Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.)
Linsmith, Gareth ; Rombauts, Stephane ; Montanari, Sara ; Deng, Cecilia H. ; Celton, Jean Marc ; Guérif, Philippe ; Liu, Chang ; Lohaus, Rolf ; Zurn, Jason D. ; Cestaro, Alessandro ; Bassil, Nahla V. ; Bakker, Linda V. ; Schijlen, Elio ; Gardiner, Susan E. ; Lespinasse, Yves ; Durel, Charles Eric ; Velasco, Riccardo ; Neale, David B. ; Chagné, David ; Peer, Yves Van de; Troggio, Michela ; Bianco, Luca - \ 2019
GigaScience 8 (2019)12. - ISSN 2047-217X
chromosome-scale assembly - Hi-C - Pac-Bio sequencing - Pyrus communis L
BACKGROUND: We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII long-read sequencing, Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. The sample selected for sequencing is a double haploid derived from the same "Bartlett" reference pear that was previously sequenced. Sequencing of di-haploid plants makes assembly more tractable in highly heterozygous species such as P. communis. FINDINGS: A total of 496.9 Mb corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 pear chromosomes. Approximately 50% (247 Mb) of the genome consists of repetitive sequences. Gene annotation confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted. CONCLUSIONS: We showed that the use of a doubled-haploid plant is an effective solution to the problems presented by high levels of heterozygosity and duplication for the generation of high-quality genome assemblies. We present a high-quality chromosome-scale assembly of the European pear Pyrus communis and demostrate its high degree of synteny with the genomes of Malus x Domestica and Pyrus x bretschneideri.
Apple whole genome sequences : recent advances and new prospects
Peace, Cameron P. ; Bianco, Luca ; Troggio, Michela ; Weg, Eric van de; Howard, Nicholas P. ; Cornille, Amandine ; Durel, Charles Eric ; Myles, Sean ; Migicovsky, Zoë ; Schaffer, Robert J. ; Costes, Evelyne ; Fazio, Gennaro ; Yamane, Hisayo ; Nocker, Steve van; Gottschalk, Chris ; Costa, Fabrizio ; Chagné, David ; Zhang, Xinzhong ; Patocchi, Andrea ; Gardiner, Susan E. ; Hardner, Craig ; Kumar, Satish ; Laurens, Francois ; Bucher, Etienne ; Main, Dorrie ; Jung, Sook ; Vanderzande, Stijn - \ 2019
Horticulture Research 6 (2019)1. - ISSN 2052-7276
In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for “what’s next” focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.
An integrated approach for increasing breeding efficiency in apple and peach in Europe
Laurens, Francois ; Aranzana, Maria José ; Arus, Pere ; Bassi, Daniele ; Bink, Marco ; Bonany, Joan ; Caprera, Andrea ; Corelli-Grappadelli, Luca ; Costes, Evelyne ; Durel, Charles Eric ; Mauroux, Jehan Baptiste ; Muranty, Hélène ; Nazzicari, Nelson ; Pascal, Thierry ; Patocchi, Andrea ; Peil, Andreas ; Quilot-Turion, Bénédicte ; Rossini, Laura ; Stella, Alessandra ; Troggio, Michela ; Velasco, Riccardo ; De Weg, Eric Van - \ 2018
Horticulture Research 5 (2018)1. - ISSN 2052-7276
Despite the availability of whole genome sequences of apple and peach, there has been a considerable gap between genomics and breeding. To bridge the gap, the European Union funded the FruitBreedomics project (March 2011 to August 2015) involving 28 research institutes and private companies. Three complementary approaches were pursued: (i) tool and software development, (ii) deciphering genetic control of main horticultural traits taking into account allelic diversity and (iii) developing plant materials, tools and methodologies for breeders. Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding, development of new, dense SNP arrays in apple and peach, new phenotypic methods for some complex traits, software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis (PBA). This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies (GWAS) on several European genebank collections. FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities. Through FruitBreedomics, significant progresses were made in the field of apple and peach breeding, genetics, genomics and bioinformatics of which advantage will be made by breeders, germplasm curators and scientists. A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public. This review covers the scientific discoveries made in this major endeavour, and perspective in the apple and peach breeding and genomics in Europe and beyond.
