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Ordidge M, Litthauer S, Venison E, Blouin-Delmas M, Fernandez-Fernandez F, Höfer M, Kägi C, Kellerhals M, Marchese A, Mariette S, Nybom H, Giovannini D. Towards a Joint International Database: Alignment of SSR Marker Data for European Collections of Cherry Germplasm. Plants (Basel) 2021; 10:1243. [PMID: 34207415 PMCID: PMC8235247 DOI: 10.3390/plants10061243] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022]
Abstract
The objective of our study was the alignment of microsatellite or simple sequence repeat (SSR) marker data across germplasm collections of cherry within Europe. Through the European Cooperative program for Plant Genetic Resources ECPGR, a number of European germplasm collections had previously been analysed using standard sets of SSR loci. However, until now these datasets remained unaligned. We used a combination of standard reference genotypes and ad-hoc selections to compile a central dataset representing as many alleles as possible from national datasets produced in France, Great Britain, Germany, Italy, Sweden and Switzerland. Through the comparison of alleles called in data from replicated samples we were able to create a series of alignment factors, supported across 448 different allele calls, that allowed us to align a dataset of 2241 SSR profiles from six countries. The proportion of allele comparisons that were either in agreement with the alignment factor or confounded by null alleles ranged from 67% to 100% and this was further improved by the inclusion of a series of allele-specific adjustments. The aligned dataset allowed us to identify groups of previously unknown matching accessions and to identify and resolve a number of errors in the prior datasets. The combined and aligned dataset represents a significant step forward in the co-ordinated management of field collections of cherry in Europe.
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Affiliation(s)
- Matthew Ordidge
- Department of Crop Science, School of Agriculture, Policy and Development, University of Reading, Reading RG6 6EU, UK;
| | - Suzanne Litthauer
- NIAB EMR, New Road, East Malling, Kent ME19 6BJ, UK; (S.L.); (F.F.-F.)
| | - Edward Venison
- Department of Crop Science, School of Agriculture, Policy and Development, University of Reading, Reading RG6 6EU, UK;
| | - Marine Blouin-Delmas
- INRAE-Unité Expérimentale Arboricole, Domaine de la Tour de Rance, 47320 Bourran, France;
| | | | - Monika Höfer
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Julius Kühn Institute, Pillnitzer Platz 3a, 01326 Dresden, Germany;
| | - Christina Kägi
- Federal Office for Agriculture, Genetic Resources and Technologies, Schwarzenburgstrasse 165, 3003 Bern, Switzerland;
| | - Markus Kellerhals
- Agroscope, Strategic Research Division Plant Breeding, Müller-Thurgau-Str. 29, 8820 Wädenswil, Switzerland;
| | - Annalisa Marchese
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze-Ed. 4, 90128 Palermo, Italy;
| | - Stephanie Mariette
- BIOGECO, INRAE, University of Bordeaux, Route d’Arcachon 69, 33612 Cestas, France;
| | - Hilde Nybom
- Balsgård-Department of Plant Breeding, Swedish University of Agricultural Sciences, Fjälkestadsvägen 459, 29194 Kristianstad, Sweden;
| | - Daniela Giovannini
- CREA-Research Centre for Olive, Fruit and Citrus Crops, via la Canapona 1 bis, 47121 Forlì, Italy;
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Urrestarazu J, Kägi C, Bühlmann A, Gassmann J, Santesteban LG, Frey JE, Kellerhals M, Miranda C. Integration of expert knowledge in the definition of Swiss pear core collection. Sci Rep 2019; 9:8934. [PMID: 31221983 PMCID: PMC6586639 DOI: 10.1038/s41598-019-44871-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/15/2019] [Indexed: 12/20/2022] Open
Abstract
Core collections (CCs) constitute a key tool for the characterization and management of genetic resources (GR). When the institutions involved in GR preservation decide to define a CC, they frequently prefer to select accessions based not only on strictly objective criteria, but also to add others following expert knowledge considerations (popularity, prestige, role in breeding history, or presence of phenotypic features of interest). The aim of this study was to evaluate the implications of approaches that combine formal analytical procedures and expert knowledge on the efficiency of CC definition through a case study to establish a pear CC from the Swiss National Pear Inventory. The CC had to represent a maximum of the genetic diversity, not to exceed 150 accessions, and required to include a priority set (SPPS) with 86 genotypes selected based on expert knowledge. In total, nine strategies were evaluated, resulting of combining compositions of the dataset sampled, sampling sizes and methods. The CCs sampled by mixed approaches provided similar scores, irrespective of the approach considered, and obtained similar efficiency in optimizing the genetic diversity retained. Therefore, mixed approaches can be an appropriate choice for applications involving genetic conservation in tree germplasm collections.
