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.
Discovering peach QTLs with multiple progeny analysis
Mora, J.R.H. ; Micheletti, D. ; Bink, M.C.A.M. ; Weg, W.E. van de; Bassi, Daniele ; Nazzicari, Nelson ; Caprera, Andrea ; Dettori, Maria Teresa ; Micali, Sabrina ; Dirlewanger, E. ; Lambert, Patrick ; Pascal, Thierry ; Banchi, E. ; Troggio, M. ; Rossini, Laura ; Verde, Ignazio ; Quilot-Turion, Bénédicte ; Laurens, F. ; Arús, Pere ; Aranzana, M.J. - \ 2017
In: 14th EUCARPIA Symposium on Fruit Breeding and Genetics International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462611689 - p. 405 - 410.
FlexQTL - FruitBreedomics - Joint progeny analysis - Maturity date - Percentage of skin color
Although many peach QTLs responsible for the variability of traits have been identified and published so far, the number of molecular markers currently used in breeding is still limited. One of the reasons is the large QTL intervals produced, in part, by the limited progeny size. Here we report a QTL mapping approach that enlarges the progeny size by analyzing jointly multiple progenies. Our analysis included 1467 individuals from eighteen Prunus progenies, 13 from intra-specific crosses and five inter-specific between peach and closely related species. The progenies were grown in five locations, with no duplication between orchards. Data from phenology, tree, flower and fruit traits, fruit quality and yield measured in different locations and years were subjected to different standardization methods and integrated in a single data file. The populations were genotyped with the 9K SNP Illumina array, which increased considerably the marker density compared to previous studies. The QTL analysis was conducted with FlexQTLTM software. Here we describe and discuss the preliminary QTLs obtained for some of the traits analyzed (maturity date, percentage of red skin color and soluble solid content). The identification of donors of favorable alleles will represent an important tool for marker-assisted breeding. This study has been conducted in the frame of the Fruit Breedomics European project.
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.
Integrated QTL detection for key breeding traits in multiple peach progenies
Hernández Mora, José R. ; Micheletti, Diego ; Bink, Marco ; Weg, Eric Van de; Cantín, Celia ; Nazzicari, Nelson ; Caprera, Andrea ; Dettori, Maria Teresa ; Micali, Sabrina ; Banchi, Elisa ; Campoy, José Antonio ; Dirlewanger, Elisabeth ; Lambert, Patrick ; Pascal, Thierry ; Troggio, Michela ; Bassi, Daniele ; Rossini, Laura ; Verde, Ignazio ; Quilot-Turion, Bénédicte ; Laurens, François ; Arús, Pere ; Aranzana, Maria José - \ 2017
BMC Genomics 18 (2017). - ISSN 1471-2164 - 15 p.
FlexQTL - PBA - Peach breeding - Peach QTL - Pedigre-based Analysis
Background: Peach (Prunus persica (L.) Batsch) is a major temperate fruit crop with an intense breeding activity. Breeding is facilitated by knowledge of the inheritance of the key traits that are often of a quantitative nature. QTLs have traditionally been studied using the phenotype of a single progeny (usually a full-sib progeny) and the correlation with a set of markers covering its genome. This approach has allowed the identification of various genes and QTLs but is limited by the small numbers of individuals used and by the narrow transect of the variability analyzed. In this article we propose the use of a multi-progeny mapping strategy that used pedigree information and Bayesian approaches that supports a more precise and complete survey of the available genetic variability. Results: Seven key agronomic characters (data from 1 to 3 years) were analyzed in 18 progenies from crosses between occidental commercial genotypes and various exotic lines including accessions of other Prunus species. A total of 1467 plants from these progenies were genotyped with a 9 k SNP array. Forty-seven QTLs were identified, 22 coinciding with major genes and QTLs that have been consistently found in the same populations when studied individually and 25 were new. A substantial part of the QTLs observed (47%) would not have been detected in crosses between only commercial materials, showing the high value of exotic lines as a source of novel alleles for the commercial gene pool. Our strategy also provided estimations on the narrow sense heritability of each character, and the estimation of the QTL genotypes of each parent for the different QTLs and their breeding value. Conclusions: The integrated strategy used provides a broader and more accurate picture of the variability available for peach breeding with the identification of many new QTLs, information on the sources of the alleles of interest and the breeding values of the potential donors of such valuable alleles. These results are first-hand information for breeders and a step forward towards the implementation of DNA-informed strategies to facilitate selection of new cultivars with improved productivity and quality.
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.
A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species
Pierro, Erica A. Di; Gianfranceschi, Luca ; Guardo, Mario Di; Koehorst-Van Putten, Herma J.J. ; Kruisselbrink, Johannes W. ; Longhi, Sara ; Troggio, Michela ; Bianco, Luca ; Muranty, Hélène ; Pagliarani, Giulia ; Bink, Marco C.A.M. ; Voorrips, Roeland E. ; Weg, Eric van de - \ 2016
Horticulture Research 3 (2016). - ISSN 2052-7276
Quantitative trait loci (QTL) mapping approaches rely on the correct ordering of molecular markers along the chromosomes, which can be obtained from genetic linkage maps or a reference genome sequence. For apple (Malus domestica Borkh), the genome sequence v1 and v2 could not meet this need; therefore, a novel approach was devised to develop a dense genetic linkage map, providing the most reliable marker-loci order for the highest possible number of markers. The approach was based on four strategies: (i) the use of multiple full-sib families, (ii) the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism (SNP) markers, (iii) the construction of a single backcross-type data set including all families, and (iv) a two-step map generation procedure based on the sequential inclusion of markers. The map comprises 15 417 SNP markers, clustered in 3 K HaploBlock markers spanning 1 267 cM, with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM. Moreover, chromosome 5 was oriented according to its homoeologous chromosome 10. This map was useful to improve the apple genome sequence, design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies. Its collinearity with the genome sequences v1 and v3 are reported. To our knowledge, this is the shortest published SNP map in apple, while including the largest number of markers, families and individuals. This result validates our methodology, proving its value for the construction of integrated linkage maps for any outbreeding species.
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.
Accuracy and responses of genomic selection on key traits in apple breeding
Muranty, Hélène ; Troggio, Michela ; Sadok, Inès Ben; Rifaï, Mehdi Al; Auwerkerken, Annemarie ; Banchi, E. ; Velasco, Riccardo ; Stevanato, P. ; Weg, W.E. van de; Guardo, M. Di; Kumar, S. ; Laurens, François ; Bink, M.C.A.M. - \ 2015
Horticulture Research 2 (2015). - ISSN 2052-7276
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.
ASSIsT: An Automatic SNP ScorIng Tool for in- and outbreeding species
Guardo, M. Di; Micheletti, D. ; Bianco, L. ; Koehorst-van Putten, H.J.J. ; Longhi, S. ; Costa, F. ; Aranzana, M.J. ; Velasco, R. ; Arus, P. ; Troggio, M. ; Weg, W.E. van de - \ 2015
Bioinformatics 31 (2015)23. - ISSN 1367-4803 - p. 3873 - 3874.
ASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays, specifically devised for custom genotyping arrays. Illumina has developed an integrated software for SNP data visualization and inspection called GenomeStudio® (GS).ASSIsT builds on GS derived data and identifies those markers that follow a bi-allelic genetic model and show reliable genotype calls. Moreover, ASSIsT re-edits SNP calls with null alleles or additional SNPs in the probe annealing site. ASSIsT can be employed in the analysis of different population types such as full-sib families and mating schemes used in the plant kingdom (backcross, F1, F2), and unrelated individuals. The final result can be directly exported in the format required by the most common software for genetic mapping and marker-trait association analysis. ASSIsT is developed in Python and runs in Windows and Linux.
