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The European Commission requested the EFSA Panel on Plant Health to prepare and deliver risk assessments for commodities listed in Commission Implementing Regulation (EU) 2018/2019 as 'High‐risk plants, plant products and other objects'. This Scientific Opinion covers plant health risks posed by defoliated 1‐ or 2‐year old bare root plants for planting (grafted or not) of 12 Prunus species (Prunus armeniaca, P. avium, P. canescens, P. cerasifera, P. cerasus, P. davidiana, P. domestica, P. dulcis, P. fontanesiana, P. persica, P. salicina, P. tomentosa) imported from Moldova, taking into account the available scientific information, including the technical information provided by the applicant country. The evaluation identified three EU‐quarantine pests, Erwinia amylovora (protected zone quarantine pest), Xiphinema rivesi non‐EU populations and Xanthomonas arboricola pv. pruni (protected zone quarantine pest), which were selected for further evaluation, based on defined criteria, including their presence in the applicant country. It should be noted that there is uncertainty regarding whether all relevant pests have been identified due to a limited number of scientific publications and pest surveys in Moldova. For the three selected pests, the risk mitigation measures proposed in the technical dossier from Moldova were evaluated taking into account the possible limiting factors. For these pests, an expert judgement is given on the likelihood of pest freedom taking into consideration the risk mitigation measures acting on it, including uncertainties associated with the assessment. The degree of pest freedom varies among the pests evaluated, with Erwinia amylovora being the pest most frequently expected on the imported plants. The Expert Knowledge Elicitation indicated, with 95% certainty, that between 9823 and 10,000 bundles (comprising 10–20 plants per bundle) out of 10,000 bundles would be free from E. amylovora. [ABSTRACT FROM AUTHOR]

Abstract The European Commission requested the EFSA Panel on Plant Health to prepare and deliver risk assessments for commodities listed in Commission Implementing Regulation (EU) 2018/2019 as ‘High‐risk plants, plant products and other objects’. This Scientific Opinion covers plant health risks posed by defoliated 1‐ or 2‐year old bare root plants for planting (grafted or not) of 12 Prunus species (Prunus armeniaca, P. avium, P. canescens, P. cerasifera, P. cerasus, P. davidiana, P. domestica, P. dulcis, P. fontanesiana, P. persica, P. salicina, P. tomentosa) imported from Moldova, taking into account the available scientific information, including the technical information provided by the applicant country. The evaluation identified three EU‐quarantine pests, Erwinia amylovora (protected zone quarantine pest), Xiphinema rivesi non‐EU populations and Xanthomonas arboricola pv. pruni (protected zone quarantine pest), which were selected for further evaluation, based on defined criteria, including their presence in the applicant country. It should be noted that there is uncertainty regarding whether all relevant pests have been identified due to a limited number of scientific publications and pest surveys in Moldova. For the three selected pests, the risk mitigation measures proposed in the technical dossier from Moldova were evaluated taking into account the possible limiting factors. For these pests, an expert judgement is given on the likelihood of pest freedom taking into consideration the risk mitigation measures acting on it, including uncertainties associated with the assessment. The degree of pest freedom varies among the pests evaluated, with Erwinia amylovora being the pest most frequently expected on the imported plants. The Expert Knowledge Elicitation indicated, with 95% certainty, that between 9823 and 10,000 bundles (comprising 10–20 plants per bundle) out of 10,000 bundles would be free from E. amylovora.

Self-incompatibility in Prunus species is governed by a single locus consisting of two highly multi-allelic and tightly linked genes, one coding for an F-box protein—i.e., SFB in Prunus- controlling the pollen specificity and one coding for an S-RNase gene controlling the pistil specificity. Genotyping the allelic combination in a fruit tree species is an essential procedure both for cross-based breeding and for establishing pollination requirements. Gel-based PCR techniques using primer pairs designed from conserved regions and spanning polymorphic intronic regions are traditionally used for this task. However, with the great advance of massive sequencing techniques and the lowering of sequencing costs, new genotyping-by-sequencing procedures are emerging. The alignment of resequenced individuals to reference genomes, commonly used for polymorphism detection, yields little or no coverage in the S-locus region due to high polymorphism between different alleles within the same species, and cannot be used for this purpose. Using the available sequences of Japanese plum S-loci concatenated in a rosary-like structure as synthetic reference sequence, we describe a procedure to accurately genotype resequenced individuals that allowed the analysis of the S-genotype in 88 Japanese plum cultivars, 74 of them are reported for the first time. In addition to unraveling two new S-alleles from published reference genomes, we identified at least two S-alleles in 74 cultivars. According to their S-allele composition, they were assigned to 22 incompatibility groups, including nine new incompatibility groups reported here for the first time (XXVII-XXXV). [ABSTRACT FROM AUTHOR]

• Contrasting and heritable proanthocyanidin profiles (catechin or epicatechin-predominant) of Chinese plum cultivars '98–99' and 'Angeleno' were confirmed throughout fruit development. • Transcription of a previously unreported MYB transcription factor (PsaMYB700) was strongly correlated with the flavan-3-ol profile and expression of PsaLAR and PsaANR biosynthetic genes. • PsaMYB700 transcription does not require the presence of a bHLH3 co-regulator. • PsabZIP5 activates the promoters of PsaMYBPA1, PsaMYB7 , and PsaMYB700 in Chinese plum Chinese plum fruits are rich in phenolic compounds from the flavan-3-ol family, including (+)-catechin and (-)-epicatechin, widely associated with sensory attributes such as bitterness and astringency, beneficial for human health, and involved in enzymatic browning. Leucoanthocyanidin reductase (LAR) and anthocyanidin reductase (ANR) enzymes catalyze (+)-catechin and (-)-epicatechin biosynthesis, respectively. It has been described that genes encoding for LAR and ANR are transcriptionally regulated by transcription factors belonging to MYB, bHLH, and bZIP families. In this study, we examined two Chinese plum cultivars ('98–99' and 'Angeleno') with different flavan-3-ol profiles to characterize MYB transcription factors involved in malus the accumulation of (+)-catechin and (-)-epicatechin in fruits. We observed that fruits of '98–99' accumulate a higher content of (+)-catechin than (-)-epicatechin, while 'Angeleno' displays an opposite profile. We identified PsaMYBPA1, PsaMYB7, and a MYB transcription factor not previously described in the literature, which we named PsaMYB700. The expression of PsaMYB700 was up to 10-fold higher in '98–99' than 'Angeleno' at the earliest fruit developmental stage. Promoter activation assays indicated that PsaMYBPA1 activates the flavan-3-ol-related genes LAR, anthocyanidin synthase (ANS), and ANR , while PsaMYB7 and PsaMYB700 activate LAR and ANS. In contrast to PsaMYBPA1 and PsaMYB7, PsaMYB700 displays high activation levels without the presence of a bHLH co-regulator. Further, the expression levels of PsaMY700 positively correlate with the higher (+)-catechin accumulation in fruits of '98–99,' compared with 'Angeleno.' Finally, we detected a PsabZIP5 with similar expression levels between cultivars, which activates the promoters of PsaMYBPA1, PsaMYB7 , and PsaMYB700. This study elucidates the roles of PsaMYBPA1, PsaMYB7, PsaMYB700 and PsabZIP5 in flavan-3-ol biosynthesis, highlighting a hierarchy of transcriptional regulation of these compounds. [ABSTRACT FROM AUTHOR]

The physiology of Prunus fruit ripening is a complex and not completely understood process. To improve this knowledge, postharvest behavior during the shelf-life period at the transcriptomic level has been studied using high-throughput sequencing analysis (RNA-Seq). Monitoring of fruits has been analyzed after different ethylene regulator treatments, including 1-MCP (ethylene-inhibitor) and Ethrel (ethylene-precursor) in two contrasting selected apricot (Prunus armeniaca L.) and Japanese plum (P. salicina L.) cultivars, 'Goldrich' and 'Santa Rosa'. KEEG and protein–protein interaction network analysis unveiled that the most significant metabolic pathways involved in the ripening process were photosynthesis and plant hormone signal transduction. In addition, previously discovered genes linked to fruit ripening, such as pectinesterase or auxin-responsive protein, have been confirmed as the main genes involved in this process. Genes encoding pectinesterase in the pentose and glucuronate interconversions pathway were the most overexpressed in both species, being upregulated by Ethrel. On the other hand, auxin-responsive protein IAA and aquaporin PIP were both upregulated by 1-MCP in 'Goldrich' and 'Santa Rosa', respectively. Results also showed the upregulation of chitinase and glutaredoxin 3 after Ethrel treatment in 'Goldrich' and 'Santa Rosa', respectively, while photosystem I subunit V psaG (photosynthesis) was upregulated after 1-MCP in both species. Furthermore, the overexpression of genes encoding GDP-L-galactose and ferredoxin in the ascorbate and aldarate metabolism and photosynthesis pathways caused by 1-MCP favored antioxidant activity and therefore slowed down the fruit senescence process. [ABSTRACT FROM AUTHOR]

The main objective of many fruit-breeding programs around the world is the release of new cultivars from interspecific hybridizations between species of the Prunus genus. Plum × apricot (Prunus salicina Lindl. × Prunus armeniaca L.) are the most widespread interspecific hybrids, which include plumcots, pluots, and apriums. In this work, 115 accessions of interspecific hybrids from different origins and 27 reference genotypes of apricot and other diploid plum species were analyzed using eight simple sequence repeat (SSR) markers to assess the population structure and current genetic diversity. A total of 149 alleles were obtained, with an average of 19 alleles per locus. The overall polymorphic information content (PIC) mean value of SSR markers was 0.81, indicating a high degree of polymorphism of the SSR. The genetic analysis revealed 141 unique genotypes and two synonyms. The unweighted pair group method with arithmetic averages (UPGMA) dendrogram and the population structure with five groups inferred through the discriminant analysis of principal components (DAPC) revealed a clear genetic differentiation between apricot genotypes and the rest of the accessions since the interspecific hybrids clustered with the Japanese plum genotypes. Repeated backcrosses between interspecific hybrids with plum genotypes could be the cause of the higher genetic proximity of the hybrids with respect to plum than with apricot genotypes. This corresponds to the fruit morphology and agronomic behavior observed in most interspecific hybrids, which also resemble plums more than apricots. [ABSTRACT FROM AUTHOR]

• Cross-compatibility in interspecific hybridization depends on the parental forms. • 'Trumlar' and D17–73 allow obtaining hybrids with apricot or myrobalan plum. • Myrobalan plum 'Amelia' is useful for obtaining myrobalan plum × apricot hybrids. • Seed germination and viability of hybrid seedlings depend on the parental forms. • Efficiency of hybridization between Japanese plum, apricot and myrobalan plum is low. In 2014–2018, a study was conducted on the interspecific cross-compatibility between various fruit-tree genotypes of three species of the genus Prunus : the Japanese plum (P. salicina Lindl) – 6 genotypes, the myrobalan plum (P. cerasifera Ehrh.) – 1 genotype, and the apricot (P. armeniaca L.) – 8 genotypes, and 1 hybrid between the Japanese plum and the myrobalan plum. It was found that incompatibility between the crossed genotypes manifests itself at various stages of hybridization – from flower pollination and fruit setting to the growth of the hybrid seedlings obtained. In the interspecific hybridization Japanese plum × apricot, fruit setting is more dependent on the Japanese plum genotype as the maternal form than on the apricot genotype as the pollen donor. Post-zygotic crossability barriers have the effect that a large number of obtained fruit contain an underdeveloped seed. Seed germination capacity and viability of the obtained hybrid seedlings depend on the interaction of the crossed parental forms. The Japanese plums 'Trumlar' and D 17–73 are useful maternal forms for obtaining hybrid seedlings of Japanese plum × apricot as well as Japanese plum × myrobalan plum. The use of the myrobalan plum 'Amelia' as the maternal parent allows obtaining hybrid seedlings of myrobalan plum × apricot. The results showed that by using these genotypes in traditional distant hybridization it is possible to obtain more hybrids of Japanese plum × apricot, Japanese plum × myrobalan plum, and also myrobalan plum × apricot than by using the other genotypes tested in the study. [ABSTRACT FROM AUTHOR]

In this study, the influence of a chitosan-based coating was assessed on qualitative traits and non-enzymatic and enzymatic antioxidant systems in Prunus salicina, 'Black Golden' Japanese Plum, during 35 days of cold storage followed by 3 days at 24 °C to evaluate its shelf life. Chitosan coating delayed the physico-chemical traits such as the total soluble solids, titratable acidity, firmness and skin color associated with the plum ripening process during cold storage and shelf life. Furthermore, the highest bioactive compounds' content and antioxidant activity in the coated plum were registered during the stored period. Chitosan-based coating enhanced the activities of superoxide dismutase and ascorbate peroxidase during cold storage and shelf-life. Moreover, this edible coating contributes to reducing membrane damages with lower lipoxygenase activity and, consequently, malondialdehyde accumulation. A multivariate statistical analysis approach identified the two key components, correlated to all analyzed traits, that influenced the changes within chitosan coated and uncoated Japanese plums during storage. Chitosan coating is a cheap and eco-friendly tool to delay ripening process and to improve the antioxidant systems and storability of the 'Black Golden' Japanese plum. [ABSTRACT FROM AUTHOR]

This study included twenty-three samples of minor fruit species and twenty-three plum cultivars. First of all, the pomological properties of the plum cultivars were assessed, where the cultivar 'Aphrodite' was determined as the cultivar with the biggest fruits (56.6 g). The selected nutritional properties were subsequently determined in all forty-six samples. The highest value of the total soluble solids in the plums was 27.3 % in 'Stanley' (Prunus domestica) and 26.1 % in 'Krasavica' (Sorbus aucuparia) in the minor fruits; the highest total content of ascorbic acid in the plums was 83.3 mg/100 g in 'Stanley' (P. domestica) and 622.9 mg/100 g in 'Krasavica' (S. aucuparia) in the minor fruits; the highest total phenolic content in the plums was 429.8 mg GAE/100 g in 'Fortune' (Prunus salicina) and 45.3 mg GAE/100 g in the minor fruits and 983.9 mg GAE/100 g in 'Vydubecký' (Cornus mas); the highest total flavonoid content in the plums was 291.5 mg CE/100 g in 'Fortune' (P. salicina) and 544.7 mg CE/100 g in 'Nero' (Sorbus melanocarpa) in the minor fruits, and the highest total antioxidant activity in the plums was 809.5 mg TE/100 g in the hybrid 'SLE2014/2' (P. domestica × P. salicina) and 849.8 mg TE/100 g in 'Amfora' (Lonicera edulis) in the minor fruits.

• 1-MCP delays apricot and plum softening, inducing hypomethylation in apricots. • Ethylene related treatments induce distinct DNA methylation patterns in both species. • Starch and sucrose metabolism displayed the highest number of methylated genes. • CoA-related genes HMG and 4CL displayed inverse expression-methylation in apricot. • PME in pentose and glucuronate pathway displayed inverse expression-methylation in plum. Apricot (Prunus armeniaca L.) and Japanese plum (Prunus salicina L.) are two of the most important stone fruit species, and their climacteric nature is a major determinant in terms of fruit shelf-life period. The role of the main genes involved in the ripening process of these species has been extensively studied, however there is a need to expand our molecular knowledge at epigenetic level. To achieve this, postharvest monitoring of 'Goldrich' apricots and 'Santa Rosa' Japanese plums after 1-MCP (ethylene inhibitor) and Ethrel (ethylene precursor) treatments was carried out to delve deep into the epigenetic level using Whole Genome Bisulfite Sequencing (WGBS). Results showed over 12,000 and 9,000 genes with differentially methylated regions (DMRs) in 'Goldrich' and 'Santa Rosa' cultivars respectively. 1-MCP-treated apricot 'Goldrich' exhibited more hypomethylated regions, suggesting lower methylation levels compared to Ethrel treatment. While starch and sucrose metabolism exhibited the greatest number of partially methylated genes, other pathways showcased more significant differences. Thus, 4-coumarate-CoA ligase in phenylpropanoid biosynthesis, DELLA protein in hormone signal transduction, GDP-L-fucose synthase in amino sugar metabolism, D-lactate dehydratase in pyruvate metabolism, and hydroxymethylglutaryl-CoA reductase in 'Goldrich', as well as homocysteine S-methyltransferase in the cysteine and methionine metabolism, 1-phosphatidylinositol-4-phosphate 5-kinase in the inositol phosphate metabolism, pectinesterase in the pentose and glucuronate interconversions, malate dehydrogenase in the carbon metabolism, photosystem I subunit VI in photosynthesis, and aquaporin-4 as a membrane transporter in Japanese plum showed inverse gene expression-methylation patterns. These findings reveal variations in epigenetic regulation during fruit ripening in apricot and plum, influenced by ethylene modulating treatments, suggesting significant role of DNA methylation in this process. [ABSTRACT FROM AUTHOR]

The red to blue hue of plant organs is caused due to anthocyanins, which are water-soluble flavonoid pigments. The accumulation of these pigments is regulated by a complex of R2R3-MYB transcription factors (TFs), basic-helix-loop-helix (bHLH), and WD-repeat (WDR) proteins (MBW complex). In Rosaceae species, R2R3-MYBs, particularly MYB10 genes, are responsible for part of the natural variation in anthocyanin colors. Japanese plum cultivars, which are hybrids of Prunus salicina, have high variability in the color hue and pattern, going from yellow-green to red and purple-blue, probably as a result of the interspecific hybridization origin of the crop. Because of such variability, Japanese plum can be considered as an excellent model to study the color determination in Rosaceae fruit tree species. Here, we cloned and characterized the alleles of the PsMYB10 genes in the linkage group LG3 region where quantitative trait loci (QTLs) for the organ color have been mapped to other Prunus species. Allele segregation in biparental populations as well as in a panel of varieties, combined with the whole-genome sequence of two varieties with contrasting fruit color, allowed the organization of the MYB10 alleles into haplotypes. With the help of this strategy, alleles were assigned to genes and at least three copies of PsMYB10.1 were identified in some varieties. In total, we observed six haplotypes, which were able to characterize 91.36% of the cultivars. In addition, two alleles of PsMYB10.1 were found to be highly associated with anthocyanin and anthocyanin-less skin. Their expression during the fruit development confirms their role in the fruit skin coloration. Here, we provide a highly efficient molecular marker for the early selection of colored or non-colored fruits in Japanese plum breeding programs.

The red to blue hue of plant organs is caused due to anthocyanins, which are water-soluble flavonoid pigments. The accumulation of these pigments is regulated by a complex of R2R3-MYB transcription factors (TFs), basic-helix-loop-helix (bHLH), and WD-repeat (WDR) proteins (MBW complex). In Rosaceae species, R2R3-MYBs, particularly MYB10 genes, are responsible for part of the natural variation in anthocyanin colors. Japanese plum cultivars, which are hybrids of Prunus salicina , have high variability in the color hue and pattern, going from yellow-green to red and purple-blue, probably as a result of the interspecific hybridization origin of the crop. Because of such variability, Japanese plum can be considered as an excellent model to study the color determination in Rosaceae fruit tree species. Here, we cloned and characterized the alleles of the PsMYB10 genes in the linkage group LG3 region where quantitative trait loci (QTLs) for the organ color have been mapped to other Prunus species. Allele segregation in biparental populations as well as in a panel of varieties, combined with the whole-genome sequence of two varieties with contrasting fruit color, allowed the organization of the MYB10 alleles into haplotypes. With the help of this strategy, alleles were assigned to genes and at least three copies of PsMYB10.1 were identified in some varieties. In total, we observed six haplotypes, which were able to characterize 91.36% of the cultivars. In addition, two alleles of PsMYB10.1 were found to be highly associated with anthocyanin and anthocyanin-less skin. Their expression during the fruit development confirms their role in the fruit skin coloration. Here, we provide a highly efficient molecular marker for the early selection of colored or non-colored fruits in Japanese plum breeding programs. [ABSTRACT FROM AUTHOR]

The main objective of many fruit-breeding programs around the world is the release of new cultivars from interspecific hybridizations between species of the Prunus genus. Plum × apricot (Prunus salicina Lindl. × Prunus armeniaca L.) are the most widespread interspecific hybrids, which include plumcots, pluots, and apriums. In this work, 115 accessions of interspecific hybrids from different origins and 27 reference genotypes of apricot and other diploid plum species were analyzed using eight simple sequence repeat (SSR) markers to assess the population structure and current genetic diversity. A total of 149 alleles were obtained, with an average of 19 alleles per locus. The overall polymorphic information content (PIC) mean value of SSR markers was 0.81, indicating a high degree of polymorphism of the SSR. The genetic analysis revealed 141 unique genotypes and two synonyms. The unweighted pair group method with arithmetic averages (UPGMA) dendrogram and the population structure with five groups inferred through the discriminant analysis of principal components (DAPC) revealed a clear genetic differentiation between apricot genotypes and the rest of the accessions since the interspecific hybrids clustered with the Japanese plum genotypes. Repeated backcrosses between interspecific hybrids with plum genotypes could be the cause of the higher genetic proximity of the hybrids with respect to plum than with apricot genotypes. This corresponds to the fruit morphology and agronomic behavior observed in most interspecific hybrids, which also resemble plums more than apricots.

In this study, the influence of a chitosan-based coating was assessed on qualitative traits and non-enzymatic and enzymatic antioxidant systems in Prunus salicina, ‘Black Golden’ Japanese Plum, during 35 days of cold storage followed by 3 days at 24 °C to evaluate its shelf life. Chitosan coating delayed the physico-chemical traits such as the total soluble solids, titratable acidity, firmness and skin color associated with the plum ripening process during cold storage and shelf life. Furthermore, the highest bioactive compounds’ content and antioxidant activity in the coated plum were registered during the stored period. Chitosan-based coating enhanced the activities of superoxide dismutase and ascorbate peroxidase during cold storage and shelf-life. Moreover, this edible coating contributes to reducing membrane damages with lower lipoxygenase activity and, consequently, malondialdehyde accumulation. A multivariate statistical analysis approach identified the two key components, correlated to all analyzed traits, that influenced the changes within chitosan coated and uncoated Japanese plums during storage. Chitosan coating is a cheap and eco-friendly tool to delay ripening process and to improve the antioxidant systems and storability of the ‘Black Golden’ Japanese plum.

This study included twenty-three samples of minor fruit species and twenty-three plum cultivars. First of all, the pomological properties of the plum cultivars were assessed, where the cultivar 'Aphrodite' was determined as the cultivar with the biggest fruits (56.6 g). The selected nutritional properties were subsequently determined in all forty-six samples. The highest value of the total soluble solids in the plums was 27.3% in 'Stanley' (Prunus domestica) and 26.1% in 'Krasavica' (Sorbus aucuparia) in the minor fruits; the highest total content of ascorbic acid in the plums was 83.3 mg/100 g in 'Stanley' (P. domestica) and 622.9 mg/100 g in 'Krasavica' (S. aucuparia) in the minor fruits; the highest total phenolic content in the plums was 429.8 mg GAE/100 g in 'Fortune' (Prunus salicina) and 45.3 mg GAE/100 g in the minor fruits and 983.9 mg GAE/100 g in 'Vydubecký' (Cornus mas); the highest total flavonoid content in the plums was 291.5 mg CE/100 g in 'Fortune' (P. salicina) and 544.7 mg CE/100 g in 'Nero' (Sorbus melanocarpa) in the minor fruits, and the highest total antioxidant activity in the plums was 809.5 mg TE/100 g in the hybrid 'SLE2014/2' (P. domestica × P. salicina) and 849.8 mg TE/100 g in 'Amfora' (Lonicera edulis) in the minor fruits. [ABSTRACT FROM AUTHOR]

The Japanese plum (Prunus salicina Lindl.) is one of the most important stone fruit crops in China. High-density linkage map is valuable resources which enhance functional genomics and genetic breeding studies. So far several Japanese plum linkage maps have been reported using different kinds of molecular markers; however, the marker numbers and chromosome coverage are limited. Recently, a newly developed strategy which genome sequencing towards specific-locus amplified fragments (SLAF) markers, has been proven to be powerful for rapid genotyping of genome-wide markers and for high-density genetic map construction. In this study, SLAF was used to genotype markers with 114 F1 seedlings from the '09–16' × 'Fortune' cross. Suitable SLAF markers (160,344 out of 343,436,902 pair-end reads) were chosen to conduct genetic map construction, 16.31% of which were polymorphic. The overall integrated map contained 3,341 high quality SLAFs and 720 loci that were grouped in eight genetic linkage groups with a total length of 869.9 cM and an average distance of 1.21 cM, and only five gaps with a genetic distance > 5 cM between adjacent markers occurred in linkage group (LG) 3 and LG6. The number of markers with each LG ranged from 82.3 cM (LG3) to 138.3 cM (LG1). Aligning the map against the peach reference genome sequence (Prunus persica L.) indicated a strictly co-linear relationship between the LGs and peach genome, demonstrating the markers on ours LGs were well ordered. Overall, our studies identified large-scale of genetic markers and constructed high-density linkage maps for Japanese plum, which will obviously provide a solid foundation for marker-assisted selection and sequence assembly of the Japanese plum reference genome. [ABSTRACT FROM AUTHOR]

Silverleaf is an important fungal trunk disease of fruit crops, such as Japanese plum (Prunus salicina). It is known that infection by Chondrostereum purpureum results in discolored wood, “silvered” foliage, and tree decline. However, effects on fruit yield and quality have not been assessed. Therefore, the objectives of this study were to determine C. purpureum pathogenicity on P. salicina and the effects on physiology, fruit yield, and quality, in Chile, in 2019 and 2020. Wood samples from affected plum trees were collected in the Chilean plum productive area. Fungi were isolated by plating wood sections from the necrosis margin on culture media. Morphological and molecular characteristics of the isolates corresponded to C. purpureum (98%). Representative isolates were inoculated from healthy plum plants and after 65-d incubation, wood necrotic lesions and silver leaves were visible. Fungi were reisolated, fulfilling Koch’s postulates. To determine Silverleaf effects, xylem water potential and fruit yield and quality were measured in healthy and Silverleaf-diseased plum trees ‘Angeleno’. Water potential was altered in diseased trees, and fruit yield was reduced by 51% (2019) and by 41% (2020) compared to fruit from healthy trees. Moreover, cover-colour, equatorial-diameter, and weight were reduced, and fruit were softer, failing to meet the criteria to be properly commercialized and exported to demanding markets.

Japanese plum (Prunus salicina Lindl.) is widely distributed in temperate zones across the world. Since its introduction to USA in the late 19th century, this species has been hybridized with up to 15 different diploid Prunus species. This high level of introgression has resulted in a wide range of traits and agronomic behaviors among currently grown cultivars. In this work, 161 Japanese plum-type accessions were genotyped using a set of eight Simple Sequence Repeats (SSR) markers to assess the current genetic diversity and population structure. A total of 104 alleles were detected, with an average of 13 alleles per locus. The overall Polymorphic Informative Content (PIC) value of SSR markers was 0.75, which indicates that these SSR markers are highly polymorphic. The Unweighted Pair Group Method with Arithmetic (UPGMA) dendrogram and the seven groups inferred by Discriminant Analysis of Principal Components (DAPC) revealed a strong correlation of the population structure to the parentage background of the accessions, supported by a moderate but highly significant genetic differentiation. The results reported herein provide useful information for breeders and for the preservation of germplasm resources.

