Phenotypic and genotypic variation in Iranian sour and duke cherries

Phenotypic and genotypic variation and structure of 29 sour cherry (P. cerasus) and duke cherry (P. x gondouinii) genotypes from different regions of Iran were identified using random amplified polymorphic DNA (RAPD) markers and morphological characters. Furthermore, one Prunus mahaleb genotype was used as an outgroup for molecular analysis. For morphological analysis, 23 variables were recorded to detect similarities between and among studied sour and duke cherries. Most studied characteristics were showing a high degree of variability. Principal component analysis showed that the first three components explained a total of 73.87 % of the whole phenotypic variability. Based on the morphological cluster analysis, studied sour and duke cherry genotypes were placed into three main clusters. The first main cluster included 16 sour cherry genotypes. The second main cluster contained all duke cherry genotypes and eight sour cherry genotypes, while, only one sour cherry genotype was placed in third main cluster. For RAPD analysis, 17 primers generated a total of 233 discernible and reproducible bands across genotypes analyzed, out of which 214 (91.51 %) were polymorphic with varied band size from 300 to 3000 bp. According to the similarity matrix, the lowest similarity was obtained between P. mahaleb, as an outgroup, and sour cherry. Dendrogram based on molecular data separated genotypes according to their species and geographic origin. Low correlation was observed between the similarity matrices obtained based on morphological and RAPD data. The information obtained here could be valuable for devising strategies for conservation of Iranian sour and duke cherries.     

Genetic relationships among cherry species with transferability of simple sequence repeat loci

Sweet and sour cherries are two economically important species in the world. The capability to distinguish among cherry genotypes in breeding, cultivation and germplasm collection is extremely important for scientific as well as economic reasons. In the present research, sixteen simple sequences repeat (SSR) loci were used to estimate the relationships among sweet, sour, duke and wild cherries. All of the SSR markers showed high transferability across the studied species that allowed us to study genetic diversity in them. Totally 96 alleles were generated with SSR loci, of which 93 were found polymorphic with 97.57 % polymorphism. Values of genetic similarity between genotypes varied from 0.16 to 0.97 which indicated high level of genetic diversity. On the basis of their genetic similarities, SSR analysis allowed to group the genotypes into three main clusters according to their species. These results have an important implication for cherry germplasm characterization, improvement, and conservation.     

Identification and genetic diversity of plum cultivars grown in Belarus

A study of the collection of sour cherry, sweet cherry, common plum, diploid and tetraploid types of plums, and apricots grown in Belarus carried out using 20 SSR markers showed that they are characterized by high genetic diversity. Among 106 genotypes, 524 polymorphic alleles were identified. The average number of alleles was 15.4 in common plum samples, 11.3 in diploid and tetraploid plum, 9.3 in sour cherry, 6.0 in apricot, and 4.9 in sweet cherry. The greatest genetic diversity is characteristic of common plum cultivars (PD = 0.811). The genetic diversity decreases as follows: diploid plum (PD = 0.741), sour cherry (PD = 0.721), apricot (PD = 0.673), and sweet cherry (PD = 0.655). Cluster analysis shows that the degree of intraspecific divergence in sour cherry and sweet cherry cultivars is less than that of common plum, diploid plum, and apricot plum. Although apricots and plums belong to the subgenus Prunophora, according to the results of SSR analysis, apricot cultivars form a cluster that is more distant from both Cerasus and Prunophora. A set of seven SSR markers (EMPA001, EMPA005, EMPA018, EMPA026 and BPPCT025, BPPCT026, BPPCT039) was selected for DNA identification of cultivars of sour cherry, sweet cherry, common plum, diploid plum, and apricot, as well as species and interspecies hybrids.     

Genetic variation in wild Prunus L. subgen. Cerasus germplasm from Iran characterized by nuclear and chloroplast SSR markers

Key message

The selected material of Cerasus subgen. will be useful for conservation and management and important for Prunus breeding programs.

Abstract

Knowledge of relationships among the cultivated and wild species of Cerasus is important for recognizing gene pools in germplasm and developing effective conservation and management strategies. In this study, genetic and phylogenetic relationships of wild Cerasus subgenus species naturally growing in Iran, including P. avium (mazzard), P. mahaleb, P. brachypetala, P. incana, P. yazdiana, P. microcarpa subsp. microcarpa, P. microcarpa subsp. diffusa and P. pseudoprostrata and three commercial species, sweet cherry (P. avium), sour cherry (P. cerasus) and duke cherry (P. x gondouinii) was investigated based on 16 nuclear SSR and five chloroplast SSR. Very high level of polymorphism was detected among the studied species based these molecular markers, indicating high inter and intraspecific genetic variation. Inter and intraspecific genetic similarity coefficients varied from 0.00 to 1.00, indicating high genetic variation in studied germplasm. These two molecular markers types could distinguish differences between all species so that accessions of each species were placed into a single group. Based on molecular markers, a close correlation was observed between intraspecific variation and geographical distribution. Furthermore, based on nuSSR primers, most wild species showed 2–4 alleles and may be tetraploid. In conclusion, the conservation of these highly diverse native populations of Iranian wild Cerasus germplasm is recommended for future breeding activity.     

Genetic diversity of some Iranian sweet cherry (<Emphasis Type="Italic">Prunus avium</Emphasis>) cultivars using microsatellite markers and morphological traits

The aim of this study was to characterize 23 important Iranian sweet cherry (Prunus avium) cultivars collected from different provinces of Iran and 1 foreign cultivar, which was used as control, considered for breeding programs by using 21 microsatellite markers and 27 morphological traits. In sweet cherry (Prunus avium) accessions, leaf, fruit, and stone morphological characters were evaluated during two consecutive years. The study revealed a high variability in the set of evaluated sweet cherry accessions. The majority of important correlations were determined among variables representing fruit and leaf size and variables related to color. Cluster analysis distinguished sweet cherry accessions into two distinct groups. Principal component analysis (PCA) of qualitative and quantitative morphological parameters explained over 86.59% of total variability in the first seven axes. In PCA, leaf traits such as leaf length and width, and fruit traits such as length, width, and weight, and fruit flesh and juice color were predominant in the first two components, indicating that they were useful for the assessment of sweet cherry germplasm characterization. Out of 21 SSR markers, 16 were polymorphic, producing 177 alleles that varied from 4 to 16 alleles (9.35 on average) with a mean heterozygosity value of 0.82 that produced successful amplifications and revealed DNA polymorphisms. Allele size varied from 95 to 290 bp. Cluster analyses showed that the studied sweet cherry genotypes were classified into five main groups based mainly on their species characteristics and SSR data. In general, our results did not show a clear structuring of genetic variability within the Iranian diffusion area of sweet cherry, so it was not possible to draw any indications on regions of provenance delimitation. The results of this study contribute to a better understanding of sweet cherry genetic variations in Iran, thus making for more efficient programs aimed at preserving biodiversity and more rational planning of the management of reproductive material.     

Physiological adaptations of five poplar genotypes grown under SRC in the semi-arid Mediterranean environment

Key message

The genotype ‘Neva’ under high plant density showed the highest biomass yield and optimal physiological strategies and could be the most suitable choice under semi-arid environment

Abstract

The poplars (Populus spp.) are the most sensitive plants to water deficit conditions among the woody species utilized for biomass production for energetic purposes; their productivity is associated with water availability in the soil. In the Mediterranean environment, crops are mainly limited by evapotranspirative demand that is not balanced by rainfall supply. As new hybrids with high growth rates and resistance to water stress are selected, the use of poplar as an energy crop may increase in Southern regions of Mediterranean Europe. The growth dynamics and physiological characteristics of poplar hybrid genotypes have been monitored for 2 years at a site with a Mediterranean climate, Apulia region, that could be used for energy crops. Unrooted cuttings of three recently selected genotypes of poplar (‘Neva’, ‘Dvina’ and ‘Lena’) and two “traditional” genotypes (‘Luisa Avanzo’ and ‘Bellini’) were planted in the spring of 2010 at two different densities: (a) low plant density = 1,667 cuttings ha^?1 (LPD); (b) high plant density = 6,667 cuttings ha^?1 (HPD). The genotypes ‘Lena’ and ‘Dvina’ showed the lowest survival rates and the poorest growth among the hybrid poplar tested. The genotype ‘Bellini’ had low stomatal sensitivity to soil water content and a moderate productive performance. The genotypes ‘Luisa Avanzo’ and ‘Neva’ had a good degree of rooting and sprouting, high values of leaf relative water content (RWC_l) and low values of stomatal conductance (g _s) during the summer months. In “Neva”, these characteristics were associated with the best yields (4 t ha^?1) in HPD.     

