Selection of mutants resistant to Alternaria blotch from in vitro -cultured apple shoots irradiated with X- and γ-rays

We produced mutants resistant to Alternaria blotch disease in several cultivars of apple (Malus × domestica Borkh.) by irradiation with X- or γ-rays. An efficient in vitro assay method was established using chemically-synthesized AM-toxin I of Alternaria alternata (Fr.) Keissler to screen for mutants resistant to Alternaria blotch disease. The frequency of necrotic lesions was investigated by applying various concentrations of AM-toxin I to leaf discs of the first, third, and fifth leaves from the shoot apex of several apple cultivars, including Jonathan, Fuji, Oorin, and Indo. In vitro-grown apple shoots of susceptible cultivars were then treated with various doses of X- or γ-ray irradiation. Several mutants resistant to AM-toxin I were obtained by combining the techniques for tissue culture of apple shoots with the AM-toxin I screening method. Following a repeat second screening test with AM-toxin I, mutant plants were sprayed with a spore suspension of A. alternata and found resistant to be the fungal pathogen. These mutants showed normal phenotypic appearance, and so far, no difference has been observed between the original plants and mutants except for the susceptibility to Alternaria blotch.     

Identification of candidate genes at the <Emphasis Type="Italic">Dp-fl</Emphasis> locus conferring resistance against the rosy apple aphid <Emphasis Type="Italic">Dysaphis plantaginea</Emphasis>

The cultivated apple is susceptible to several pests including the rosy apple aphid (RAA; Dysaphis plantaginea Passerini), control of which is mainly based on chemical treatments. A few cases of resistance to aphids have been described in apple germplasm resources, laying the basis for the development of new resistant cultivars by breeding. The cultivar ‘Florina’ is resistant to RAA, and recently, the Dp-fl locus responsible for its resistance was mapped on linkage group 8 of the apple genome. In this paper, a chromosome walking approach was performed by using a ‘Florina’ bacterial artificial chromosome (BAC) library. The walking started from the available tightly linked molecular markers flanking the resistance region. Various walking steps were performed in order to identify the minimum tiling path of BAC clones covering the Dp-fl region from both the “resistant” and “susceptible” chromosomes of ‘Florina’. A genomic region of about 279 Kb encompassing the Dp-fl resistance locus was fully sequenced by the PacBio technology. Through the development of new polymorphic markers, the mapping interval around the resistance locus was narrowed down to a physical region of 95 Kb. The annotation of this sequence resulted in the identification of four candidate genes putatively involved in the RAA resistance response.     

Rapid location of Glomerella leaf spot resistance gene locus in apple by whole genome re-sequencing

Glomerella leaf spot (GLS) is a new fungal disease of apple that damages apple leaves mainly during the summer in China. For efficient GLS-resistant apple breeding by marker-assisted selection (MAS) and a better understanding of the molecular mechanisms of the resistance, it is important to find molecular markers that are tightly linked to GLS resistance genes and construct fine mapping. However, the development and selection of DNA markers are time-consuming and labor-intensive processes. Next-generation sequencing technology provides a powerful tool to overcome this limitation and is faster and more efficient in establishing the association of GLS resistance with molecular markers or searching for candidate genes. In this study, we report a method for rapid location of a GLS resistance gene locus (R _gls ) in apple by whole genome re-sequencing technology coupled with bulked segregant analysis (BSA). A total of 3,399,950 single nucleotide polymorphisms (SNPs) were identified. Through the genome-wide comparison of SNP profiles between the resistant and the susceptible bulks constructed from F₁ individuals derived from a cross between “Golden Delicious” and “Fuji,” the R _gls locus was identified on apple chromosome 15 between 2 and 5 Mb. In this region, eight SNP markers were validated using high resolution melting (HRM), and the fine genetic mapping of the eight markers was constructed. The R _gls locus was sandwiched by two flanking markers SNP4208 and SNP4257, with the recombination frequency of 0.97% (2/207). The marker SNP4236 co-segregated with R _gls . The physical size of the R _gls locus was estimated to be 49 kb. In this genetic interval, nine genes were predicted. Our study provides an effective method for rapid identification of genomic regions and development of the diagnostic markers for MAS. This strategy is potentially useful for other agronomic traits or plant species.     