‘Schmidt's Antonovka’ is identical to ‘Common Antonovka’, an apple cultivar widely used in Russia in breeding for biotic and abiotic stresses
Pikunova, A. ; Madduri, M. ; Sedov, E. ; Noordijk, Y. ; Peil, A. ; Troggio, M. ; Bus, V.G.M. ; Visser, R.G.F. ; Weg, W.E. van de - \ 2014
Tree Genetics and Genomes 10 (2014)2. - ISSN 1614-2942 - p. 261 - 271.
x-domestica borkh. - resistance gene - linkage map - scab - genome
Progenies of ‘Schmidt's Antonovka’ (SA) have been widely used in Western breeding programs as a source of scab resistance. The identity of SA has remained obscure, especially due to the existence of a series of ‘Antonovka’ cultivars with different origins. In this paper we show Schmidt's Antonovka to be identical to ¿¿¿¿´¿¿¿¿¿ ¿¿¿¿¿¿¿¿¿¿¿¿ or ‘Common Antonovka’ (CA), an old Russian cultivar of unknown origin, by comparing simple sequence repeat (SSR) and SNP genotyping data from several first-generation descendants of SA from two European collections and a CA accession from the germplasm collection held at VNIISPK (The All-Russian Research Institute of Horticultural Breeding, Orel, Russia). The use of CA in Russian breeding programs is also briefly reviewed.
Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array
Antanaviciute, L. ; Fernández-Fernández, F. ; Jansen, J. ; Banchi, E. ; Evans, K.M. ; Viola, R. ; Velasco, R. ; Dunwell, J.M. ; Troggio, M. ; Sargent, D.J. - \ 2012
BMC Genomics 13 (2012). - ISSN 1471-2164
domestica borkh. - construction - alleles
Background: A whole-genome genotyping array has previously been developed for Malus using SNP data from 28 Malus genotypes. This array offers the prospect of high throughput genotyping and linkage map development for any given Malus progeny. To test the applicability of the array for mapping in diverse Malus genotypes, we applied the array to the construction of a SNP-based linkage map of an apple rootstock progeny. Results: Of the 7,867 Malus SNP markers on the array, 1,823 (23.2%) were heterozygous in one of the two parents of the progeny, 1,007 (12.8%) were heterozygous in both parental genotypes, whilst just 2.8% of the 921 Pyrus SNPs were heterozygous. A linkage map spanning 1,282.2 cM was produced comprising 2,272 SNP markers, 306 SSR markers and the S-locus. The length of the M432 linkage map was increased by 52.7 cM with the addition of the SNP markers, whilst marker density increased from 3.8 cM/marker to 0.5 cM/marker. Just three regions in excess of 10 cM remain where no markers were mapped. We compared the positions of the mapped SNP markers on the M432 map with their predicted positions on the 'Golden Delicious' genome sequence. A total of 311 markers (13.7% of all mapped markers) mapped to positions that conflicted with their predicted positions on the 'Golden Delicious' pseudo-chromosomes, indicating the presence of paralogous genomic regions or mis-assignments of genome sequence contigs during the assembly and anchoring of the genome sequence. Conclusions: We incorporated data for the 2,272 SNP markers onto the map of the M432 progeny and have presented the most complete and saturated map of the full 17 linkage groups of M. pumila to date. The data were generated rapidly in a high-throughput semi-automated pipeline, permitting significant savings in time and cost over linkage map construction using microsatellites. The application of the array will permit linkage maps to be developed for QTL analyses in a cost-effective manner, and the identification of SNPs that have been assigned erroneous positions on the 'Golden Delicious' reference sequence will assist in the continued improvement of the genome sequence assembly for that variety.
Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple
Chagné, D. ; Crowhurst, R.N. ; Troggio, M. ; Davey, M.W. ; Gilmore, B. ; Lawley, C. ; Vanderzande, S. ; Hellens, R.P. ; Kumar, S. ; Cestaro, A. ; Velasco, R. ; Main, D. ; Rees, J.D. ; Iezzoni, A.F. ; Mockler, T. ; Wilhelm, L. ; Weg, W.E. van de; Gardiner, S.E. ; Bassil, N. ; Peace, C. - \ 2012
PLoS ONE 7 (2012)2. - ISSN 1932-6203
x-domestica borkh. - single-nucleotide polymorphisms - transcription factor - malus-domestica - genus vitis - shelf-life - fruit - markers - diversity - discovery
As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of ‘Golden Delicious’, SNPs were identified using SoapSNP. A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple