Dissecting apple tree architecture into genetic, ontogenetic and environmental effects: mixed linear modelling of repeated spatial and temporal measures

The present study aimed to dissect tree architectural plasticity into genetic, ontogenetic and environmental effects over the first 4 yr of growth of an apple (Malus x domestica) F1 progeny by means of mixed linear modelling of repeated data. Traits related to both growth and branching processes were annually assessed on different axes of the trees planted in a staggered-start design. Both spatial repetitions, (i.e. different axis types) and temporal repetitions (i.e. successive ages of trees) were considered in a mixed linear model of repeated data. A significant genotype effect was found for most studied traits and interactions between genotype and year and/or age were also detected. The analysis of repeated temporal measures highlighted that the magnitude of the decrease in primary growth is mainly determined by the first year of growth, and the decrease in bottom diameter increment is concomitant with the first fruiting occurrence. This approach allowed us to distinguish among the traits that were under genetic control, those for which this control is exerted differentially throughout tree life or depending on climatic conditions or an axis type. Mapping quantitative trait loci (QTL) that are specific to these different effects will constitute the next step in the research.     

Factors that effect leaf regeneration efficiency in apple,and effect of antibiotics in morphogenesis

Several factors that affect the frequency of organogenesis in apple leaf explants were examined for the scion cultivars Empire, Freedom, Golden Delicious, Liberty, McIntosh, and Mutsu and for the rootstocks Malling 7A and Malling 26. The main factors affecting morphogenesis were BA concentration, basal medium, leaf explant origin and maturity, explant orientation, and photosynthetic photon flux. Depending on the genotype, optimal regeneration was obtained using either 22.2 or 31.1 M BA and the N6 basal medium, with the exception of Golden Delicious which regenerated better on MS medium. After 6 weeks, the average number of shoots per segment varied from 5 to 16, and the percentage of regeneration between 70 and 100%, depending on the genotype tested and the maturity of the explant. Regeneration capacity increased dramatically from the tip towards the base of the leaf, and was higher from the middle to the proximal end.Cefotaxime and carbenicillin, two antibiotics commonly used during transformation studies to eliminate Agrobacterium tumefaciens from plant tissue, were tested to determine their effect on morphogenesis. Cefotaxime at a dose of 250 mg 1^-1 enhanced regeneration and shoot development, whereas carbenicillin at a dose of 500 mg l^-1 induced abundant callus formation and inhibited regeneration. Kanamycin, a widely used selection agent for plant transformation, strongly inhibited regeneration even at very low doses. Schemes for selection and recovery of transgenic apple plants when kanamycin is used as the selection agent are discussed.Abbreviations BA benzyladenine - Cef cefotaxime - Crb carbenicillin - IBA indolebutyric acid - Kan kanamycin - LS Linsmaier and Skoog (1965) medium - M Malling - MS Murashige and Skoog (1962) medium - NAA naphthaleneacetic acid - N6 medium (Chu et al. 1975) as modified by Welander (1988) - PPF photosynthetic photon flux     

Repeat flowering in apple caused by water stress or defoliation

Summary A series of experiments involving defoliation or water stress at different dates indicated that either of these treatments can make potted apple trees flower a second time in any one year, as long as the treatment is given near the end of July. The results suggest that the reflowering after a period of water stress was primarily a result of the loss of leaves that occurred when the plants were subsequently rewatered. Reflowering normally occurred only if flower primordia had already differentiated at the time of the treatment. There was an indication that in early July water stress was more effective than defoliation at stimulating reflowering.     

Identification and mapping of the novel apple scab resistance gene Vd3

Apple scab, caused by the fungal pathogen Venturia inaequalis, is one of the most devastating diseases for the apple growing in temperate zones with humid springs and summers. Breeding programs around the world have been able to identify several sources of resistance, the Vf from Malus floribunda 821 being the most frequently used. The appearance of two new races of V. inaequalis (races 6 and 7) in several European countries that are able to overcome the resistance of the Vf gene put in evidence the necessity of the combination of different resistance genes in the same genotype (pyramiding). Here, we report the identification and mapping of a new apple scab resistance gene (Vd3) from the resistant selection “1980-015-25” of the apple breeding program at Plant Research International, The Netherlands. This selection contains also the Vf gene and the novel V25 gene for apple scab resistance. We mapped Vd3 on linkage group 1, 1 cM to the south of Vf in repulsion phase to it. Based on pedigree analysis and resistance tests, it could be deduced that 1980-015-25 had inherited Vd3 from the founder “D3.” This gene provides resistance to the highly virulent EU-NL-24 strain of race 7 of V. inaequalis capable of overcoming the resistance from Vf and Vg. JMS and SGJ contributed equally to this work     