Weighted gene co-expression network analysis (WGCNA) is a widely used software tool that is used to establish relationships between phenotypic traits and gene expression data. It generates gene modules and then correlates their first principal component to phenotypic traits, proposing a functional relationship expressed by the correlation coefficient. However, gene modules often contain thousands of genes of different functional backgrounds. Here, we developed a stochastic optimization algorithm, known as genetic algorithm (GA), optimizing the trait to gene module relationship by gradually increasing the correlation between the trait and a subset of genes of the gene module. We exemplified the GA on a Japanese plum hormone profile and an RNA-seq dataset. The correlation between the subset of module genes and the trait increased, whereas the number of correlated genes became sufficiently small, allowing for their individual assessment. Gene ontology (GO) term enrichment analysis of the gene sets identified by the GA showed an increase in specificity of the GO terms associated with fruit hormone balance as compared with the GO enrichment analysis of the gene modules generated by WGCNA and other methods. [ABSTRACT FROM AUTHOR]

• Three unique early-flowering natural mutants have been identified in apricot and plum. • Mutant genotypes flowered one to four weeks before their wild types. • Earliness in mutants was stable over three years. • Molecular fingerprinting suggests that mutants derive from their wild types. Flowering time is one of the most important traits in temperate fruit trees. Flowering time correlates with chilling requirements and ripening time. The mechanism controlling flowering time in these species could be conserved as suggested by the co-localization of QTL and the candidate genes for flowering time in several Prunus species. Currently, the molecular mechanisms underlying the regulation of flowering time remain poorly understood. In this study, three promising natural early-flowering/low-chilling-requirement mutants were identified and characterized: 'Rojo Pasión Precoz' and 'Búlida Precoz' in apricot (Prunus armeniaca L.) and 'Santa Rosa Precoz' in Japanese plum (Prunus salicina L.). The advancement in flowering date with respect to the wild types was around one week in the case of 'Rojo Pasion Precoz' apricot cultivar, more than two weeks in 'Bulida Precoz' apricot cultivar, and between 9–27 days in the case of 'Santa Rosa Precoz' Japanese plum cultivar. In addition, they were fingerprinted using 44 SSR (Simple Sequence Repeats) and 21 SNPs (Single Nucleotide Polymorphism) markers. Fingerprinting analysis confirmed identical marker profiles between the wild types and their mutants. These results support the hypothesis that a somatic mutation or a stable epi-allele may underlay the early-flowering phenotype. [ABSTRACT FROM AUTHOR]

Biophysical fruit growth depends on a balance among the vascular and transpiration flows entering/exiting the fruit via phloem, xylem and through the epidermis. There is no information on vascular flows of Japanese plums, a species characterized by high-sugar content of its fruit at harvest. Vascular flows of Angeleno plums were monitored by fruit gauges during late fruit development, under the dry environment of the Goulburn Valley, Victoria, Australia. Phloem, xylem flows and skin transpiratory losses were determined, as well as diurnal leaf, stem and fruit pressure potentials. Fruit seasonal development, skin conductance and dry matter accumulation were also monitored. Fruit grew following a double-sigmoid pattern, but fruit size increased only 3.1 g over the last 3 weeks of development. Fruit grew very little in the morning, primarily due to phloem inflows (0.05 g fruit−1hr−1), while water left the fruit via the xylem. Negligible skin transpiration was recorded for vapour pressure deficit (VPD) values below 3 kPa. This growth pattern, in the absence of skin transpiration, suggests apoplastic phloem unloading. However, at VPD values over 3 kPa (e.g. from early afternoon to a peak around 18:00 h), transpiratory losses through the skin (up to 0.25 g fruit−1hr−1) caused fruit to shrink, leading to enhanced phloem and xylem inflows (ca. 0.15 g fruit−1hr−1), a scenario that would correspond to symplastic phloem unloading. Over 24 h the fruit showed a slightly negative total growth, consistent with fruit growth measured in situ during the season at weekly intervals. A few fruit species are known to alter their phloem unloading mechanism, switching from symplastic to apoplastic during the season. Our data support the coexistence in Japanese plum of different phloem unloading strategies within the same day. [ABSTRACT FROM AUTHOR]

Genotyping by sequencing (GBS) provides a large quantity of useful data suitable for the identification of single nucleotide polymorphisms (SNPs), facilitating accurate genomic studies in plant species. In this study, GBS-based SNPs were used to characterise 11 Japanese plum cultivars and to explore their natural allelic diversity in relation to the most important phenology events (flowering date, ripening date and fruit development period) and fruit quality traits (weight, shape, skin and flesh colour, over colour, skin and flesh chlorophyll index, flesh firmness and soluble solids concentration). GBS-based SNPs were shown to be a powerful tool for genetic diversity and other genomic studies where SNP markers were related to several traits, particularly for flowering date, ripening date, fruit development period, skin chlorophyll degradation, flesh chlorophyll degradation and flesh colour. These results represent a preliminary approach using GBS as a possible breeding tool in current and new Japanese plum breeding programmes. [ABSTRACT FROM AUTHOR]

