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The bacterial pathogen Erwinia amylovora causes fire blight on rosaceous plants, including apples and their wild relatives. The pathogen uses the type III secretion pathogenicity island to inject effector proteins, such as Eop1, into host plants, leading to disease phenotypes in susceptible genotypes. In contrast, resistant genotypes exhibit quantitative resistance associated with genomic regions and/or R-gene-mediated qualitative resistance to withstand the pathogen. In Malus, strong resistance is observed in some wild species accessions, for example, in Malus xarnoldiana accession MAL0004. The resistance locus FB_Mar12, previously identified on linkage group 12 (LG12) of MAL0004, is one of two gene loci in Malus proven to withstand highly virulent North American strains of E. amylovora. This suggests the influence of a major gene, with a few candidate genes proposed within the FB_Mar12 region. In this report, we provide evidence that this gene locus is completely broken down by a mutant strain of the E. amylovora effector protein Eop1 (Δeop1) following artificial shoot inoculations of an ‘Idared’ × MAL0004 F1 progeny set, indicating a gene-for-gene interaction. Interestingly, Δeop1 does not overcome the resistance of the FB_Mar12 donor MAL0004 itself, but only the QTL on LG12, an indication that other resistance factors, possibly QTLs/genes are contributing to the fire blight resistance of MAL0004.

ABBA (Apple, Bee, Bacteria, Antagonists) onFire (Fire Blight) is a three-year internal consortium project at the Julius Kühn Institute (JKI), in which six JKI institutes are involved. In this project, an innovative treatment approach based on natural tailocin-producing bacteria is being investigated to combat the fire blight pathogen Erwinia amylovora in organic pome fruit cultivation. In addition to effectiveness, the project also assesses potential impacts on non-target organisms and the environment. The project aims to verify the benefits of microbial genomic mining, through a proof-of-concept using the pathogen Erwinia amylovora. The objective is to search for natural antagonists against this plant pathogenic bacterium in organic farming and thus to develop a practical, specific control concept. The overall aim of the project is to develop an approach that can also be transferred to other harmful bacteria and be used for prophylactic treatments in organic farming.

Sour cherry (Prunus cerasus L.) is an important allotetraploid cherry species that evolved in the Caspian Sea and Black Sea regions from a hybridization of the tetraploid ground cherry (Prunus fruticosa Pall.) and an unreduced pollen of the diploid sweet cherry (P. avium L.) ancestor. Details of when and where the evolution of this species occurred are unclear, as well as the effect of hybridization on the genome structure. To gain insight, the genome of the sour cherry cultivar ‘Schattenmorelle’ was sequenced using Illumina NovaSeqTM and Oxford Nanopore long-read technologies, resulting in a ~629-Mbp pseudomolecule reference genome. The genome could be separated into two subgenomes, with subgenome PceS_a originating from P. avium and subgenome PceS_f originating from P. fruticosa. The genome also showed size reduction compared to ancestral species and traces of homoeologous sequence exchanges throughout. Comparative analysis confirmed that the genome of sour cherry is segmental allotetraploid and evolved very recently in the past.

Mendels Einfluss auf die moderne Obstzüchtung ist unverkennbar. Die von ihm aufgestellten Vererbungsregeln haben es Züchtern ermöglicht, Kreuzungsprogramme gezielt zu designen, Vorhersagen über den möglichen Erfolg zu treffen und die Selektion von Nachkommen mit verbesserten Merkmalskombinationen mithilfe molekulargenetischer Marker kostengünstig und effizient zu gestalten. Am Beispiel des Apfels und der Süßkirsche als Vertreter für Kern- und Steinobst werden ausgewählte mendelnde Merkmale vorgestellt, die von besonderer Bedeutung für die Züchtung sind. Darüber hinaus wird der derzeitige Stand an molekularen Markern und genetischen Karten bei diesen Kulturen präsentiert. Sie beeinflussen die Effizienz in der Obstzüchtung enorm. Ihre Entwicklung wäre jedoch ohne Mendels Erkenntnisse nicht möglich gewesen. Beim Apfel, der bedeutendsten einheimischen Obstart, gibt es eine Vielzahl von wirtschaftlich inte­ressanten mendelnden Merkmalen. Einige von ihnen, wie der Säulenwuchs, die rote Fruchtfleischfarbe, das Kältebedürfnis zum Brechen der Winterknospenruhe, die Samenlosigkeit der Früchte sowie gefüllte Blüten für den Anbau als Ziergehölz und die Resistenz gegenüber Schorf und Mehltau sind phänotypisch einfach zu erfassen. Eine Selektion auf der Basis des Phänotyps ist bei diesen Merkmalen meist problemlos möglich, wenngleich sie mithilfe molekularer Marker noch effektiver gestaltet werden kann. Andere Merkmale, wie die Resistenz gegenüber Insekten, verschiedenen Lagerkrankheiten oder der bakteriellen Feuerbrandkrankheit sind nicht so einfach anhand des Phänotyps zu bestimmen. Hier sind für eine erfolgreiche Züchtung molekulare Marker unabdingbar. Das gilt auch für die rote Färbung der Fruchtschale. Bei Süßkirschen ist die Situation sehr ähnlich. Zu den mendelnden Merkmalen mit ökonomischer Bedeutung gehören hier neben der Selbstfertilität auch die Mehltauresistenz und die ­Farbe der Fruchtschale.

