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Verdu CF, Guichoux E, Quevauvillers S, De Thier O, Laizet Y, Delcamp A, Gévaudant F, Monty A, Porté AJ, Lejeune P, Lassois L, Mariette S. Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L. Ecol Evol 2016; 6:7323-7333. [PMID: 28725400 PMCID: PMC5513258 DOI: 10.1002/ece3.2466] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/18/2016] [Accepted: 08/19/2016] [Indexed: 12/20/2022] Open
Abstract
The RADseq technology allows researchers to efficiently develop thousands of polymorphic loci across multiple individuals with little or no prior information on the genome. However, many questions remain about the biases inherent to this technology. Notably, sequence misalignments arising from paralogy may affect the development of single nucleotide polymorphism (SNP) markers and the estimation of genetic diversity. We evaluated the impact of putative paralog loci on genetic diversity estimation during the development of SNPs from a RADseq dataset for the nonmodel tree species Robinia pseudoacacia L. We sequenced nine genotypes and analyzed the frequency of putative paralogous RAD loci as a function of both the depth of coverage and the mismatch threshold allowed between loci. Putative paralogy was detected in a very variable number of loci, from 1% to more than 20%, with the depth of coverage having a major influence on the result. Putative paralogy artificially increased the observed degree of polymorphism and resulting estimates of diversity. The choice of the depth of coverage also affected diversity estimation and SNP validation: A low threshold decreased the chances of detecting minor alleles while a high threshold increased allelic dropout. SNP validation was better for the low threshold (4×) than for the high threshold (18×) we tested. Using the strategy developed here, we were able to validate more than 80% of the SNPs tested by means of individual genotyping, resulting in a readily usable set of 330 SNPs, suitable for use in population genetics applications.
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Affiliation(s)
- Cindy F Verdu
- Forest Management Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium
| | | | - Samuel Quevauvillers
- Forest Management Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium
| | - Olivier De Thier
- Forest Management Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium
| | | | | | | | - Arnaud Monty
- Biodiversity and Landscape Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium
| | | | - Philippe Lejeune
- Forest Management Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium
| | - Ludivine Lassois
- Forest Management Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium.,Biodiversity and Landscape Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium
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Verdu CF, Guyot S, Childebrand N, Bahut M, Celton JM, Gaillard S, Lasserre-Zuber P, Troggio M, Guilet D, Laurens F. QTL analysis and candidate gene mapping for the polyphenol content in cider apple. PLoS One 2014; 9:e107103. [PMID: 25271925 PMCID: PMC4182701 DOI: 10.1371/journal.pone.0107103] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [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: 01/28/2014] [Accepted: 08/12/2014] [Indexed: 11/25/2022] Open
Abstract
Polyphenols have favorable antioxidant potential on human health suggesting that their high content is responsible for the beneficial effects of apple consumption. They control the quality of ciders as they predominantly account for astringency, bitterness, color and aroma. In this study, we identified QTLs controlling phenolic compound concentrations and the average polymerization degree of flavanols in a cider apple progeny. Thirty-two compounds belonging to five groups of phenolic compounds were identified and quantified by reversed phase liquid chromatography on both fruit extract and juice, over three years. The average polymerization degree of flavanols was estimated in fruit by phloroglucinolysis coupled to HPLC. Parental maps were built using SSR and SNP markers and used for the QTL analysis. Sixty-nine and 72 QTLs were detected on 14 and 11 linkage groups of the female and male maps, respectively. A majority of the QTLs identified in this study are specific to this population, while others are consistent with previous studies. This study presents for the first time in apple, QTLs for the mean polymerization degree of procyanidins, for which the mechanisms involved remains unknown to this day. Identification of candidate genes underlying major QTLs was then performed in silico and permitted the identification of 18 enzymes of the polyphenol pathway and six transcription factors involved in the apple anthocyanin regulation. New markers were designed from sequences of the most interesting candidate genes in order to confirm their co-localization with underlying QTLs by genetic mapping. Finally, the potential use of these QTLs in breeding programs is discussed.
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Affiliation(s)
- Cindy F. Verdu
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- Université d'Angers, EA921 Laboratoire de Substances d'Origine Naturelle et Analogues Structuraux, SFR 4207 Quasav, PRES L'UNAM, Angers, France
| | - Sylvain Guyot
- INRA, UR1268 Biopolymères, Interactions & Assemblages, Equipe « Polyphénols, Réactivité & Procédés », Le Rheu, France
| | - Nicolas Childebrand
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Muriel Bahut
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Jean-Marc Celton
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Sylvain Gaillard
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Pauline Lasserre-Zuber
- INRA-UBP, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, TN, Italy
| | - David Guilet
- Université d'Angers, EA921 Laboratoire de Substances d'Origine Naturelle et Analogues Structuraux, SFR 4207 Quasav, PRES L'UNAM, Angers, France
| | - François Laurens
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
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Verdu CF, Childebrand N, Marnet N, Lebail G, Dupuis F, Laurens F, Guilet D, Guyot S. Polyphenol variability in the fruits and juices of a cider apple progeny. J Sci Food Agric 2014; 94:1305-1314. [PMID: 24115016 DOI: 10.1002/jsfa.6411] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [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: 02/11/2013] [Revised: 05/30/2013] [Accepted: 10/01/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND Polyphenols have a favourable antioxidant potential on human health, suggesting that their high content in apple is responsible for the beneficial effects of apple consumption. They are also linked to the quality of apple juices and ciders since they are predominantly responsible for astringency, bitterness and colour. Major phenolic compounds were quantified by liquid chromatography in fruits and juices from a cider apple progeny harvested for 3 years. The total content of procyanidins and their average degree of polymerisation (DPn) were also determined in fruits by phloroglucinolysis. Variability and extraction yield of these compounds were determined. RESULTS The variability observed in the progeny was representative of the variability observed in many cider apple varieties. Hydroxycinnamic acids were the most extractable group, with an average extraction yield of 67%, whereas flavonols and anthocyanins were the least. CONCLUSION This study is the first to introduce variability and extraction yields of the main phenolic compounds in both fruits and juices of a cider apple progeny. This dataset will be used for an upcoming QTL mapping study, an original approach that has never been undertaken for cider apple.
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Affiliation(s)
- Cindy F Verdu
- Université d'Angers, EA 921, Laboratoire de Substances d'Origine Naturelle et Analogues Structuraux, SFR 4207 QUASAV, PRES L'UNAM, 49045, Angers, France; Université d'Angers, UMR1345, Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, 49045, Angers, France; AgroCampus-Ouest, UMR1345, Institut de Recherche en Horticulture et Semences, 49045, Angers, France; INRA, UMR1345, Institut de Recherche en Horticulture et Semences, 49071, Beaucouzé, France
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Verdu CF, Gatto J, Freuze I, Richomme P, Laurens F, Guilet D. Comparison of two methods, UHPLC-UV and UHPLC-MS/MS, for the quantification of polyphenols in cider apple juices. Molecules 2013; 18:10213-27. [PMID: 23973994 PMCID: PMC6270524 DOI: 10.3390/molecules180910213] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [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: 07/11/2013] [Revised: 08/12/2013] [Accepted: 08/12/2013] [Indexed: 12/04/2022] Open
Abstract
The aim of this study was to develop faster and more efficient phenotyping methods for in-depth genetic studies on cider apple progeny. The UHPLC chromatographic system was chosen to separate polyphenolic compounds, and quantifications were then simultaneously performed with a UV-PDA detector and an ESI-triple quadrupole mass analyzer (SRM mode). Both quantification methods were validated for 15 major compounds using two apple juice samples, on the basis of linearity, limits of detection and quantification, recovery and precision tests. The comparison between UV and SRM quantifications in 120 different samples of a cider apple progeny showed an excellent correlation for major compounds quantified with both methods. However, an overestimation was revealed for five compounds with the UV detector and the mass analyzer. Co-elution and matrix effects are discussed to explain this phenomenon. SRM methods should therefore be considered with restrictions in some cases for quantification measurements when several phenolic compounds are simultaneously quantified in complex matrices such as apple juices. For both methods, analyses were carried out over short periods of time while maintaining a high quality for the simultaneous quantification of phenolic compounds in apple juice. Each method is relevant for more in-depth genetic studies of the polyphenol content of apple juice.
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Affiliation(s)
- Cindy F. Verdu
- Laboratoire SONAS, Université d’Angers, SFR QUASAV, Angers 49045, France; E-Mails: (C.F.V.); (J.G.); (P.R.)
- Institut de Recherche en Horticulture et Semences, UMR1345, INRA, Université d’Angers, AgroCampus-Ouest, SFR QUASAV, Angers 49045, France; E-Mail:
| | - Julia Gatto
- Laboratoire SONAS, Université d’Angers, SFR QUASAV, Angers 49045, France; E-Mails: (C.F.V.); (J.G.); (P.R.)
| | - Ingrid Freuze
- Plateforme d’Ingénierie et Analyses Moléculaires, Université d’Angers, Angers 49045, France; E-Mail:
| | - Pascal Richomme
- Laboratoire SONAS, Université d’Angers, SFR QUASAV, Angers 49045, France; E-Mails: (C.F.V.); (J.G.); (P.R.)
- Plateforme d’Ingénierie et Analyses Moléculaires, Université d’Angers, Angers 49045, France; E-Mail:
| | - François Laurens
- Institut de Recherche en Horticulture et Semences, UMR1345, INRA, Université d’Angers, AgroCampus-Ouest, SFR QUASAV, Angers 49045, France; E-Mail:
| | - David Guilet
- Laboratoire SONAS, Université d’Angers, SFR QUASAV, Angers 49045, France; E-Mails: (C.F.V.); (J.G.); (P.R.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +33-241-226-676; Fax: +33-241-226-634
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