2020

Ballini E, Tavaud M, Ducasse A, Sanchez D, Paux E, Kitt J, Charmet G, Audigeos D, Roumet P, David J and Morel JB (2020) Genome wide association mapping for resistance to multiple fungal pathogens in a panel issued from a broad composite cross-population of tetraploid wheat Triticum turgidum. Euphytica, 216, 92.

Concia L, Veluchamy A, Ramirez-Prado JS, Martin-Ramirez A, Huang Y, Perez M, Domenichini S, Rodriguez Granados NY, Kim S, Blein T, Duncan S, Pichot C, Manza-Mianza D, Juery C, Paux E, Moore G, Hirt H, Bergounioux C, Crespi M, Mahfouz MM, Bendahmane A, Liu C, Hall A, Raynaud C, Latrasse D and Benhamed M (2020) Wheat chromatin architecture is organized in genome territories and transcription factories. Genome Biol, 21, 104.

Falque M, Jebreen K, Paux E, Knaak C, Mezmouk S and Martin OC (2020) CNVmap: A Method and Software To Detect and Map Copy Number Variants from Segregation Data. Genetics, 214, 561-576.

Ben-Sadoun S, Rincent R, Auzanneau J, Oury FX, Rolland B, Heumez E, Ravel C, Charmet G and Bouchet S (2020) Economical optimization of a breeding scheme by selective phenotyping of the calibration set in a multi-trait context: application to bread making quality. Theor Appl Genet, 133, 2197-2212.

Charmet G, Tran LG, Auzanneau J, Rincent R and Bouchet S (2020) BWGS: A R package for genomic selection and its application to a wheat breeding programme. PLoS One, 15, e0222733.

Lovegrove A, Wingen LU, Plummer A, Wood A, Passmore D, Kosik O, Freeman J, Mitchell RAC, Hassall K, Ulker M, Tremmel-Bede K, Rakszegi M, Bedo Z, Perretant MR, Charmet G, Pont C, Salse J, Waite ML, Orford S, Burridge A, Pellny TK, Shewry PR and Griffiths S (2020) Identification of a major QTL and associated molecular marker for high arabinoxylan fibre in white wheat flour. PLoS One, 15, e0227826.

Ravel C, Faye A, Ben-Sadoun S, Ranoux M, Dardevet M, Dupuits C, Exbrayat F, Poncet C, Sourdille P and Branlard G (2020) SNP markers for early identification of high molecular weight glutenin subunits (HMW-GSs) in bread wheat. Theor Appl Genet, 133, 751-770.

2019

Balfourier F, Bouchet S, Robert S, De Oliveira R, Rimbert H, Kitt J, Choulet F, International Wheat Genome Sequencing C, BreedWheat C and Paux E (2019) Worldwide phylogeography and history of wheat genetic diversity. Sci Adv, 5, eaav0536.

Coriton O, Faye A, Paux E, Lemoine J, Huteau V, Branlard G and Jahier J (2019) Development of 1AS.1AL-1DL durum wheat chromosome carrying Glu-D1a locus encoding high molecular weight glutenin subunits 2 + 12. Mol Breed, 39, 32.

Tulpova Z, Luo MC, Toegelova H, Visendi P, Hayashi S, Vojta P, Paux E, Kilian A, Abrouk M, Bartos J, Hajduch M, Batley J, Edwards D, Dolezel J and Simkova H (2019) Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies. N Biotechnol, 48, 12-19.

Pont C, Leroy T, Seidel M, Tondelli A, Duchemin W, Armisen D, Lang D, Bustos-Korts D, Goue N, Balfourier F, Molnar-Lang M, Lage J, Kilian B, Ozkan H, Waite D, Dyer S, Letellier T, Alaux M, Wheat, Barley Legacy for Breeding Improvement c, Russell J, Keller B, van Eeuwijk F, Spannagl M, Mayer KFX, Waugh R, Stein N, Cattivelli L, Haberer G, Charmet G and Salse J (2019) Tracing the ancestry of modern bread wheats. Nat Genet, 51, 905-911.

 2018

Alaux M, Rogers J, Letellier T, Flores R, Alfama F, Pommier C, Mohellibi N, Durand S, Kimmel E, Michotey C, Guerche C, Loaec M, Laine M, Steinbach D, Choulet F, Rimbert H, Leroy P, Guilhot N, Salse J, Feuillet C, International Wheat Genome Sequencing C, Paux E, Eversole K, Adam-Blondon AF and Quesneville H (2018) Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. Genome Biol, 19, 111.

Handa H, Kanamori H, Tanaka T, Murata K, Kobayashi F, Robinson SJ, Koh CS, Pozniak CJ, Sharpe AG, Paux E, International Wheat Genome Sequencing C, Wu J and Nasuda S (2018) Structural features of two major nucleolar organizer regions (NORs), Nor-B1 and Nor-B2, and chromosome-specific rRNA gene expression in wheat. Plant J, 96, 1148-1159.

Ilc T, Arista G, Tavares R, Navrot N, Duchene E, Velt A, Choulet F, Paux E, Fischer M, Nelson DR, Hugueney P, Werck-Reichhart D and Rustenholz C (2018) Annotation, classification, genomic organization and expression of the Vitis vinifera CYPome. PLoS One, 13, e0199902.

International Wheat Genome Sequencing Consortium (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science, 361.

Jordan KW, Wang S, He F, Chao S, Lun Y, Paux E, Sourdille P, Sherman J, Akhunova A, Blake NK, Pumphrey MO, Glover K, Dubcovsky J, Talbert L and Akhunov ED (2018) The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping. Plant J, 95, 1039-1054.

Ly D, Huet S, Gauffreteau A, Rincent R, Touzy G, Mini A, Jannink J-L, Cormier F, Paux E, Lafarge S, Le Gouis J and Charmet G (2018) Whole-genome prediction of reaction norms to environmental stress in bread wheat (Triticum aestivum L.) by genomic random regression. Field Crops Res, 216, 32-41.

Ramirez-Gonzalez RH, Borrill P, Lang D, Harrington SA, Brinton J, Venturini L, Davey M, Jacobs J, van Ex F, Pasha A, Khedikar Y, Robinson SJ, Cory AT, Florio T, Concia L, Juery C, Schoonbeek H, Steuernagel B, Xiang D, Ridout CJ, Chalhoub B, Mayer KFX, Benhamed M, Latrasse D, Bendahmane A, International Wheat Genome Sequencing C, Wulff BBH, Appels R, Tiwari V, Datla R, Choulet F, Pozniak CJ, Provart NJ, Sharpe AG, Paux E, Spannagl M, Brautigam A and Uauy C (2018) The transcriptional landscape of polyploid wheat. Science, 361.

Rimbert H, Darrier B, Navarro J, Kitt J, Choulet F, Leveugle M, Duarte J, Riviere N, Eversole K, International Wheat Genome Sequencing C, Le Gouis J, on behalf The BreedWheat C, Davassi A, Balfourier F, Le Paslier MC, Berard A, Brunel D, Feuillet C, Poncet C, Sourdille P and Paux E (2018) High throughput SNP discovery and genotyping in hexaploid wheat. PLoS One, 13, e0186329.

Rincent R, Charpentier JP, Faivre-Rampant P, Paux E, Le Gouis J, Bastien C and Segura V (2018) Phenomic Selection Is a Low-Cost and High-Throughput Method Based on Indirect Predictions: Proof of Concept on Wheat and Poplar. G3 (Bethesda), 8, 3961-3972.

Wicker T, Gundlach H, Spannagl M, Uauy C, Borrill P, Ramirez-Gonzalez RH, De Oliveira R, International Wheat Genome Sequencing C, Mayer KFX, Paux E and Choulet F (2018) Impact of transposable elements on genome structure and evolution in bread wheat. Genome Biol, 19, 103.

 2017

Darrier B, Rimbert H, Balfourier F, Pingault L, Josselin AA, Servin B, Navarro J, Choulet F, Paux E and Sourdille P (2017) High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism. Genetics, 206, 1373-1388.

Gouache D, Bogard M, Pegard M, Thepot S, Garcia C, Hourcade D, Paux E, Oury F-X, Rousset M, Deswarte J-C and Le Bris X (2017) Bridging the gap between ideotype and genotype: Challenges and prospects for modelling as exemplified by the case of adapting wheat (Triticum aestivum L.) phenology to climate change in France. Field Crops Res, 202, 108-121.

Holusova K, Vrana J, Safar J, Simkova H, Balcarkova B, Frenkel Z, Darrier B, Paux E, Cattonaro F, Berges H, Letellier T, Alaux M, Dolezel J and Bartos J (2017) Physical Map of the Short Arm of Bread Wheat Chromosome 3D. Plant Genome, 10.

Oury FX, Lasme P, Michelet C, Dubat A, Gardet O, Heumez E, Rolland B, Rousset M, Abecassis J, Bar L'Helgouac'h C and Lullien-Pellerin V (2017) Bread wheat milling behavior: effects of genetic and environmental factors, and modeling using grain mechanical resistance traits. Theor Appl Genet, 130, 929-950.

Rincent R, Kuhn E, Monod H, Oury FX, Rousset M, Allard V and Le Gouis J (2017) Optimization of multi-environment trials for genomic selection based on crop models. Theor Appl Genet, 130, 1735-1752.

Bouchet S, Bertin P, Presterl T, Jamin P, Coubriche D, Gouesnard B, Laborde J, Charcosset A (2017) Association mapping for phenology and plant architecture in maize shows higher power for developmental traits compared with growth influenced traits. Heredity, 118, 249-259.

Ly D, Chenu K, Gauffreteau A, Rincent R, Huet S, Gouache D, Martre P, Bordes J and Charmet G (2017) Nitrogen nutrition index predicted by a crop model improves the genomic prediction of grain number for a bread wheat core collection. Field Crops Res, 214, 331-340.

 2016

Cubizolles N, Rey E, Choulet F, Rimbert H, Laugier C, Balfourier F, Bordes J, Poncet C, Jack P, James C, Gielen J, Argillier O, Jaubertie JP, Auzanneau J, Rohde A, Ouwerkerk PB, Korzun V, Kollers S, Guerreiro L, Hourcade D, Robert O, Devaux P, Mastrangelo AM, Feuillet C, