Apple Genetic Resources Research Articles

Fruit quality of old local Bulgarian apple genetic resources

Fruit quality of old local Bulgarian apple genetic resources

Genetic Characterization of the Norwegian Apple Collection

Commercial fruit production in Norway is located at around latitude 60° north, demanding a careful choice of adapted cultivars. The most comprehensive collection of apple genetic resources in Norway is being kept in the Norwegian Apple Collection (NAC) at the Njøs Fruit and Berry Centre (NJØS). The collection contains around 350 accessions and was recently genotyped with a single nucleotide polymorphism (SNP) array. Curated SNP data were used for the assessment of structure and diversity, pedigree confirmation, and core collection development. In the following SNP analysis, we identified several duplicates and parent-child relationships. Across the geographic regions represented, the collection was equally diverse. Different methods for analyzing population structure were applied. K-means clustering and a Bayesian modeling approach with prior assumptions of the data revealed five subpopulations associated with geographic breeding centers. The collection has a distinct genetic structure and low relatedness among the accessions; hence, two core collections with 100 accessions in each were created. These new core collections will allow breeders and researchers to use the NAC efficiently. The results from this study suggest that several of the accessions in the Norwegian Apple Collection could be of high importance for breeding purposes.

Using High-Density SNP Array to Investigate Genetic Relationships and Structure of Apple Germplasm in Bosnia and Herzegovina

Apple accessions, currently maintained within the two main ex situ collections in Bosnia and Herzegovina (B&H), have previously been genotyped using microsatellite markers. The obtained molecular data provided insight into mislabeled accessions and redundancies, as well as the overall genetic structure of the germplasm. The available dataset enabled the creation of a core collection consisting of 52 accessions. The reliability and usefulness of microsatellites has made this low-density marker system a norm in studies on apple germplasm. However, the increased access to medium- and high-density SNP arrays, developed specifically for apples, has opened new avenues of research into apple genetic resources. In this study, 45 apple genotypes consisting of 33 diploid core collection accessions from B&H and 12 international reference cultivars were genotyped using an Axiom® Apple 480 K SNP array in order to examine their genetic relationships, population structure and diversity, as well as to compare the obtained results with those calculated on previously reported SSR profiles. The SNPs displayed a better ability to differentiate apple accessions based on their origin, as well as to cluster them according to their pedigree. Calculating identity by descent revealed 16 pairings with first-degree relationships and uncovered the introgression of ‘Delicious’ and ‘Golden Delicious’ into the core collection.

EVALUATION OF SCAB AND POWDERY MILDEW RESISTANCE OF APPLE GERMPLASM COLECTTED AT RIFG PITESTI

The rising incidence of biotic and abiotic stresses makes commercial fruit production increasingly difficult in Europe, especially apple orchards which are affected by fungal diseases, like scab and powdery mildew, caused by Venturia inaequalis Cooke Winter and Podosphaera leucotricha Ellis & Everh. Salmon. Releasing and planting of apple resistant cultivars is a promising strategy. A set of 527 apple cultivars from the apple gene bank collected at Research Institute for Fruit Growing (RIFG) Pitești was evaluated for the incidence of scab (on leaves and fruits) and powdery mildew (on leaves and top shoots) in three consecutive years (2018, 2019 and 2020). Phenotypic results were compared to data reported at the evaluation made in 2006. Unfortunately, the incidence of both scab and powdery mildew increased significantly in the last years. In 2021, 48 Romanian apple cultivars were analyzed with molecular markers linked to Rvi2, Rvi4, Rvi5, Rvi6, Rvi8 and Plw. The markers linked to Rvi6 was detected in 31 cultivars. Alleles linked to Plw were expressed from three cultivars. The information on resistance / susceptibility of apple genetic resources towards economically important diseases is important for breeding. Using a systematic screening of the apple cultivar collection, several cultivars with high value for resistance breeding and sustainable growing were identified.

Validation Assay of Md-ACS1, Md-ACO1, and Md-PG1 Molecular Markers Associated with Storability in Apples

The purpose of this study was to examine the potential utility of marker-assisted selection (MAS) based on storability-associated molecular markers in apple breeding and to provide genotype information for the markers Md-ACS1, Md-ACO1, and Md-PG1 in apple genetic resources as basic data for the use of breeding materials. We analyzed 750 apple genetic resources to assess the allelic composition of Md-ACS1 and Md-ACO1, which play roles in the ethylene biosynthesis pathway, and Md-PG1, which is involved in cell wall degradation. For 108 of the genetic resources used for genotyping, we measured fruit firmness using a texture analyzer (10 mm plunger) at harvest and after 20 days of room temperature (20~25℃) storage. Md-ACS1 and Md-PG1 were found to be associated with changes in fruit firmness (the difference between firmness at harvest and after storage), with ACS1-2/2, PG1-1/1, and PG1-2/2 showing the lowest changes in fruit firmness. In addition, we found that changes in fruit firmness were smallest in late-harvest species, even for the same genotype. In contrast, Md-ACO1 appeared to be unrelated to the storability of fruit. Of the 750 apple genetic resources screened, the genotypes ACS1-2/2, and PG1-1/1 or PG1-2/2 were detected in 3.6% of accessions, including ‘Fuji’, bud mutation cultivars of ‘Fuji’, ‘Chubu’, and ‘Iwakami’. The Md-ACS1 and Md-PG1 markers could have potential utility in assessments of storability and applied in MAS to improve the efficiency of apple breeding.

Some Important Horticultural Properties of Summer Apple Genotypes from Coruh Valley in Turkey

ABSTRACT Coruh Valley located in Northeastern part of Turkey is accepted one of the 34 hotspots for plant biodiversity area by International Union for Conservation of Nature. In this study, 22 seed propagated summer apple genotypes were evaluated using a number of phenological, morphological, and biochemical markers. Phenological, morphological, and sensory traits were highly differed among genotypes. Harvest dates of genotypes were found quite variable ranging from 9 July to 8 August. Fruit weight were found between 81.3 and 125.4 g. Round, conic, and oblate were the common fruit shapes of genotypes. Fruit firmness and stalk length recorded in the range of 3.10–6.11 kg/cm2 and 4.0–8.0 mm, respectively. High total phenols and antioxidant capacity were found for genotypes CVE 16 and CVE2. This study could help promote the commercialization of promising summer apple genotypes, which are rich in bioactive compounds for use in for nutraceutical purposes. CVE2 and CVE16 genotypes displayed superior traits as summer apple genetic resources, and they could be important for future breeding activities.

Analysis of Genetic Diversity Among ‘Misket’ Apple Clones Using AFLP, SSR and RAPD Markers

Knowledge of genetic relationship among genotypes is an important concern for utilization of germplasm resources in breeding. The need for knowledge in local apple cultivars is increasing and molecular marker analysis has contributed to understanding of the apple genetic diversity and phylogenetic relationship between genotypes. Three different DNA-based techniques, random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) were used for detecting genetic variation among the 30 local ‘Misket’ apple genotypes. A total of 423 bands amplified and 205 polymorphic band were obtained with three marker techniques. Thirty RAPD primers amplified 207 bands, of which 91 were polymorphic (40.1%), 10 SSR primers produced 33 bands and 26 of them were polymorphic (78.78%) and 5 AFLP combinations amplified 183 bands of which 88 were polymorphic (48.08%). The average numbers of polymorphic marker per primer combination were 17.6, 3.03 and 2.6 for AFLP, RAPD and SSR respectively. Our results indicate that SSR was less informative in characterizing closely related ‘Misket’ apple genotypes, compared with RAPD and AFLP markers. AFLP seemed to best suited for evaluating the genetic relationship among the apple genotypes. Closely related genotypes may require more than one marker technique. The findings will be useful to identify and evaluate the local growing apple genetic resources.

Phenotypic and molecular characterization of apple (Malus × domestica Borkh) genetic resources in Greece

Phenotypic and molecular characterization of apple (Malus × domestica Borkh) genetic resources in Greece

Analyses of fruit attributes by multidimensional scaling method of apple genetic resources from coastal zone of North Eastern Anatolia, Turkey

Abstract North Eastern Anatolia had a significant contribution to development of cultivated apple. A lot of local apple genotypes have been successfully grown without any pesticide applications despite to high rainfall (900–2300 mm) and humidity (70–85%) especially at the coastal part of the Eastern Black Sea Region of North Eastern Anatolia. We have investigated and selected local apple genotypes from the region which could be of importance for apple breeding by fruit attributes. In this study, sensory characteristics (186 accessions) and quantitative characteristics (176 accessions) determined based on Apple Descriptor, and were analyzed by Multidimensional Scaling analysis. Harvest maturity dates classified the genotypes into early season (19), mid-season (13) and late season (154) apples. Among the genotypes, 39.25% had medium-sized fruits, 53.23% had intermediate attractiveness, 50% had ground color of green-yellow, 59.68% had skin over color of red, 61.29% had good eating quality and 53.76% had fine flesh texture. Quantitative characters showed large variation that fruit weight ranged from 27.4 g to 246.4 g, SSC from 8.6% to 15.4%, TA from 0.08% to 2.24%. Multidimensional Scaling analysis indicated that the genotypes harvested in early and mid-season exhibited larger variation for sensory and quantitative characteristics than did late season apples. Although several genotypes were differentiated for investigated characteristics and/or variables in early and late season groups, mid-season apples did not tend to form any cluster.

Analysis of the genetic diversity and structure of the Spanish apple genetic resources suggests the existence of an Iberian genepool

AbstractThe nature and structure of genetic diversity in the Spanish apple germplasm preserved at the national level was widely unknown, since studies performed to date on this topic have been exclusively carried out at the regional scale. Here, 1453 accessions from Spanish collections of Malus × domestica were evaluated with a common set of 13 SSR (Simple Sequence Repeats) markers in order to estimate genetic diversity, to identify the underlying genetic structure and to unravel the relationships among them and among a wide set of international cultivars for reference. In total, 737 unique genotypes were identified, 581 diploids and 156 triploids. Using a model‐based Bayesian clustering procedure, two reconstructed populations were obtained for diploid genotypes; one retaining only Spanish cultivars (42% of genotypes), and a second containing all foreign cultivars the latter exhibiting evidence supporting the existence of a secondary sub‐structure. Similarly, analysis performed on the 156 triploid genotypes also revealed two reconstructed populations; one exclusively associated with local Spanish genotypes (44%). The Jaccard coefficient allowed clustering by UPGMA (Unweighted Pair Group Method) diploid and triploid genotypes, and remarkable differences in allelic composition among the different partitioning levels were found. AMOVA analyses showed moderate but significant differentiation among the main groups (0.08 ≤ FST ≤ 0.12). Our results highlight an important fraction of the Spanish apple germplasm that constitutes a differentiated genepool with respect to the international and commercial apple cultivars. Moreover, the extent of the Spanish genetic diversity was spatially distributed along the northern Iberian Peninsula, suggesting an extensive migration of genotypes along the country. This study is the first valuable action for genetic conservation of apple at the national scale, and constitutes a decisive step towards the definition of a Spanish core collection that will be useful for further studies in dissecting the genetic control of important horticultural traits through genome‐wide association analysis in apple.

Heritability and genetic variation of plant biomass, transpiration, and water use efficiency for an apple core-collection

To study the heritability and genetic variation of plant biomass, transpiration and water use efficiency (WUE) in apple (Malus × domestica Borkh.), 193 genotypes from an INRA apple core-collection were evaluated in 2014. Four grafted replicates per genotype grown as one-year-old scions were studied in a high-throughput phenotyping platform (PhenoArch). Individual pot weight was recorded twice a day and irrigation was scheduled to maintain constant soil water content (SWC) and avoid any water stress during 46 days. Plant 3D pictures were automatically taken every two days. Analysis of pictures and pot weights differences allowed the estimation of whole-plant biomass and transpiration during the experiment. WUE was calculated as the ratio of accumulated biomass to transpiration. For each trait, we tested nine mixed models to account for the genetic effect and spatial variability inside PhenoArch. The Best Linear Unbiased Predictors (BLUPs) of genetic values were estimated after model selection. For each trait, broad-sense heritability (H2) was calculated from variance estimates. Plant biomass, transpiration and WUE had H2 values of 0.76, 0.54, and 0.73, respectively. The H2 value of WUE is high enough to consider that this trait is under genetic control in apple. The genetic variation of WUE indicated that apple genetic resources such as the INRA core-collection could be extremely useful to improve apple plant material for the use of water.

A strategy to conserve worldwide apple genetic resources: survey results

A strategy to conserve worldwide apple genetic resources: survey results

Unravelling genetic diversity and cultivar parentage in the Danish apple gene bank collection

Characterization of apple germplasm is important for conservation management and breeding strategies. A set of 448 Malus domestica accessions, primarily of local Danish origin, were genotyped using 15 microsatellite markers. Ploidy levels were determined by flow cytometry. Special emphasis was given to pedigree reconstruction, cultivar fingerprinting and genetic clustering. A reference set of cultivars, mostly from other European countries, together with a private nursery collection and a small set of Malus sieversii, Malus sylvestris and small-fruited, ornamental Malus cultivars, was also included. The microsatellite markers amplified 17–30 alleles per loci with an average degree of heterozygosity at 0.78. We identified 104 (23%) duplicate genotypes including colour sports. We could infer first-degree relationships for many cultivars with previously unknown parentages. STRUCTURE analysis provided no evidence for a genetic structure but allowed us to present a putative genetic assembly that was consistent with both PCA analysis and parental affiliation. The Danish cultivar collection contains 10% duplicate genotypes including colour sports and 22% triploids. Many unique accessions and considerable genetic diversity make the collection a valuable resource within the European apple germplasm. The findings presented shed new light on the origin of Danish apple cultivars. The fingerprints can be used for cultivar identification and future management of apple genetic resources. In addition, future genome-wide association studies and breeding programmes may benefit from the findings concerning genetic clustering and diversity of cultivars.

Redundancies and Genetic Structure among ex situ Apple Collections in Norway Examined with Microsatellite Markers

Apple genetic resources in Norway are currently conserved within a number of local clonal archives. However, during establishment of these ex situ collections, primary focus was not on capturing as much of the diversity as possible, but instead on preserving cultivars of particular importance to specific fruit-growing areas. To identify redundancies within the collection as well as to assess the genetic diversity and structure of apple germplasm currently being conserved in Norway, eight microsatellites were used in genetic characterization of 181 apple accessions. Overall, 14 cases of synonym or possibly mislabeled accessions were identified, as well as several homonyms and duplicates within and among the analyzed collections. The information obtained should contribute to overall better management of the preserved germplasm. Bayesian analysis of genetic structure revealed two major clusters, one containing most of the foreign cultivars, while the other consisted mainly of traditional Scandinavian cultivars, but also some very winter-hardy genotypes such as ‘Charlamovsky’, ‘Gravenstein’, ‘Transparente Blanche’, and ‘Wealthy’. Analyses of molecular variance (AMOVA) detected a significant genetic differentiation among the clusters (fCT = 0.077; P < 0.01). The results of the Bayesian analyses do not indicate a strong differentiation between the foreign and the Norwegian apple accessions, however, they do suggest that climate adaptation has had a significant influence on the genetic structure of the preserved germplasm. Overall, apple accessions currently maintained ex situ in Norway represent a diverse germplasm which could be very valuable in future breeding programs, especially for the Scandinavian climate.

Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level.

BackgroundThe amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North + East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe.ResultsA Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST = 0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST = 0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars.ConclusionsThe variation found at group and subgroup levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0818-0) contains supplementary material, which is available to authorized users.

Genetic Diversity, Population Structure, Parentage Analysis, and Construction of Core Collections in the French Apple Germplasm Based on SSR Markers

In-depth characterization of apple genetic resources is a prerequisite for genetic improvement and for germplasm management. In this study, we fingerprinted a very large French collection of 2163 accessions with 24 SSR markers in order to evaluate its genetic diversity, population structure, and genetic relationships, to link these features with cultivar selection date or usage (old or modern, dessert or cider cultivars), and to construct core collections. Most markers were highly discriminating and powerful for varietal identification, with a probability of identity P (ID) over the 21 retained SSR loci close to 10−28. Pairwise comparisons revealed 34 % redundancy and 18.5 % putative triploids. The results showed that the germplasm is highly diverse with an expected heterozygosity H e of 0.82 and observed heterozygosity H o of 0.83. A Bayesian model-based clustering approach revealed a weak but significant structure in three subgroups (FST = 0.014–0.048) corresponding, albeit approximately, to the three subpopulations defined beforehand (Old Dessert, Old Cider, and Modern Cultivars). Parentage analyses established already known and yet unknown relationships, notably between old cultivars, with the frequent occurrence of cultivars such as “King of Pippin” and “Calville Rouge d’Hiver” as founders. Finally, core collections based on allelic diversity were constructed. A large dessert core collection of 278 cultivars contained 90 % of the total dessert allelic diversity, whereas a dessert subcore collection of 48 cultivars contained 71 % of diversity. For cider apples, a 48-cultivar core collection contained 83 % of the total cider allelic diversity.

Morphological Characterization of Autochthonous Apple Genetic Resources in Montenegro

Autochthonous apple varieties are still keeping their importance in Montenegro and they are valuable resources as human food and an important part of rural landscape. The aim of this study was to study and preserve morphological diversity of 30 autochthonous apple varieties in Montenegro between 2008 and 2010. We found a great variation on blooming period and maturation time among varieties and classified them as very early, early, mid and late for blooming and early, middle, late and very late for maturation. Fruit weight varied in wide range from 40.76 g to 206.74 g and ‘Krupnaja’, ‘Krstovaca’ and ‘Babovaca’ produced biggest fruits (191.83–206.74 g). Soluble solid content (SSC) varied between 11.0 to 16.1 % among varieties and ‘Borovaca’, ‘Aleksandrija’, ‘Krstovaca’, ‘Dapsicanka’, ‘Bosnika’, ‘Rebraca’ and ‘Babovaca’ had the highest SSC values imply that they can be commercially used in production of spirits, wine, concentrate and jam and also for drying. Based on 3-year average data for 25 properties, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) dendrogram showed a high degree of variability among the studied varieties dividing them into 5 groups and 3 independent accessions.

The vulnerability of US apple (Malus) genetic resources

Apple (Malus × domestica Borkh.) is one of the top three US fruit crops in production and value. Apple production has high costs for land, labor and inputs, and orchards are a long-term commitment. Production is dominated by only a few apple scion and rootstock cultivars, which increases its susceptibility to dynamic external threats. Apple crop wild relatives, including progenitor species Malus sieversii (Ledeb.) M. Roem., Malus orientalis Uglitzk., Malus sylvestris (L.) Mill., and Malus prunifolia (Willd.) Borkh., as well as many other readily hybridized species, have a wide range of biotic and abiotic stress resistances as well as desirable productivity and fruit quality attributes. However, access to wild materials is limited and wild Malus throughout the world is at risk of loss due to human encroachment and changing climatic patterns. The USDA-ARS National Plant Germplasm System (NPGS) Malus collection, maintained by the Plant Genetic Resources Unit in Geneva, NY, US is among the largest collections of cultivated apple and Malus species in the world. The collection currently has 5004 unique accessions in the field and 1603 seed accessions representing M. × domestica, 33 Malus species, and 15 hybrid species. Of the trees in the field, 3,070 are grafted and are represented by a core collection of 258 individuals. Many wild species accessions are represented as single seedlings (non-grafted). The crop vulnerability status of apple in the US is moderate because although there are a few breeders developing new commercial cultivars who also access Malus species, threats and challenges include new diseases, pests, and changing climate combined with industry needs and consumer demands, with a limited number of cultivars in production.

Crop‐to‐wild gene flow and spatial genetic structure in the closest wild relatives of the cultivated apple

Crop‐to‐wild gene flow have important evolutionary and ecological consequences and require careful consideration in conservation programs for wild genetic resources of potential use in breeding programs and in assessments of the risk of transgene escape into natural ecosystems. Using 26 microsatellites and a set of 1181 trees, we investigated the extent of introgression from the cultivated apple, Malus domestica, to its three closest wild relatives, M. sylvestris in Europe, M. orientalis in the Caucasus, and M. sieversii in Central Asia. We found footprints of introgression from M. domestica to M. orientalis (3.2% of hybrids), M. sieversii (14.8%), and M. sylvestris (36.7%). Malus sieversii and M. orientalis presented weak, but significant genetic structures across their geographic range. Malus orientalis displayed genetic differentiation with three differentiated populations in Turkey, Armenia, and Russia. Malus sieversii consisted of a main population spread over Central Asia and a smaller population in the Tian Shan Mountains. The low Sp values suggest high dispersal capacities for the wild apple relatives. High potential for crop‐to‐wild gene flow in apples needs to be considered in the implementation of in situ and ex situ actions for the conservation of wild apple genetic resources potentially useful to plant breeding.

Comparison of genetic diversity structure analyses of SSR molecular marker data within apple (Malus×domestica) genetic resources

The aim of this study was to compare traditional hierarchical clustering techniques and principal coordinate analysis (PCoA) with the model-based Bayesian cluster analyses in relation to subpopulation differentiation based on breeding history and geographical origin of apple (Malus×domestica Borkh.) cultivars and landraces. We presented the use of a set of 10 microsatellite (SSR) loci for genetic diversity structure analyses of 273 apple accessions from national genetic resources. These SSR loci yielded a total of 113 polymorphic SSR alleles, with 5-18 alleles per locus. SSR molecular data were successfully used in binary and allelic input format for all genetic diversity analyses, but allelic molecular data did not reveal reliable results with the NTSYS-pc and BAPS softwares. A traditional cluster analysis still provided an easy and effective way for determining genetic diversity structure in the apple germplasm collection. A model-based Bayesian analysis also provided the clustering results in accordance to traditional cluster analysis, but the analyses were distorted by the presence of a dominant group of apple genetic resources owing to the narrow origin of the apple genome. PCoA confirmed that there were no noticeable differences in genetic diversity structure of apple genetic resources during the breeding history. The results of our analyses are useful in the context of enhancing apple collection management, sampling of core collections, and improving breeding processes.