Novel Rosaceae plant elicitor peptides as sustainable tools to control Xanthomonas arboricola pv. pruni in Prunus spp.

Fruit crops are regarded as important health promoters and constitute a major part of global agricultural production, and Rosaceae species are of high economic impact. Their culture is threatened by bacterial diseases, whose control is based on preventative treatments using compounds of limited efficacy and negative environmental impact. One of the most economically relevant examples is the pathogen Xanthomonas arboricola pv. pruni (Xap) affecting Prunus spp. The plant immune response against pathogens can be triggered and amplified by plant elicitor peptides (Peps), perceived by specific receptors (PEPRs). Although they have been described in various angiosperms, scarce information is available on Rosaceae species. Here, we identified the Pep precursor (PROPEP), Pep and PEPR orthologues of 10 Rosaceae species and confirmed the presence of the Pep/PEPR system in this family. We showed the perception and elicitor activity of Rosaceae Peps using the Prunus–Xap pathosystem as proof‐of‐concept. Treatment with nanomolar doses of Peps induced the corresponding PROPEP and a set of defence‐related genes in Prunus leaves, and enhanced resistance against Xap. Peps from the same species had the highest efficiencies. Rosaceae Peps could potentially be used to develop natural, targeted and environmentally friendly strategies to enhance the resistance of Prunus species against biotic attackers.     

Phylogenetic analysis of morphology in Prunus reveals extensive homoplasy

Prunus is a large and economically important genus with considerable morphological variation. The evolution of vegetative and reproductive characters are examined here by parsimony reconstruction on trees obtained from data of ITS, trnL-trnF, trnS-trnG, and 25 morphological characters of 37 species of Prunus and representatives of eight other genera of Rosaceae. Prunus grayana is supported as the sister species to the rest of Prunus and the common ancestor of Prunus is reconstructed as having deciduous and serrated leaves, leafy racemes and fruit with well-developed pericarp. All diagnostic characters used in classification of the raceme-bearing species show some degree of convergent evolution and do not reflect phylogenetic relatedness. Some character states, such as evergreen foliage and entire leaf margin, are likely adaptations to environments with higher humidity and mean temperature. However, these hypotheses need to be tested by including species formerly classified in genus Pygeum, which were not available for this study. A clade consisting of subgenera Prunus, Amygdalus, Emplectocladus and section Microcerasus (formerly in subgenus Cerasus) is characterized by having axillary buds organized in groups of three, two of which give rise to flowers or inflorescences and one to a vegetative shoot. Fruits with thin pericarps are common in Prunus but they arose more than once independently. Dry fruits also evolved more than once, and only in species of Prunus living in arid environments, suggesting that this feature is another example of adaptation. Maddenia hypoleuca is nested within Prunus and the morphological characters used to segregate it from Prunus have been misinterpreted or are also found in species of Prunus previously classified in genus Pygeum.     

Phylogenetics of Eurasian plums, <Emphasis Type="Italic">Prunus</Emphasis> L. section <Emphasis Type="Italic">Prunus</Emphasis> (Rosaceae), according to coding and non-coding chloroplast DNA sequences

The genus Prunus contains the subgenus Prunus incorporating the European plums (section Prunus), the North American plums (section Prunocerasus) and the apricots (section Armeniaca). In section Prunus, there are approximately 20 species, which occur in three levels of ploidy, diploid ( 2n = 2x = 16 ) \left( {2n = 2x = 16} \right) , tetraploid ( 2n = 4x = 32 ) \left( {2n = 4x = 32} \right) and hexaploid ( 2n = 6x = 48 ) \left( {2n = 6x = 48} \right) . Despite a clear distinction between section Prunus and the other sections, phylogenetic relationships between species within the section are unclear. We performed a phylogenetic analysis on members of the section Prunus and three outgroup species using sequence data from four single-copy phylogenetically informative chloroplast DNA regions (atpB-rbcL, matK, rpl16, and trnL-trnF). After alignment, the analysed regions totalled 4,696 bp of sequence, containing 68 parsimony-informative sites and 14 parsimony-informative indels. Data were analysed using both maximum parsimony and Bayesian likelihood and phylogenetic trees were reconstructed. The analyses recovered trees with congruent topologies and similar levels of statistical support for relationships between taxa. They confirmed that species belonging to section Prunus form a monophyletic clade within Prunus. The section is resolved into four well-supported clades, which correspond to the geographical distribution of the species. The hexaploid species could not be resolved into distinct species clades but formed a well-supported group separate from the tetraploid species, highlighting the distinct evolutionary origins of the different polyploid groups. The close relationship between the hexaploids and Prunus divaricata, Prunus cerasifera and Prunus ursina indicates the former may have derived from an ancestor of P. cerasifera and its allies.     

Biotechnological approaches for improvement and conservation of Prunus species

Biotechnology has contributed to improvement and conservation of Prunus species. Biotechnological approaches involving in vitro tissue culture, genetic transformation, molecular marker development and cryopreservation were applied to various Prunus species. This report provides an overview of biotechnological research on Prunus species, with an emphasis on ornamental Prunus.     

Looking into flowering time in almond (Prunus dulcis (Mill) D. A. Webb): the candidate gene approach

Blooming time is one of the most important agronomic traits in almond. Biochemical and molecular events underlying flowering regulation must be understood before methods to stimulate late flowering can be developed. Attempts to elucidate the genetic control of this process have led to the identification of a major gene (Lb) and quantitative trait loci (QTLs) linked to observed phenotypic differences, but although this gene and these QTLs have been placed on the Prunus reference genetic map, their sequences and specific functions remain unknown. The aim of our investigation was to associate these loci with known genes using a candidate gene approach. Two almond cDNAs and eight Prunus expressed sequence tags were selected as candidate genes (CGs) since their sequences were highly identical to those of flowering regulatory genes characterized in other species. The CGs were amplified from both parental lines of the mapping population using specific primers. Sequence comparison revealed DNA polymorphisms between the parental lines, mainly of the single nucleotide type. Polymorphisms were used to develop co-dominant cleaved amplified polymorphic sequence markers or length polymorphisms based on insertion/deletion events for mapping the candidate genes on the Prunus reference map. Ten candidate genes were assigned to six linkage groups in the Prunus genome. The positions of two of these were compatible with the regions where two QTLs for blooming time were detected. One additional candidate was localized close to the position of the Evergrowing gene, which determines a non-deciduous behaviour in peach.     

Development of a new SSR-based linkage map in apricot and analysis of synteny with existing Prunus maps

Linkage maps of the apricot accessions ‘Lito’ and ‘BO 81604311’ were constructed using a total of 185 simple sequence repeat (SSR) markers sampled from those isolated in peach, almond, apricot and cherry; 74 were derived from a new apricot genomic library enriched for AG/CT microsatellite repeats (UDAp series), and in total, 98 had never been mapped in Prunus before. Eight linkage groups putatively corresponding to the eight haploid apricot chromosomes were identified for each parent. The two maps were 504 and 620 cM long, respectively, with 96 anchor markers showing a complete co-linearity between the two genomes. As few as three gaps larger than 15 cM were present in ‘Lito’ and six in the male parent; the maps align well with all the available SSR-based Prunus maps through the many common anchor loci. Only occasionally inverted positions between adjacent markers were found, and this can be explained by the small size of cross populations analysed in these Prunus maps and in those reported in literature. The newly developed apricot SSRs will help saturating the existing Prunus maps and will extend the choice of markers in the development of genetic maps for new breeding populations.     

