Search

Implementation of genomic tools is desirable to increase the efficiency of apple breeding. Recently, the multi-environment apple reference population (apple REFPOP) proved useful for rediscovering loci, estimating genomic predictive ability, and studying genotype by environment interactions (G × E). So far, only two phenological traits were investigated using the apple REFPOP, although the population may be valuable when dissecting genetic architecture and reporting predictive abilities for additional key traits in apple breeding. Here we show contrasting genetic architecture and genomic predictive abilities for 30 quantitative traits across up to six European locations using the apple REFPOP. A total of 59 stable and 277 location-specific associations were found using GWAS, 69.2% of which are novel when compared with 41 reviewed publications. Average genomic predictive abilities of 0.18-0.88 were estimated using main-effect univariate, main-effect multivariate, multi-environment univariate, and multi-environment multivariate models. The G × E accounted for up to 24% of the phenotypic variability. This most comprehensive genomic study in apple in terms of trait-environment combinations provided knowledge of trait biology and prediction models that can be readily applied for marker-assisted or genomic selection, thus facilitating increased breeding efficiency., This work was partially supported by the project RIS3CAT (COTPA-FRUIT3CAT) financed by the European Regional Development Fund through the FEDER frame of Catalonia 2014-2020 and by the CERCA Program from Generalitat de Catalunya. We acknowledge financial support from the Spanish Ministry of Economy and Competitiveness through the “Severo Ochoa Programme for Centres of Excellence in R&D” 2016-2019 (SEV-20150533) and 2020-2023 (CEX2019-000902-S)., With funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000902-S)

Implementation of genomic tools is desirable to increase the efficiency of apple breeding. The apple reference population (apple REFPOP) proved useful for rediscovering loci, estimating genomic prediction accuracy, and studying genotype by environment interactions (G×E). Here we show contrasting genetic architecture and genomic prediction accuracies for 30 quantitative traits across up to six European locations using the apple REFPOP. A total of 59 stable and 277 location-specific associations were found using GWAS, 69.2% of which are novel when compared with 41 reviewed publications. Average genomic prediction accuracies of 0.18–0.88 were estimated using single-environment univariate, single-environment multivariate, multi-environment univariate, and multi-environment multivariate models. The G×E accounted for up to 24% of the phenotypic variability. This most comprehensive genomic study in apple in terms of trait-environment combinations provided knowledge of trait biology and prediction models that can be readily applied for marker-assisted or genomic selection, thus facilitating increased breeding efficiency.

International audience; Apple scab, caused by Venturia inaequalis, is a major disease worldwide. To control this disease, up to 20-25 fungicide applications may be needed depending on the year and the production system. Cultivation of scab-resistant apple cultivars would reduce the chemical footprint of apple production. Breeding for durable scab resistance is an objective of most apple breeding programmes. One way to achieve durable resistance is to pyramid multiple apple scab resistance genes in a cultivar. Currently, more than 18 different apple scab resistance genes have been reported. Molecular markers are available for most of these and can be used to select seedlings carrying multiple resistance genes. Apple scab isolates are virulent to specific apple scab resistance genes. Choice of optimal resistance genes for use in a breeding program, should therefore take regional presence of these apple scab isolates into consideration. In order to learn more about the geographical distribution of apple scab isolates, the VINQUEST project (www.vinquest.ch) was initiated in 2009. Ten years after the launch of this initiative, 24 partners from 14 countries are regularly contributing data. Results obtained from the data collected during the first 10 years provide the first insights into which apple scab resistance genes may hold most promise for breeding cultivars with durable resistance.

In the original publication, the positions of the SNP markers from the 50K SNP array are given according toGDDH13 v1.0 version of the apple reference genome and not according to GDDH13 v1.1 version as stated in the original publication.

Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection candidates. Genomics-assisted breeding utilizes genomic and phenotypic information to increase the selection efficiency in breeding programs, and measurements of phenotypes in different environments can facilitate the application of the approach under various climatic conditions. Here we present an apple reference population: the apple REFPOP, a large collection formed of 534 genotypes planted in six European countries, as a unique tool to accelerate apple breeding. The population consisted of 269 accessions and 265 progeny from 27 parental combinations, representing the diversity in cultivated apple and current European breeding material, respectively. A high-density genome-wide dataset of 303,239 SNPs was produced as a combined output of two SNP arrays of different densities using marker imputation with an imputation accuracy of 0.95. Based on the genotypic data, linkage disequilibrium was low and population structure was weak. Two well-studied phenological traits of horticultural importance were measured. We found marker–trait associations in several previously identified genomic regions and maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date, respectively. With decreasing SNP density, the detection of significant marker–trait associations varied depending on trait architecture. Regardless of the trait, 10,000 SNPs sufficed to maximize genomic prediction ability. We confirm the suitability of the apple REFPOP design for genomics-assisted breeding, especially for breeding programs using related germplasm, and emphasize the advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era., This work was partially supported by the project RIS3CAT (COTPA-FRUIT3CAT) financed by the European Regional Development Fund through the FEDER frame of Catalonia 2014–2020 and by the CERCA Program from Generalitat de Catalunya. We acknowledge financial support from the Spanish Ministry of Economy and Competitiveness through the “Severo Ochoa Program for Centres of Excellence in R&D” 2016–2019 (SEV‐20150533). This work has been partially funded by the EU seventh Framework Program, the FruitBreedomics project No. 265582: Integrated Approach for Increasing Breeding Efficiency in Fruit Tree Crops.