Stone fruit trees of genus Prunus, like other temperate woody species, need to accumulate a cultivar-specific amount of chilling during endodormancy, and of heat during ecodormancy to flower properly in spring. Knowing the requirements of a cultivar can be critical in determining if it can be adapted to a particular area. Growers can use this information to anticipate the future performance of their orchards and the adaptation of new cultivars to their region. In this work, the available information on chilling- and heat-requirements of almond, apricot, plum, peach, and sweet cherry cultivars is reviewed. We pay special attention to the method used for the determination of breaking dormancy, the method used to quantify chilling and heat temperatures, and the place where experiments were conducted. The results reveal different gaps in the information available, both in the lack of information of cultivars with unknown requirements and in the methodologies used. The main emerging challenges are the standardization of the conditions of each methodology and the search for biological markers for dormancy. These will help to deal with the growing number of new cultivars and the reduction of winter cold in many areas due to global warming.

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The genetic diversity of 14 Japanese plum (Prunus salicina Lindl) landraces adapted to an ecosystem of alternating flooding and dry conditions was characterized using neutral simple sequence repeat (SSR) markers. Twelve SSRs located in six chromosomes of the Prunus persica reference genome resulted to be polymorphic, thus allowing identification of all the evaluated landraces. Differentiation between individuals was moderate to high (average shared allele distance (DAS) = 0.64), whereas the genetic diversity was high (average indices polymorphism information content (PIC) = 0.62, observed heterozygosity (Ho) = 0.51, unbiased expected heterozygosity (uHe) = 0.70). Clustering and genetic structure approaches grouped all individuals into two major groups that correlated with flesh color. This finding suggests that the intuitive breeding practices of growers tended to select plum trees according to specific phenotypic traits. These neutral markers were adequate for population genetic studies and cultivar identification. Furthermore, we assessed the SSR flanking genome regions (25 kb) in silico to search for candidate genes related to stress resistance or associated with other agronomic traits of interest. Interestingly, at least 26 of the 118 detected genes seem to be related to fruit quality, plant development, and stress resistance. This study suggests that the molecular characterization of specific landraces of Japanese plum that have been adapted to extreme agroecosystems is a useful approach to localize candidate genes which are potentially interesting for breeding.

Marker-assisted selection (MAS) in stone fruit (Prunus species) breeding is currently difficult to achieve due to the polygenic nature of themost relevant agronomic traits linked to fruit quality. Genotyping by sequencing (GBS), however, provides a large quantity of useful data suitable for finemapping using Single Nucleotide Polymorphisms (SNPs) from a reference genome. In this study, GBS was used to genotype 272 seedlings of three F1 Japanese plum (Prunus salicina Lindl) progenies derived from crossing "98-99" (as a common female parent) with "Angeleno," "September King," and "September Queen" as male parents. Raw sequences were aligned to the Peach genome v1, and 42,909 filtered SNPs were obtained after sequence alignment. In addition, 153 seedlings from the "98-99" × "Angeleno" cross were used to develop a genetic map for each parent. A total of 981 SNPs were mapped (479 for "98-99" and 502 for "Angeleno"), covering a genetic distance of 688.8 and 647.03 cM, respectively. Fifty five seedlings from this progeny were phenotyped for different fruit quality traits including ripening time, fruit weight, fruit shape, chlorophyll index, skin color, flesh color, over color, firmness, and soluble solids content in the years 2015 and 2016. Linkage-based QTL analysis allowed the identification of genomic regions significantly associated with ripening time (LG4 of both parents and both phenotyping years), fruit skin color (LG3 and LG4 of both parents and both years), chlorophyll degradation index (LG3 of both parents in 2015) and fruit weight (LG7 of both parents in 2016). These results represent a promising situation for GBS in the identification of SNP variants associated to fruit quality traits, potentially applicable in breeding programs through MAS, in a highly heterozygous crop species such as Japanese plum. [ABSTRACT FROM AUTHOR]

The growth, phenology and fruit yield of 14 Japanese plum cultivars (Prunus salicina Lindl) were studied in two newly established experimental orchards under organic and conventional management. The experiment was conducted during 2005-2011 in the province of Seville (SW Spain), an important region of Japanese plum culture. Trunk cross-section areas (TCSA), flowering, yield and tree defoliation before winter dormancy were analysed over several years. After one year, TCSA were larger in the organically managed orchard (OMO) for most of the cultivars, in the next two years they were equal, and from the fourth year, several cultivars showed significantly larger TCSA in the conventionally managed orchard (CMO). Flowering in the conventional orchard started from 2 to 6 days before and lasted for 3 to 5 days more than in the OMO. Several cultivars produced significantly more fruit in the CMO, being the average fruit yield in the organic orchard about 72% of the conventionally managed orchard. Autumn defoliation was significantly advanced in the organic orchard, especially in cultivars highly susceptible to rust (Tranzschelia pruni spinosae), a disease not adequately controlled in the organic orchard.