With the ongoing cost decrease of genotyping and sequencing technologies, accurate and fast phenotyping remains the bottleneck in the utilizing of plant genetic resources for breeding and breeding research. Although cost-efficient high-throughput phenotyping platforms are emerging for specific traits and/or species, manual phenotyping is still widely used and is a time- and money-consuming step. Approaches that improve data recording, processing or handling are pivotal steps towards the efficient use of genetic resources and are demanded by the research community. Therefore, we developed PhenoApp, an open-source Android app for tablets and smartphones to facilitate the digital recording of phenotypical data in the field and in greenhouses. It is a versatile tool that offers the possibility to fully customize the descriptors/scales for any possible scenario, also in accordance with international information standards such as MIAPPE (Minimum Information About a Plant Phenotyping Experiment) and FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. Furthermore, PhenoApp enables the use of pre-integrated ready-to-use BBCH (Biologische Bundesanstalt für Land- und Forstwirtschaft, Bundessortenamt und CHemische Industrie) scales for apple, cereals, grapevine, maize, potato, rapeseed and rice. Additional BBCH scales can easily be added. The simple and adaptable structure of input and output files enables an easy data handling by either spreadsheet software or even the integration in the workflow of laboratory information management systems (LIMS). PhenoApp is therefore a decisive contribution to increase efficiency of digital data acquisition in genebank management but also contributes to breeding and breeding research by accelerating the labour intensive and time-consuming acquisition of phenotyping data.

Abstract Objective The proposed candidate gene underlying the Malus fusca fire blight resistance locus on chromosome 10 was previously predicted to possess 880 amino acids and 8 exons. Eight base pair (8 bp) insertion/deletion in the first exon potentially distinguished resistant genotypes from susceptible ones. This study aimed at analyzing the candidate gene sequence in another set of original resistant and susceptible progeny, characterizing the sequence in a transgenic line transformed with the candidate gene under its own native promoter, as well as deciphering the potential genomic differences between this candidate gene and its homolog in the ‘Golden Delicious’ doubled haploid genome (GDDH13). Results Sequences of amplicons of part of the candidate gene amplified in two progenies that showed resistant and susceptible fire blight phenotypes, confirmed the 8 bp insertion that distinguishes susceptible and resistant progenies. The transgenic line was positive for the candidate gene sequence, confirming a successful transfer into the background of apple cultivar ‘Pinova’, and possessed the same genomic sequence as the progeny with a resistant phenotype. Sequence analysis showed that the homolog gene on GDDH13 possesses a significant 18 bp deletion in exon 1 leading to a difference of 15 amino acid from the protein sequence of the candidate gene.

Abstract Most of the commercial apple cultivars are highly susceptible to fire blight, which is the most devastating bacterial disease affecting pome fruits. Resistance to fire blight is described especially in wild Malus accessions such as M. × robusta 5 (Mr5), but the molecular basis of host resistance response to the pathogen Erwinia amylovora is still largely unknown. The bacterial effector protein AvrRpt2EA was found to be the key determinant of resistance response in Mr5. A wild type E. amylovora strain and the corresponding avrRpt2 EA deletion mutant were used for inoculation of Mr5 to induce resistance or susceptible response, respectively. By comparison of the transcriptome of both responses, 211 differentially expressed genes (DEGs) were identified. We found that heat-shock response including heat-shock proteins (HSPs) and heat-shock transcription factors (HSFs) are activated in apple specifically in the susceptible response, independent of AvrRpt2 EA . Further analysis on the expression progress of 81 DEGs by high-throughput real-time qPCR resulted in the identification of genes that were activated after inoculation with E. amylovora. Hence, a potential role of these genes in the resistance to the pathogen is postulated, including genes coding for enzymes involved in formation of flavonoids and terpenoids, ribosome-inactivating enzymes (RIPs) and a squamosa promoter binding-like (SPL) transcription factor.

Winter dormancy – a period of low metabolic activity and no visible growth – appears as an adaptation to harsh winter conditions and can be divided into different phases. It is tightly controlled by environmental cues, with ambient temperature playing a major role. During endodormancy, a cultivar-specific amount of cold needs to be perceived, and during ecodormancy, heat hours accumulate before bud burst and anthesis in spring. Expression analysis, performed in several key fruit tree species, proved to be very useful in elucidating the molecular control of onset and release of dormancy. However, the time resolution of these experiments has been limited. Therefore, in this study, dense time-series expression analysis was conducted for 40 candidate genes involved in dormancy control, under the cool-temperate climate conditions in Dresden. Samples were taken from the cultivars ‘Pinova’ and ‘Gala,’ which differ in flowering time. The set of candidate genes included well-established dormancy genes such as DAM genes, MdFLC-like, MdICE1, MdPRE 1, and MdPIF4. Furthermore, we tested genes from dormancy-associated pathways including the brassinosteroid, gibberellic acid, abscisic acid (ABA), cytokinin response, and respiratory stress pathways. The expression patterns of well-established dormancy genes were confirmed and could be associated with specific dormancy phases. In addition, less well-known transcription factors and genes of the ABA signaling pathway showed associations with dormancy progression. The three ABA signaling genes HAB1_chr15, HAI3, and ABF2 showed a local minimum of gene expression in proximity of the endodormancy to ecodormancy transition. The number of sampling points allowed us to correlate expression values with temperature data, which revealed significant correlations of ambient temperature with the expression of the Malus domestica genes MdICE1, MdPIF4, MdFLC-like, HAB1chr15, and the type-B cytokinin response regulator BRR9. Interestingly, the slope of the linear correlation of temperature with the expression of MdPIF4 differed between cultivars. Whether the strength of inducibility of MdPIF4 expression by low temperature differs between the ‘Pinova’ and ‘Gala’ alleles needs to be tested further.

Abstract Background Although the most common path of infection for fire blight, a severe bacterial disease on apple, is via host plant flowers, quantitative trait loci (QTLs) for fire blight resistance to date have exclusively been mapped following shoot inoculation. It is not known whether the same mechanism underlies flower and shoot resistance. Results We report the detection of a fire blight resistance QTL following independent artificial inoculation of flowers and shoots on two F1 segregating populations derived from crossing resistant Malus ×robusta 5 (Mr5) with susceptible ‘Idared’ and ‘Royal Gala’ in experimental orchards in Germany and New Zealand, respectively. QTL mapping of phenotypic datasets from artificial flower inoculation of the ‘Idared’ × Mr5 population with Erwinia amylovora over several years, and of the ‘Royal Gala’ × Mr5 population in a single year, revealed a single major QTL controlling floral fire blight resistance on linkage group 3 (LG3) of Mr5. This QTL corresponds to the QTL on LG3 reported previously for the ‘Idared’ × Mr5 and an ‘M9’ × Mr5 population following shoot inoculation in the glasshouse. Interval mapping of phenotypic data from shoot inoculations of subsets from both flower resistance populations re-confirmed that the resistance QTL is in the same position on LG3 of Mr5 as that for flower inoculation. These results provide strong evidence that fire blight resistance in Mr5 is controlled by a major QTL on LG3, independently of the mode of infection, rootstock and environment. Conclusions This study demonstrates for the first time that resistance to fire blight caused by Erwinia amylovora is independent of the mode of inoculation at least in Malus ×robusta 5.