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Affiliation(s)
- J Urrestarazu
- Department of Agronomy, Biotechnology and Food Science, Public University of Navarre, 31006, Pamplona, Spain.
| | - C Kägi
- Federal Office for Agriculture, 3003, Bern, Switzerland
| | | | | | - L G Santesteban
- Department of Agronomy, Biotechnology and Food Science, Public University of Navarre, 31006, Pamplona, Spain
| | - J E Frey
- Agroscope, 8820, Wädenswil, Switzerland
| | | | - C Miranda
- Department of Agronomy, Biotechnology and Food Science, Public University of Navarre, 31006, Pamplona, Spain
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Urrestarazu J, Denancé C, Ravon E, Guyader A, Guisnel R, Feugey L, Poncet C, Lateur M, Houben P, Ordidge M, Fernandez-Fernandez F, Evans KM, Paprstein F, Sedlak J, Nybom H, Garkava-Gustavsson L, Miranda C, Gassmann J, Kellerhals M, Suprun I, Pikunova AV, Krasova NG, Torutaeva E, Dondini L, Tartarini S, Laurens F, Durel CE. Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level. BMC Plant Biol 2016; 16:130. [PMID: 27277533 PMCID: PMC4898379 DOI: 10.1186/s12870-016-0818-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/23/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North + East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe. RESULTS A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST = 0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST = 0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars. CONCLUSIONS The variation found at group and subgroup levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.
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Affiliation(s)
- Jorge Urrestarazu
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
- Department of Agricultural Sciences, University of Bologna, Viale Giuseppe Fanin 44, 40127, Bologna, Italy
- Public University of Navarre (UPNA), Campus Arrosadia, 31006, Pamplona, Spain
| | - Caroline Denancé
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Elisa Ravon
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Arnaud Guyader
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Rémi Guisnel
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Laurence Feugey
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Charles Poncet
- Plateforme Gentyane, INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 63100, Clermont-Ferrand, France
| | - Marc Lateur
- CRA-W, Centre Wallon de Recherches Agronomiques, Plant Breeding & Biodiversity, Bâtiment Emile Marchal, Rue de Liroux, 4 - 5030, Gembloux, Belgium
| | - Patrick Houben
- CRA-W, Centre Wallon de Recherches Agronomiques, Plant Breeding & Biodiversity, Bâtiment Emile Marchal, Rue de Liroux, 4 - 5030, Gembloux, Belgium
| | - Matthew Ordidge
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, RG6 6AR, UK
| | | | - Kate M Evans
- Washington State University Tree Fruit Research and Extension Center, 1100 N Western Ave, Wenatchee, WA, 98801, USA
| | - Frantisek Paprstein
- RBIPH, Research and Breeding Institute of Pomology Holovousy Ltd., 508 01, Horice, Czech Republic
| | - Jiri Sedlak
- RBIPH, Research and Breeding Institute of Pomology Holovousy Ltd., 508 01, Horice, Czech Republic
| | - Hilde Nybom
- Department of Plant Breeding, Balsgård, Fjälkestadsvägen 459, Swedish University of Agricultural Sciences, 291 94, Kristianstad, Sweden
| | - Larisa Garkava-Gustavsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, 230 53, Alnarp, Sweden
| | - Carlos Miranda
- Public University of Navarre (UPNA), Campus Arrosadia, 31006, Pamplona, Spain
| | - Jennifer Gassmann
- Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.O. Box, 8820, Wädenswil, Switzerland
| | - Markus Kellerhals
- Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.O. Box, 8820, Wädenswil, Switzerland
| | - Ivan Suprun
- NCRRIH&V, North Caucasian Regional Research Institute of Horticulture and Viticulture, 39, 40-letiya Pobedy street, Krasnodar, 350901, Russian Federation
| | - Anna V Pikunova
- VNIISPK, The All Russian Research Institute of Fruit Crop Breeding, 302530, p/o Zhilina, Orel district, Russian Federation
| | - Nina G Krasova
- VNIISPK, The All Russian Research Institute of Fruit Crop Breeding, 302530, p/o Zhilina, Orel district, Russian Federation
| | - Elnura Torutaeva
- Kyrgyz National Agrarian University, 68 Mederova Street, 720005, Bishkek, Kyrgyzstan
| | - Luca Dondini
- Department of Agricultural Sciences, University of Bologna, Viale Giuseppe Fanin 44, 40127, Bologna, Italy
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Viale Giuseppe Fanin 44, 40127, Bologna, Italy
| | - François Laurens
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Charles-Eric Durel
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.
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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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Costa F, Cappellin L, Zini E, Patocchi A, Kellerhals M, Komjanc M, Gessler C, Biasioli F. QTL validation and stability for volatile organic compounds (VOCs) in apple. Plant Sci 2013; 211:1-7. [PMID: 23987805 DOI: 10.1016/j.plantsci.2013.05.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 05/28/2013] [Accepted: 05/31/2013] [Indexed: 05/22/2023]
Abstract
The aroma trait in apple is a key factor for fruit quality strongly affecting the consumer appreciation, and its detection and analysis is often an extremely laborious and time consuming procedure. Molecular markers associated to this trait can to date represent a valuable selection tool to overcome these limitations. QTL mapping is the first step in the process of targeting valuable molecular markers to be employed in marker-assisted breeding programmes (MAB). However, a validation step is usually required before a newly identified molecular marker can be implemented in marker-assisted selection. In this work the position of a set of QTLs associated to volatile organic compounds (VOCs) was confirmed and validated in three different environments in Switzerland, namely Wädenswil, Conthey and Cadenazzo, where the progeny 'Fiesta×Discovery' was replicated. For both QTL identification and validation, the phenotypic data were represented by VOCs produced by mature apple fruit and assessed with a Proton Transfer Reaction-Mass Spectrometer (PTR-MS) instrument. The QTL-VOC combined analysis performed among these three locations validated the presence of important QTLs in three specific genomic regions, two located in the linkage group 2 and one in linkage group 15, respectively, for compounds related to esters (m/z 43, 61 and 131) and to the hormone ethylene (m/z 28). The QTL set presented here confirmed that in apple some compounds are highly genetically regulated and stable across environments.
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Affiliation(s)
- Fabrizio Costa
- Research and Innovation Centre, Foundation Edmund Mach, Via Mach 1, San Michele all'Adige (TN), Italy.