Epistatic fire blight resistance QTL alleles in the apple cultivar ‘Enterprise’ and selection X-6398 discovered and characterized through pedigree-informed analysis
Weg, Eric van de; Guardo, Mario Di; Jänsch, Melanie ; Socquet-Juglard, Didier ; Costa, Fabrizio ; Baumgartner, Isabelle ; Broggini, Giovanni A.L. ; Kellerhals, Markus ; Troggio, Michela ; Laurens, François ; Durel, Charles Eric ; Patocchi, Andrea - \ 2018
Molecular Breeding 38 (2018)1. - ISSN 1380-3743
Epistasis - Erwinia amylovora - FlexQTL™ - Malus × domestica - Pedigree-based analyses
Most cultivated apple cultivars are highly susceptible to fire blight, caused by Erwinia amylovora. However, differences in resistance levels are observed among cultivars and could be used in breeding. In this paper, we investigated the genetic basis of fire blight resistance of the cultivar ‘Enterprise’ and the advanced breeding selection X-6398. Genotyped pedigrees were used for validating and curating historic pedigree records. Various quantitative trait locus (QTL) discovery approaches were applied on the full-sib families ‘Gala’ × ‘Enterprise’ (GaEn) and X-6398 × X-6683 (IW) with the software FlexQTL™ and MapQTL®. The paternal lineage of ‘Enterprise’ was reconstructed and showed to include ‘Cox’s Orange Pippin’. The QTLs found varied with the software used. Using FlexQTL™, two were found on linkage groups (LGs) 7 and 13, favourable alleles inherited by Enterprise from ‘Cox’s Orange Pippin’ and ‘Golden Delicious’, respectively. The former was identical to the previously named FB_F7 allele from ‘Fiesta’, while the latter is new and has been named FB_13GD. X-6398 had a QTL at the same position as FB_F7. Its favourable allele was new, originating from the unknown grandfather of X-4598, and was named FB_7X-6398. Using MapQTL® on GaEn, FB_F7 was also identified. Performing the same analysis on the subset of offspring that carried the favourable allele of FB_F7, two putative QTLs on LG8 and on top of LG13 were identified, which showed interactions with FB_F7. Implication of the findings for breeding for fire blight-resistant apples is discussed. Single nucleotide polymorphism data on Enterprise and its ancestors are provided.
Genome-wide association mapping of flowering and ripening periods in apple
Urrestarazu, Jorge ; Muranty, Hélène ; Denancé, Caroline ; Leforestier, Diane ; Ravon, Elisa ; Guyader, Arnaud ; Guisnel, Rémi ; Feugey, Laurence ; Aubourg, Sébastien ; Celton, Jean Marc ; Daccord, Nicolas ; Dondini, Luca ; Gregori, Roberto ; Lateur, Marc ; Houben, Patrick ; Ordidge, Matthew ; Paprstein, Frantisek ; Sedlak, Jiri ; Nybom, Hilde ; Garkava-Gustavsson, Larisa ; Troggio, Michela ; Bianco, Luca ; Velasco, Riccardo ; Poncet, Charles ; Théron, Anthony ; Moriya, Shigeki ; Bink, Marco C.A.M. ; Laurens, François ; Tartarini, Stefano ; Durel, Charles Eric - \ 2017
Frontiers in Plant Science 8 (2017). - ISSN 1664-462X
Adaptive traits - Association genetics - Germplasm collection - GWAS - Malus × domestica Borkh - Microsynteny - Quantitative trait loci - SNP
Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.
Genome wide association study of two phenology traits (flowering time and maturity date) in apple
Muranty, Hélène ; Urrestarazu, J. ; Denancé, C. ; Leforestier, D. ; Ravon, E. ; Guyader, A. ; Guisnel, R. ; Feugey, L. ; Tartarini, S. ; Dondini, L. ; Gregori, R. ; Lateur, M. ; Houben, E.H.P. ; Sedlak, J. ; Paprstein, F. ; Ordidge, M. ; Nybom, H. ; Garkava-Gustavsson, L. ; Troggio, M. ; Bianco, L. ; Velasco, R. ; Poncet, C. ; Théron, Anthony ; Bink, M.C.A.M. ; Laurens, F. ; Durel, C.E. - \ 2017
In: 14th EUCARPIA Symposium on Fruit Breeding and Genetics International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462611689 - p. 411 - 417.