Podosphaera pannosa (syn. Sphaerotheca pannosa) on Rosa and Prunus spp.: Characterization of Pathotypes by Differential Plant Reactions and ITS Sequences

The powdery mildew fungus Podosphaera pannosa (Wallr.: Fr.) de Bary (syn. Sphaerotheca pannosa) is a major problem on roses worldwide. Twenty‐six monoconidial isolates of Podosphaera collected on roses and Prunus spp. in Belgium, Germany, France, Denmark, Israel and The Netherlands were characterized on the basis of differential reactions on in vitro rose genotypes and Prunus avium L. and by DNA sequence analysis of the rDNA ITS (internal transcribed spacer) region. Twenty‐four isolates were determined as P. pannosa. Amongst these, different groups could be distinguished. A first group of 18 isolates was highly virulent on rose and avirulent or very weakly virulent on P. avium. A second group of four isolates was highly virulent on both rose and P. avium. Analysis of the ITS sequence could discriminate these two groups of P. pannosa strains by a one base pair difference. Finally, two isolates of powdery mildew collected on Prunus sp. could be classified as P. pannosa based on their ITS sequence, which was identical to the ITS sequence of the isolates only highly virulent on roses. However, these two isolates were not able to infect roses. These results indicate that different strains of P. pannosa exist with varying host specificity. We demonstrated by ITS sequencing and plant reactions that the host range of P. pannosa comprises roses and Prunus spp.     

<Emphasis Type="Italic">Prunus</Emphasis> microsatellite marker transferability across rosaceous crops

A total of 145 microsatellite primer pairs from Prunus DNA sequences were studied for transferability in a set of eight cultivars from nine rosaceous species (almond, peach, apricot, Japanese plum, European plum, cherry, apple, pear, and strawberry), 25 each of almond genomic, peach genomic, peach expressed sequence tags (EST), and Japanese plum genomic, 22 of almond EST, and 23 of apricot (13 EST and 10 genomic), all known to produce single-locus and polymorphic simple-sequence repeats in the species where they were developed. Most primer pairs (83.6%) amplified bands of the expected size range in other Prunus. Transferability, i.e., the proportion of microsatellites that amplified and were polymorphic, was also high in Prunus (63.9%). Almond and Japanese plum were the most variable among the diploid species (all but the hexaploid European plum) and peach the least polymorphic. Thirty-one microsatellites amplified and were polymorphic in all Prunus species studied, 12 of which, covering its whole genome, are proposed as the “universal Prunus set”. In contrast, only 16.3% were transferable in species of other Rosaceae genera (apple, pear, and strawberry). Polymorphic Prunus microsatellites also detected lower levels of variability in the non-congeneric species. No significant differences were detected in transferability and the ability to detect variability between microsatellites of EST and genomic origin.     

Recent advances and prospects in Prunus virology

The stone fruit genus Prunus, within the family Rosaceae, comprises more than 230 species, some of which have great importance or value as ornamental or fruit crops. Prunus are affected by numerous viruses and viroids linked to the vegetative propagation practices in many of the cultivated species. To date, 44 viruses and three viroids have been described in the 9 main cultivated Prunus species. Seven of these viruses and one viroid have been identified in Prunus hosts within the last 5 years. This work addresses recent advances and prospects in the study of viruses and viroids affecting Prunus species, mostly concerning the detection and characterisation of the agents involved, pathogenesis analysis and the search for new control tools. New sequencing technologies are quickly reshaping the way we can identify and characterise new plant viruses and isolates. Specific efforts aimed at virus identification or data mining of high‐throughput sequencing data generated for plant genomics‐oriented purposes can efficiently reveal the presence of known or novel viruses. These technologies have also been used to gain a deeper knowledge of the pathogenesis mechanisms at the gene and miRNA expression level that underlie the interactions between Prunus spp. and their main viruses and viroids. New biotechnological control tools include the transfer of resistance by grafting, the use of new sources of resistance and the development of gene silencing strategies using genetic transformation. In addition, the application of next generation sequencing and genome editing techniques will contribute to improving our knowledge of virus–host interactions and the mechanisms of resistance. This should be of great interest in the search to obtain new Prunus cultivars capable of dealing both with known viruses and viroids and with those that are yet to be discovered in the uncertain scenario of climate change.     

