Isolation and <Emphasis Type="Italic">S</Emphasis>-genotyping application of <Emphasis Type="Italic">S</Emphasis>-allelic polymorphic <Emphasis Type="Italic">MdSLFB</Emphasis>s in apple (<Emphasis Type="Italic">Malus domestica</Emphasis> Borkh.)

Apple (Malus domestica Borkh.) possesses gametophytic self-incompatibility (GSI) which is controlled by S-RNase in the pistil as well as a pollen S-determinant that has not been well characterized. The identification of S-locus F-box brother (SFBB) genes, which are good candidates for the pollen S-determinant in apple and pear, indicated the presence of multiple S-allelic polymorphic F-box genes at the S-locus. In apple, two SFBB gene groups have been described, while there are at least three groups in pear. In this report, we identified five MdSLFB (S-RNase-linked F-box) genes from four different S-genotypes of apple. These genes showed pollen- and S-allele-specific expression with a high polymorphism among S-alleles. The phylogenetic tree suggested that some of them belong to SFBBα or β groups as described previously, while others appear to be different from SFBBs. In particular, the presence of MdSLFB3 and MdSLFB9 suggested that there are more S-allelic polymorphic F-box gene groups in the S-locus besides α and β. Based on the sequence polymorphism of MdSLFBs, we developed an S-genotyping system for apple cultivars. In addition, we isolated twelve MdSLFB-like genes, which showed pollen-specific expression without S-allelic polymorphism.     

Dating and functional characterization of duplicated genes in the apple (<Emphasis Type="Italic">Malus domestica</Emphasis> Borkh.) by analyzing EST data

Background  

Gene duplication is central to genome evolution. In plants, genes can be duplicated through small-scale events and large-scale duplications often involving polyploidy. The apple belongs to the subtribe Pyrinae (Rosaceae), a diverse lineage that originated via allopolyploidization. Both small-scale duplications and polyploidy may have been important mechanisms shaping the genome of this species.     

Maize <Emphasis Type="Italic">Lc</Emphasis> transcription factor enhances biosynthesis of anthocyanins,distinct proanthocyanidins and phenylpropanoids in apple (<Emphasis Type="Italic">Malus domestica</Emphasis> Borkh.)

Flavonoids are a large family of polyphenolic compounds with manifold functions in plants. Present in a wide range of vegetables and fruits, flavonoids form an integral part of the human diet and confer multiple health benefits. Here, we report on metabolic engineering of the flavonoid biosynthetic pathways in apple (Malus domestica Borkh.) by overexpression of the maize (Zea mays L.) leaf colour (Lc) regulatory gene. The Lc gene was transferred into the M. domestica cultivar Holsteiner Cox via Agrobacterium tumefaciens-mediated transformation which resulted in enhanced anthocyanin accumulation in regenerated shoots. Five independent Lc lines were investigated for integration of Lc into the plant genome by Southern blot and PCR analyses. The Lc-transgenic lines contained one or two Lc gene copies and showed increased mRNA levels for phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), flavanone 3 beta-hydroxylase (FHT), dihydroflavonol 4-reductase (DFR), leucoanthocyanidin reductases (LAR), anthocyanidin synthase (ANS) and anthocyanidin reductase (ANR). HPLC-DAD and LC-MS analyses revealed higher levels of the anthocyanin idaein (12-fold), the flavan 3-ol epicatechin (14-fold), and especially the isomeric catechin (41-fold), and some distinct dimeric proanthocyanidins (7 to 134-fold) in leaf tissues of Lc-transgenic lines. The levels of phenylpropanoids and their derivatives were only slightly increased. Thus, Lc overexpression in Malus domestica resulted in enhanced biosynthesis of specific flavonoid classes, which play important roles in both phytopathology and human health.     

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.     