Germplasm collections - Malus × domestica - Marker-assisted selection
The aim of Genome Wide Association Studies (GWAS) is to identify markers in tight linkage disequilibrium with loci controlling quantitative trait variation. These markers can then be used in marker-assisted selection (MAS) in fruit crops such as apple. The GWAS approach involves both phenotyping of a large population of mostly unrelated individuals for the traits of interest, and genotyping at high marker density. In the EU-FP7 project FruitBreedomics, almost 1,200 European diploid dessert apple accessions (old and/or local cultivars) from six germplasm collections were genotyped with the Affymetrix Axiom-Apple480K array (487,000 SNPs). Phenotypic data on a large number of traits have been gathered during the project. Here we focus on flowering period and harvesting date. Knowledge of the genetic control of these traits is necessary to develop cultivars that can face the challenges imposed by global climate change and to target cultivar development as a function of a prolonged vegetation period in the production regions. Different models were tested, including control for effects of population structure and relatedness between cultivars. The full model, controlling for both structure and relatedness, was shown to be the most appropriate to avoid spurious marker-trait associations. When analyzing data over all collections, one significant marker-trait association was obtained for each trait, on chromosomes 9 and 3, for flowering period and harvesting date, respectively. Thereby, genomic locations previously identified in bi-parental populations could now be confirmed for a genetically diverse germplasm.
High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development
Daccord, Nicolas ; Celton, Jean-Marc ; Linsmith, Gareth ; Becker, Claude ; Choisne, Nathalie ; Schijlen, Elio ; Geest, Henri van de; Bianco, Luca ; Micheletti, Diego ; Velasco, Riccardo ; Pierro, Erica Adele Di; Gouzy, Jérôme ; Rees, D.J.G. ; Guérif, Philippe ; Muranty, Hélène ; Durel, Charles Eric ; Laurens, François ; Lespinasse, Yves ; Gaillard, Sylvain ; Aubourg, Sébastien ; Quesneville, Hadi ; Weigel, Detlef ; Weg, Eric van de; Troggio, Michela ; Bucher, Etienne - \ 2017
Nature Genetics 49 (2017)7. - ISSN 1061-4036 - p. 1099 - 1106.
Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.
Development and validation of the Axiom®Apple480K SNP genotyping array
Bianco, Luca ; Cestaro, Alessandro ; Linsmith, Gareth ; Muranty, Hélène ; Denancé, Caroline ; Théron, Anthony ; Poncet, Charles ; Micheletti, Diego ; Kerschbamer, Emanuela ; Pierro, Erica A. Di; Larger, Simone ; Pindo, Massimo ; De Weg, Eric Van; Davassi, Alessandro ; Laurens, François ; Velasco, Riccardo ; Durel, Charles Eric ; Troggio, Michela - \ 2016
The Plant Journal 86 (2016)1. - ISSN 0960-7412 - p. 62 - 74.
genome-wide association study - genotyping - linkage mapping - Malus × domestica Borkh. - SNP chip - validation
Cultivated apple (Malus × domestica Borkh.) is one of the most important fruit crops in temperate regions, and has great economic and cultural value. The apple genome is highly heterozygous and has undergone a recent duplication which, combined with a rapid linkage disequilibrium decay, makes it difficult to perform genome-wide association (GWA) studies. Single nucleotide polymorphism arrays offer highly multiplexed assays at a relatively low cost per data point and can be a valid tool for the identification of the markers associated with traits of interest. Here, we describe the development and validation of a 487K SNP Affymetrix Axiom® genotyping array for apple and discuss its potential applications. The array has been built from the high-depth resequencing of 63 different cultivars covering most of the genetic diversity in cultivated apple. The SNPs were chosen by applying a focal points approach to enrich genic regions, but also to reach a uniform coverage of non-genic regions. A total of 1324 apple accessions, including the 92 progenies of two mapping populations, have been genotyped with the Axiom®Apple480K to assess the effectiveness of the array. A large majority of SNPs (359 994 or 74%) fell in the stringent class of poly high resolution polymorphisms. We also devised a filtering procedure to identify a subset of 275K very robust markers that can be safely used for germplasm surveys in apple. The Axiom®Apple480K has now been commercially released both for public and proprietary use and will likely be a reference tool for GWA studies in apple.
Virulence characterization of Venturia inaequalis reference isolates on the differential set of Malus hosts
Caffier, V. ; Patocchi, A. ; Expert, P. ; Bellanger, M.N. ; Durel, C.E. ; Hilber-Bodmer, M. ; Broggini, G.A.L. ; Groenwold, R. ; Bus, V. - \ 2015
Plant Disease 99 (2015)3. - ISSN 0191-2917 - p. 370 - 375.