Interactions of Apple and the Alternaria alternata Apple Pathotype

Apple is one of the most cultivated tree fruits worldwide, and is susceptible to many diseases. Understanding the interactions between the host and pathogen is critical in implementing disease management strategies and developing resistant cultivars. This review provides an update on the interactions of apple with Alternaria alternata apple pathotype, which causes Alternaria blotch, with a brief history about the discovery of the disease and pathogen and its damage and epidemiology. The focus of the review is placed on the physiological and genetic response of the host to pathogen infection, including resistance and susceptibility, and the molecular markers associated with them. Of the response of the pathogen to the host, the emphasis is placed on the role of the selective toxins on pathogenicity and their genetic controls and regulations. The review ends with a perspective on future directions in the research on the apple-A. alternata pathosystem in the era of genomics and post genomics, particularly on how to identify candidate genes from both host and pathogen for potential genetic engineering for disease resistant cultivars.     

Laboratory tests carried out onMicrothrix inconspicuella [Lep.: Pyralidae], a biological control agent forEmex australis in Australia

Host specificity tests of the moth,Microthrix inconspicuella Ragonot in Australia, indicated that larvae could feed and develop on young apple leaves. Additional tests in South Africa on leaves and fruit of the 4 apple varieties, Jonathan, Starking (Red Delicious), Granny Smith and Golden Delicious, showed that apples were not a preferred food. Little feeding occurred and pupation happened infrequently. No 2^nd generation resulted whenM. inconspicuella colonies were confined on apple fruit or leaves.      

Effect of storage conditions on virulence of Fusarium avenaceum and Alternaria alternata on apple fruits

To overcome difficulty in phytopathogenic fungi control during storage of apple fruits, the effect of different storage conditions on the occurrence and development of Fusarium avenaceum and Alternaria alternata infections on apple cultivar “Cripps Pink” was investigated during and after storage. Inhibitory effects of wild oregano essential oil on apple fruit rots caused by F. avenaceum and A. alternata were also tested as possible rot control measure. Artificially inoculated apple fruits were kept in cold storage with normal (NA) and controlled (CA) atmosphere for 95 days and at room temperature only. The obtained results indicated that different storage conditions significantly affect necrosis development on apple fruits caused by F. avenaceum and A. alternata after storage, as well as during shelf life.     

Expression of an endochitinase gene from <Emphasis Type="Italic">Trichoderma virens</Emphasis> confers enhanced tolerance to <Emphasis Type="Italic">Alternaria</Emphasis> blight in transgenic <Emphasis Type="Italic">Brassica juncea</Emphasis> (L.) czern and coss lines

An endochitinase gene ‘ech42’ from the biocontrol fungus ‘Trichoderma virens’ was introduced to Brassica juncea (L). Czern and Coss via Agrobaterium tumefaciens mediated genetic transformation method. Integration and expression of the ‘ech42’ gene in transgenic lines were confirmed by PCR, RT-PCR and Southern hybridization. Transgenic lines (T₁) showed expected 3:1 Mendelian segregation ratio when segregation analysis for inheritance of transgene ‘hpt’ was carried out. Fluorimetric analysis of transgenic lines (T₀ and T₁) showed 7 fold higher endochitinase activity than the non-transformed plant. Fluorimetric zymogram showed presence of endochitinase (42 kDa) in crude protein extract of transgenic lines. In detached leaf bioassay with fungi Alternaria brassicae and Alternaria brassicicola, transgenic lines (T₀ and T₁) showed delayed onset of lesions as well as 30–73 % reduction in infected leaf area compared to non-transformed plant.     

Proteome Analysis of Pathogen-Responsive Proteins from Apple Leaves Induced by the Alternaria Blotch Alternaria alternata

Understanding the defence mechanisms used by apple leaves against Alternaria alternate pathogen infection is important for breeding purposes. To investigate the ultrastructural differences between leaf tissues of susceptible and resistant seedlings, in vitro inoculation assays and transmission electron microscopy (TEM) analysis were conducted with two different inoculation assays. The results indicated that the resistant leaves may have certain antifungal activity against A. alternate that is lacking in susceptible leaves. To elucidate the two different host responses to A. alternate infection in apples, the proteomes of susceptible and resistant apple leaves that had or had not been infected with pathogen were characterised using two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionisation time-of-flight tandem mass spectrometry (MALDI-TOF-TOF MS). MS identified 43 differentially expressed proteins in two different inoculation assays. The known proteins were categorised into 5 classes, among these proteins, some pathogenesis-related (PR) proteins, such as beta-1,3-glucanase, ascorbate peroxidase (APX), glutathione peroxidase (GPX) and mal d1, were identified in susceptible and resistant hosts and were associated with disease resistance of the apple host. In addition, the different levels of mal d1 in susceptible and resistant hosts may contribute to the outstanding anti-disease properties of resistant leaves against A. alternate. Taken together, the resistance mechanisms of the apple host against A. alternate may be a result of the PR proteins and other defence-related proteins. Given the complexity of the biology involved in the interaction between apple leaves and the A. alternate pathogen, further investigation will yield more valuable insights into the molecular mechanisms of suppression of the A. alternate pathogen. Overall, we outline several novel insights into the response of apple leaves to pathogen attacks. These findings increase our knowledge of pathogen resistance mechanisms, and the data will also promote further investigation into the regulation of the expression of these target proteins.     