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Fahrentrapp J, Broggini G, Gessler C, Peil A, Kellerhals M, Malnoy M, Richter K. FINE MAPPING OF FIRE BLIGHT RESISTANCE LOCUS IN MALUS × ROBUSTA 5 ON LINKAGE GROUP 3. ACTA ACUST UNITED AC 2011. [DOI: 10.17660/actahortic.2011.896.32] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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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Baumgartner I, Patocchi A, Franck L, Kellerhals M, Broggini G. FIRE BLIGHT RESISTANCE FROM 'EVERESTE' AND MALUS SIEVERSII USED IN BREEDING FOR NEW HIGH QUALITY APPLE CULTIVARS: STRATEGIES AND RESULTS. ACTA ACUST UNITED AC 2011. [DOI: 10.17660/actahortic.2011.896.56] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [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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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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Khan MA, Durel CE, Duffy B, Drouet D, Kellerhals M, Gessler C, Patocchi A. Development of molecular markers linked to the ‘Fiesta’ linkage group 7 major QTL for fire blight resistance and their application for marker-assisted selection. Genome 2007; 50:568-77. [PMID: 17632578 DOI: 10.1139/g07-033] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [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
A fire blight resistance QTL explaining 34.3%–46.6% of the phenotypic variation was recently identified on linkage group 7 of apple cultivar ‘Fiesta’ (F7). However, markers flanking this QTL were AFLP and RAPD markers unsuitable for marker-assisted selection (MAS). Two RAPD markers bracketing the QTL have been transformed into SCAR (sequence-characterized amplified region) markers, and an SSR marker specific for the region was developed. Pedigree analysis of ‘Fiesta’ with these markers enabled tracking of the F7 QTL allele back to ‘Cox’s Orange Pippin’. Stability of the effect of this QTL allele in different backgrounds was analyzed by inoculating progeny plants of a cross between ‘Milwa’, a susceptible cultivar, and ‘1217’, a moderately resistant cultivar, and a set of cultivars that carry or lack the allele conferring increased fire blight resistance. Progenies and cultivars that carried both markers were significantly more resistant than those that did not carry both markers, indicating high stability of the F7 QTL allele in different backgrounds. This stability and the availability of reproducible markers bracketing the QTL make this locus promising for use in MAS.
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Affiliation(s)
- Muhammad A Khan
- Plant Pathology, Institute of Integrative Biology (IBZ), ETH Zurich, CH-8092, Zurich, Switzerland
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Gygax M, Gianfranceschi L, Liebhard R, Kellerhals M, Gessler C, Patocchi A. Molecular markers linked to the apple scab resistance gene Vbj derived from Malus baccata jackii. Theor Appl Genet 2004; 109:1702-9. [PMID: 15365630 DOI: 10.1007/s00122-004-1803-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Accepted: 08/19/2004] [Indexed: 05/23/2023]
Abstract
Breeding for scab-resistant apple cultivars by pyramiding several resistance genes in the same genetic background is a promising way to control apple scab caused by the fungus Venturia inaequalis. To achieve this goal, DNA markers linked to the genes of interest are required in order to select seedlings with the desired resistance allele combinations. For several apple scab resistance genes, molecular markers are already available; but until now, none existed for the apple scab resistance gene Vbj originating from the crab apple Malus baccata jackii. Using bulk segregant analysis, three RAPD markers linked to Vbj were first identified. These markers were transformed into more reliable sequence-characterised amplified region (SCAR) markers that proved to be co-dominant. In addition, three SSR markers and one SCAR were identified by comparing homologous linkage groups of existing genetic maps. Discarding plants showing genotype-phenotype incongruence (GPI plants) plants, a linkage map was calculated. Vbj mapped between the markers CH05e03 (SSR) and T6-SCAR, at 0.6 cM from CH05e03 and at 3.9 cM from T6-SCAR. Without the removal of the GPI plants, Vbj was placed 15 cM away from the closest markers. Problems and pitfalls due to GPI plants and the consequences for mapping the resistance gene accurately are discussed. Finally, the usefulness of co-dominant markers for pedigree analysis is also demonstrated.
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Affiliation(s)
- M Gygax
- Plant Pathology, Institute of Plant Sciences, Swiss Federal Institute of Technology, 8092 Zurich, Switzerland
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Abstract
Reports from several European countries of the breakdown of the Vf resistance, the most frequently used source of resistance in breeding programs against apple scab, emphasize the urgency of diversifying the basis of apple scab resistance and pyramiding different apple scab resistances with the use of their associated molecular markers. GMAL 2473 is an apple scab resistant selection thought to carry the resistance gene Vr. We report the identification by BSA of three AFLP markers and one RAPD marker associated with the GMAL 2473 resistance gene. SSRs associated with the resistance gene were found by (1) identifying the linkage group carrying the apple scab resistance and (2) testing the SSRs previously mapped in the same region. One such SSR, CH02c02a, mapped on linkage group 2, co-segregates with the resistance gene. GAML 2473 was tested with molecular markers associated with other apple scab resistance genes, and accessions carrying known apple scab resistance genes were tested with the SSR linked to the resistance gene found in GMAL 2473. The results indicate that GMAL 2473 does not carry Vr, and that a new apple scab resistance gene, named Vr2, has been identified.
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Affiliation(s)
- A Patocchi
- Plant Pathology Group, Institute of Plant Sciences, Swiss Federal Institute of Technology, Zürich, Switzerland.
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15
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Liebhard R, Kellerhals M, Pfammatter W, Jertmini M, Gessler C. Mapping quantitative physiological traits in apple (Malus x domestica Borkh.). Plant Mol Biol 2003; 52:511-26. [PMID: 12956523 DOI: 10.1023/a:1024886500979] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Efficient breeding and selection of high-quality apple cultivars requires knowledge and understanding of the underlying genetics. The availability of genetic linkage maps constructed with molecular markers enables the detection and analysis of major genes and quantitative trait loci contributing to the quality traits of a genotype. A segregating population of the cross between the apple varieties 'Fiesta' (syn. 'Red Pippin') and 'Discovery' has been observed over three years at three different sites in Switzerland and data on growth habit, blooming behaviour, juvenile period and fruit quality has been recorded. QTL analyses were performed, based on a genetic linkage map consisting of 804 molecular markers and covering all 17 apple chromosomes. With the maximum likelihood based interval mapping method, the investigated complex traits could be dissected into a number of QTLs affecting the observed characters. Genomic regions participating in the genetic control of stem diameter, plant height increment, leaf size, blooming time, blooming intensity, juvenile phase length, time of fruit maturity, number of fruit, fruit size and weight, fruit flesh firmness, sugar content and fruit acidity were identified and compared with previously mapped QTLs in apple. Although 'Discovery' fruit displayed a higher acid content, both acidity QTLs were attributed to the sweeter parent 'Fiesta'. This indicated homozygosity at the acidity loci in 'Discovery' preventing their detection in the progeny due to the lack of segregation.
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Affiliation(s)
- R Liebhard
- Swiss Federal Institute of Technology, Institute of Plant Science/Phytopathology, Universitätstrasse 2, 8092 Zurich, Switzerland
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16
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Liebhard R, Koller B, Patocchi A, Kellerhals M, Pfammatter W, Jermini M, Gessler C. Mapping Quantitative Field Resistance Against Apple Scab in a 'Fiesta' x 'Discovery' Progeny. Phytopathology 2003; 93:493-501. [PMID: 18944365 DOI: 10.1094/phyto.2003.93.4.493] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT Breeding of resistant apple cultivars (Malus x domestica) as a disease management strategy relies on the knowledge and understanding of the underlying genetics. The availability of molecular markers and genetic linkage maps enables the detection and the analysis of major resistance genes as well as of quantitative trait loci (QTL) contributing to the resistance of a genotype. Such a genetic linkage map was constructed, based on a segregating population of the cross between apple cvs. Fiesta (syn. Red Pippin) and Discovery. The progeny was observed for 3 years at three different sites in Switzerland and field resistance against apple scab (Venturia inaequalis) was assessed. Only a weak correlation was detected between leaf scab and fruit scab. A QTL analysis was performed, based on the genetic linkage map consisting of 804 molecular markers and covering all 17 chromosomes of apple. With the maximum likelihood-based interval mapping method, eight genomic regions were identified, six conferring resistance against leaf scab and two conferring fruit scab resistance. Although cv. Discovery showed a much stronger resistance against scab in the field, most QTL identified were attributed to the more susceptible parent 'Fiesta'. This indicated a high degree of homozygosity at the scab resistance loci in 'Discovery', preventing their detection in the progeny due to the lack of segregation.
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Ren Q, Sierro N, Kellerhals M, Kessler B, Witholt B. Properties of engineered poly-3-hydroxyalkanoates produced in recombinant Escherichia coli strains. Appl Environ Microbiol 2000; 66:1311-20. [PMID: 10742205 PMCID: PMC91986 DOI: 10.1128/aem.66.4.1311-1320.2000] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [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: 11/20/2022] Open
Abstract
To prepare medium-chain-length poly-3-hydroxyalkanoates (PHAs) with altered physical properties, we generated recombinant Escherichia coli strains that synthesized PHAs with altered monomer compositions. Experiments with different substrates (fatty acids with different chain lengths) or different E. coli hosts failed to produce PHAs with altered physical properties. Therefore, we engineered a new potential PHA synthetic pathway, in which ketoacyl-coenzyme A (CoA) intermediates derived from the beta-oxidation cycle are accumulated and led to the PHA polymerase precursor R-3-hydroxyalkanoates in E. coli hosts. By introducing the poly-3-hydroxybutyrate acetoacetyl-CoA reductase (PhbB) from Ralstonia eutropha and blocking the ketoacyl-CoA degradation step of the beta-oxidation, the ketoacyl-CoA intermediate was accumulated and reduced to the PHA precursor. Introduction of the phbB gene not only caused significant changes in the monomer composition but also caused changes of the physical properties of the PHA, such as increase of polymer size and loss of the melting point. The present study demonstrates that pathway engineering can be a useful approach for producing PHAs with engineered physical properties.
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Affiliation(s)
- Q Ren
- Institute of Biotechnology, Swiss Federal Institute of Technology, CH-8093 Zürich, Switzerland
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Gianfranceschi L, Koller B, Seglias N, Kellerhals M, Gessler C. Molecular selection in apple for resistance to scab caused by Venturia inaequalis. Theor Appl Genet 1996; 93:199-204. [PMID: 24162218 DOI: 10.1007/bf00225746] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/1995] [Accepted: 01/26/1996] [Indexed: 05/04/2023]
Abstract
Large-scale marker-assisted selection requires highly reproducible, consistent and simple markers. The use of genetic markers is important in woody plant breeding in general, and in apple in particular, because of the high level of heterozygosity present in Malus species. We present here the transformation of two RAPD markers, which we found previously to be linked to the major scab resistance gene Vf, into more reliable and reproducible markers that can be applied directly to apple breeding. We give an example of how the use of such markers can speed up selection for the introduction of scab resistance genes into the same plant, reducing labour and avoiding time-consuming test crosses. We discuss the nature and relationship of the scab resistance gene Vf to the one present in Nova Easygro, thought to be Vr.
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Affiliation(s)
- L Gianfranceschi
- Phytopathology Group, Institute of Plant Sciences, Swiss Federal Institute of Technology, Universitätsstraße 2, CH-8092, Zürich, Switzerland
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Kellerhals M, Fouillet A, Lespinasse Y. Effect of the scab inoculum and the susceptible parent on resistance to apple scab (Venturia inaequalis) in the progenies of crosses to the scab resistant cv 'Florina'. ACTA ACUST UNITED AC 1993. [DOI: 10.1051/agro:19930707] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Kellerhals M, Diehl P, Lounila J, Wasser R. Determination of the rα-structure of cyclopropane by NMR of partially oriented molecules allowing for the correlation between vibration and rotation. J Mol Struct 1987. [DOI: 10.1016/0022-2860(87)87029-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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