A set of differential hosts has recently been identified for 17 apple scab resistance genes in an updated system for defining gene-for-gene (GfG) relationships in the Venturia inaequalis-Malus pathosystem. However, a set of reference isolates characterized for their complementary avirulence alleles is not yet available. In this paper, we report on improving the set of differential hosts for h(7) and propose the apple genotype LPG3-29 as carrying the single major resistance gene Rvi7. We characterized a reference set of 23 V. inaequalis isolates on 14 differential apple hosts carrying major resistance genes under controlled conditions. We identified isolates that were virulent on at least one of the following defined resistance gene hosts: h(1), h(2), h(3), h(4), h(5), h(6), h(7), h(8), h(9), h(10) and h(13). Sixteen different virulence patterns were observed. In general, the isolates carried one to three virulences, but some of them were more complex, with up to six virulences. This set of well-characterized isolates will be helpful for the identification of additional apple scab resistance genes in apple germplasm and the characterization of new GfG relationships to help improve our understanding of the host-pathogen interactions in the V. inaequalis-Malus pathosystem.
Bayesian QTL analyses using pedigreed families of an outcrossing specis, with application to fruit firmness in apple
Bink, M.C.A.M. ; Jansen, J. ; Madduri, M. ; Voorrips, R.E. ; Durel, C.E. ; Kouassi, A.B. ; Laurens, F. ; Mathis, F. ; Gessler, C. ; Gobbin, D. ; Rezzonico, F. ; Patocchi, A. ; Kellerhals, M. ; Boudichevskaia, A. ; Dunemann, F. ; Peil, A. ; Nowicka, A. ; Lata, B. ; Stankiewicz-Kosyl, M. ; Jeziorek, K. ; Pitera, E. ; Soska, A. ; Tomala, K. ; Evans, K.M. ; Fernández-Fernández, F. ; Guerra, W. ; Korbin, M. ; Keller, S. ; Lewandowski, M. ; Plocharski, W. ; Rutkowski, K. ; Zurawicz, E. ; Costa, F. ; Sansavini, S. ; Tartarini, S. ; Komjanc, M. ; Mott, D. ; Antofie, A. ; Lateur, M. ; Rondia, A. ; Gianfranceschi, L. ; Weg, W.E. van de - \ 2014
Theoretical and Applied Genetics 127 (2014)5. - ISSN 0040-5752 - p. 1073 - 1090.
quantitative trait loci - x domestica borkh. - quality traits - plant-populations - phenotypic data - genome - relatedness - prediction - cultivars - selection
Key message - 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. Abstract - 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.
Cisgenic Approach for improved disease resistance in apple
Broggini, G.A.L. ; Durel, C.E. ; Vergne, E. ; Chevreau, E. ; Fahrentrapp, J. ; Vanblaere, T. ; Peil, A. ; Flachowsky, H. ; Hanke, M.V. ; Krens, F.A. ; Schouten, H.J. ; Gessler, C. - \ 2013
In: II Genetically Modified Organisms in Horticulture Symposium. - White River, South Africa : ISHS - ISBN 9789066050976 - p. 117 - 121.
Swiss and more generally European apple (Malus × domestica) production is hampered by several diseases, the most destructive being fire blight, caused by Erwinia amylovora. On the other hand, there are apple scab, caused by Venturia inaequalis and powdery mildew, caused by Podosphaera leucotricha, which represent the major phytosanitary problems. Classical breeding has produced many scab and mildew resistant cultivars and efforts to breed also fire blight resistant cultivars are currently undertaken. Marker assisted selection (MAS) increases efficiency by allowing early non-destructive screening of seedlings and identifying genotypes showing pyramids of resistance genes. If the development of markers for MAS was the primary goal of genetic analysis in the 1990s, identification and cloning of resistance genes is now the goal. The first and until now the sole resistance gene which has been isolated and transformed into a susceptible apple cultivar is the gene HcrVf2 (Rvi6), responsible for the Vf scab resistance present in most classically bred scab resistant cultivars. Much effort is currently spent in the identification and positional cloning of other apple genes conferring resistance to apple scab and fire blight. In our labs, we identified the putative scab resistance gene Rvi15 and two fire blight resistance genes namely from ‘Evereste’ and Malus × robusta 5. The functionality of these candidate genes is currently under scrutiny by complementation experiments. However, the final goal is the creation of a product, e.g., an improved apple cultivar that is resistant to scab and fire blight. The ideal product would have advantages to the environment and producer, and should raise as little concern as possible with consumers. To accomplish this ‘ideal product’, we opted for the cisgenic approach by introducing the scab resistance gene HcrVf2 with its own regulatory sequences into the highly susceptible apple cultivar, ‘Gala’, through Agrobacterium transformation. All marker genes were eliminated after transformation. Similarly, we are currently introducing into both the readily developed cisgenic ‘Gala’ and in the untransformed ‘Gala’ the putative Malus own fire blight resistance gene candidates, aiming at both proof of functionality of the identified candidates and possibly at rapid development of a fire blight and scab resistant cisgenic apple.
Genotyping of pedigreed apple breeding material with a genome covering set of SSRs: Trueness to type of cultivars and their parentages
Evans, K.M. ; Patocchi, A. ; Rezzonico, F. ; Mathis-Jeanneteau, F. ; Durel, C.E. ; Fernandez-Fernandez, F. ; Boudichevskaia, A. ; Dunemann, F. ; Stankiewicz-Kosyl, M. ; Gianfranceschi, L. ; Komjanc, M. ; Lateur, M. ; Madduri, M. ; Noordijk, Y. ; Weg, W.E. van de - \ 2011
Molecular Breeding 28 (2011)4. - ISSN 1380-3743 - p. 535 - 547.
plant-populations - resistance - traits
Apple cultivars and breeding lines that represent much of the diversity currently present in major European breeding programmes and are genetically related by their pedigree were examined for the trueness of their identity and parentage by consistency in marker scores using a genome-covering set of 80 microsatellite (SSR) markers and an ‘identity-by-descent’ approach. One hundred and twenty-five individuals were validated for the trueness-to-type of both their parents and 49 were validated for one of their parents, their second being unknown (23 individuals) or not available in this study (26 individuals). In addition, 15 individuals for which we lacked one of or both the direct parents were validated by consistency with tested parents of earlier generations. Furthermore, the identity of 28 founder cultivars was validated, their marker scores being consistent with descending cultivars and breeding lines. Four of the eight triploids identified were clearly shown to have arisen from unreduced egg cells. The assumed pedigree of 15 further individuals was found to be incorrect; fully consistent pedigrees were suggested for three of the cultivars. The pedigrees of a further eight individuals were confirmed through inference from the molecular data
Estimation of genetic parameters and prediction of breeding values for apple fruit-quality traits using pedigreed plant material in Europe
Kouassi, A.B. ; Durel, C.E. ; Costa, F. ; Tartarini, S. ; Weg, W.E. van de; Evans, K. ; Fernandez-Fernandez, F. ; Govan, C. ; Boudichevskaja, A. ; Dunemann, F. ; Antofie, A. ; Lateur, M. ; Stankiewicz-Kosyl, M. ; Soska, A. ; Tomala, K. ; Lewandowski, M. ; Rutkovski, K. ; Zurawicz, E. ; Guerra, W. ; Laurens, F. - \ 2009
Tree Genetics and Genomes 5 (2009)4. - ISSN 1614-2942 - p. 659 - 672.
sensory interpretation - variance-components - information
Genetic parameters for apple (Malus x domestica) fruit external traits (fruit size, ground colour, proportion of over colour and attractiveness) and sensory traits (firmness, crispness, texture, juiciness, flavour, sugar, acidity and global taste) were estimated using 2,207 pedigreed genotypes from breeding programmes in six European countries. Data were scored for 3 years and four periods during storage. Analyses were performed with a restricted maximum likelihood method using VCE 5.1.2 software. Heritability estimates ranged from medium to high for instrumental traits. Genetic correlations between firmness and sugar were medium and low between firmness and acidity. Sensory traits showed low to high heritability, acidity and flavour being, respectively, the most and the less heritable. Global taste was strongly correlated with texture, juiciness, and flavour and relatively less correlated with crispness and acidity. Sensory sugar and acidity showed highly negative correlations whereas their instrumental measurements showed low and increasing positive correlations from harvest to 4 months post-harvest. Sugar exhibited a higher sensory/instrumental divergence. Conversely, instrumental and sensory firmness were highly correlated. Fruit external characteristics had medium heritability. Fruit attractiveness had highest and lowest correlations with fruit size and ground colour, respectively. Best linear unbiased predictors of breeding values were computed for all genotypes with the software PEST. The results were analysed with regard to the dynamic and the reliability of genetic parameters according to the scoring dates. Original issues of the study and the importance of the obtained results for efficient designs of further apple fruit quality breeding programmes were discussed.
