cross between a susceptible line 'changchunmici' and IL52. Interestingly, pm was co-localized with the major-effect DMR QTL dm5.2 confirmed by combining linkage analysis and BSA-seq, which was consistent with the observed linkage of DMR and PMR in IL52. Further, phenotype-genotype correlation analysis of DMR and PMR in the RILs indicated that the co-localized locus pm/dm5.2 confers complete resistance to PM and partial resistance to DM. Seven candidate genes for DMR were identified within dm5.2 by BSA-seq analysis, of which Csa5M622800.1, Csa5M622830.1 and Csa5M623490.1 were also the same candidate genes for PMR. A single nucleotide polymorphism that is present in the 3' untranslated region (3'UTR) of Csa5M622830.1 co-segregated perfectly with PMR. The GATA transcriptional factor gene Csa5M622830.1 may be a likely candidate gene for DMR and PMR. This study has provided a clear evidence for the relationship between DMR and PMR in IL52 and sheds new light on the potential value of IL52 for cucumber DMR and PMR breeding program.

Comparative genome analyses reveal sequence features reflecting distinct modes of host-adaptation between dicot and monocot powdery mildew

BACKGROUND

Powdery mildew (PM) is one of the most important and widespread plant diseases caused by biotrophic fungi. Notably, while monocot (grass) PM fungi exhibit high-level of host-specialization, many dicot PM fungi display a broad host range. To understand such distinct modes of host-adaptation, we sequenced the genomes of four dicot PM biotypes belonging to Golovinomyces cichoracearum or Oidium neolycopersici.

RESULTS

We compared genomes of the four dicot PM together with those of Blumeria graminis f.sp. hordei (both DH14 and RACE1 isolates), B. graminis f.sp. tritici, and Erysiphe necator infectious on barley, wheat and grapevine, respectively. We found that despite having a similar gene number (6620-6961), the PM genomes vary from 120 to 222 Mb in size. This high-level of genome size variation is indicative of highly differential transposon activities in the PM genomes. While the total number of genes in any given PM genome is only about half of that in the genomes of closely related ascomycete fungi, most (~ 93%) of the ascomycete core genes (ACGs) can be found in the PM genomes. Yet, 186 ACGs were found absent in at least two of the eight PM genomes, of which 35 are missing in some dicot PM biotypes, but present in the three monocot PM genomes, indicating remarkable, independent and perhaps ongoing gene loss in different PM lineages. Consistent with this, we found that only 4192 (3819 singleton) genes are shared by all the eight PM genomes, the remaining genes are lineage- or biotype-specific. Strikingly, whereas the three monocot PM genomes possess up to 661 genes encoding candidate secreted effector proteins (CSEPs) with families containing up to 38 members, all the five dicot PM fungi have only 116-175 genes encoding CSEPs with limited gene amplification.

CONCLUSIONS

Compared to monocot (grass) PM fungi, dicot PM fungi have a much smaller effectorome. This is consistent with their contrasting modes of host-adaption: while the monocot PM fungi show a high-level of host specialization, which may reflect an advanced host-pathogen arms race, the dicot PM fungi tend to practice polyphagy, which might have lessened selective pressure for escalating an with a particular host.

Genetic mapping of psl locus and quantitative trait loci for angular leaf spot resistance in cucumber (Cucumis sativus L.)

One of the most important cucumber diseases is bacterial angular leaf spot (ALS), whose increased occurrence in open-field production has been observed over the last years. To map ALS resistance genes, a recombinant inbred line (RIL) mapping population was developed from a narrow cross of cucumber line Gy14 carrying psl resistance gene and susceptible B10 line. Parental lines and RILs were tested under growth chamber conditions as well as in the field for angular leaf spot symptoms. Based on simple sequence repeat and DArTseq, genotyping a genetic map was constructed, which contained 717 loci in seven linkage groups, spanning 599.7 cM with 0.84 cM on average between markers. Monogenic inheritance of the lack of chlorotic halo around the lesions, which is typical for ALS resistance and related with the presence of recessive psl resistance gene, was confirmed. The psl locus was mapped on cucumber chromosome 5. Two major quantitative trait loci (QTL) psl5.1 and psl5.2 related to disease severity were found and located next to each other on chromosome 5; moreover, psl5.1 was co-located with psl locus. Identified QTL were validated in the field experiment. Constructed genetic map and markers linked to ALS resistance loci are novel resources that can contribute to cucumber breeding programs.