Effects of fruit thinning agents on apple tree canopy photosynthesis and dark respiration

Effects on photosynthesis of the fruit thinning agents naphthaleneaceticacid (NAA) and three commercial plant growth regulator formulations,naphthaleneacetic acid ('Rhodofix') and naphthaleneacetamide('Amidthin') and 2-chloroethylphosphonic acid('Ethrel')were evaluated with respect to the stress they impose on the fruit tree, usingthe alternate-bearing sensitive apple cv. 'Elstar'. This work wasbased on the hypothesis that plant stress in the form of large reductions inleaf photosynthesis are a pre-requisite for successful fruit thinning. A newtechnology was employed for continuous recording of tree canopyphotosynthesis, dark respiration and carbon balance of apple trees. This wasbased on six canopy chambers, which enclosed apple trees under naturalconditions in the field, with on-line measurements and continuous analysis ofCO₂ exchange and automated data acquisition. All employed thinningagents reduced whole tree canopy photosynthesis consistently by3–34% on the five days following their application, withphotosynthesis still declining thereafter in the case of the NAA and'Amid-thin' application. The reduction after application of either'Rhodofix' or 'Ethrel', declined within five days, suchthat most of the original photosynthetic potential was restored, indicatingacceptable phytotoxicity of these three plant growth regulators at theconcentrations used. The effects on dark respiration differed markedly. NAA and'Ethrel' increased dark respirationover-proportionally by up to 106%, whereas 'Amid-thin' and'Rhodofix' decreased it by up to 46%inthe first night after application, thereby drastically affecting the carbonbalance of the tree in opposite ways. These results are integrated into ahypothesis linking basipetal auxin transport, phloem loading, translocation anddeficiency of photoassimilates.     

Relative developmental, environmental, and tree-to-tree variability in buds from field-grown apple trees

High-throughput genomic technologies are becoming more accessible to nonmodel plant species, and therefore, tissue collected outside controlled environments is being increasingly used for microarray analyses. In this study, we present a 15,720-feature apple microarray analysis of the variability of gene expression in buds from field-grown apple trees. Tree-to-tree and day-to-day variances were assessed during two different seasons: summer, when the meristems in the buds were undergoing the first stages of floral development, and autumn, when the buds were undergoing transition to winter dormancy. We found that apple trees with the same scion and rootstock cultivars, grown in a standard orchard environment, had small tree-to-tree variation. Gene expression differences caused by season was the dominant cause of variance while using false discovery rate control with a threshold of α* = 0.01 to select significantly different expression between genes. At this threshold, the environmental and location effects accounted for less than 10% of the genes selected. Consequently, we have shown that field microarray experiments are a viable approach for measuring seasonal changes in gene expression during apple bud development. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

QTL analysis for aphid resistance and growth traits in apple

The rosy apple aphid (Dysaphis plantaginea), the leaf-curling aphid (Dysaphis cf. devecta) and the green apple aphid (Aphis pomi) are widespread pest insects that reduce growth of leaves, fruits and shoots in apple (Malus × domestica). Aphid control in apple orchards is generally achieved by insecticides, but alternative management options like growing resistant cultivars are needed for a more sustainable integrated pest management (IPM). A linkage map available for a segregating F₁-cross of the apple cultivars ‘Fiesta’ and ‘Discovery’ was used to investigate the genetic basis of resistance to aphids. Aphid infestation and plant growth characteristics were repeatedly assessed for the same 160 apple genotypes in three different environments and 2 consecutive years. We identified amplified fragment length polymorphism (AFLP) markers linked to quantitative trait loci (QTLs) for resistance to D. plantaginea (‘Fiesta’ linkage group 17, locus 57.7, marker E33M35–0269; heritability: 28.3%), and to D. cf. devecta (‘Fiesta’ linkage group 7, locus 4.5, marker E32M39–0195; heritability: 50.2%). Interactions between aphid species, differences in climatic conditions and the spatial distribution of aphid infestation were identified as possible factors impeding the detection of QTLs. A pedigree analysis of simple sequence repeat (SSR) marker alleles closely associated with the QTL markers revealed the presence of the alleles in other apple cultivars with reported aphid resistance (‘Wagener’, ‘Cox’s Orange Pippin’), highlighting the genetic basis and also the potential for gene pyramiding of aphid resistance in apple. Finally, significant QTLs for shoot length and stem diameter were identified, while there was no relationship between aphid resistance and plant trait QTLs. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The use of the phosphomannose-isomerase/mannose selection system to recover transgenic apple plants