Development and test of 21 multiplex PCRs composed of SSRs spanning most of the apple genome
Patocchi, A. ; Fernandez-Fernandez, F. ; Evans, K. ; Gobbin, D. ; Rezzonico, F. ; Boudichevskaia, A. ; Dunemann, F. ; Stankiewicz-Kosyl, M. ; Mathis-Jeanneteau, F. ; Durel, C.E. ; Gianfranceschi, L. ; Costa, F. ; Toller, C. ; Cova, V. ; Mott, D. ; Komjanc, M. ; Barbaro, E. ; Kodde, L.P. ; Rikkerink, E.H.A. ; Gessler, C. ; Weg, W.E. van de - \ 2009
Tree Genetics and Genomes 5 (2009)1. - ISSN 1614-2942 - p. 211 - 223.
x-domestica borkh. - microsatellite markers - pear - polymorphism - populations - resistance - japanese - qtl - l.
A series of 21 multiplex (MP) polymerase chain reactions containing simple sequence repeat (SSR) markers spanning most of the apple genome has been developed. Eighty-eight SSR markers, well distributed over all 17 linkage groups (LGs), have been selected. Eighty-four of them were included in 21 different MPs while four could not be included in any MPs. The 21 MPs were then used to genotype approximately 2,000 DNA samples from the European High-quality Disease-Resistant Apples for a Sustainable agriculture project. Two SSRs (CH01d03 and NZAL08) were discarded at an early stage as they did not produce stable amplifications in the MPs, while the scoring of the multilocus (ML) SSR Hi07d11 and CN44794 was too complex for large-scale genotyping. The testing of the remaining 80 SSRs over a large number of different genotypes allowed: (1) a better estimation of their level of polymorphism; as well as of (2) the size range of the alleles amplified; (3) the identification of additional unmapped loci of some ML SSRs; (4) the development of methods to assign alleles to the different loci of ML SSRs and (5) conditions at which an SSR previously described as ML would amplify alleles of a single locus to be determined. These data resulted in the selection of 75 SSRs out of the 80 that are well suited and recommended for large genotyping projects.
Construction of an integrated consensus map of the Apple genome based on four mapping populations
N'Diaye, A. ; Weg, W.E. van de; Kodde, L.P. ; Koller, B. ; Dunemann, F. ; Thiermann, M. ; Tartarini, S. ; Gennari, F. ; Durel, C.E. - \ 2008
Tree Genetics and Genomes 4 (2008)4. - ISSN 1614-2942 - p. 727 - 743.
quantitative trait loci - genetic-linkage map - x-domestica borkh. - malus-pumila mill. - zea-mays l - scab resistance - venturia-inaequalis - rapd markers - qtl analysis - microsatellite markers
An integrated consensus genetic map for apple was constructed on the basis of segregation data from four genetically connected crosses (C1¿=¿Discovery × TN10-8, C2¿=¿Fiesta × Discovery, C3¿=¿Discovery × Prima, C4¿=¿Durello di Forli × Fiesta) with a total of 676 individuals using CarthaGene® software. First, integrated female¿male maps were built for each population using common female¿male simple sequence repeat markers (SSRs). Then, common SSRs over populations were used for the consensus map integration. The integrated consensus map consists of 1,046 markers, of which 159 are SSR markers, distributed over 17 linkage groups reflecting the basic chromosome number of apple. The total length of the integrated consensus map was 1,032 cM with a mean distance between adjacent loci of 1.1 cM. Markers were proportionally distributed over the 17 linkage groups (¿ 2¿=¿16.53, df¿=¿16, p¿=¿0.41). A non-uniform marker distribution was observed within all of the linkage groups (LGs). Clustering of markers at the same position (within a 1-cM window) was observed throughout LGs and consisted predominantly of only two to three linked markers. The four integrated female¿male maps showed a very good colinearity in marker order for their common markers, except for only two (CH01h01, CH05g03) and three (CH05a02z, NZ02b01, Lap-1) markers on LG17 and LG15, respectively. This integrated consensus map provides a framework for performing quantitative trait locus (QTL) detection in a multi-population design and evaluating the genetic background effect on QTL expression.
