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Peace CP, Bianco L, Troggio M, van de Weg E, Howard NP, Cornille A, Durel CE, Myles S, Migicovsky Z, Schaffer RJ, Costes E, Fazio G, Yamane H, van Nocker S, Gottschalk C, Costa F, Chagné D, Zhang X, Patocchi A, Gardiner SE, Hardner C, Kumar S, Laurens F, Bucher E, Main D, Jung S, Vanderzande S. Apple whole genome sequences: recent advances and new prospects. Hortic Res 2019; 6:59. [PMID: 30962944 PMCID: PMC6450873 DOI: 10.1038/s41438-019-0141-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 05/19/2023]
Abstract
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.
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Affiliation(s)
- Cameron P. Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Luca Bianco
- Computational Biology, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - Michela Troggio
- Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - Eric van de Weg
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Nicholas P. Howard
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108 USA
- Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky Universität, 26129 Oldenburg, Germany
| | - Amandine Cornille
- GQE – Le Moulon, Institut National de la Recherche Agronomique, University of Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Charles-Eric Durel
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
| | - Sean Myles
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
| | - Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
| | - Robert J. Schaffer
- The New Zealand Institute for Plant and Food Research Ltd, Motueka, 7198 New Zealand
- School of Biological Sciences, University of Auckland, Auckland, 1142 New Zealand
| | - Evelyne Costes
- AGAP, INRA, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Gennaro Fazio
- Plant Genetic Resources Unit, USDA ARS, Geneva, NY 14456 USA
| | - Hisayo Yamane
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan
| | - Steve van Nocker
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Chris Gottschalk
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Fabrizio Costa
- Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, 4474 New Zealand
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, 100193 Beijing, China
| | | | - Susan E. Gardiner
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, 4474 New Zealand
| | - Craig Hardner
- Queensland Alliance of Agriculture and Food Innovation, University of Queensland, St Lucia, 4072 Australia
| | - Satish Kumar
- New Cultivar Innovation, Plant and Food Research, Havelock North, 4130 New Zealand
| | - Francois Laurens
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
| | - Etienne Bucher
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
- Agroscope, 1260 Changins, Switzerland
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Stijn Vanderzande
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
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Laurens F, Aranzana MJ, Arus P, Bassi D, Bink M, Bonany J, Caprera A, Corelli-Grappadelli L, Costes E, Durel CE, Mauroux JB, Muranty H, Nazzicari N, Pascal T, Patocchi A, Peil A, Quilot-Turion B, Rossini L, Stella A, Troggio M, Velasco R, van de Weg E. An integrated approach for increasing breeding efficiency in apple and peach in Europe. Hortic Res 2018; 5:11. [PMID: 29507735 PMCID: PMC5830435 DOI: 10.1038/s41438-018-0016-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 12/23/2017] [Indexed: 05/02/2023]
Abstract
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.
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Affiliation(s)
- Francois Laurens
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Université Bretagne Loire, 42 rue Georges Morel, Beaucouzé, 49071 France
| | - Maria José Aranzana
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona Spain
| | - Pere Arus
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona Spain
| | - Daniele Bassi
- Università degli Studi di Milano - DiSAA, Via Celoria 2, Milan, 20133 Italy
| | - Marco Bink
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708PB The Netherlands
- Present Address: Hendrix Genetics Research, Technology & Services, Boxmeer, 5830 AC The Netherlands
| | - Joan Bonany
- IRTA-Mas Badia, Mas Badia, La Tallada, 17134 Spain
| | - Andrea Caprera
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900 Italy
| | | | | | - Charles-Eric Durel
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Université Bretagne Loire, 42 rue Georges Morel, Beaucouzé, 49071 France
| | | | - Hélène Muranty
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Université Bretagne Loire, 42 rue Georges Morel, Beaucouzé, 49071 France
| | - Nelson Nazzicari
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900 Italy
| | | | - Andrea Patocchi
- Agroscope, Research Division Plant Breeding, Schloss 1, Wädenswil, 8820 Switzerland
| | - Andreas Peil
- Julius Kühn-Institute (JKI); Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, Dresden, 01326 Germany
| | | | - Laura Rossini
- Università degli Studi di Milano - DiSAA, Via Celoria 2, Milan, 20133 Italy
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900 Italy
| | - Alessandra Stella
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900 Italy
| | - Michela Troggio
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Riccardo Velasco
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
- CREA-VE, Center of Viticulture and Enology, via XXVIII Aprile 26, Conegliano (TV), 31015 Italy
| | - Eric van de Weg
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, P.O.Box 386, Wageningen, 6700AJ The Netherlands
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Bianco L, Cestaro A, Sargent DJ, Banchi E, Derdak S, Di Guardo M, Salvi S, Jansen J, Viola R, Gut I, Laurens F, Chagné D, Velasco R, van de Weg E, Troggio M. Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh). PLoS One 2014; 9:e110377. [PMID: 25303088 PMCID: PMC4193858 DOI: 10.1371/journal.pone.0110377] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 09/12/2014] [Indexed: 01/08/2023] Open
Abstract
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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Affiliation(s)
- Luca Bianco
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Alessandro Cestaro
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Daniel James Sargent
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Elisa Banchi
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Sophia Derdak
- CNAG – Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona, Spain
| | - Mario Di Guardo
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
| | | | - Johannes Jansen
- Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Roberto Viola
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Ivo Gut
- CNAG – Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona, Spain
| | - Francois Laurens
- INRA, UMR1345 Institut de Recherche en Horticulture and Semences, Beaucouzé, France
| | - David Chagné
- Plant & Food Research, Palmerston North Research Centre, Palmerston North, New Zealand
| | - Riccardo Velasco
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Eric van de Weg
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
- * E-mail:
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Bink MCAM, Jansen J, Madduri M, Voorrips RE, Durel CE, Kouassi AB, 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 KM, 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, van de Weg WE. Bayesian QTL analyses using pedigreed families of an outcrossing species, with application to fruit firmness in apple. Theor Appl Genet 2014; 127:1073-90. [PMID: 24567047 DOI: 10.1007/s00122-014-2281-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 01/31/2014] [Indexed: 05/18/2023]
Abstract
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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Affiliation(s)
- M C A M Bink
- Biometris, Wageningen University and Research Centre, Droevendaalsesteeg 1, P.O. Box 16, 6700 AA, Wageningen, The Netherlands,
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Galvez-Lopez D, Laurens F, Quéméner B, Lahaye M. Variability of cell wall polysaccharides composition and hemicellulose enzymatic profile in an apple progeny. Int J Biol Macromol 2011; 49:1104-9. [DOI: 10.1016/j.ijbiomac.2011.09.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 08/25/2011] [Accepted: 09/07/2011] [Indexed: 11/24/2022]
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Bus V, Rikkerink E, Aldwinckle H, Caffier V, Durel C, Gardiner S, Gessler C, Groenwold R, Laurens F, Le Cam B, Luby J, Meulenbroek B, Kellerhals M, Parisi L, Patocchi A, Plummer K, Schouten H, Tartarini S, van de Weg W. A PROPOSAL FOR THE NOMENCLATURE OF VENTURIA INAEQUALIS RACES. ACTA ACUST UNITED AC 2009. [DOI: 10.17660/actahortic.2009.814.125] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Costes E, Lauri P, Laurens F, Moutier N, Belouin A, Delort F, Legave J, Regnard J. MORPHOLOGICAL AND ARCHITECTURAL TRAITS ON FRUIT TREES WHICH COULD BE RELEVANT FOR GENETIC STUDIES: A REVIEW. ACTA ACUST UNITED AC 2004. [DOI: 10.17660/actahortic.2004.663.60] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Bus V, van de Weg W, Durel C, Gessler C, Calenge F, Parisi L, Rikkerink E, Gardiner S, Patocchi A, Meulenbroek M, Schouten H, Laurens F. DELINEATION OF A SCAB RESISTANCE GENE CLUSTER ON LINKAGE GROUP 2 OF APPLE. ACTA ACUST UNITED AC 2004. [DOI: 10.17660/actahortic.2004.663.3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Durel CE, Parisi L, Laurens F, Van de Weg WE, Liebhard R, Jourjon MF. Genetic dissection of partial resistance to race 6 of Venturia inaequalis in apple. Genome 2003; 46:224-34. [PMID: 12723038 DOI: 10.1139/g02-127] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Scab, caused by the fungus Venturia inaequalis, is one of the most important diseases of apple (Malus x domestica). The major resistance gene, Vf, has been widely used in apple breeding programs, but two new races of the fungus (races 6 and 7) are able to overcome this gene. A mapped F1 progeny derived from a cross between the cultivars Prima and Fiesta has bee n inoculated with two monoconidial strains of race 6. These strains originated from sporulating leaves of 'Prima' and a descendant of 'Prima' that were grown in an orchard in northern Germany. 'Prima' carries the Vf resistance gene, whereas 'Fiesta' lacks Vf. A large variation in resistance and (or) susceptibility was observed among the individuals of the progeny. Several quantitative trait loci (QTLs) for resistance were identified that mapped on four genomic regions. One of them was located in the very close vicinity of the Vf resistance gene on linkage group LG-1 of the 'Prima' genetic map. This QTL is isolate specific because it was only detected with one of the two isolates. Two out of the three other genomic regions were identified with both isolates (LG-11 and LG-17). On LG-11, a QTL effect was detected in both parents. The genetic dissection of this QTL indicated a favourable intra-locus interaction between some parental alleles.
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Affiliation(s)
- C E Durel
- Unité d'Amélioration des Espèces Fruitières et Omementales, BP 57, 49071, Beaucouzd CEDEX, France.
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