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      Rvi4 and Rvi15 are the same apple scab resistance genes

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          Abstract

          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.

          Supplementary Information

          The online version contains supplementary material available at 10.1007/s11032-023-01421-0.

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          Most cited references33

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          Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh)

          High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ∼3.7K validated SNPs from the IRSC 8K array. The array has already been used in other studies where ∼15.8K SNP markers were mapped with an average of ∼6.8K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs.
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            Microsatellite markers spanning the apple (Malus x domestica Borkh.) genome

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              Bayesian QTL analyses using pedigreed families of an outcrossing species, with application to fruit firmness in apple.

              Proof of concept of Bayesian integrated QTL analyses across pedigree-related families from breeding programs of an outbreeding species. Results include QTL confidence intervals, individuals' genotype probabilities and genomic breeding values. Bayesian QTL linkage mapping approaches offer the flexibility to study multiple full sib families with known pedigrees simultaneously. Such a joint analysis increases the probability of detecting these quantitative trait loci (QTL) and provide insight of the magnitude of QTL across different genetic backgrounds. Here, we present an improved Bayesian multi-QTL pedigree-based approach on an outcrossing species using progenies with different (complex) genetic relationships. Different modeling assumptions were studied in the QTL analyses, i.e., the a priori expected number of QTL varied and polygenic effects were considered. The inferences include number of QTL, additive QTL effect sizes and supporting credible intervals, posterior probabilities of QTL genotypes for all individuals in the dataset, and QTL-based as well as genome-wide breeding values. All these features have been implemented in the FlexQTL(™) software. We analyzed fruit firmness in a large apple dataset that comprised 1,347 individuals forming 27 full sib families and their known ancestral pedigrees, with genotypes for 87 SSR markers on 17 chromosomes. We report strong or positive evidence for 14 QTL for fruit firmness on eight chromosomes, validating our approach as several of these QTL were reported previously, though dispersed over a series of studies based on single mapping populations. Interpretation of linked QTL was possible via individuals' QTL genotypes. The correlation between the genomic breeding values and phenotypes was on average 90 %, but varied with the number of detected QTL in a family. The detailed posterior knowledge on QTL of potential parents is critical for the efficiency of marker-assisted breeding.
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                Author and article information

                Contributors
                andreas.peil@julius-kuehn.de
                nick.howard@fresh-forward.nl
                simone.buehlmann-schuetz@agroscope.admin.ch
                ines.hiller@julius-kuehn.de
                henk.schouten@wur.nl
                henryk.flachowsky@julius-kuehn.de
                andrea.patocchi@agroscope.admin.ch
                Journal
                Mol Breed
                Mol Breed
                Molecular Breeding : New Strategies in Plant Improvement
                Springer Netherlands (Dordrecht )
                1380-3743
                1572-9788
                11 October 2023
                11 October 2023
                October 2023
                : 43
                : 10
                : 74
                Affiliations
                [1 ]Julius Kühn Institut (JKI)—Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, ( https://ror.org/022d5qt08) Pillnitzer Platz 3a, 01326 Dresden, Pillnitz Germany
                [2 ]Fresh Forward Breeding and Marketing B.V., Hogewoerd 1C, 6851 ET Huissen, The Netherlands
                [3 ]Research Division Plant Breeding, Agroscope, ( https://ror.org/04d8ztx87) Müller-Thurgau-Strasse 29, 8820 Wädenswil, Switzerland
                [4 ]Department of Plant Breeding, Wageningen University & Research, ( https://ror.org/04qw24q55) Droevendaalsesteeg 1, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
                Author information
                https://orcid.org/0000-0002-5461-4441
                https://orcid.org/0000-0001-7094-2229
                https://orcid.org/0009-0007-3378-690X
                https://orcid.org/0000-0003-4495-1951
                https://orcid.org/0000-0003-1440-1895
                http://orcid.org/0000-0002-0919-2702
                Article
                1421
                10.1007/s11032-023-01421-0
                10564682
                37830083
                0a1a8f78-9a48-4bf3-b720-f2ecbecff955
                © The Author(s) 2023

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 16 August 2023
                : 2 October 2023
                Funding
                Funded by: Agroscope
                Categories
                Article
                Custom metadata
                © Springer Nature B.V. 2023

                Animal science & Zoology
                malus x domestica,venturia inaequalis,resistance breeding,marker-assisted selection

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