A new versatile database created for geneticists and breeders to link molecular and phenotypic data in perennial crops: the AppleBreed DataBase
Antofie, A. ; Lateur, M. ; Oger, R. ; Patocchi, A. ; Durel, C.E. ; Weg, W.E. van de - \ 2007
Bioinformatics 23 (2007)7. - ISSN 1367-4803 - p. 882 - 891.
genome database - plant genome - zmdb
Objective: AppleBreed DataBase (DB) aims to store genotypic and phenotypic data from multiple pedigree verified plant populations (crosses, breeding selections and commercial cultivars) so that they are easily accessible for geneticists and breeders. It will help in elucidating the genetics of economically important traits, in identifying molecular markers associated with agronomic traits, in allele mining and in choosing the best parental cultivars for breeding. It also provides high traceability of data over generations, years and localities. AppleBreed DB could serve as a generic database design for other perennial crops with long economic lifespans, long juvenile periods and clonal propagation. Results: AppleBreed DB is organized as a relational database. The core element is the GENOTYPE entity, which has two sub-classes at the physical level: TREE and DNA-SAMPLE. This approach facilitates all links between plant material, phenotypic and molecular data. The entities TREE, DNA-SAMPLE, PHENOTYPE and MOLECULAR DATA allow multi-annual observations to be stored as individual samples of individual trees, even if the nature of these observations differs greatly (e.g. molecular data on parts of the apple genome, physico-chemical measurements of fruit quality traits, and evaluation of disease resistance). AppleBreed DB also includes synonyms for cultivars and pedigrees. Finally, it can be loaded and explored through the web, and comes with tools to present basic statistical overviews and with validation procedures for phenotypic and marker data to certify data quality. AppleBreed DB was developed initially as a tool for scientists involved in apple genetics within the framework of the European project, `High-quality Disease Resistance in Apples for Sustainable Agriculture¿ (HiDRAS), but it is also applicable to many other perennial crops.
Microsatellite markers spanning the apple (Malus x domestica Borkh.) genome
Silfverberg-Dilworth, E. ; Matasci, C.L. ; Weg, W.E. van de; Kaauwen, M.P.W. van; Walser, M. ; Kodde, L.P. ; Soglio, V. ; Gianfranceschi, L. ; Durel, C.E. ; Costa, F. ; Yamamoto, T. ; Koller, B. ; Gessler, C. ; Patocchi, A. - \ 2006
Tree Genetics and Genomes 2 (2006)4. - ISSN 1614-2942 - p. 202 - 224.
simple sequence repeats - scab resistance gene - fire-blight resistance - venturia-inaequalis - linkage maps - mildew resistance - pumila mill. - identification - pear - l.
A new set of 148 apple microsatellite markers has been developed and mapped on the apple reference linkage map Fiesta x Discovery. One-hundred and seventeen markers were developed from genomic libraries enriched with the repeats GA, GT, AAG, AAC and ATC; 31 were developed from EST sequences. Markers derived from sequences containing dinucleotide repeats were generally more polymorphic than sequences containing trinucleotide repeats. Additional eight SSRs from published apple, pear, and Sorbus torminalis SSRs, whose position on the apple genome was unknown, have also been mapped. The transferability of SSRs across Maloideae species resulted in being efficient with 41% of the markers successfully transferred. For all 156 SSRs, the primer sequences, repeat type, map position, and quality of the amplification products are reported. Also presented are allele sizes, ranges, and number of SSRs found in a set of nine cultivars. All this information and those of the previous CH-SSR series can be searched at the apple SSR database (http://www.hidras.unimi.it) to which updates and comments can be added. A large number of apple ESTs containing SSR repeats are available and should be used for the development of new apple SSRs. The apple SSR database is also meant to become an international platform for coordinating this effort. The increased coverage of the apple genome with SSRs allowed the selection of a set of 86 reliable, highly polymorphic, and overall the apple genome well-scattered SSRs. These SSRs cover about 85% of the genome with an average distance of one marker per 15 cM
Identification of a major QTL together with several minor additive or epistatic QTLs for resistance to fire blight in apple in two related progenies
Calenge, F. ; Drouet, D. ; Denance, C. ; Weg, W.E. van de; Brisset, M.N. ; Paulin, J.P. ; Durel, C.E. - \ 2005
Theoretical and Applied Genetics 111 (2005)1. - ISSN 0040-5752 - p. 128 - 135.