Malus ×arnoldiana accession MAL0004 has been found to be resistant to moderately and highly virulent strains of the fire blight causal pathogen – the Gram-negative bacterium, Erwinia amylovora. Genetic analyses with an F1 segregating population derived from crossing the highly susceptible apple cultivar ‘Idared’ and MAL0004 led to the detection and mapping of the fire blight resistance locus of M. ×arnoldiana to linkage group (LG)12 (FB_Mar12). FB_Mar12 mapped at the distal end of LG12 below the apple SSR Hi07f01 in an interval of approximately 6 cM (Centimorgan), where both the fire blight resistance loci of M. floribunda 821 and ‘Evereste’ were located. We fine mapped the region containing FB_Mar12 using 892 progenies. Mining of the region of interest (ROI) on the ‘Golden Delicious’ doubled haploid genome (GDDH13) identified the presence of 2.3 Mb (megabases) in the homologous region. Of 40 primer pairs designed within this region, 20 were polymorphic and nine were mapped, leading to the identification of 24 significant recombinant individuals whose phenotypes were informative in determining the precise position of the locus within a 0.57 cM interval. Analyses of tightly linked marker sequences on the M. baccata draft genome revealed scaffolds of interest putatively harboring the resistance loci of M. ×arnoldiana, a hybrid between M. baccata and M. floribunda. Open reading frame (ORF) analyses led to the prediction of first fire blight resistance candidate genes with serine/threonine kinase and leucine-rich repeat domains, including homologs of previously identified ‘Evereste’ candidate genes. We discuss the implications of these results on breeding for resistance to fire blight.

Genomics: New resources for apple and pear breeding A Europe-led effort to bridge the gap between genomics and breeding offers a new resource to support apple and peach production. A team led by François Laurens from the Research Institute in Horticulture and Seeds (IRHS) in Angers, France, review the tools, methodologies and scientific discoveries made through FruitBreedomics, a project that ran between 2011 and 2015 and involved 28 different research and private companies from around the world. These new molecular and bioinformatics tools include DNA arrays for mapping genetic diversity, computer software for analyzing genetic information and novel methods for understanding commercially important traits such as fruit quality and resistance to stresses. The project’s materials should help apple and peach producers better plan their breeding programs so as to meet grower and consumer demand for high-quality fruit with desired characteristics.

The bacterium, Erwinia amylovora, deposits effector proteins such as AvrRpt2EA into hosts through the type III secretion pathogenicity island to cause fire blight in susceptible Malus genotypes. A single nucleotide polymorphism in the AvrRpt2EA effector plays a key role in pathogen virulence on Malus hosts by exchanging one cysteine to serine in the effector protein sequence. Fire blight resistance quantitative trait loci (QTLs) were detected in a few apple cultivars and wild Malus genotypes with the resistance of wild apples generally found to be stronger than their domestic relatives. The only candidate and functionally analyzed fire blight resistance genes proposed are from wild apple genotypes. Nevertheless, the aforementioned AvrRpt2EA SNP and a couple of effector mutants of E. amylovora are responsible for the breakdown of resistance from a few Malus donors including detected QTLs and underlying R-genes. This review summarizes a key finding related to the molecular basis underpinning an aspect of virulence of E. amylovora on Malus genotypes, as well as mechanisms of host recognition and specificity, and their implications on the results of genetic mapping and phenotypic studies within the last 5–6 years. Although the knowledge gained has improved our understanding of the Malus–E. amylovora system, more research is required to fully grasp the resistance mechanisms in this genus especially as they pertain to direct interactions with pathogen effectors.

A set of 680 apple cultivars from the Fruit Gene bank in Dresden Pillnitz was evaluated for the incidence of powdery mildew and scab in two consecutive years. The incidence of both scab and powdery mildew increased significantly in the second year. Sixty and 43 cultivars with very low incidence in both years of scab and powdery mildew, respectively, were analysed with molecular markers linked to known resistance genes. Thirty-five cultivars were identified to express alleles or combinations of alleles linked to Rvi2, Rvi4, Rvi6, Rvi13, Rvi14, or Rvi17. Twenty of them, modern as well as a few traditional cultivars known before the introduction or Rvi6 from Malus floribunda 821, amplified the 159 bp fragment of marker CH_Vf1 that is linked to Rvi6. Alleles linked to Pl1, Pld, or Plm were expressed from five cultivars resistant to powdery mildew. Eleven cultivars were identified to have very low susceptibility to both powdery mildew and scab. The information on resistance/susceptibility of fruit genetic resources towards economically important diseases is important for breeding and for replanting traditional cultivars. Furthermore, our work provides a well-defined basis for the discovery of undescribed, new scab, and powdery mildew resistance.

Black and red raspberries (Rubus occidentalis L. and Rubus idaeus L.) are the prominent members of the genus Rubus (Rosaceae family). Breeding programs coupled with the low costs of high-throughput sequencing have led to a reservoir of data that have improved our understanding of various characteristics of Rubus and facilitated the mapping of different traits. Gene B controls the waxy bloom, a clearly visible epicuticular wax on canes. The potential effects of this trait on resistance/susceptibility to cane diseases in conjunction with other morphological factors are not fully studied. Previous studies suggested that gene H, which controls cane pubescence, is closely associated with gene B. Here, we used tunable genotyping-by-sequencing technology to identify the de novo SNPs of R. occidentalis and R. idaeus using an interspecific population that segregates for the waxy bloom phenotype. We created linkage maps of both species and mapped the identified SNPs to the seven chromosomes (Ro01–Ro07) of Rubus. Importantly, we report, for the first time, the mapping of gene B to chromosome 2 of R. occidentalis using a genetic map consisting of 443 markers spanning 479.76 cM. We observed the poor transferability of R. idaeus SSRs to R. occidentalis and discrepancies in their previously reported chromosome locations.

This study investigated the impact of constitutively expressed Trichoderma atroviride genes encoding exochitinase nag70 or endochitinase ech42 in transgenic lines of the apple cultivar Pinova on the symbiosis with arbuscular mycorrhizal fungi (AMF). We compared the exo- and endochitinase activities of leaves and roots from non-transgenic Pinova and the transgenic lines T386 and T389. Local and systemic effects were examined using own-rooted trees and trees grafted onto rootstock M9. Scab susceptibility was also assessed in own-rooted and grafted trees. AMF root colonization was assessed microscopically in the roots of apple trees cultivated in pots with artificial substrate and inoculated with the AMF Glomus intraradices and Glomus mosseae. Own-rooted transgenic lines had significantly higher chitinase activities in their leaves and roots compared to non-transgenic Pinova. Both of the own-rooted transgenic lines showed significantly fewer symptoms of scab infection as well as significantly lower root colonization by AMF. Biomass production was significantly reduced in both own-rooted transgenic lines. Rootstock M9 influenced chitinase activities in the leaves of grafted scions. When grafted onto M9, the leaf chitinase activities of non-transgenic Pinova (M9/Pinova) and transgenic lines (M9/T386 and M9/T389) were not as different as when grown on their own roots. M9/T386 and M9/T389 were only temporarily less infected by scab than M9/Pinova. M9/T386 and M9/T389 did not differ significantly from M9/Pinova in their root chitinase activities, AMF root colonization and biomass.