Growth inhibition effect of pyroligneous acid on pathogenic fungus,<Emphasis Type="Italic">Alternaria mali</Emphasis>, the agent of Alternaria blotch of apple

We investigated the growth inhibition effect of pyroligneous acid on the pathogenic fungus,Alternaria mali, which is known to be the agent of Alternaria blotch of apple plants. Chemical control ofA. mali could be achieved through the use of agrochemical fungicides, while the substitute for agrochemical control is gradually increasing. It was observed that pyroligneous acid exhibited antifungal activity against some plant pathogenic fungi. More specifically, the growth ofA. mali was completely inhibited in pyroligneous acid at a dilution of 1∶32. When its antifungal activity was compared to that of polyoxin B, which is used for the chemical control of Alternaria blotch of apple, it was observed that the antifungal activity of pyroligneous acid diluted at 1∶32 corresponded to 2.0 mg/mL of polyoxin B. Consequently, it is concluded that the diluted pyroligneous acid can substitute for polyoxin B, thereby reducing the use of the agrochemical for the control of Alternaria blotch of apple.     

Identification of a leucine-rich repeat receptor-like serine/threonine-protein kinase as a candidate gene for <Emphasis Type="Italic">Rvi12 (Vb)</Emphasis>-based apple scab resistance

Apple scab caused by Venturia inaequalis is the most important fungal disease of apples (Malus × domestica). Currently, the disease is controlled by up to 15 fungicide applications to the crop per year. Resistant apple cultivars will help promote the sustainable control of scab in commercial orchards. The breakdown of the Rvi6 (Vf) major-gene based resistance, the most used resistance gene in apple breeding, prompted the identification and characterization of new scab resistance genes. By using a large segregating population, the Rvi12 scab resistance gene was previously mapped to a genetic location flanked by molecular markers SNP_23.599 and SNP_24.482. Starting from these markers, utilizing chromosome walking of a Hansen’s baccata #2 (HB2) BAC-library; a single BAC clone spanning the Rvi12 interval was identified. Following Pacific Biosciences (PacBio) RS II sequencing and the use of the hierarchical genome assembly process (HGAP) assembly of the BAC clone sequence, the Rvi12 resistance locus was localized to a 62.3-kb genomic region. Gene prediction and in silico characterization identified a single candidate resistance gene. The gene, named here as Rvi12_Cd5, belongs to the LRR receptor-like serine/threonine-protein kinase family. In silico comparison of the resistance allele from HB2 and the susceptible allele from Golden Delicious (GD) identified the presence of an additional intron in the HB2 allele. Conserved domain analysis identified the presence of four additional LRR motifs in the susceptible allele compared to the resistance allele. The constitutive expression of Rvi12_Cd5 in HB2, together with its structural similarity to known resistance genes, makes it the most likely candidate for Rvi12 scab resistance in apple.     

Characterization of Small RNAs and Their Targets from <Emphasis Type="Italic">Fusarium oxysporum</Emphasis> Infected and Noninfected Cotton Root Tissues

Genes for host-plant resistant do exist in cotton (Gossypium spp.) but improvement of cotton cultivars with resistance is difficult due to intensive breeding. Identifying molecular-genetic mechanisms associated with disease resistance can offer a new way to combat a serious threat such as Fusarium oxysporum f. sp. vasinfectum (FOV). Here, we captured and annotated “top-layer” of abundantly and specifically expressed cotton root small RNA (sRNA) including microRNA (miR) sequences during FOV pathogenesis using size-directed and adenylated linker-based sRNA cloning strategy. A total of 4116 candidate sRNA sequences with 16 to 30 nucleotide (nt) length were identified from four complementary DNA (cDNA) libraries of noninfected and FOV race 3-infected roots of susceptible (“11970”) versus resistant (“Mebane B-1”) cotton genotypes (G. hirsutum L.). The highest numbers of sRNA signatures were those with 19–24 nt long in all libraries, and interestingly, the number of sRNAs substantially increased during FOV infection in a resistant genotype, while it sharply decreased in a susceptible genotype. In BLAST analysis, more than 73 % of sRNAs matched Gossypium (G. arboretum L., G. hirsutum, and G. barbadense L.) ESTs. A small percentage of sRNAs matched A. thaliana (1.68 %), T. cacao (1.26 %), fungal (2 %), and other organism (21.33 %) ESTs. mirBase comparisons showed that 4 % of sRNAs were homologous to previously reported plant miRs, among which we predicted novel cotton Ghr-miR-160 that was not registered in the cotton miR database. These major representative sRNA signatures targeted proteins associated with the key biological processes and molecular functions, explaining the molecular mechanisms of the host defense response during the FOV pathogenesis in cotton.     