A selection system based on the phosphomannose-isomerase gene (pmi) as a selectable marker and mannose as the selective agent was evaluated for the transformation of apple (Malus domestica Borkh.). Mannose is an unusable carbon source for many plant species. After uptake, mannose is phosphorylated by endogenous hexokinases to mannose-6-phosphate. The accumulation of mannose-6-phosphate leads to a block in glycolysis by inhibition of phosphoglucose-isomerase, resulting in severe growth inhibition. The phosphomannose-isomerase is encoded by the manA gene from Escherichia coli and catalyzes the conversion of mannose-6-phosphate to fructose-6-phosphate, an intermediate of glycolysis. Transformed cells expressing the manA gene can therefore utilize mannose as a carbon and survive on media containing mannose. The manA gene along with a β-glucuronidase (GUS) gene was transferred into apple cv. ‘Holsteiner Cox’ via Agrobacterium tumefaciens-mediated transformation. Leaf explants were selected on medium supplemented with different concentrations and combinations of mannose and sorbitol to establish an optimized mannose selection protocol. Transgenic lines were regenerated after an initial selection pressure of 1–2 g l⁻¹ mannose in combination with 30 g l⁻¹ sorbitol followed by a stepwise increase in the mannose concentration up to 10 g l⁻¹ and simultaneous decrease in the sorbitol concentration. Integration of transgenes in the apple genome of selected plants was confirmed by PCR and southern blot analysis. GUS histochemical and chlorophenol red (CPR) assays confirmed activity of both transgenes in regenerated plants. The pmi/mannose selection system is shown to be highly efficient for producing transgenic apple plants without using antibiotics or herbicides.     

Identifying ontogenetic, environmental and individual components of forest tree growth

Background and Aims

This study aimed to identify and characterize the ontogenetic, environmental and individual components of forest tree growth. In the proposed approach, the tree growth data typically correspond to the retrospective measurement of annual shoot characteristics (e.g. length) along the trunk.

Methods

Dedicated statistical models (semi-Markov switching linear mixed models) were applied to data sets of Corsican pine and sessile oak. In the semi-Markov switching linear mixed models estimated from these data sets, the underlying semi-Markov chain represents both the succession of growth phases and their lengths, while the linear mixed models represent both the influence of climatic factors and the inter-individual heterogeneity within each growth phase.

Key Results

On the basis of these integrative statistical models, it is shown that growth phases are not only defined by average growth level but also by growth fluctuation amplitudes in response to climatic factors and inter-individual heterogeneity and that the individual tree status within the population may change between phases. Species plasticity affected the response to climatic factors while tree origin, sampling strategy and silvicultural interventions impacted inter-individual heterogeneity.

Conclusions

The transposition of the proposed integrative statistical modelling approach to cambial growth in relation to climatic factors and the study of the relationship between apical growth and cambial growth constitute the next steps in this research.     

Construction of an integrated consensus map of the apple genome based on four mapping populations