A genome-wide identification and comparative analysis of the lentil MLO genes

Powdery mildew is a widespread fungal plant disease that can cause significant losses in many crops. Some MLO genes (Mildew resistance locus O) have proved to confer a durable resistance to powdery mildew in several species. Resistance granted by the MLO gene family members has prompted an increasing interest in characterizing these genes and implementing their use in plant breeding. Lentil (Lens culinaris Medik.) is a widely grown food legume almost exclusively consumed as dry seed with an average world production of 4.5 million tons. Powdery mildew causes severe losses on certain lentil cultivars under particular environmental conditions. Data mining of the lentil CDC Redberry draft genome allowed to identify up to 15 gene sequences with homology to known MLO genes, designated as LcMLOs. Further characterization of these gene sequences and their deduced protein sequences demonstrated conformity with key MLO protein characteristics such as the presence of transmembrane and calmodulin binding domains, as well as that of other conserved motifs. Phylogenetic and other comparative analyses revealed that LcMLO1 and LcMLO3 are the most likely gene orthologs related to powdery mildew response in other species, sharing a high similarity with other known resistance genes of dicot species, such as pea PsMLO1 and Medicago truncatula MtMLO1 and MtMLO3. Sets of primers were designed as tools to PCR amplify the genomic sequences of LcMLO1 and LcMLO3, also to screen lentil germplasm in search of resistance mutants. Primers were used to obtain the complete sequences of these two genes in all of the six wild lentil relatives. Respective to each gene, all Lens sequences shared a high similarity. Likewise, we used these primers to screen a working collection of 58 cultivated and 23 wild lentil accessions in search of length polymorphisms present in these two genes. All these data widen the insights on this gene family and can be useful for breeding programs in lentil and close related species.

QTL mapping of downy and powdery mildew resistances in PI 197088 cucumber with genotyping-by-sequencing in RIL population

Host resistances in PI 197088 cucumber to downy and powdery mildew pathogens are conferred by 11 (3 with major effect) and 4 (1 major effect) QTL, respectively, and three of which are co-localized. The downy mildew (DM) and powdery mildew (PM) are the two most important foliar diseases of cucurbit crops worldwide. The cucumber accession PI 197088 exhibits high-level resistances to both pathogens. Here, we reported QTL mapping results for DM and PM resistances with 148 recombinant inbred lines from a cross between PI 197088 and the susceptible line 'Coolgreen'. Phenotypic data on responses to natural DM and PM infection were collected in multi-year and multi-location replicated field trials. A high-density genetic map with 2780 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing and 55 microsatellite markers was developed, which revealed genomic regions with segregation distortion and mis-assemblies in the '9930' cucumber draft genome. QTL analysis identified 11 and 4 QTL for DM and PM resistances accounting for more than 73.5 and 63.0% total phenotypic variance, respectively. Among the 11 DM resistance QTL, dm5.1, dm5.2, and dm5.3 were major-effect contributing QTL, whereas dm1.1, dm2.1, and dm6.2 conferred susceptibility. Of the 4 QTL for PM resistance, pm5.1 was the major-effect QTL explaining 32.4% phenotypic variance and the minor-effect QTL pm6.1 contributed to disease susceptibility. Three PM QTL, pm2.1, pm5.1, and pm6.1, were co-localized with DM QTL dm2.1, dm5.2, and dm6.1, respectively, which was consistent with the observed linkage of PM and DM resistances in PI 197088. The genetic architecture of DM resistance in PI 197088 and another resistant line WI7120 (PI 330628) was compared, and the potential of using PI 197088 in cucumber breeding for downy and powdery mildew resistances is discussed.

