Apple Breeding Research Articles

Profiling apple volatile organic compounds in a New Zealand collection of germplasm as a resource for breeding cultivars with desirable flavors

Flavor is a major component of the apple eating experience, along with taste, texture and appearance. Apples produce a wide array of volatile organic compounds that impart particular flavors. Cultivars producing increased or novel flavors may have more desirability for consumers and help to differentiate the fruit. Efficiently breeding more flavorful apples requires understanding the volatiles present in apple germplasm and their potential sensory impact. As an initial step towards the development of more flavorful apple cultivars, a New Zealand collection of germplasm was surveyed, and seventy-three volatiles were identified as being present in at least half the accessions. Substantial differences in the presence and relative abundance of specific volatiles were uncovered across the accessions and could sometimes be linked to an apple’s flavor profile. The large number of volatiles analyzed allowed relationships between and among molecule classes to be established. Esters were found to be the main drivers of volatile differentiation across accessions. Apples tended to produce either ethyl or acetate esters, suggesting there is different genetic control for these two ester types. Additionally, esters generally had larger broad-sense heritabilities, indicating they could be easier targets for modifying apple flavor. This volatile dataset is a valuable resource for apple breeding, and increases the understanding of an important consumer trait.

Evaluation of the Carbohydrate Composition of Crabapple Fruit Tissues Native to Northern Asia.

A comprehensive comparative analysis of the carbohydrate composition (soluble sugars and pectins) of fruit tissues of Malus baccata, Malus mandshurica, Malus chamardabanica, and Malus sachalinensis, characteristic of the vast territory of Eastern Siberia and the Far East, was carried out. It was shown that a large part of the soluble carbohydrates of the studied species were represented by transport sugars-sorbitol and sucrose. These compounds also provided the main variability in the carbohydrate composition of fruits in the studied material. The polymers pectins and protopectins isolated from the studied fruits were highly methoxylated (up to 60-70%), and their content averaged about 6% of dry weight. The greatest length of pectin polymers was found in the fruit tissues of M. chamardabanica and M. sachalinensis. Data on elemental analysis of fractions of pectins and protopectins of all studied species showed the absence of potentially toxic concentrations of heavy metals. Of note is the rather high content of calcium in both polymer fractions of the four studied species, while its content in protopectin is significantly higher. In addition, in all cases, the presence of low-molecular-weight oligosaccharide molecules with a low-dispersed linear structure was revealed in the tissues of the fruits. It is worth noting that the high content of ascorbic acid was observed in the fruits of all studied species. In addition to being of fundamental interest, information about the carbohydrate composition of the wild Malus species can be useful for apple breeding when choosing sources of genes underlying useful traits.

Rvi4 and Rvi15 are the same apple scab resistance genes

The apple (Malus x domestica) scab (Venturia inaequalis) resistance genes Rvi4 and Rvi15 were mapped to a similar region on the top of linkage group 2 and both resistance genes elicit the same type of resistance reaction, i.e., a hypersensitive response; hence, it is suspected that the two genes may be the same. As the two resistance genes Rvi4 and Rvi15 are currently used in apple breeding, it is important to clarify whether the two resistance genes are the same or not. Several approaches were used to make this determination. First, the pedigree of the genotype GMAL 2473, the source of Rvi15, was reconstructed. GMAL 2473 was found to be an F1 of ‘Russian seedling’, the genotype, which is known to also be the source of Rvi4. Next, it was further demonstrated that ‘Regia’, a cultivar known to carry Rvi4 (and Rvi2), carries the same gene (Vr2-C), which was demonstrated to be the gene inducing Rvi15 resistance. Finally, it was shown that transgenic lines carrying Vr2-C are compatible with race 4 apple scab isolates. Taken all together, these results definitively demonstrate that Rvi4 and Rvi15 are the same resistance gene. For future studies, we suggest referring to this resistance with the first name that was assigned to this gene, namely Rvi4.