Microsatellite Loci Polymorphism of Apple (<Emphasis Type="Italic">Malus domestica</Emphasis> Borkh.) Genotypes with Different Ploidy Level

In this paper, the microsatellite (SSR) loci analysis was used to study apple genotypes with different levels of ploidy. A total of 47 samples were studied (9 diploids, 21 triploids, and 17 tetraploids) for seven microsatellite loci (GD147, Hi02C07, CH02c11, CH04c07, CH03d07, CH02c09, and GD12). It was possible to refine the pedigrees for some forms. It was established that the tetraploidss 20-9-30 and 20-9-27, selected in a hybrid family from the crossing of Wealthy 4x and Antonovka Obyknovennaya, were probably obtained from the self-pollination of the maternal form, since in the most loci they did not inherit alleles from the paternal form. As a result of the alleles distribution analysis, the spontaneous triploid cultivars Nizkorosloe and Sinap Orlovsky were revealed to be formed from the merge of an unreduced ovum and haploid pollen, since in the heterozygous loci both alleles are inherited from the maternal form and only one from the paternal form. According to the obtained data, studied tetraploids may be divided into two groups, which also reflect the features of tetraploids origin. The first group includes tetraploids inherited alleles from one initial diploid form (including spontaneous and induced tetraploids, as well as forms from self-pollination of the tetraploid maternal form). These teraploids, like diploids, amplify 1–2 alleles per locus (on average, for all 7 loci, one genotype amplifies 13 alleles). The second group includes tetraploids carrying alleles from several initial diploid forms. Tetraploids of this group are highly heterozygous and amplify 3–4 alleles at most loci (the maximum number of alleles at all loci, 24 alleles, was identified in the form 30-47-88). Tetraploids of the second group have a greater potential for the genetic diversity of its offspring. Analysis of polymorphism of microsatellite loci can be used (1) as an alternative or additional method for identifying the triploid hybrids from heteroploid crosses of orthoploid forms, which is based on the analysis of the loci most polymorphic in parental forms, and (2) for the analysis of true hybridity (verification of pedigrees), including tetraploid forms. Moreover, we identified the most polymorphic loci suitable for the above purposes. The aspects of qualitative and quantitative interpretation of the fragment analysis of microsatellite loci results are considered. The possibilities and limitations of the SSR analysis for detection of apple ploidy level are discussed.     

Photosystem 2 is more tolerant to high temperature in apple (<Emphasis Type="Italic">Malus domestica</Emphasis> Borkh.) leaves than in fruit peel

Tolerance of photosystem 2 (PS2) to high temperature in apple (Malus domestica Borkh. cv. Cortland) leaves and peel was investigated by chlorophyll a fluorescence (OJIP) transient after exposure to 25 (control), 40, 42, 44, and 46 °C in the dark for 30 min. The positive L-step was more pronounced in a peel than in leaves when exposed to 44 °C. Heat-induced K-step became less pronounced in leaves than in peel when exposed to 42 °C or higher temperature. Leaves had negative L-and K-steps relative to the peel. The decrease of oxygen-evolving complex (OEC) by heat stress was higher in the peel than in the leaves. OJIP transient from the 46 °C treated peel could not reach the maximum fluorescence (F_m). The striking thermoeffect was the big decrease in the relative variable fluorescence at 30 ms (V_I), especially in the leaves. Compared with the peel, the leaves had less decreased maximum PS2 quantum efficiency (F_v/F_m), photochemical rate constant (K_P), F_m and performance index (PI) on absorption basis (PI_abs) and less increased minimum fluorescence (F₀) and non-photochemical rate constant (K_N), but more increased reduction of end acceptors at PS1 electron acceptor side per cross section (RE₀/CS₀) and per reaction center (RE₀/RC₀), quantum yield of electron transport from Q_A ⁻ to the end acceptors (ϕ _R0) and total PI (PI_abs,total) when exposed to 44 °C. In conclusion, PS2 is more thermally labile than PS1. The reduction of PS2 activity by heat stress primarily results from an inactivation of OEC. PS2 was more tolerant to high temperature in the leaves than in the peel.     

Md-ACS1 and Md-ACO1 genotyping of apple (<Emphasis Type="Italic">Malus</Emphasis> x <Emphasis Type="Italic">domestica</Emphasis> Borkh.) breeding parents and suitability for marker-assisted selection

Fruit ethylene production genotypes for Md-ACS1 and Md-ACO1 were determined for 60 apple cultivars and 35 advanced breeding selections. Two alleles for each gene are commonly found in cultivated apple. Earlier studies showed that genotypes homozygous for the ACS1-2 allele produce less ethylene and have firmer fruit than ACS1-1/2 and ACS1-1/1 genotypes. ACO1 plays a minor role compared to ACS1, with homozygous ACO1-1 having lower ethylene production. In this study, ACS1-2 and ACO1-1 homozygotes had firmer fruit at harvest and after 60 days of 0–1°C cold storage compared to other genotypes. These genotypes, ACS1-2/2 and ACO1-1/1, were observed for the following 8 of 95 cultivars/selections: “Delblush”, “Fuji”, “Pacific Beauty”, “Sabina” and four breeding selections. Cultivars/selections that were homozygous ACS1-2 but not ACO1-1 were: “Ambrosia”, “Aurora Golden Gala”, “CrimsonCrisp”, “Gala”, “GoldRush”, “Huaguan”, “Pacific Rose, “Pacific Queen”, “Pinova”, “Sansa”, “Sonja”, “Sundance”, “Zestar”, and 17 breeding selections. Cultivars with the heterozygous ACS1-1/2 genotype were “Arlet”, “Braeburn”, “Cameo”, “Delicious”, “Delorgue”, “Empire”, “Enterprise”, “Ginger Gold”, “Golden Delicious”, “Granny Smith”, “Honeycrisp”, “Orin”, “Pink Lady”, “Silken”, “Suncrisp”, “Sundowner”, “Sunrise” and 11 breeding selections. No cultivars were detected homozygous for both ACS1-1 and ACO1-1, or for both ACS1-2 and ACO1-2. This study is the first large-scale allelic genotyping of both ethylene synthesis genes for a comprehensive set of apple breeding parents used in an ongoing breeding project. The data reported here are important for informative selection of parent combinations and marker-assisted selection of progeny for breeding low ethylene-producing apple cultivars for better storability and improved consumer acceptance.     

A Genomics Approach Using Expressed Sequence Tags and Microarrays in Ripening Apple Fruit (<Emphasis Type="Italic">Malus domestica</Emphasis> Borkh.)

Apple (Malus domestica Borkh.), an important horticultural crop, produces human health-promoting metabolites during fruit ripening. Because that process, which involves complex biochemical and physiological changes, is genetically programmed, molecular and genetic approaches have been taken to understand the associated cellular mechanisms. The release of 151,687 apple expressed sequence tags (ESTs) into a public database has made possible large-scale studies of expression. Analysis of apple ESTs allows for the identification and characterization of genes with potential roles in fruit development, particularly those related to aroma production and protein degradation during ripening. Apple cDNA and oligonucleotide microarrays have been generated for more comprehensive examinations. Such tools are powerful means for elucidating the molecular events involved in metabolite biosynthesis and physiological changes and will also enable researchers to understand how to control that ripening process.     

A Phytocystatin Gene from <Emphasis Type="Italic">Malus prunifolia</Emphasis> (Willd.) Borkh., <Emphasis Type="Italic">MpCYS5</Emphasis>, Confers Salt Stress Tolerance and Functions in Endoplasmic Reticulum Stress Response in <Emphasis Type="Italic">Arabidopsis</Emphasis>

Cystatins, or phytocystatins (PhyCys), comprise a family of plant-specific inhibitors of cysteine proteinases. They are thought to help regulate endogenous processes and protect plants against biotic or abiotic stresses, such as heat, salinity, cold, water deficit, chilling, and abscisic acid (ABA) treatment. We isolated and identified a novel cystatin gene from Malus prunifolia, MpCYS5. Its expression was typically induced by salt stress treatment; ectopic expression in Arabidopsis enhanced salt tolerance. Physiological parameters confirmed this phenotype, with the transgenics having remarkably lower electrolyte leakage (EL) values, higher chlorophyll concentrations, and lower levels of malondialdehyde (MDA) upon salt treatment. In addition, the accumulation of reactive oxygen species was markedly regulated by MpCYS5 under stress conditions, as shown by fluctuations in the concentrations of hydrogen peroxide and superoxide radicals and the activities of antioxidant enzymes. We also noted that this gene modulated tunicamycin (TM)-induced endoplasmic reticulum (ER) stress tolerance and functioned in the unfolded protein response (UPR)-signaling pathway in Arabidopsis. This was confirmed by the expression of eight ER stress-responsive genes. All marker genes examined were strongly induced in the wild type, while most of them maintained relatively stable over time in the transgenics. These results demonstrated that ectopic expression of a cystatin gene is associated with salt-tolerant and TM-tolerant phenotypes. Therefore, the discovery of MpCYS5 from M. prunifolia might establish a molecular link between the ER stress response and salt tolerance in plants.     

Molecular markers linked to the apple scab resistance gene <Emphasis Type="Italic">Vbj</Emphasis> derived from <Emphasis Type="Italic">Malus baccata jackii</Emphasis>

Breeding for scab-resistant apple cultivars by pyramiding several resistance genes in the same genetic background is a promising way to control apple scab caused by the fungus Venturia inaequalis. To achieve this goal, DNA markers linked to the genes of interest are required in order to select seedlings with the desired resistance allele combinations. For several apple scab resistance genes, molecular markers are already available; but until now, none existed for the apple scab resistance gene Vbj originating from the crab apple Malus baccata jackii. Using bulk segregant analysis, three RAPD markers linked to Vbj were first identified. These markers were transformed into more reliable sequence-characterised amplified region (SCAR) markers that proved to be co-dominant. In addition, three SSR markers and one SCAR were identified by comparing homologous linkage groups of existing genetic maps. Discarding plants showing genotype–phenotype incongruence (GPI plants) plants, a linkage map was calculated. Vbj mapped between the markers CH05e03 (SSR) and T6-SCAR, at 0.6 cM from CH05e03 and at 3.9 cM from T6-SCAR. Without the removal of the GPI plants, Vbj was placed 15 cM away from the closest markers. Problems and pitfalls due to GPI plants and the consequences for mapping the resistance gene accurately are discussed. Finally, the usefulness of co-dominant markers for pedigree analysis is also demonstrated.     

Characterisation of microRNAs from apple (<Emphasis Type="Italic">Malus domestica</Emphasis>'Royal Gala') vascular tissue and phloem sap

Background  

Plant microRNAs (miRNAs) are a class of small, non-coding RNAs that play an important role in development and environmental responses. Hundreds of plant miRNAs have been identified to date, mainly from the model species for which there are available genome sequences. The current challenge is to characterise miRNAs from plant species with agricultural and horticultural importance, to aid our understanding of important regulatory mechanisms in crop species and enable improvement of crops and rootstocks.     

Frequency of a natural truncated allele of <Emphasis Type="Italic">MdMLO19</Emphasis> in the germplasm of <Emphasis Type="Italic">Malus domestica</Emphasis>

Podosphaera leucotricha is the causal agent of powdery mildew (PM) in apple. To reduce the amount of fungicides required to control this pathogen, the development of resistant apple cultivars should become a priority. Resistance to PM was achieved in various crops by knocking out specific members of the MLO gene family that are responsible for PM susceptibility (S-genes). In apple, the knockdown of MdMLO19 resulted in PM resistance. However, since gene silencing technologies such as RNAi are perceived unfavorably in Europe, a different approach that exploits this type of resistance is needed. This work evaluates the presence of non-functional naturally occurring alleles of MdMLO19 in apple germplasm. The screening of the re-sequencing data of 63 apple individuals led to the identification of 627 single nucleotide polymorphisms (SNPs) in five MLO genes (MdMLO5, MdMLO7, MdMLO11, MdMLO18, and MdMLO19), 127 of which were located in exons. The T-1201 insertion of a single nucleotide in MdMLO19 caused the formation of an early stop codon, resulting in a truncated protein lacking 185 amino acids, including the calmodulin-binding domain. The presence of the insertion was evaluated in 115 individuals. It was heterozygous in 64 and homozygous in 25. Twelve of the 25 individuals carrying the insertion in homozygosity were susceptible to PM. After barley, pea, cucumber, and tomato, apple would be the fifth species for which a natural non-functional mlo allele has been found.     

Assessing nitrogen fluxes from roots to soil associated to rhizodeposition by apple (<Emphasis Type="Italic">Malus domestica</Emphasis>) trees

The mass transfer from root to soil by means of rhizodeposition has been studied in grasses and forest trees, but its role in fruit trees is still unknown. In this study, N fluxes from roots to soil were estimated by applying a ¹⁵N mass balance technique to the soil–tree system. Apple (Malus domestica) trees were pre-labelled with ¹⁵N and then grown outdoors in 40 L pots for one vegetative season in (1) a coarse-textured, low organic matter soil, (2) a coarse-textured, high organic matter soil, and (3) a fine-textured, high organic matter soil. At tree harvest the ¹⁵N abundance of the soils was higher than at transplanting, but the total amount of ¹⁵N present in the tree–soil system was similar at transplanting and tree harvest. The soils had a strong effect on N fluxes from and to the soil. In the fine-textured soil, 11% of the total plant-derived nitrogen was transferred to the soil, compared with 2–5% in the two coarse-textured soils. Rhizodeposition was higher in the fine soil (18% of the primary production) than in the coarse-textured soils, whereas higher soil organic matter depressed rhizodeposition. Nitrogen uptake was almost double in the coarse-textured, high organic matter soil versus the other soils. Our results indicate that belowground primary productivity is significantly underestimated if based on root production data only. Rhizodeposition represents a major process, whose role should not be underestimated in carbon and nitrogen cycles in orchard ecosystems.     

Genetic transformation of apple (<Emphasis Type="Italic">Malus</Emphasis> x <Emphasis Type="Italic">domestica</Emphasis>) without use of a selectable marker gene

Selectable marker genes are widely used for the efficient transformation of crop plants. In most cases, antibiotic or herbicide resistance marker genes are preferred because they tend to be most efficient. Due mainly to consumer and grower concerns, considerable effort is being put into developing strategies (site-specific recombination, homologous recombination, transposition, and cotransformation) to eliminate the marker gene from the nuclear or chloroplast genome after selection. For the commercialization of genetically transformed plants, use of a completely marker-free technology would be desirable, since there would be no involvement of antibiotic resistance genes or other marker genes with negative connotations for the public. With this goal in mind, a technique for apple transformation was developed without use of any selectable marker. Transformation of the apple genotype “M.26” with the constructs pPin2Att35SGUSintron and pPin2MpNPR1 was achieved. In different experiments, 22.0–25.4% of regenerants showed integration of the gene of interest. Southern analysis in some transformed lines confirmed the integration of one copy of the gene. Some of these transformed lines have been propagated and used to determine the uniformity of transformed tissues in the plantlets. The majority of the lines are uniformly transformed plants, although some lines are chimeric, as also occurs with the conventional transformation procedure using a selectable marker gene. A second genotype of apple, “Galaxy,” was also transformed with the same constructs, with a transformation efficiency of 13%.