Trans-specific <Emphasis Type="Italic">S</Emphasis>-RNase and SFB alleles in <Emphasis Type="Italic">Prunus</Emphasis> self-incompatibility haplotypes

Self-incompatibility in the genus Prunus is controlled by two genes at the S-locus, S-RNase and SFB. Both genes exhibit the high polymorphism and high sequence diversity characteristic of plant self-incompatibility systems. Deduced polypeptide sequences of three myrobalan and three domestic plum S-RNases showed over 97% identity with S-RNases from other Prunus species, including almond, sweet cherry, Japanese apricot and Japanese plum. The second intron, which is generally highly polymorphic between alleles was also remarkably well conserved within these S-allele pairs. Degenerate consensus primers were developed and used to amplify and sequence the co-adapted polymorphic SFB alleles. Sequence comparisons also indicated high degrees of polypeptide sequence identity between three myrobalan and the three domestic plum SFB alleles and the corresponding Prunus SFB alleles. We discuss these trans-specific allele identities in terms of S-allele function, evolution of new allele specificities and Prunus taxonomy and speciation. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

III. Variation in plant viruses: Variation in ryegrass mosaic virus in relation to resistance

Prunus necrotic ringspot and apple mosaic viruses have been described separately but they are distantly related serologically and intermediate strains occur in hop and rose. They may therefore be regarded as type strains of two serotypic groups of a single virus (Prunus necrotic ringspot virus which was the first to be described). The host range of both serotypes is wide, mostly amongst woody plants and there have long been recurring difficulties of diagnosis based on symptoms produced in woody or herbaceous indicator plants. These problems have been overcome by the application of enzyme-linked immunosorbent assay which provides a rapid and convenient means of detecting and serotyping the various strains encountered.     

Merging Maddenia with the morphologically diverse Prunus (Rosaceae)

Maddenia (Rosaceae) has been distinguished from Prunus on the basis of its tepaloid perianth and one‐ to two‐carpellate gynoecium. These distinctive morphological traits nonetheless overlap with several Prunus spp. Maddenia has previously been shown to be nested within Prunus, more specifically within a clade containing members of subgenera Laurocerasus and Padus, but its phylogenetic position within that clade has not been defined precisely. This study clarifies the position of Maddenia within Prunus through phylogenetic analyses of nuclear ribosomal internal transcribed spacer (ITS) and plastid ndhF sequences, with an expanded sampling of tropical species of subgenus Laurocerasus and the inclusion of three Maddenia spp. The monophyly of Maddenia is supported by both the ITS and ndhF analyses, but both datasets support the inclusion of Maddenia in Prunus. All trees from the ITS analysis and some trees from the ndhF analysis also support a close alliance of Maddenia with a clade comprising temperate species of subgenera Laurocerasus and Padus. On the basis of these results, all recognized species of Maddenia are herein formally transferred to Prunus, which requires four new combinations and one new name: Prunus fujianensis (Y.T.Chang) J.Wen, comb. nov. ; Prunus himalayana J.Wen, nom. nov. ; Prunus hypoleuca (Koehne) J.Wen, comb. nov. ; Prunus hypoxantha (Koehne) J.Wen, comb. nov. ; and Prunus incisoserrata (T.T.Yü & T.C.Ku) J.Wen, comb. nov. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164 , 236–245.     

Construction of an intra-specific sweet cherry (<Emphasis Type="Italic">Prunus avium</Emphasis> L.) genetic linkage map and synteny analysis with the <Emphasis Type="Italic">Prunus</Emphasis> reference map