disease resistance - venturia-inaequalis - erwinia-amylovora - scab resistance - linkage maps - genes - organization - cultivars - evolution
Although fire blight, caused by the bacterium Erwinia amylovora, is one of the most destructive diseases of apple (Malus x domestica) worldwide, no major, qualitative gene for resistance to this disease has been identified to date in apple. We conducted a quantitative trait locus (QTL) analysis in two F-1 progenies derived from crosses between the cultivars Fiesta and either Discovery or Prima. Both progenies were inoculated in the greenhouse with the same strain of E. amylovora, and the length of necrosis was scored 7 days and 14 days after inoculation. Additive QTLs were identified using the MAPQTL software, and digenic epistatic interactions, which are an indication of putative epistatic QTLs, were detected by two-way analyses of variance. A major QTL explaining 34.3-46.6% of the phenotypic variation was identified on linkage group (LG) 7 of Fiesta in both progenies at the same genetic position. Four minor QTLs were also identified on LGs 3, 12 and 13. In addition, several significant digenic interactions were identified in both progenies. These results confirm the complex polygenic nature of resistance to fire blight in the progenies studied and also reveal the existence of a major QTL on LG7 that is stable in two distinct genetic backgrounds. This QTL could be a valuable target in marker-assisted selection to obtain new, fire blight-resistant apple cultivars and forms a starting point for discovering the function of the genes underlying such QTLs involved in fire blight control.
Resistance gene analogues identified through the NBS-profiling method map close to major genes and QTL for disease resistance in apple
Calenge, F. ; Linden, C.G. van der; Weg, W.E. van de; Schouten, H.J. ; Arkel, G. van; Denance, C. ; Durel, C.E. - \ 2005
Theoretical and Applied Genetics 110 (2005)4. - ISSN 0040-5752 - p. 660 - 668.
quantitative trait loci - venturia-inaequalis - scab resistance - mildew resistance - defense genes - co-localize - arabidopsis - homologs - potato - progeny
We used a new method called nucleotide-binding site (NBS) profiling to identify and map resistance gene analogues (RGAs) in apple. This method simultaneously allows the amplification and the mapping of genetic markers anchored in the conserved NBS-encoding domain of plant disease resistance genes. Ninety-four individuals belonging to an F1 progeny derived from a cross between the apple cultivars Discovery and TN10-8 were studied. Two degenerate primers designed from the highly conserved P-loop motif within the NBS domain were used together with adapter primers. Forty-three markers generated with NBS profiling could be mapped in this progeny. After sequencing, 23 markers were identified as RGAs, based on their homologies with known resistance genes or NBS/leucine-rich-repeat-like genes. Markers were mapped on 10 of the 17 linkage groups of the apple genetic map used. Most of these markers were organized in clusters. Twenty-five markers mapped close to major genes or quantitative trait loci for resistance to scab and mildew previously identified in different apple progenies. Several markers could become efficient tools for marker-assisted selection once converted into breeder-friendly markers. This study demonstrates the efficiency of the NBS-profiling method for generating RGA markers for resistance loci in apple
QTL analysis of the genetic architecture determining resistance to fire blight in an apple progeny
Calenge, F. ; Drouet, D. ; Weg, W.E. van de; Brisset, M.N. ; Paulin, J.P. ; Durel, C.E. - \ 2004
Acta Horticulturae 663 (2004). - ISSN 0567-7572 - p. 141 - 146.
Fire blight, caused by the bacterial pathogen Erwinia amylovora, is one of the most destructive diseases of apple (Malus x domestica). In order to analyse the genetic determinism of resistance to fire blight in apple, a quantitative trait analysis (QTL) approach was used. A F1 progeny of 164 individuals derived from a cross between the apple cultivars `Prima¿ and `Fiesta¿ was inoculated in greenhouse conditions. Seven copies per genotype were used. The length of the necrosis observed on shoots was scored 7 and 14 days after inoculation. The MapQTL software was used for QTL analyses, using two previously built maps of the parents, and the symptoms scored on shoots. Digenic interactions between all pairwise combinations of genetic markers were tested using a two-way ANOVA model with the SAS software. QTL were detected at the same locations both 7 and 14 days after inoculation. Two weak effect QTL deriving from `Prima¿ were detected on linkage groups (LG) 3 and LG16. One strong effect QTL deriving from `Fiesta¿ was detected on LG7 that explained 46.6% of the phenotypic variation observed in the progeny. Two additional significant (P