苹果炭疽叶枯病菌致病力分析及苹果种质抗病性鉴定

苹果炭疽叶枯病是由胶孢炭疽菌(Colletotrichum gloeosporioides)引起的一种真菌病害,现已上升为世界苹果生产中的主要病害之一。了解不同来源的苹果炭疽叶枯病菌致病力差异及明确苹果种质资源对苹果炭疽叶枯病的抗性,对品种选育、品种合理布局以及控制病害的流行具有重要的参考价值。本研究对不同来源的79株病原菌进行了室内致病力测定,获知该菌致病力差异明显,其中强致病力菌株所占比例大。同时,本研究也对327份苹果种质资源进行了室内抗病性鉴定,其中高抗资源160份,中抗资源6份,中感资源22份,高感资源139份。表明我国现保存的苹果种质资源中存在丰富抗病种质。进一步按苹果分类系统分析发现,抗病资源在当前栽培的主要品种群中均有分布,特别是红玉品种群、富士品种群抗病资源最为丰富。     

Genome-wide identification of <Emphasis Type="Italic">SERK</Emphasis> genes in apple and analyses of their role in stress responses and growth

Background

Somatic embryogenesis receptor-like kinases (SERKs) are leucine-rich repeat receptor-like kinases associated with various signaling pathways. These kinases have a relationship with stress signals, and they are also believed to be important for regulating plant growth. However, information about this protein family in apple is limited.

Results

Twelve apple SERK genes distributed across eight chromosomes were identified. These genes clustered into three distinct groups in a phylogenetic analysis. All of the encoded proteins contained typical SERK domains. The chromosomal locations, gene/protein structures, synteny, promoter sequences, protein–protein interactions, and physicochemical characteristics of MdSERK genes were analyzed. Bioinformatics analyses demonstrated that gene duplications have likely contributed to the expansion and evolution of SERK genes in the apple genome. Six homologs of SERK genes were identified between apple and Arabidopsis. Quantitative real-time PCR analyses revealed that the MdSERK genes showed different expression patterns in various tissues. Eight MdSERK genes were responsive to stress signals, such as methyl jasmonate, salicylic acid, abscisic acid, and salt (NaCl). The application of exogenous brassinosteroid and auxin increased the growth and endogenous hormone contents of Malus hupehensis seedlings. The expression levels of seven MdSERK genes were significantly upregulated by brassinosteroid and auxin. In addition, several MdSERK genes showed higher expression levels in standard trees of ‘Nagafu 2’ (CF)/CF than in dwarf trees of CF/‘Malling 9’ (M.9), and in CF than in the spur-type bud mutation “Yanfu 6” (YF).

Conclusion

This study represents the first comprehensive investigation of the apple SERK gene family. These data indicate that apple SERKs may function in adaptation to adverse environmental conditions and may also play roles in controlling apple tree growth.

     

Cloning and characterization of a cyclic peptide synthetase gene from Alternaria alternata apple pathotype whose product is involved in AM-toxin synthesis and pathogenicity

Afternaria afternata apple pathotype causes Alternaria blotch of susceptible apple cultivars through the production of a cyclic peptide host-specific toxin, AM-toxin. PCR (polymerase chain reaction), with primers designed to conserved domains of peptide synthetase genes, amplified several products from A. alternata apple pathotype that showed high similarity to other fungal peptide synthetases and were specific to the apple pathotype. Screening of a Lambda Zap genomic library with these PCR-generated probes identified overlapping clones containing a complete cyclic peptide synthetase gene of 13.1 kb in length with no introns. Disruption of this gene, designated AM-toxin synthetase (AMT), by transformation of wild-type A. afternata apple pathotype with disruption vectors resulted in toxin-minus mutants, which were also unable to cause disease symptoms on susceptible apple cultivars. AM-toxin synthetase is therefore a primary determinant of virulence and specificity in the A. alternata apple pathotype/apple interaction.