Identification of incompatibility alleles in the tetraploid species sour cherry

The incompatibility genetics of sour cherry (Prunus cerasus), an allotetraploid species thought to be derived from sweet cherry (diploid) and ground cherry (tetraploid), were investigated by test crossing and by analysis of stylar ribonucleases which are known to be the products of incompatibility alleles in sweet cherry. Stylar extracts of 36 accessions of sour cherry were separated electrophoretically and stained for ribonuclease activity. The zymograms of most accessions showed three bands, some two or four. Of the ten bands seen, six co-migrated with bands that in sweet cherry are attributed to the incompatibility alleles S ₁ , S ₃ , S ₄ , S _6, S ₉ and S ₁₃ . aanski Rubin, Erdi Botermo B, Koro and Ujfehertoi Furto, which showed bands apparently corresponding to S ₁ and S ₄ , were test pollinated with the sweet cherry Merton Late (S ₁ S ₄ ). Monitoring pollen tube growth, and, in one case, fruit set, showed that these crosses were incompatible and that the four sour cherries indeed have the alleles S ₁ and S ₄ . Likewise, test pollination of Marasca Piemonte, Marasca Savena and Morello, Dutch with Noble (S ₆ S ₁₃ ) showed that these three sour cherries have the alleles S ₆ and S ₁₃ . S ₁₃ was very frequent in sour cherry cultivars, but is rare in sweet cherry cultivars, whereas with S ₃ the situation is reversed. It was suggested that the other four bands are derived from ground cherry and one of these, provisionally attributed to S _B , occurred frequently in a small set of ground cherry accessions surveyed. Analysing some progenies from sour by sweet crosses by S allele-specific PCR and monitoring the success of some sweet by sour crosses were informative. They indicated mostly disomic inheritance, with sweet cherry S alleles belonging to one locus and, presumably, the ground cherry alleles to the other, and helped clarify the genomic arrangement of the alleles and the interactions in heteroallelic pollen.Communicated by H.F. Linskens     

High-density linkage maps constructed in sweet cherry (<Emphasis Type="Italic">Prunus avium</Emphasis> L.) using cross- and self-pollination populations reveal chromosomal homozygosity in inbred families and non-syntenic regions with the peach genome

The landrace sweet cherry (Prunus avium L.) cultivar ‘Cristobalina’ is a useful resource for sweet cherry breeding due to several important traits, including low chilling requirement, early maturity date, and self-compatibility. In this work, three families (N?=?325), derived from ‘Cristobalina’, were used to develop high-density genetic maps using the RosBREED 6K Illumina Infinium® cherry SNP array. Two of the families were derived from self-pollination, which allowed construction of the first F₂ genetic maps in the species. The other map developed was from an interspecific cross of cultivars ‘Vic’?×?‘Cristobalina’. The maps developed include 511 to 816 mapped SNPs covering 622.4 to 726.0 cM. Mapped SNP marker order and position were compared to the sweet cherry and peach genome sequences, and a high degree of synteny was observed. However, inverted and small translocated regions between peach and sweet cherry genomes were observed with the most noticeable inversion at the top of LG5. The progeny resulting from self-pollination also revealed a high level of homozygosity, as large presumably homozygous regions as well as entire homozygous LGs were observed. These maps will be used for genetic analysis of relevant traits in sweet cherry breeding by QTL analysis, and self-pollination populations will be useful for investigating inbreeding depression in a naturally outbreeding species.     