An integrated consensus genetic map for apple was constructed on the basis of segregation data from four genetically connected crosses (C1?=?Discovery × TN10-8, C2?=?Fiesta × Discovery, C3?=?Discovery × Prima, C4?=?Durello di Forli × Fiesta) with a total of 676 individuals using CarthaGene® software. First, integrated female–male maps were built for each population using common female–male simple sequence repeat markers (SSRs). Then, common SSRs over populations were used for the consensus map integration. The integrated consensus map consists of 1,046 markers, of which 159 are SSR markers, distributed over 17 linkage groups reflecting the basic chromosome number of apple. The total length of the integrated consensus map was 1,032 cM with a mean distance between adjacent loci of 1.1 cM. Markers were proportionally distributed over the 17 linkage groups (χ ²?=?16.53, df?=?16, p?=?0.41). A non-uniform marker distribution was observed within all of the linkage groups (LGs). Clustering of markers at the same position (within a 1-cM window) was observed throughout LGs and consisted predominantly of only two to three linked markers. The four integrated female–male maps showed a very good colinearity in marker order for their common markers, except for only two (CH01h01, CH05g03) and three (CH05a02z, NZ02b01, Lap-1) markers on LG17 and LG15, respectively. This integrated consensus map provides a framework for performing quantitative trait locus (QTL) detection in a multi-population design and evaluating the genetic background effect on QTL expression.     

Strong synergistic effects of gibberellins with the synthetic cytokinin N-(2-chloro-4-pyridyl)-N-phenylurea on parthenocarpic fruit set and some other fruit characteristics of apple

The induction of parthenocarpic fruit set was investigated using the apple cvs. Golden Delicious and Jonagold. The gibberellins GA₃, GA₄, GA₅ and GA₇ and the synthetic phenylurea-type cytokinin CPPU (N-(2-chloro-4-pyridyl)-N-phenylurea), were applied alone and in combination to unpollinated flowers at the end of petal fall. Gibberellins induced only a marginal final set of parthenocarpic fruits. CPPU sprays were more effective, particularly in the first year. When applied in combination, CPPU and gibberellins had a positive synergistic effect on parthenocarpic fruit set and fruit size, but a negative effect on flower induction the next year. After CPPU + GA sprays, percent fruit set was similar, or greater, compared to natural pollinated trees. The parthenocarpic fruits induced by CPPU + GA had an increased length to diameter ratio. CPPU stimulated, and GA₄ and GA₇ reduced, the russeting of the parthenocarpic fruits. The internal quality of the fruits was hardly affected, but Ca-deficiency symptoms occurred more frequently in parthenocarpic fruits.     

Medium,container and genotype all influence in vitro cold storage of apple germplasm

The goal of this study was to evaluate the in vitro storage of apple germplasm by screening a range of genotypes followed by more comprehensive testing of multiple parameters on two genotypes of differing species, Malus domestica cultivar Grushovka Vernenskaya and wild Malus sieversii selection TM-6. Stored plants were rated on a 6 point scale (0 low to 5 high) for plant appearance at 3 month intervals after storage at 4°C. Combinations of carbon source (sucrose and/or mannitol), nitrate nitrogen content (25, 50 or 100%) and plant growth regulators (ABA, BAP, IBA) were studied in three types of containers (tissue culture bags, test tubes or jars). An initial screen of 16 genotypes stored in tissue culture bags indicated that plantlets could be stored at 4°C for 9–14 months without subculture on standard 3% sucrose Murashige and Skoog (1962) (MS) medium with no plant growth regulators (PGRs). In subsequent in-depth studies on the two genotypes, ANOVA indicated highly significant interactions of medium, container and genotype. ‘Grushovka Vernenskaya’ shoots with no PGRs and 3% sucrose remained viable (ratings of ≥1) for 21 months of storage in bags. Storage on reduced nitrogen (MS with 25% nitrogen), PGRs, and 3% sucrose kept ‘Grushovka Vernenskaya’ shoot condition rated >2 at 21 months. Addition of 0.5 or 1 mg⁻¹ abscisic acid (ABA) also improved plant ratings at 21 months. The longest storage for ‘Grushovka Vernenskaya’ was 33–39 months with PGRs and 3% sucrose in either tubes or jars. Addition of abscisic acid (ABA) to the medium did not improve storage of plantlets in jars and tubes at 15 months. TM-6 stored best in tubes on 3% sucrose with PGRs or in jars on 2% mannitol and 2% sucrose. Overall it appears that cold storage of apple shoot cultures can be successful for 21 months in tissue culture bags with 25% MS nitrate nitrogen, 3% sucrose, and no PGRs or for 33 months in jars or tubes on MS with 3% sucrose and PGRs. Preliminary RAPD analysis found no significant differences between plants stored for 39 months and non-stored controls.     