Linkage maps of the sweet cherry cultivar ‘Emperor Francis’ (EF) and the wild forest cherry ‘New York 54’ (NY) were constructed using primarily simple sequence repeat (SSR) markers and gene-derived markers with known positions on the Prunus reference map. The success rate for identifying SSR markers that could be placed on either the EF or NY maps was only 26% due to two factors: a reduced transferability of other Prunus-species-derived markers and a low level of polymorphism in the mapping parents. To increase marker density, we developed four cleaved amplified polymorphic sequence markers (CAPS), 19 derived CAPS markers, and four insertion–deletion markers for cherry based on 101 Prunus expressed sequence tags. In addition, four gene-derived markers representing orthologs of a tomato vacuolar invertase and fruit size gene and two sour cherry sorbitol transporters were developed. To complete the linkage analysis, 61 amplified fragment length polymorphism and seven sequence-related amplified polymorphism markers were also used for map construction. This analysis resulted in the expected eight linkage groups for both parents. The EF and NY maps were 711.1 cM and 565.8 cM, respectively, with the average distance between markers of 4.94 cM and 6.22 cM. A total of 82 shared markers between the EF and NY maps and the Prunus reference map showed that the majority of the marker orders were the same with the Prunus reference map suggesting that the cherry genome is colinear with that of the other diploid Prunus species. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Prior reproduction and weather affect berry crops in central Ontario, Canada

Populations of many perennial plants intermittently produce large seed crops—a phenomenon referred to as mast seeding or masting. Masting may be a response to spatially correlated environmental conditions (the Moran effect), an adaptive reproductive strategy reflecting economies of scale, or a consequence of the internal resource budgets of individual plants. Fruit production by endozoochorous plants representing eight genera varied synchronously over much of central Ontario, Canada, 1998–2009. We tested for effects of weather and prior reproduction on fruit production by comparing AIC_c values among regression models fit to time series of fruit production scores and partitioning contributions by different predictors to multiple R ² into independent and joint contributions. Fruit production by mountain ash (Sorbus spp.), juneberry (Amelanchier spp.), dogwoods (Cornus spp.), nannyberry (Viburnum lentago), and possibly cherries (Prunus spp.) was inversely related to production in the previous year. These effects were independent of weather conditions, suggesting that intrinsic factors such as internal resource budgets or an adaptive strategy of variable reproductive output influenced fruit production. To our knowledge, this is the first evidence of masting in members of the genera Cornus, Viburnum, and Amelanchier, and in members of Prunus and Sorbus in North America. All species produced fewer fruits when weather conditions were dry, so the Moran effect could have synchronized fruit production both within and among species. Patterns and causes of variation in berry crops have implications for ecosystem dynamics, particularly in boreal and subArctic environments where berry crops are important wildlife foods.     

Hydroxynitrile Lyases from Prunus Seeds in the Preparation of Cyanohydrins

The hydroxynitrile lyase (HNL) activity of nine defatted Prunus seeds was compared for catalyzing the addition of HCN to aromatic, heteroaromatic and α,β-unsaturated aldehydes. Although the conversion and enantiomeric excess (ee) of the corresponding cyanohydrins were both influenced by the HNL source and the chemical structure of the aldehyde, Prunus HNLs were all suitable for the enantioselective preparation of cyanohydrins.     

Microbial inoculation influences arbuscular mycorrhizal fungi community structure and nutrient dynamics in temperate tree restoration

Soil microbial communities have a profound influence on soil chemical processes and subsequently influence tree nutrition and growth. This study examined how the addition of a commercial inoculum or forest‐collected soils influenced nitrogen (N) and phosphorus (P) dynamics, soil microbial community structure, and growth in Liriodendron tulipifera and Prunus serotina tree saplings. Inoculation method was an important determinant of arbuscular mycorrhizal fungi (AMF) community structure in both species and altered soil N dynamics in Prunus and soil P dynamics in Liriodendron. Prunus saplings receiving whole forest soil transfers had a higher rhizosphere soil carbon/nitrogen ratio and ammonia content at the end of the first growing season when compared to unmanipulated control saplings. Inoculation with whole forest soil transfers resulted in increased inorganic phosphorus in Liriodendron rhizosphere soils. The number of AMF terminal restriction fragments was significantly greater in rhizosphere soils of Liriodendron saplings inoculated with whole forest soil transfers and Prunus saplings receiving either inoculum source than control saplings. Forest soil inoculation also increased AMF colonization and suppressed stem elongation in Liriodendron after 16 months; conversely, Prunus AMF colonization was unchanged and stem elongation was significantly greater when saplings were inoculated with whole forest soil transfers. Longer term monitoring of tree response to inoculation will be essential to assess whether early costs of AMF colonization may provide long‐term benefits. This study provides insight into how practitioners can use microbial inoculation to alter AMF community structure and functioning, subsequently influencing tree growth and nutrient cycling during the restoration of degraded lands.     