Differences in body size and egg loads of Rhagoletis indifferens (Diptera: Tephritidae) from introduced and native cherries

The western cherry fruit fly, Rhagoletis indifferens Curran, infests introduced, domesticated sweet [Prunus avium (L.) L.], and tart cherries (Prunus cerasus L.) as well as native bitter cherry, Prunus emarginata (Douglas) Eaton. Bitter cherries are smaller than sweet and tart cherries and this could affect various life history traits of flies. The objectives of the current study were to determine 1) if body size and egg loads of flies infesting sweet, tart, and bitter cherries differ from one another; and 2) if any observed body size differences are genetically based or caused by the host fruit environment. Pupae and adults of both sexes reared from larval-infested sweet and tart cherries collected in Washington and Montana were larger than those reared from bitter cherries. In addition, flies of both sexes caught on traps in sweet and tart cherry trees were larger than those caught in bitter cherry trees and females trapped from sweet and tart cherry trees had 54.0-98.8% more eggs. The progeny of flies from naturally-infested sweet and bitter cherries reared for one generation in the laboratory on sweet cherry did not differ in size. The same also was true for progeny of sweet and bitter cherry flies reared in the field on bitter cherry. The results suggest that the larger body sizes of flies from sweet and tart cherries than bitter cherries in the field are caused by host fruit and not genetic factors.     

Comparative responses of ‘Gala’ and ‘Fuji’ apple trees to deficit irrigation: Placement versus volume effects

Aims

Climate, soil water potential (SWP), leaf relative water content (RWC), stomatal conductance (g_s), fruit and shoot growth, and carbohydrate levels were monitored during the 2008 and 2009 growing seasons to study the responses of ‘Gala’ and ‘Fuji’ apple trees to irrigation placement or volume.

Methods

Three irrigation treatments were imposed, conventional irrigation (CI), partial root-zone drying (PRD, 50% of CI water on one side of the root-zone, which was alternated periodically), and continuous deficit irrigation (DI, 50% of CI water on both sides of the root-zone).

Results

After each irrigation season, DI generated twice the soil water deficit (SWD_int) than PRD (average of dry and wet sides) and a greater integrated leaf water deficit (LWD_int) than PRD and CI. Both PRD and DI reduced g_s by 9 and 15% over the irrigation period. RWC of both PRD and DI was directly related to SWP and inversely related (non-linear) to vapor pressure deficit (VPD), whereas it was unrelated to g_s. Considering individual sampling days, g_s of ‘Gala’ leaves was inversely related to VPD mainly until early August (fruit at cell expansion phase and high VPD), while it was directly related to VPD in September (no fruit and low VPD). On the contrary, g_s of ‘Fuji’ leaves was inversely related to VPD from late August until mid October (low VPD and fruit at cell expansion phase). Fruit growth was not affected by irrigation, whereas shoot and trunk growth was reduced by DI. Irrigation induced sporadic and inconsistent changes in carbohydrate contents or partitioning, with a general tendency of DI leaves to degrade and PRD to accumulate sorbitol and sucrose in dry periods.

Conclusions

‘Gala’ trees exhibited a more conservative water use than ‘Fuji’ trees due primarily to different timing of fruit growth and crop loads. Different levels of SWD_int, rather than changes in stomatal control and carbohydrate partitioning, seem to play a major role in determining a better water status in PRD than in DI trees.     

Characterization of self-compatibility in sweet cherry varieties by crossing experiments and molecular genetic analysis

Self-compatibility is a major breeding objective in sweet cherry. The identification and characterization of new sources of self-compatibility will be useful for breeding and research purposes. In this work, self-compatibility of four local Spanish sweet cherry varieties was investigated by crossing experiments and molecular genetic analysis of two self-incompatibility loci. Crossing experiments included self- and cross-pollinations in the laboratory followed by microscopic observation of pollen tube growth and fruit set assay in the field. After crossing experiments, two accessions, ‘Son Miró’ and ‘Talegal Ahín’, were self-compatible while the other two were self-incompatible. Inheritance of S-locus and microsatellite EMPaS02 (linked to self-compatibility, Sc) were investigated in self-pollination progeny of both self-compatible genotypes. Results indicate that self-compatibility in ‘Talegal Ahín’ is similar to self-compatibility described in sweet cherry ‘Cristobalina’ and may be caused by the same mutation. That is a pollen part mutation not linked to the S-locus but linked to microsatellite EMPaS02 in cherry LG3. In ‘Son Miró’ self-compatibility seems more complex, affecting pollen and style function, and probably involving more than one mutation not described previously in sweet cherry. Together with ‘Cristobalina’, the newly described self-compatible varieties ‘Son Miró’ and ‘Talegal Ahín’ confirm the existence of unique self-compatible plant material in local germplasm from Spain that should be conserved and characterized for its use in breeding and research.     