Regeneration of androgenic embryos in apple (<Emphasis Type="Italic">Malus x domestica</Emphasis> Brokh.) <Emphasis Type="Italic">via</Emphasis> anther and microspore culture

Based on optimized protocols for anther and microspore culture in apple (Malus x domestica Borkh.), the regeneration phase and the efficiency of the processes in general were compared by using the same androgenic material of two experimental years. Microspore culture resulted in an increase in embryo induction depending on the genotype (Höfer 2004), however anther culture was superior to microspore culture in the total number of regenerated plants. The regeneration process in anther and microspore culture is similar. Two developmental pathways were observed: 1) secondary embryogenesis followed by adventitious shoot formation and 2) direct adventitious shoot formation from primary embryos. Induction and regeneration processes are delayed in microspore culture as compared with anther culture. The reasons for the reduced regeneration efficiency in microspore culture are discussed.     

Identification and stability of QTLs for fruit quality traits in apple

Breeding for fruit quality traits is complex due to the polygenic (quantitative) nature of the genetic control of these traits. Therefore, to improve the speed and efficiency of genotype selection, attention in recent years has focused on the identification of quantitative trait loci (QTLs) and molecular markers associated with these QTLs. However, despite the huge potential of molecular markers in breeding programmes, their implementation in practice has been limited by the lack of information on the stability of QTLs across different environments and within different genetic backgrounds. Here, we present the results from a comprehensive analysis of the inheritance of fruit quality traits within a population derived from a cross between the apple cultivars ‘Telamon’ and ‘Braeburn’ over two successive seasons. A total of 74 different QTLs were identified for all the major fruit physiological traits including fruit height, diameter, weight and stiffness, flesh firmness, rate of flesh browning, acidity, the oBrix content and harvest date. Seventeen of these QTLs were ‘major’ QTLs, accounting for over 20% of the observed population variance of the trait. However, only one third (26) of the identified QTLs were stable over both harvest years, and of these year-stable QTLs only one was a major QTL. A direct comparison with published QTL results obtained using other populations (King et al., Theor Appl Genet 102:1227–1235, 2001; Liebhard et al., Plant Mol Biol 52:511–526, 2003) is difficult because the linkage maps do not share a sufficient number of common markers and due to differences in the trait evaluation protocols. Nonetheless, our results suggest that for the six fruit quality traits which were measured in all populations, nine out of a total of 45 QTLs were common or stable across all population × environments combinations. These results are discussed in the framework of the development and application of molecular markers for fruit quality trait improvement.     

The effects of pollen diversity on plant reproduction: insights from apple

For many plants, the number of pollen genotypes deposited on a flower’s stigma is positively related to fruit maturation and seed number; however, the mechanisms underlying this effect are less understood. Here we examined whether diversity of pollen (1, 3, or 5 donors) affects reproductive success in self-incompatible apple (Malus × domestica). Using paternity analysis, we then assessed the siring rate of individual donors to test whether diversity effects are related to the presence of a superior pollen donor or to donor × donor interactions. Increasing the diversity of compatible pollen enhanced seed number and reduced seed abortion in some but not all recipient genotypes. This effect was associated with an increased number of sires per fruit and non-random siring success among pollen donors. Two donors had consistently high siring rates, regardless of recipient genotype; however, the siring success of pollen donors was not correlated with their siring success in single-donor pollinations. Rather, siring success was affected by the identity of other pollen genotypes present on the stigma. Our results therefore suggest that the effects of pollen diversity are variable but may enhance fecundity by fostering interactions between pollen donors.     

Micropropagation of thirteen Malus cultivars and rootstocks,and effect of antibiotics on proliferation