Transcriptome profiling of pumpkin (Cucurbita moschata Duch.) leaves infected with powdery mildew

Cucurbit powdery mildew (PM) is one of the most severe fungal diseases, but the molecular mechanisms underlying PM resistance remain largely unknown, especially in pumpkin (Cucurbita moschata Duch.). The goal of this study was to identify gene expression differences in PM-treated plants (harvested at 24 h and 48 h after inoculation) and untreated (control) plants of inbred line “112–2” using RNA sequencing (RNA-Seq). The inbred line “112–2” has been purified over 8 consecutive generations of self-pollination and shows high resistance to PM. More than 7600 transcripts were examined in pumpkin leaves, and 3129 and 3080 differentially expressed genes (DEGs) were identified in inbred line “112–2” at 24 and 48 hours post inoculation (hpi), respectively. Based on the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway database and GO (Gene Ontology) database, a complex regulatory network for PM resistance that may involve hormone signal transduction pathways, transcription factors and defense responses was revealed at the transcription level. In addition, the expression profiles of 16 selected genes were analyzed using quantitative RT-PCR. Among these genes, the transcript levels of 6 DEGs, including bHLH87 (Basic Helix-loop-helix transcription factor), ERF014 (Ethylene response factor), WRKY21 (WRKY domain), HSF (heat stress transcription factor A), MLO3 (Mildew Locus O), and SGT1 (Suppressor of G-Two Allele of Skp1), in PM-resistant “112–2” were found to be significantly up- or down-regulated both before 9 hpi and at 24 hpi or 48 hpi; this behavior differed from that observed in the PM-susceptible material (cultivar “Jiujiangjiaoding”). The transcriptome data provide novel insights into the response of Cucurbita moschata to PM stress and are expected to be highly useful for dissecting PM defense mechanisms in this major vegetable and for improving pumpkin breeding with enhanced resistance to PM.

A D-genome-originated Ty1/Copia-type retrotransposon family expanded significantly in tetraploid cottons

Retrotransposons comprise of a major fraction of higher plant genomes, and their proliferation and elimination have profound effects on genome evolution and gene functions as well. Previously we found a D-genome-originated Ty1/Copia-type LTR (DOCL) retrotransposon in the chromosome A08 of upland cotton. To further characterize the DOCL retrotransposon family, a total of 342 DOCL retrotransposons were identified in the sequenced cotton genomes, including 73, 157, and 112 from Gossypium raimondii, G. hirsutum, and G. barbadense, respectively. According to phylogenetic analysis, the DOCL family was divided into nine groups (G1-G9), among which five groups (G1-G4 and G9, including 292 members) were proliferated after the formation of tetraploid cottons. It was found that the majority of DOCL retrotransposons (especially those in G2, G3 and G9) inserted in non-allelic loci in G. hirsutum and G. barbadense, suggesting that their proliferations were relatively independent in different tetraploid cottons. Furthermore, DOCL retrotransposons inserted in coding regions largely eliminated expression of the targeted genes in G. hirsutum or G. barbadense. Our data suggested that recent proliferation of retrotransposon families like DOCL was one of important evolutionary forces driving diversification and evolution of tetraploid cottons.

Transposable Elements Direct The Coevolution between Plants and Microbes

Transposable elements are powerful drivers of genome evolution in many eukaryotes. Although they are mostly considered as 'selfish' genetic elements, increasing evidence suggests that they contribute to genetic variability; particularly under stress conditions. Over the past few years, the role of transposable elements during host-microbe interactions has been recognised. It has been proposed that many pathogenic microbes have evolved a 'two-speed' genome with regions that show increased variability and that are enriched in transposable elements and pathogenicity-related genes. Plants similarly display structured genomes with transposable-element-rich regions that mediate accelerated evolution. Immune receptor genes typically reside in such regions. Various mechanisms have recently been identified through which transposable elements contribute to the coevolution between plants and their associated microbes.

Functional characterization of cucumber (Cucumis sativus L.) Clade V MLO genes

BACKGROUND

Powdery mildew (PM) causing fungi are well-known pathogens, infecting over 10.000 plant species, including the economically important crop cucumber (Cucumis sativus L.). Loss-of-function mutations in clade V MLO genes have previously been shown to lead to recessively inherited broad-spectrum resistance to PM in several species. In cucumber, one clade V MLO homolog (CsaMLO8) was previously identified as being a susceptibility factor to PM. Two other closely related homologs (CsaMLO1 and CsaMLO11) were found, but their function was not yet unravelled.