Bayesian QTL analyses using pedigreed families of an outcrossing species,with application to fruit firmness in apple

Key message

Proof of concept of Bayesian integrated QTL analyses across pedigree-related families from breeding programs of an outbreeding species. Results include QTL confidence intervals, individuals’ genotype probabilities and genomic breeding values.

Abstract

Bayesian QTL linkage mapping approaches offer the flexibility to study multiple full sib families with known pedigrees simultaneously. Such a joint analysis increases the probability of detecting these quantitative trait loci (QTL) and provide insight of the magnitude of QTL across different genetic backgrounds. Here, we present an improved Bayesian multi-QTL pedigree-based approach on an outcrossing species using progenies with different (complex) genetic relationships. Different modeling assumptions were studied in the QTL analyses, i.e., the a priori expected number of QTL varied and polygenic effects were considered. The inferences include number of QTL, additive QTL effect sizes and supporting credible intervals, posterior probabilities of QTL genotypes for all individuals in the dataset, and QTL-based as well as genome-wide breeding values. All these features have been implemented in the FlexQTL^? software. We analyzed fruit firmness in a large apple dataset that comprised 1,347 individuals forming 27 full sib families and their known ancestral pedigrees, with genotypes for 87 SSR markers on 17 chromosomes. We report strong or positive evidence for 14 QTL for fruit firmness on eight chromosomes, validating our approach as several of these QTL were reported previously, though dispersed over a series of studies based on single mapping populations. Interpretation of linked QTL was possible via individuals’ QTL genotypes. The correlation between the genomic breeding values and phenotypes was on average 90 %, but varied with the number of detected QTL in a family. The detailed posterior knowledge on QTL of potential parents is critical for the efficiency of marker-assisted breeding.     

Detection and Identification of ‘Candidatus Phytoplasma prunorum’, ‘Candidatus Phytoplasma mali’ and ‘Candidatus Phytoplasma pyri’ in Stone Fruit Trees in Poland

A survey was made to determine the incidence of phytoplasmas in 39 sweet and sour cherry, peach, nectarine, apricot and plum commercial and experimental orchards in seven growing regions of Poland. Nested polymerase chain reaction (PCR) using the phytoplasma‐universal primer pairs P1/P7 followed by R16F2n/R16R2 showed the presence of phytoplasmas in 29 of 435 tested stone fruit trees. The random fragment length polymorphism (RFLP) patterns obtained after digestion of the nested PCR products separately with RsaI, AluI and SspI endonucleases indicated that selected Prunus spp. trees were infected by phytoplasmas belonging to three different subgroups of the apple proliferation group (16SrX‐A, ‐B, ‐C). Nucleotide sequence analysis of 16S rDNA fragment amplified with primers R16F2n/R16R2 confirmed the PCR/Restriction Fragment Length Polymorphism (RFLP) results and revealed that phytoplasma infecting sweet cherry cv. Regina (Reg), sour cherry cv. Sokowka (Sok), apricots cv. Early Orange (EO) and AI/5, Japanese plum cv. Ozark Premier (OzPr) and peach cv. Redhaven (RedH) was closely related to isolate European stone fruit yellows‐G1 of the ‘Candidatus Phytoplasma prunorum’ (16SrX‐B). Sequence and phylogenetic analyses resulted in the highest similarity of the 16S rDNA fragment of phytoplasma from nectarine cv. Super Queen (SQ) with the parallel sequence of the strain AP15 of the ‘Candidatus Phytoplasma mali’ (16SrX‐A). The phytoplasma infecting sweet cherry cv. Kordia (Kord) was most similar to the PD1 strain of the ‘Candidatus Phytoplasma pyri’ (16SrX‐C). This is the first report of the occurrence of ‘Ca. P. prunorum’, ‘Ca. P. mali’ and ‘Ca. P. pyri’ in naturally infected stone fruit trees in Poland.     

Morphological and histological impacts of the laurina mutation on fructification and seed characteristics in Coffea arabica L.

Key message

The comparison between the cultivar Bourbon and its mutant, the Bourbon pointu, of Coffea arabica led to five novel findings on fruit development and three main impacts of the mutation.