Several factors that affect in vitro establishment, proliferation, and rooting of thirteen Malus cultivars and rootstocks were studied. Apple shoot tips (1.5±0.5 cm in length) were established using ascorbic and citric acids as antioxidants. Four proliferation media containing 1.0 mg 1^–1 BA and different concentrations of IBA and GA₃ were tested. Proliferation rates varied depending on the genotype and medium used. The highest proliferation rate was obtained for a rootstock that produced 11.6±2.5 shoots (1.5±0.8 cm in length) per tube per month. Rooting was induced with IBA for all the genotypes tested. The optimal IBA concentration was cultivar dependent (between 0.1 and 1.0 mg 1^–1 IBA), and lower concentrations were necessary to induce rooting in liquid rather than in solid medium.The effects on shoot-tip proliferation of cefotaxime, carbenicillin and kanamycin, three antibiotics commonly used for transformation studies, were also evaluated. Cefotaxime at 200 mg 1^–1 stimulated shoot growth and development, but at 500 mg 1^–1 caused abnormal shoot morphology. Carbenicillin at 500 mg 1^–1, alone or in combination with cefotaxime at 200 mg 1^–1, inhibited proliferation and caused excessive enlargement of the basal leaves, inducing callus formation and release of phenolic compounds in the medium. Kanamycin at 50 mg 1^–1 was phytotoxic and caused shoot chlorosis and necrosis. Consideration of the toxicity of these antibiotics is critical when designing transformation schemes for selection and recovery of transgenic apple plants.Abbreviations BA benzyladenine - cef cefotaxime - crb carbenicillin - GA₃ gibberellic acid - IBA indole-3-butyric acid - Kan kanamycin - ms Murashige and Skoog [19] macro- and micro-nutrients - NAA naphthalene-acetic acid     

A new,efficient method using 8-hydroxy-quinolinol-sulfate for the initiation and establishment of tissue cultures of apple from adult material

Applying the new method for culture initiation 16 different cultivars of Malus domestica could be established in vitro from shoot tips of adult orchard trees. Actively growing shoot tips were cleaned and surface disinfested, dissected to 2–3 mm and placed on a modified MS-medium with 4.4 M BA. Explants were covered for 24 h with 200 l of a 0.1% solution of 8-hydroxy-quinolinol-sulfate (8-HQS) and transferred to a medium containging both auxin and cytokinin after 2 weeks. The application of 8-HQS induced a strong reduction of the infection rate and inhibited the browning of the explants and the media. After 7 days yields of 50–90% sterile explants could be obtained in comparison to 100% losses of untreated shoot tips. After 60 days variable rates of actively growing shoots could be observed, depending on the genotypes. The described method allows a successful establishment of fruit trees from adult orchard material on one hand by strongly reducing the browning, caused by the oxidation of polyphenolic compounds by polyphenoloxidases, and on the other hand 8-HQS can strongly increase the yield of explants without contamination, independently from the vegetation period and the phytosanitary state of the donor material.Abbreviations BA 6-benzyladenine - IBA indolebutyric acid - 8-HQS 8-hydroxy-quinolinol-sulfate     

How rainfall, relative humidity and temperature influence volatile emissions from apple trees in situ

Headspace volatiles from apple-bearing twigs were collected in the field with a Radiello sampler during three different diurnal periods over the complete fruit growing season. Analyses by thermal desorption-GC-MS identified a total of 62 compounds in changing quantities, including the terpenoids alpha-pinene, camphene, beta-pinene, limonene, beta-caryophyllene and (E,E)-alpha-farnesene, the aldehydes (E)-2-hexenal, benzaldehyde and nonanal, and the alcohol (Z)-3-hexen-1-ol. The variations in emission of these plant odours were statistically related to temperature, humidity and rainfall in the field. Remarkably, rainfall had a significant positive influence on changes in volatile release during all three diurnal periods, and further factors of significance were temperature and relative humidity around noon, relative humidity in the late afternoon, and temperature and relative humidity during the night. Rainfall was associated consistently with an increase in the late afternoon in terpene and aldehyde volatiles with a known repellent effect on the codling moth, one of the key pests of apple fruit. During the summer of 2003, a season characterized by below-average rainfall, some postulated effects of drought on trees were tested by establishing correlations with rainfall. Emissions of the wood terpenes alpha-pinene, beta-pinene and limonene were negatively correlated with rainfall. Another monoterpene, camphene, was only detected in this summer but not in the previous years, and its emissions were negatively correlated with rainfall, further supporting the theory that drought can result in higher formation of secondary metabolites. Finally, the two green leaf volatiles (E)-2-hexenal and (Z)-3-hexen-1-ol were negatively correlated with rainfall, coinciding well with the expectation that water deficit stress increases activity of lipoxygenase. To our knowledge, this work represents the first empirical study concerning the influence of abiotic factors on volatile emissions from apple trees in situ.