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Phenomic selection in wheat breeding: identification and optimisation of factors influencing prediction accuracy and comparison to genomic selection

Pauline Robert , Jérôme Auzanneau , Ellen Goudemand , François-Xavier Oury , Bernard Rolland et al.
TAG Theoretical and Applied Genetics, 2022, 135 (3), pp.895-914. ⟨10.1007/s00122-021-04005-8⟩
Journal articles hal-03524817v1
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Phenomic selection in wheat breeding: prediction of the genotype-by-environment interaction in multi-environment breeding trials

Pauline Robert , Ellen Goudemand , Jérôme Auzanneau , François-Xavier Oury , Bernard Rolland et al.
TAG Theoretical and Applied Genetics, 2022, 135, pp.3337-3356. ⟨10.1007/s00122-022-04170-4⟩
Journal articles hal-03765277v1
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A genomics resource for genetics, physiology, and breeding of West African sorghum

Jacques M Faye , Fanna Maina , Eyanawa A Akata , Bassirou Sine , Cyril Diatta et al.
Plant Genome, 2021, ⟨10.1002/tpg2.20075⟩
Journal articles hal-03274357v1
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Evolution of recombination landscapes in diverging populations of bread wheat

Alice Danguy Des Déserts , Sophie Bouchet , Pierre Sourdille , Bertrand Servin
Genome Biology and Evolution, 2021, 13 (8), ⟨10.1093/gbe/evab152⟩
Journal articles hal-03290674v1
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Integration of genomic selection into winter-type bread wheat breeding schemes: a simulation pipeline including economic constraints

Sarah Ben-Sadoun , Aline Fugeray-Scarbel , Jérôme Auzanneau , Gilles Charmet , Stephane Lemarié et al.
Crop Breeding,Genetics and Genomics , 2021, 3, ⟨10.20900/cbgg20210008⟩
Journal articles hal-03359314v1
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Dissecting adaptive traits with nested association mapping: genetic architecture of inflorescence morphology in sorghum

Marcus Olatoye , Sandeep Marla , Zhenbin Hu , Sophie Bouchet , Ramasamy Perumal et al.
G3, 2020, 10 (5), pp.1785-1796. ⟨10.1534/g3.119.400658⟩
Journal articles hal-02911856v1
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Economical optimization of a breeding scheme by selective phenotyping of the calibration set in a multi-trait context: application to bread making quality

S. Ben-Sadoun , R. Rincent , J. Auzanneau , François-Xavier Oury , B. Rolland et al.
TAG Theoretical and Applied Genetics, 2020, 133 (7), pp.2197-2212. ⟨10.1007/s00122-020-03590-4⟩
Journal articles hal-02553534v1
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BWGS: A R package for genomic selection and its application to a wheat breeding programme

Gilles Charmet , Louis-Gautier Tran , Jerome Auzanneau , Renaud Rincent , Sophie Bouchet et al.
PLoS ONE, 2020, 15 (4), pp.1-20. ⟨10.1371/journal.pone.0222733⟩
Journal articles hal-02571067v1
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Worldwide phylogeography and history of wheat genetic diversity

François Balfourier , Sophie Bouchet , Sandra Robert , Romain de Oliveira , Hélène Rimbert et al.
Science Advances , 2019, 5 (5), pp.eaav0536. ⟨10.1126/sciadv.aav0536⟩
Journal articles hal-02172516v1

Population genomics of sorghum (Sorghum bicolor) across diverse agroclimatic zones of Niger

Fanna Maina , Sophie Bouchet , Sandeep R. Marla , Zhenbin Hu , Jianan Wang et al.
Genome, 2018, 61 (4), pp.223-232. ⟨10.1139/gen-2017-0131⟩
Journal articles hal-02625927v1

Increased Power To Dissect Adaptive Traits in Global Sorghum Diversity Using a Nested Association Mapping Population.

Sophie Bouchet , Marcus O Olatoye , Sandeep R Marla , Ramasamy Perumal , Tesfaye Tesso et al.
Genetics, 2017, 206 (2), pp.573-585. ⟨10.1534/genetics.116.198499⟩
Journal articles hal-02627749v1

Association mapping for phenology and plant architecture in maize shows higher power for developmental traits compared with growth influenced traits

Sophie Bouchet , Pascal Bertin , T Presterl , Philippe Jamin , Denis Coubriche et al.
Heredity, 2017, 118 (3), pp.249-259. ⟨10.1038/hdy.2016.88⟩
Journal articles hal-01481767v1
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Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): Comparative analysis of global accessions and Senegalese landraces

Zhenbin Hu , Bassirou Mbacké , Ramasamy Perumal , Mame Codou Guèye , Ousmane Sy et al.
BMC Genomics, 2015, 16 (1), ⟨10.1186/s12864-015-2255-0⟩
Journal articles hal-01342372v1

Dent and flint maize diversity panels reveal important genetic potential for increasing biomass production

Renaud Rincent , Stephane S. Nicolas , Sophie Bouchet , T. Altmann , Dominique D. Brunel et al.
TAG Theoretical and Applied Genetics, 2014, 127 (11), pp.2313-2331. ⟨10.1007/s00122-014-2379-7⟩
Journal articles hal-02637142v1
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An initial assessment of linkage disequilibrium (LD) in coffee trees: LD patterns in groups of Coffea canephora Pierre using microsatellite analysis

Philippe Cubry , Fabien de Bellis , Komlan Avia , Sophie Bouchet , David Pot et al.
BMC Genomics, 2013, 14, 15 p. ⟨10.1186/1471-2164-14-10⟩
Journal articles hal-02643249v1
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Massive sorghum collection genotyped with SSR markers to enhance use of global genetic resources

Claire Billot , Punna Ramu , Sophie Bouchet , Jacques Chantereau , Monique Deu et al.
PLoS ONE, 2013, 8 (4), pp.e59714. ⟨10.1371/journal.pone.0059714⟩
Journal articles hal-01595265v1
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Adaptation of maize to temperate climates: mid-density genome-wide association genetics and diversity patterns reveal key genomic regions, with a major contribution of the Vgt2 (ZCN8) locus

Sophie Bouchet , Bertrand Servin , Pascal Bertin , Delphine D. Madur , Valerie V. Combes et al.
PLoS ONE, 2013, 8 (8), ⟨10.1371/journal.pone.0071377⟩
Journal articles hal-02652500v1
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Genetic structure, linkage disequilibrium and signature of selection in Sorghum: lessons from physically anchored DArT markers

Sophie Bouchet , David Pot , Monique Deu , Jean-François Rami , Claire Billot et al.
PLoS ONE, 2012, 7 (3), ⟨10.1371/journal.pone.0033470⟩
Journal articles hal-01268396v1

Genetic diversity of taro (Colocasia esculenta (L.) Schott) in Vanuatu (Oceania): an appraisal of the distribution of allelic diversity (DAD) with SSR markers

Julie Sardos , Jean-Louis Noyer , Sophie Bouchet , Vincent Lebot
Genetic Resources and Crop Evolution, 2012, 59 (5), pp.805 - 820. ⟨10.1007/s10722-011-9720-7⟩
Journal articles hal-01268335v1

Flowering Time in Maize: Linkage and Epistasis at a Major Effect Locus

Eléonore Durand , Sophie Bouchet , Pascal Bertin , Adrienne Ressayre , Philippe Jamin et al.
Genetics, 2012, 190 (4), pp.1547 - +. ⟨10.1534/genetics.111.136903⟩
Journal articles hal-02648939v1

Genetic diversity, structure, gene flow and evolutionary relationships within the Sorghum bicolor wild-weedy-crop complex in a western African region

Fabrice Sagnard , Monique Deu , Dékoro Dembélé , Raphaël Leblois , Lassana Touré et al.
TAG Theoretical and Applied Genetics, 2011, 123 (7), pp.1231-1246. ⟨10.1007/s00122-011-1662-0⟩
Journal articles hal-02649865v1
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A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers

Emma S Mace , Jean-Francois Rami , Sophie Bouchet , Patricia E Klein , Robert R Klein et al.
BMC Plant Biology, 2009, 9 (13), ⟨10.1186/1471-2229-9-13⟩
Journal articles hal-01338089v1

Leaf tip necrosis, molecular markers and β1-proteasome subunits associated with the slow rusting resistance genes Lr46/Yr29

G. M. Rosewarne , R. P. Singh , J. Huerta-Espino , H. M. William , Sophie Bouchet et al.
TAG Theoretical and Applied Genetics, 2006, 112 (3), pp.500-508. ⟨10.1007/s00122-005-0153-6⟩
Journal articles hal-01338628v1

Identification of factors influencing predictive ability of phenomic selection and comparison to genomic selection in wheat breeding programs

P Robert , Francois-Xavier Oury , Jérôme Auzanneau , Bernard Rolland , Emmanuel E. Heumez et al.
6th Conference on Cereal Biotechnology and Breeding,CBB6, EUCARPIA; AKCongress, Nov 2021, Budapest, Hungary
Conference papers hal-03480325v1

Prédiction génomique de la valeur boulangère

Sarah Ben Sadoun , Sophie Bouchet , Gilles Charmet
Phloème 2020 : biennales de l’innovation céréalière, Arvalis - Institut du végétal, Jan 2020, Paris, France
Conference papers hal-03113799v1

Historical recombination maps estimated with two diverging european and asian populations on bread wheat 3B chromosome

Alice Danguy Des Deserts , Ludovic Duvaux , Pierre Sourdille , Sophie Bouchet
"Quantitative Genetics and Genomics" Gordon Research Conference, Gordon Research Conference., Feb 2019, Barga, Italy
Conference papers hal-02289531v1

Bread-making quality predictions: multi-trait assisted genomic selection in bread wheat

Sarah Ben Sadoun , Renaud Rincent , Jerome Auzanneau , Francois-Xavier Oury , Bernard Rolland et al.
"Quantitative Genetics and Genomics" Gordon Research Conference, Gordon Research Conference., Feb 2019, Barga, Italy
Conference papers hal-02289536v1

Bread-making quality predictions of multi-trait assisted genomic selection

Sarah Ben Sadoun , Renaud Rincent , Jerome Auzanneau , Francois-Xavier Oury , Bernard Rolland et al.
1. International Wheat Congress, International Wheat Congress; Wheat inititive, Jul 2019, Saskatoon, Canada
Conference papers hal-02942672v1

Selection and characterization of a winter wheat diversity panel

Jacques Le Gouis , Agathe Mini , Sophie Bouchet , Etienne Paux , Stéphane Lafarge et al.
7. Congress and Associate Symposiums of Breads of the future: genomics, genetics, breeding, Federal research center “Vavilov all-Russian Institute of Plant Genetic Resources” – VIR., Jun 2019, St Petersbourg, Russia
Conference papers hal-02289527v1

Optimization of breeding schemes using genomic predictions and simulations

Sophie Bouchet , Stephane Lemarié , Aline Fugeray-Scarbel , Jerome Auzanneau , Gilles Charmet et al.
4. Conference on Cereal Biotechnology and Breeding (CBB4), EUCARPIA Cereal Section., Nov 2017, Budapest, Hungary
Conference papers hal-02786724v1
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De la modélisation des schémas de sélection à l'analyse de l'efficacité économique de la sélection génomique : méthode et quelques cas d'application

Aline Fugeray-Scarbel , Stephane Lemarié , Sophie Bouchet , Gilles Charmet , Jean Michel Elsen et al.
Séminaire SelGen 2017 : "La sélection génomique, bilan et perspectives", Sep 2017, Clichy, France. 1 p
Conference papers hal-01595570v1

Virtual selection for comparing wheat breeding schemes at constant total cost

Gilles Charmet , Sophie Bouchet , Jerome Auzanneau , Aline Fugeray-Scarbel , Stephane Lemarié et al.
13. International Wheat Genetics Symposium, Apr 2017, Tulln, Austria
Conference papers hal-02340466v1

Analyzing the economic effectiveness of genomic selection relative to conventional breeding approaches

Aline Fugeray-Scarbel , Sarah Ben-Sadoun , Sophie Bouchet , Stephane Lemarié
Nourollah Ahmadi; Jérôme Bartholomé. Complex Trait Prediction, 2467, Springer US, pp.619-644, 2022, Methods in Molecular Biology, 978-1-0716-2205-6. ⟨10.1007/978-1-0716-2205-6_22⟩
Book sections hal-03652408v1