Abstract

Coffea arabica ‘Laurina’ (Bourbon pointu) is a natural mutant of Coffea arabica ‘Bourbon’. Relative to the ‘Bourbon’ cultivar, it is characterized by internode dwarfism, a Christmas tree shape, and lower caffeine content. The effects of the laurina mutation on fructification over time, the fruit structure and seed characteristics were studied here. Fruits of ‘Bourbon’ and ‘Bourbon pointu’ were monitored. The trees were grown in the same plot and flowered on the same day. Harvesting was done every 2 weeks from the 6th to the 26th week after flowering. Histological observations were carried out using multiphoton and conventional microscopes. The measurements concerned the fruit, parchment and seed. Five novel findings on fructification development were obtained: (1) a sigmoid model and non-linear regression efficiently described the phenomenon; (2) a precise relationship was defined between the qualitative stages of fructification and quantitative observations, thus revealing key weeks in this process; (3) the parchment had a mesocarpic origin; (4) a meristematic zone was present close to the parchment; and (5) an endocarp with three cell layers was visible in young fruits. Three effects of the laurina mutation were highlighted: (1) fruit growth ended 1 week earlier in ‘Bourbon’, but without difference in fruit length. In contrast, fruits were wider on average in ‘Bourbon’; (2) the parchment of narrow seeds in ‘Bourbon pointu’ was thicker than in other ‘Bourbon pointu’ and ‘Bourbon’ seeds; and (3) the narrow seed frequency in ‘Bourbon pointu’ depended on environmental conditions.     

Wild and Rare Self-Incompatibility Allele S17 Found in 24 Sweet Cherry (Prunus avium L.) Cultivars

The pollination of self-incompatible diploid sweet cherry is determined by the S-locus alleles. We resolved the S-alleles of 50 sweet cherry cultivars grown in Estonia and determined their incompatibility groups, which were previously unknown for most of the tested cultivars. We used consensus primers SI-19/20, SI-31/32, PaConsI, and PaConsII followed by allele-specific primers and sequencing to identify sweet cherry S-genotypes. Surprisingly, 48% (24/50) of the tested cultivars, including 17 Estonian cultivars, carry the rare S-allele S₁₇, which had initially been described in wild sweet cherries in Belgium and Germany. The S₁₇-allele in Estonian cultivars could originate from ‘Leningradskaya tchernaya’ (S₆|S₁₇), which has been extensively used in Estonian sweet cherry breeding. Four studied cultivars carrying S₁₇ are partly self-compatible, whereas the other 20 cultivars with S₁₇ have not been reported to be self-compatible. The recommended pollinator of seven self-incompatible sweet cherries is of the same S-genotype, including four with S₁₇-allele, suggesting heritable reduced effectiveness of self-infertility. We classified the newly genotyped sweet cherry cultivars into 15 known incompatibility groups, and we proposed four new incompatibility groups, 64–67, for S-locus genotypes S₃|S₁₇, S₄|S₁₇, S₅|S₁₇, and S₆|S₁₇, respectively, which makes them excellent pollinators all across Europe. Alternatively, the frequency of S₁₇ might be underestimated in Eastern European populations and some currently unidentified sweet cherry S-alleles might potentially be S₁₇.

     

Combined heat and controlled atmosphere quarantine treatments for control of western cherry fruit fly in sweet cherries

Nonchemical quarantine treatments, using a combination of short duration high temperatures under low oxygen, elevated carbon dioxide atmospheric environment were developed to control western cherry fruit fly, Rhagoletis indifferens Curran, in sweet cherries, Prunus avium (L.). The two treatments developed use a chamber temperature of 45 degrees C for 45 min and a chamber temperature of 47 degreesd C for 25 min, both under a 1% oxygen, 15% carbon dioxide, -2 degrees C dew point environment. Both these treatments have been shown to provide control of all life stages of western cherry fruit fly while preserving commodity market quality. There was no definitive egg or larval stage, which was demonstrated to be the most tolerant to either controlled atmosphere temperature treatment system treatment. Efficacy tests for both treatments resulted in 100% mortality of >5000 western cherry fruit flies in each treatment. These treatments may provide, with further study, quarantine security in exported sweet cherries where western cherry fruit fly is a quarantine concern and fumigation with methyl bromide is not desired.