Für die vergleichende Kartierung von Feuerbrandresistenz bei Malus wurden vier Populationen bearbeitet, die als einen Elter einen Donor für Feuerbrandresistenz und als zweiten Elter die anfällige Sorte ‘Idared’ hatten. Als Donoren für Widerstandsfähigkeit wurden definierte Abstammungen der Wildarten M. baccata, M. fusca, M. ×robusta und die widerstandsfähige Pillnitzer Apfelsorte ‘Rewena’ genutzt. Die Phänotypisierung der Populationen erfolgte in unterschiedlichen Jahren durch Inokulation von vege­tativen Trieben mit dem Erwinia amylovora-Isolat Ea222 und anderen definierten Isolaten unter Gewächshaus­bedingungen. Der Befall der Triebe wurde als Befallsrate, dem Verhältnis der befallenen Trieblänge zur Gesamt­trieblänge, ermittelt. Je nach Isolat und Population va­riierte die durchschnittliche Befallsrate zwischen 10 bis 82%. Die Genotypisierung der Nachkommen zur Erstellung genetischer Karten erfolgte mit Mikrosatelliten-, SNP- und DArT-Markern. Die genetischen Kopplungs­karten wurden mittels Joinmap 4.0 und die Resistenz gegenüber Feuerbrand mit MapQTL5.0 kartiert. Major-QTLs konnten für M. ×robusta auf Kopplungsgruppe 3, für M. baccata auf Kopplungsgruppe 12 und für M. fusca auf Kopplungsgruppe 10 detektiert werden. Während die Feuerbrand-QTLs von M. ×robusta 5 und M. fusca je nach Jahr bis zu ca. 87% der phänotypischen Varianz erklären können, erklärt der QTL von M. baccata nur ca. 45%, was die Existenz eines zweiten QTL nahe legt. Für die resistente Sorte ‘Rewena’ konnte kein QTL detektiert werden. Mit den Markern, die im Bereich der detektierten QTLs liegen, kann auf Resistenz gegenüber Feuerbrand selektiert werden. Damit ist eine Kombinierung unterschiedlicher Feuerbrandresistenz-QTLs möglich. Auf dieser Basis können zukünftig Sorten gezüchtet werden, die dauerhaft widerstandsfähig gegenüber Feuerbrand sind, um diese dann dem deutschen Obstbau zur Verfügung stellen zu können. DOI: 10.5073/JfK.2014.12.02, https://doi.org/10.5073/JfK.2014.12.02

With the ongoing cost decrease of genotyping and sequencing technologies, accurate and fast phenotyping remains the bottleneck in the utilizing of plant genetic resources for breeding and breeding research. Although cost-efficient high-throughput phenotyping platforms are emerging for specific traits and/or species, manual phenotyping is still widely used and is a time- and money-consuming step. Approaches that improve data recording, processing or handling are pivotal steps towards the efficient use of genetic resources and are demanded by the research community. Therefore, we developed PhenoApp, an open-source Android app for tablets and smartphones to facilitate the digital recording of phenotypical data in the field and in greenhouses. It is a versatile tool that offers the possibility to fully customize the descriptors/scales for any possible scenario, also in accordance with international information standards such as MIAPPE (Minimum Information About a Plant Phenotyping Experiment) and FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. Furthermore, PhenoApp enables the use of pre-integrated ready-to-use BBCH (Biologische Bundesanstalt für Land- und Forstwirtschaft, Bundessortenamt und CHemische Industrie) scales for apple, cereals, grapevine, maize, potato, rapeseed and rice. Additional BBCH scales can easily be added. The simple and adaptable structure of input and output files enables an easy data handling by either spreadsheet software or even the integration in the workflow of laboratory information management systems (LIMS). PhenoApp is therefore a decisive contribution to increase efficiency of digital data acquisition in genebank management but also contributes to breeding and breeding research by accelerating the labour intensive and time-consuming acquisition of phenotyping data.

With the ongoing cost decrease of genotyping and sequencing technologies, accurate and fast phenotyping remains the bottleneck in the utilizing of plant genetic resources for breeding and breeding research. Although cost-efficient high-throughput phenotyping platforms are emerging for specific traits and/or species, manual phenotyping is still widely used and is a time- and money-consuming step. Approaches that improve data recording, processing or handling are pivotal steps towards the efficient use of genetic resources and are demanded by the research community. Therefore, we developed PhenoApp, an open-source Android app for tablets and smartphones to facilitate the digital recording of phenotypical data in the field and in greenhouses. It is a versatile tool that offers the possibility to fully customize the descriptors/scales for any possible scenario, also in accordance with international information standards such as MIAPPE (Minimum Information About a Plant Phenotyping Experiment) and FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. Furthermore, PhenoApp enables the use of pre-integrated ready-to-use BBCH (Biologische Bundesanstalt für Land- und Forstwirtschaft, Bundessortenamt und CHemische Industrie) scales for apple, cereals, grapevine, maize, potato, rapeseed and rice. Additional BBCH scales can easily be added. The simple and adaptable structure of input and output files enables an easy data handling by either spreadsheet software or even the integration in the workflow of laboratory information management systems (LIMS). PhenoApp is therefore a decisive contribution to increase efficiency of digital data acquisition in genebank management but also contributes to breeding and breeding research by accelerating the labour intensive and time-consuming acquisition of phenotyping data.