International audience; Apple scab, caused by Venturia inaequalis, is a major fungal disease worldwide. Cultivation of scab-resistant cultivars would reduce the chemical footprint of apple production. However, new apple cultivars carrying durable resistances should be developed to prevent or at least slow the breakdown of resistance against races of V. inaequalis. One way to achieve durable resistance is to pyramid multiple scab resistance genes in a cultivar. The choice of the resistance genes to be combined in the pyramids should take into account the frequency of resistance breakdown and the geographical distribution of apple scab isolates able to cause such breakdowns. In order to acquire this information and to make it available to apple breeders, the VINQUEST project (www.vinquest.ch) was initiated in 2009. Ten years after launching this project, 24 partners from 14 countries regularly contribute data. From 2009 to 2018 nearly 9000 data points have been collected. This information has been used to identify the most promising apple scab resistance genes for developing cultivars with durable resistance, which to date are: Rvi5, Rvi11, Rvi12, Rvi14 and Rvi15. As expected, Rvi1, together with Rvi3 and Rvi8, were often overcome, hence have little value for scab resistance breeding. Rvi10 may also belong to this group. On the other hand Rvi2, Rvi4, Rvi6, Rvi7, Rvi9, and Rvi13 are still useful for the breeding, but their use is recommended only in extended pyramids of (≥3) resistance genes.

Acidity and sweetness are important qualities for apple breeders and understanding their genetic regulation can improve the breeding process. In previous QTL studies, fruit quality assessments were performed using instrumental measurements, leading to the identification of two major QTL Ma and Ma3. Here, we use sensorial data to investigate the role of known and unknown genetic factors in the perception of acidity and sweetness in three pedigreed full-sib families. For 2 years, these families were phenotyped by a trained panel, at harvest and after 2 months of cold storage, and genotyped with a new 50 K SNP array. FlexQTLTM analyses using both an additive and an additive + dominance model resulted in the identification of Ma and Ma3 for acidity as well as sweetness, whereas the use of the additive model yielded decisive evidence for the discovery of two additional QTL on LG1 and LG6 for acidity. QTL genotypes were qualified as the inverse of each other, which indicates that individuals with the less-acidity alleles of Ma and Ma3 are perceived sweeter. Due to the genetic configuration in the families studied, resulting from a link with the Pale Green Disorder locus, no incomplete dominance effect could be detected for the Ma locus, although previously reported in the literature. For the Ma3 locus, however, an incomplete dominance effect (58%) is reported here for the first time. The Ma3 locus was also further confined to a 2–4-cM region and a predictive marker for this locus was identified.

Apple scab causes significant losses in the production of this fruit. A timely and more site-specific monitoring and spraying of the disease could reduce the number of applications of fungicides in the fruit industry. The aim of this leaf-scale study therefore lies in the early detection of apple scab infections in a non-invasive and non-destructive way. In order to attain this objective, fluorescence- and hyperspectral imaging techniques were used. An experiment was conducted under controlled environmental conditions, linking hyperspectral reflectance and fluorescence imaging measurements to scab infection symptoms in a susceptible apple cultivar (Malus x domestica Borkh. cv. Braeburn). Plant stress was induced by inoculation of the apple plants with scab spores. The quantum efficiency of Photosystem II (PSII) photochemistry was derived from fluorescence images of leaves under light adapted conditions. Leaves inoculated with scab spores were expected to have lower PSII quantum efficiency than control (mock) leaves. However, besides scab-induced, also immature leaves exhibited low PSII quantum efficiency. Therefore, this study recommends the simultaneous use of fluorescence imaging and hyperspectral techniques. A shortwave infrared narrow-waveband ratio index (R1480/R2135) is presented in this paper as a promising tool to identify scab stress before symptoms become visible to the naked eye. Low PSII quantum efficiency attended by low narrow waveband R1480/R2135 index values points out scab stress in an early stage. Apparent high PSII quantum efficiency together with high overall reflectance in VIS and SWIR spectral domains indicate a severe, well-developed scab infection.

A surprisingly strong correlation between the date of commercial harvest and the mean vitamin C (L-ascorbate, L-AA) contents of fruits from Belgian-grown Malus × domestica cultivars was reported recently (Davey MW and Keulemans J, J Agric Food Chem 52:8031–8038 (2004)). The study has been extended to show that this correlation remains consistent over different production years and that harvest date is also significantly correlated with fruit L-AA and total antioxidant activities but not with glutathione (GSH) levels or other physiological parameters of fruits. L-AA concentrations were also found to be negatively correlated with mean preharvest daytime temperature; however, since preharvest temperature and harvest date themselves are closely linked, it was not possible to definitively separate the relative contributions of genetic and environmental factors to these traits. It is also shown that the susceptibility of fruits of different apple genotypes to postharvest infection with Botrytris cinerea decreases with increasing harvest date and that this susceptibility is correlated with fruit vitamin C but not GSH levels. There is no such relationship underlying the susceptibility of fruits to postharvest infection with Gloeosporium fructigenum. These results are discussed in the context of low-input breeding for improved fruit quality and disease resistance via selection of fruits with improved antioxidant defence capabilities. Copyright © 2007 Society of Chemical Industry

International audience; The application of genomic selection in fruit tree crops is expected to enhance breeding efficiency by increasing prediction accuracy, increasing selection intensity and decreasing generation interval. The objectives of this study were to assess the accuracy of prediction and selection response in commercial apple breeding programmes for key traits. The training population comprised 977 individuals derived from 20 pedigreed full-sib families. Historic phenotypic data were available on 10 traits related to productivity and fruit external appearance and genotypic data for 7829 SNPs obtained with an Illumina 20K SNP array. From these data, a genome-wide prediction model was built and subsequently used to calculate genomic breeding values of five application full-sib families. The application families had genotypes at 364 SNPs from a dedicated 512 SNP array, and these genotypic data were extended to the high-density level by imputation. These five families were phenotyped for 1 year and their phenotypes were compared to the predicted breeding values. Accuracy of genomic prediction across the 10 traits reached a maximum value of 0.5 and had a median value of 0.19. The accuracies were strongly affected by the phenotypic distribution and heritability of traits. In the largest family, significant selection response was observed for traits with high heritability and symmetric phenotypic distribution. Traits that showed non-significant response often had reduced and skewed phenotypic variation or low heritability. Among the five application families the accuracies were uncorrelated to the degree of relatedness to the training population. The results underline the potential of genomic prediction to accelerate breeding progress in outbred fruit tree crops that still need to overcome long generation intervals and extensive phenotyping costs.

The effects of nematode infection and mulching on plantain cv. Agbagba (Musa spp., AAB-group, false horn) yield and plantation longevity were examined in a field experiment at the High Rainfall Station of the International Institute of Tropical Agriculture (IITA) at Onne in southeastern Nigeria. The 2nd, 3rd and 4th crop cycles (1st, 2nd and 3rd ratoon, respectively) following the plant crop cycle (mother crop) were examined in nematode inoculated or non-inoculated and mulched or non-mulched treatments. Nematodes (Radopholus similis, Helicotylenchus multicinctus and, to a lesser extent, Helicotylenchus dihystera, Hoplolaimus pararobustus and Meloidogyne spp.) were inoculated at planting of the mother plant, but were also present in relatively high population densities in the non-inoculated treatments at harvest of the 1st crop cycle. Plants inoculated with nematodes failed to reach harvest and neither did plants in the non-inoculated non-mulched treatments in any ratoon. Only non-inoculated mulched plants reached harvest, producing 0.85, 1.22 and 0.2 Mg ha−1, respectively in the 1st, 2nd and 3rd ratoon, taking toppled, broken and dead plants into consideration. Mulched plants were larger, had more suckers, survived longer and had healthier root systems compared with non-mulched plants. Damage to roots was greater in the inoculated plants compared with the non-inoculated plants for the 1st and 2nd ratoons but not for the 3rd ratoon. Radopholus similis was most strongly associated with root damage (percentage root necrosis and dead roots), although H. multicinctus population densities were also positively correlated with percentage root necrosis. At flowering of the 1st ratoon, 71% of the inoculated non-mulched plants were dead compared with only 1% of the non-inoculated mulched plants. Helicotylenchus multicinctus remained the most abundant nematode throughout the experiment. Together with R. similis, it comprised over 95% of the plant-parasitic nematode population.