METHODS

CsaMLO1 and CsaMLO11 were cloned from cucumber and overexpressed in a tomato mlo mutant. The transcript abundances of all three CsaMLO genes in different cucumber tissues were quantified using qRT-PCR and RNA-seq, with and without inoculation with the cucumber PM fungus Podosphaera xanthii. Allelic variation of CsaMLO1 and CsaMLO11 was screened in silico in sequenced cucumber germplasm.

RESULTS

Heterologous overexpression of all three CsaMLO genes in the tomato mlo mutant restored susceptibility to PM caused by Oidium neolycopersici, albeit to a different extent: whereas overexpression of CsaMLO1 or CsaMLO8 completely restored susceptibility, overexpression of CsaMLO11 was only partially able to restore PM susceptibility. Furthermore, it was observed by qRT-PCR and RNA-seq that CsaMLO8 was significantly higher expressed in non-inoculated cucumber compared to the other two MLO genes. However, inoculation with P. xanthii led to upregulation of CsaMLO1, but not to upregulation of CsaMLO8 or CsaMLO11.

CONCLUSIONS

Both CsaMLO1 and CsaMLO11 are functional susceptibility genes, although we conclude that based on the transcript abundance CsaMLO8 is probably the major clade V MLO gene in cucumber regarding providing susceptibility to PM. Potential loss-of-function mutations in CsaMLO1 and CsaMLO11 have not been identified. The generation and analysis of such mutants are interesting subjects for further investigation.

mlo-Based Resistance: An Apparently Universal "Weapon" to Defeat Powdery Mildew Disease

Loss-of-function mutations of one or more of the appropriate Mildew resistance locus o (Mlo) genes are an apparently reliable "weapon" to protect plants from infection by powdery mildew fungi, as they confer durable broad-spectrum resistance. Originally detected as a natural mutation in an Ethiopian barley landrace, this so-called mlo-based resistance has been successfully employed in European barley agriculture for nearly four decades. More recently, mlo-mediated resistance was discovered to be inducible in virtually every plant species of economic or scientific relevance. By now, mlo resistance has been found (as natural mutants) or generated (by induced mutagenesis, gene silencing, and targeted or nontargeted gene knock-out) in a broad range of monocotyledonous and dicotyledonous plant species. Here, we review features of mlo resistance in barley, discuss approaches to identify the appropriate Mlo gene targets to induce mlo-based resistance, and consider the issue of pleiotropic effects often associated with mlo-mediated immunity, which can harm plant yield and quality. We portray mlo-based resistance as an apparently universal and effective weapon to defeat powdery mildew disease in a multitude of plant species.

Frequency of a natural truncated allele of MdMLO19 in the germplasm of Malus domestica

Podosphaera leucotricha is the causal agent of powdery mildew (PM) in apple. To reduce the amount of fungicides required to control this pathogen, the development of resistant apple cultivars should become a priority. Resistance to PM was achieved in various crops by knocking out specific members of the MLO gene family that are responsible for PM susceptibility (S-genes). In apple, the knockdown of MdMLO19 resulted in PM resistance. However, since gene silencing technologies such as RNAi are perceived unfavorably in Europe, a different approach that exploits this type of resistance is needed. This work evaluates the presence of non-functional naturally occurring alleles of MdMLO19 in apple germplasm. The screening of the re-sequencing data of 63 apple individuals led to the identification of 627 single nucleotide polymorphisms (SNPs) in five MLO genes (MdMLO5, MdMLO7, MdMLO11, MdMLO18, and MdMLO19), 127 of which were located in exons. The T-1201 insertion of a single nucleotide in MdMLO19 caused the formation of an early stop codon, resulting in a truncated protein lacking 185 amino acids, including the calmodulin-binding domain. The presence of the insertion was evaluated in 115 individuals. It was heterozygous in 64 and homozygous in 25. Twelve of the 25 individuals carrying the insertion in homozygosity were susceptible to PM. After barley, pea, cucumber, and tomato, apple would be the fifth species for which a natural non-functional mlo allele has been found.