Two new fossil woods ofAcer and a new combination ofPrunus from the Tertiary of Japan

Two new species ofAcer fossil woods,A. momijiyamense andA. Watarianum, are described and a short review of fossil wood of this genus from the Tertiary of Japan is given. In the course of a study on three fossil wood species which have been described asAcer andAcernium from Japan, it is noticed thatAcernium iwatense Watari does not belong toAcer but toPrunus of the Rosaceae, and is therafore transferred intoPrunus asPrunus iwatense comb. nov.     

Identification of a recently active Prunus‐specific non‐autonomous Mutator element with considerable genome shaping force

Miniature inverted‐repeat transposable elements (MITEs) are known to contribute to the evolution of plants, but only limited information is available for MITEs in the Prunus genome. We identified a MITE that has been named Falling Stones, FaSt. All structural features (349‐bp size, 82‐bp terminal inverted repeats and 9‐bp target site duplications) are consistent with this MITE being a putative member of the Mutator transposase superfamily. FaSt showed a preferential accumulation in the short AT‐rich segments of the euchromatin region of the peach genome. DNA sequencing and pollination experiments have been performed to confirm that the nested insertion of FaSt into the S‐haplotype‐specific F‐box gene of apricot resulted in the breakdown of self‐incompatibility (SI). A bioinformatics‐based survey of the known Rosaceae and other genomes and a newly designed polymerase chain reaction (PCR) assay verified the Prunoideae‐specific occurrence of FaSt elements. Phylogenetic analysis suggested a recent activity of FaSt in the Prunus genome. The occurrence of a nested insertion in the apricot genome further supports the recent activity of FaSt in response to abiotic stress conditions. This study reports on a presumably active non‐autonomous Mutator element in Prunus that exhibits a major indirect genome shaping force through inducing loss‐of‐function mutation in the SI locus.     

Characterization of the <Emphasis Type="Italic">RMja</Emphasis> gene for resistance to root-knot nematodes in almond: spectrum,location, and interest for <Emphasis Type="Italic">Prunus</Emphasis> breeding

In Prunus spp., resistance genes to root-knot nematodes (RKN), Meloidogyne arenaria, Meloidogyne incognita, Meloidogyne javanica, and Meloidogyne floridensis, confer either a complete spectrum, e.g., the Ma and Rjap genes in Myrobalan and Japanese plums (subgenus Prunophora), respectively, or a more restricted spectrum, e.g., the RMia gene (M. arenaria + M. incognita) in peach (subgenus Amygdalus). We report here characterization data of the RMja gene from the almond Alnem1, another Amygdalus source. The study of its spectrum is hampered by the inability of almond to be propagated by cuttings; we overcame this problem by using F1 and BC1 crosses with previously genotyped Myrobalan plums that conferred their rooting ability to hybrids for simultaneous evaluation to different RKN. As expected from a homozygous dominant resistance, BC1 progenies of Alnem1 segregated for resistance to M. javanica but were uniformly susceptible to M. incognita and M. floridensis, demonstrating that RMja controlled M. javanica but not M. incognita nor M. floridensis. SSR markers covering the Prunus reference map placed RMja on LG7 in the same region as Ma and Rjap and thus showed its independence from the RMia gene (LG2) of the botanically closer peach. The spectrum of this gene allows the theoretical construction of interspecific rootstocks, Myrobalan plum × (almond × peach), which cumulate RMja with Ma and RMia and are protected from each of the predominant RKN affecting Prunus, i.e., M. arenaria, M. incognita, and M. javanica, by at least two genes. This pyramiding strategy should offer to rootstock material an unprecedented guarantee of durable RKN resistance.