A comparison of new and existing rootstocks to reduce canker of apple trees caused by Neonectria ditissima (Nectriaceae, Hypocreales)

The grafting of apple rootstocks on to scions confers benefits including reduced tree size/dwarfing for trellis based growing systems, increased tolerance to physiological stress, and pest and disease management. The current study investigated the effect of rootstock selection on canker and tree death using eight common rootstocks M9 337, M9 337 with Golden Delicious (GD) interstock, M9 EMLA, MM106, M116, M26, Geneva® G11 and G41, in addition to six advanced selections from the NIAB East Malling apple breeding programme EMR-001—EMR-006, all grafted with Gala scions. One of the rootstocks, M9 377 was also grafted with a GD interstock. Two locations in England were selected, the first at East Malling, Kent, the second, at Newent, Gloucestershire. Several variables were analysed including cumulative numbers of dead trees per rootstock from 2017 to 2020, number of rootstock ‘A type’ cankers, number of scion mainstem ‘B type’ cankers, and number of peripheral ‘C + D + E’ branch cankers at the Kent and Gloucestershire locations in the fourth and final assessment year of 2020. Kendall’s rank correlation was used to test if trunk circumference (a measure of tree vigour) and canker were statistically dependant. Results showed that in Kent, there were significant differences between rootstocks for scion B cankers and peripheral C + D + E cankers. There were no significant differences found between rootstocks for rootstock A cankers at Kent, or any of the three canker types in Gloucestershire. There were up to 31.25% dead trees in Kent (EMR-004), and 30% in Gloucestershire (M9 337 with GD interstock, M26), but there were no significant differences in number of dead trees due to rootstock type in either Kent or Gloucestershire. The Kendall’s rank correlation analysis indicated there was almost no dependence of trunk circumference on canker. The three rootstocks with the overall lowest susceptibility to canker were M116, EMR-006, and EMR-004. The industry standard rootstocks M9 EMLA and M9 337 were ranked 12 and 14, and with EMR-001 were the three worst performing rootstocks. The Geneva® rootstocks G11 was ranked 6, and G41 was ranked 11. An interplay of factors are likely involved in the development of canker including location and environmental effects—rainfall, relative humidity, temperature, wind, soil type, topography, aspect, and other seasonal infection processes including pathogen inoculum load, and rainsplash of inoculum between trees and within individual trees, the genetics and physiology of each scion/rootstock combination, water and nutritional status of trees, hormonal and molecular signalling, and orchard management including pruning and removal of cankers.

Evaluation of allelic polymorphism of apple tree resistance genes to scab

The article presents the data of molecular genetic analysis for several genes of the Rvi system of resistance to Venturia inaequalis (Cooke) G. Winter (Rvi1, Rvi6, Rvi8, Rvi9, Rvi11, Rvi14, Rvi16, Rvi17) of the collection and new breeding material of the apple tree (Malus ? domestica Borkh.) of different ploidy, ecological, geographic and genetic origin. We used the CTAB method, which was previously modified in FSBSI NCFSCHVW for more complete purification of DNA samples during extraction. SSR-markers and SCAR-markers linked to the desired 9 genes were used: Rvi1 – CH01D03; Rvi4 – CH02c02a; Rvi6 – CH-Vf1, VfC; Rvi8 – OPL19; Rvi9, Rvi11 – CH05e03; Rvi14 – HB09; Rvi16 – NH030a; Rvi17 – CH-Vf1. The experiment was carried out with the participation of 53 apple samples, including: 17 varieties, 4 elite and 32 hybrid forms of domestic breeding. According to the data obtained, the following genes were classified as quite rare in the studied sample of samples: Rvi9, Rvi16; the presence of genes has not been established: Rvi8, Rvi11, Rvi17. Revealed that among the new breeding material of the apple tree, the Rvi6 gene is the most common, its frequency of occurrence is 62.5%. The study of the allelic polymorphism of several target genes of the Rvi set made it possible to identify promising apple samples for breeding use – carriers of 2–3 resistance genes to Venturia inaequalis (Cooke) G. Winter. According to the DNA marking data, varieties and forms of domestic breeding were selected: Zarya Stavropol'ya, Nika, 12/2-20-75, 17/1-6-72 (carriers of the Rvi1, Rvi6, Rvi14 genes) as promising donors to enhance the efficiency of apple breeding technology for long-term resistance to scab. The data obtained are important for the formation of an identified collection of Malus Mill., the selection of new valuable donors to optimize a number of key stages of the breeding process for long-term resistance to the pathogen by pyramiding the target genes.

Role of the transcription factor MdABF2 in abscisic acid-induced volatile compound biosynthesis in ‘Ruixue’ (Malus × domestica) apple during storage

Fruit aroma, which is conferred by an array of volatile compounds, strongly influences both consumer acceptance and market competitiveness. The phytohormone abscisic acid (ABA) regulates volatile compound biosynthesis during fruit ripening. However, the regulatory mechanism by which ABA may alter the production of volatile compounds in apple remains unknown. In this study, ABA treatment accelerated fruit ripening and volatile compound production, whereas treatment with the ABA biosynthesis inhibitor nordihydroguaiaretic acid (NDGA) resulted in the opposite effects. We identified a nuclear-localized ABA-responsive transcription factor (TF), MdABF2, which was upregulated by exogenous ABA. Overexpression of MdABF2 resulted in enhanced production of volatile compounds and biosynthesis gene expression, and these effects were further enhanced by ABA treatment. Moreover, MdABF2 was found to bind directly to the MdLOX1a, MdLOX5a, MdAAT1, and MdAAT2 promoters, activating their expression. The results presented here contribute to our understanding of the mechanism by which ABA regulates volatile compound biosynthesis. Furthermore, these data will be beneficial for the molecular breeding and improvement of apple for better flavor and aroma.

QTL mapping of generative bud break to promote breeding of apple cultivars resilient to climate change

QTL mapping of generative bud break to promote breeding of apple cultivars resilient to climate change

QTL mapping combined RNA-seq technology identified potential genes involved in regulation of apple size

Fruit size is an important external indicator of apple quality. However, fruit-size breeding is complicated because multiple factors, including cultivar management, plant hormones and genetic factors, influence the final fruit size. Genetic factors are the most fundamental determinants of fruit size, mainly through cell division and expansion. Hence, the genes involved in regulation of cell development and plant hormone signalling are important regulators of fruit size. This work presents a dense genetic linkage map constructed using a 'Golden Delicious' × 'Fuji' population. Two algorithms: Kruskal-Wallis (KW) and Interval Mapping (IM) was used to identify the quantitative trait loci (QTL) for fruit size. Several size QTLs were detected, generating three genomic regions for fruit size and analysing the biological functions revealed 339 genes from the three regions as possible candidate genes controlling apple fruit size. Meanwhile, the transcriptome profiles of fruit flesh between large (LF) and small fruits (SF) at 30 and 60 days after full bloom (DAFB) revealed 2635 and 3922 DEGs at 30 DAFB and 60 DAFB, respectively. The 339 genes identified by QTL-Mapping revealed 41 DEGs, with 23 genes at both 30 and 60 DAFB (five genes in common), as the final candidate genes controlling fruit size. These results maybe reveal the molecular regulation mechanism of fruit size and provide basic evidence for developing gene markers for apple breeding.

Correlation of Types of Fruit Formations, Yield and Economic Indicators of New Breeding Apple Cultures in Azerbaijan

The results of a long-term study of biological and economic indicators of new apple breeding varieties, including the number of fruits, fruit weight, yield and comparative economic evaluation of the variety, are presented. Selected by a set of valuable traits for widespread introduction into industrial gardens varieties: Nigar, Zaka, Zafar, Udvi, Watan, Emil, Elvin, Sevinj, Gobustan, Gyzyl taj, Mahmari, Sadaf, Sahil and Shabran.

Forty years of scab resistance breeding in apple at Agroscope

Forty years of scab resistance breeding in apple at Agroscope

Malus Species with Diverse Bloom Times Exhibit Variable Rates of Floral Development

In response to challenges caused by climate change, apple (Malus ×domestica) breeding programs must quickly develop more resilient cultivars. One strategy is to breed for various bloom times. Members of the genus Malus, including domesticated apple, wild species, and hybrids, exhibit striking variations in the bloom date. Although bloom time is strongly influenced by chilling requirements, other aspects of floral development in Malus and their contributions to bloom time are less known. The purpose of this study was to investigate potential connections between predormancy flower development and final bloom time in Malus species. We performed a phenological analysis of flower development in wild and domesticated apple with extreme differences in bloom time over the course of one developmental season. We tracked histological changes in the floral apex of representatives of three early-blooming Malus genotypes (M. ×domestica ‘Anna’ PI 280400, M. orthocarpa PI 589392, M. sylvestris PI 633824) and three late-blooming genotypes (M. angustifolia PI 589763, M. angustifolia PI 613880, M. ×domestica ‘Koningszuur’ PI 188517). Our study documented their floral meristem progression and organ development and expanded on current staging systems for apple flower development to describe the changes observed. The developmental trajectories of each genotype did not group according to bloom category, and we observed variations in the floral development stage at the time of dormancy onset.

Approaches to implement genomic selection in three Swiss apple breeding programs

Approaches to implement genomic selection in three Swiss apple breeding programs

Cider apple breeding in France

Cider apple breeding in France

Evaluation of Malus Germplasm Identifies Genetic Sources of Powdery Mildew and Frogeye Leaf Spot Resistance for Apple Breeding.

Apple is an important fruit crop of temperate regions. The narrow genetic base of commercially cultivated apples has resulted in its vulnerability to a large number of fungal, bacterial, and viral pathogens. Apple breeders are always seeking new sources of resistance within the cross-compatible Malus species that can be deployed into elite genetic backgrounds. We have evaluated resistance to two major fungal diseases of apples: powdery mildew and frogeye leaf spot, using a germplasm collection of 174 Malus accessions to identify novel sources of genetic resistance. In 2020 and 2021, we evaluated these accessions for the incidence and severity of powdery mildew and frogeye leaf spot diseases at Cornell AgriTech, Geneva, New York, in a partially managed orchard. The severity and incidence of powdery mildew and frogeye leaf spot, as well as weather parameters were recorded in June, July, and August. Total incidence of powdery mildew and frogeye leaf spot infections increased from 33 to 38%, and 56 to 97% in 2020 and 2021, respectively. Our analysis showed that relative humidity and precipitation correlate with powdery mildew and frogeye leaf spot susceptibility. The predictor variables with highest impact to the variability of powdery mildew were accessions and relative humidity in May. A total of 65 Malus accessions were found to be resistant to powdery mildew, and only one accession showed moderate resistance to frogeye leaf spot. Several of these accessions belong to Malus hybrid species and domesticated apples and can therefore be potential sources of novel resistance alleles for apple breeding.

Quantitative Traits of Interest in Apple Breeding and Their Implications for Selection.

Apple breeding is a laborious and long-lasting process that requires qualified resources, land, time, and funds. In this study, more than 5000 F1 apple hybrids from direct and testcrosses were analyzed. The results revealed how the phenotypic expression of the main quantitative traits of interest assessed in five half-sib families was controlled by the additive genetic effects and by non-additive effects of dominance and epistasis. The statistical number of hybrids required to ensure efficient selection increased exponentially with the number of desirable traits. The minimum number of progenies required to obtain a hybrid with associated quantitative traits of agronomic interest was highly variable. For two independent traits essential in selection (fruit size and quality), but incorporated together in the same hybrid, the statistical number was between about 30 and 300. If three more cumulative traits were added (a large number of fruits per tree, resistance/tolerance to apple scab, and powdery mildew attack), the limits increased to between 1500 and 18,000. The study highlighted the need for new apple varieties due to the narrowing of the genetic diversity of the cultivated species and how the choice of parents used in hybridizations (as well as the objectives pursued in the selection) can increase the efficiency of apple breeding.

Deducing genotypes for loci of interest from SNP array data via haplotype sharing, demonstrated for apple and cherry.

Breeders, collection curators, and other germplasm users require genetic information, both genome-wide and locus-specific, to effectively manage their genetically diverse plant material. SNP arrays have become the preferred platform to provide genome-wide genetic profiles for elite germplasm and could also provide locus-specific genotypic information. However, genotypic information for loci of interest such as those within PCR-based DNA fingerprinting panels and trait-predictive DNA tests is not readily extracted from SNP array data, thus creating a disconnect between historic and new data sets. This study aimed to establish a method for deducing genotypes at loci of interest from their associated SNP haplotypes, demonstrated for two fruit crops and three locus types: quantitative trait loci Ma and Ma3 for acidity in apple, apple fingerprinting microsatellite marker GD12, and Mendelian trait locus Rf for sweet cherry fruit color. Using phased data from an apple 8K SNP array and sweet cherry 6K SNP array, unique haplotypes spanning each target locus were associated with alleles of important breeding parents. These haplotypes were compared via identity-by-descent (IBD) or identity-by-state (IBS) to haplotypes present in germplasm important to U.S. apple and cherry breeding programs to deduce target locus alleles in this germplasm. While IBD segments were confidently tracked through pedigrees, confidence in allele identity among IBS segments used a shared length threshold. At least one allele per locus was deduced for 64-93% of the 181 individuals. Successful validation compared deduced Rf and GD12 genotypes with reported and newly obtained genotypes. Our approach can efficiently merge and expand genotypic data sets, deducing missing data and identifying errors, and is appropriate for any crop with SNP array data and historic genotypic data sets, especially where linkage disequilibrium is high. Locus-specific genotypic information extracted from genome-wide SNP data is expected to enhance confidence in management of genetic resources.

Transcriptome Analysis Identifies Genes Associated with Chlorogenic Acid Biosynthesis during Apple Fruit Development

As a predominant phenolic compound in apple fruits, chlorogenic acid (CGA) benefits human health due to its various antioxidant properties. However, little has been known regarding the molecular mechanism underlying the CGA accumulation in apple fruits. In this study, we measured the CGA content and relative enzymes’ activities during fruit development in two different flesh-colored cultivars ‘Huashuo’ and ‘Red Love’. The CGA content in both cultivars decreased sharply from 30 days after full bloom (DAFB) to 60 DAFB. Notably, the CGA content in fruit flesh was relatively higher than that in the peel. Further, the activities of C3H and HCT enzymes downstream of the CGA biosynthesis showed the similar changing trend as CGA content. Based on the transcriptome data of ‘Huashuo’ fruit at 30 DAFB and 60 DAFB, 23 differentially expressed CGA synthesis-related genes were screened. Gene expression analyses further showed that MdHCT1/2/4/5/6 and MdC3H1/2/3 were positively correlated to the variation of CGA content in two cultivars. These findings establish a theoretical foundation for further mechanism study on CGA biosynthesis and provide guidance for nutrient improvement in apple breeding programs.

Progress in apple breeding for resistance to fire blight

The paper presents the most important issues concerning the breeding of apple trees resistant to fire blight, which creates great op­portunities to increase the efficiency of apple fruit production without the use of other protection methods, including the chemical treatment. The phenotypic assessment of susceptibility of apple genotypes to the disease is based on observations on the occurrence of symptoms in field and/or closed facilities, e.g. in the greenhouse. Molecular biology methods, including identification of resistance mark­ers, and biotechnology are valuable tools to accelerate the breeding process. Breeding programs conducted in various research centers around the world use wild species of the genus Malus and commercial cultivars of apple. Apple rootstocks with very high resistance to fire blight (USA) and a number of scab-resistant cultivars, also showing high resistance to the disease (Germany, Switzerland) have already been bred. In recent years cultivar Early Szampion and clone No. 69 (J-2003-05) have been bred in Poland. Both genotypes are characterized by a very high resistance, and produce attractive tasty fruit. They have the prospect of being used in breeding programs and commercial plantings.

Elucidation and characterization of QTLs for Russet formation on apple fruit in ‘Honeycrisp’-derived breeding germplasm

Russet formation in apples (Malus domestica Borkh.) is a superficial skin disorder that detracts from fruit appearance and therefore is a breeding target in many apple scion breeding programs. Previous studies have reported quantitative trait loci (QTLs) for russet formation, but these results have been limited to a narrow genetic background, which reduces breeding utility. In this study, 14 breeding parents were represented in 13-full sib families, nine of which were ‘Honeycrisp’-derived while the other four were derived from ‘Minneiska’, an offspring of ‘Honeycrisp.’ Two previously reported QTLs, on linkage group (LG) 2 and LG6, were confirmed and characterized for the first time in ‘Honeycrisp’-derived germplasm. Five other putative QTLs were also detected. The QTLs characterized in this study could be targeted for DNA test development to be used in marker-assisted selection. Non-additive interactions were observed at and between the LG2 and LG6 QTLs. Future work should include validation of QTL and haplotype effects in other germplasm, development of trait-predictive DNA tests for use in apple breeding programs, and exploration of genome-wide prediction models for russet formation.

Production and Biological Assessment of VNIISPK Cultivars of Various Ploidy for the Zone of Temperate Continental Climate.

Increasing the reliability of fruit crops in unstable weather conditions of a temperate continental climate has become particularly relevant. This research was carried out based on a bioresource collection from the Russian Research Institute of Fruit Crop Breeding (VNIISPK BRC). Apple cultivars (diploids and triploids) of different maturation periods were studied. Triploid cultivars (3×) of summer maturation were developed using diploid gametes of the ‘Papirovka tetraploid’ cultivar as a donor (2-4-4-4×), triploids of winter maturation were developed using 13-6-106 (Suvorovetz: open pollination), and ‘Wealthy tetraploid’ (2-4-4-4×) or ‘Giant Spy’ (2-4-4-4×) were used as donors of diploid gametes. ‘Antonovka’ and ‘Melba’ were taken as control cultivars. The aim of this work was to evaluate the apple breeding cultivars according to the main economic and biological indicators and to determine the threshold of resistance to unfavorable conditions of the winter period for possible cultivation in specific conditions of a temperate continental climate. As a result of using the method of modeling damaging factors, apple cultivars that withstood not only the critical temperatures of January, but also especially dangerous frosts after thaws at the end of winter were identified, with the stability of vital tissues at the level of ‘Antonovka’ (a control cultivar), scab immune cultivars (RVi6) ‘Ivanovskoye’, ‘Zdorovie’ and ‘Pamyati Hitrovo’, and immune triploids (3×) ‘Vavilovskoye’, ‘Aleksandr Boyko’, Rozhdestvenskoye’ and ‘Academic Saveliev’. During the whole winter, the winter resistance of summer scab immune triploids, ‘Zhilinskoye’, ‘Maslovskoye’, ‘Yablochny Spas’ and ‘Spasskoye’, was at the level of ‘Antonovka’, but was higher than ‘Melba’. The high precocity of scab-immune cultivars, ’Afrodita’, ‘Ivanovskoye’, ‘Veniaminovskoye’, and ‘Yubiley Moskvy’, and triploids ‘Patriot’ and ‘Rozhdestvenskoye’, have been identified. Triploid cultivars are superior to diploid cultivars and control ‘Antonovka’ in fruit size. According to the complex of characteristics, promising apple cultivars were identified for planting in intensive orchards of the temperate continental climate zones, namely ‘Avgusta’ and ‘Solnyshko’ (summer cultivars), and ‘Aleksandr Boyko’, ‘Vavilovskoye’, ‘Venyaminovskoye’, ‘Ivanovskoye’ and ‘Rozhdestvenskoye’ (winter cultivars).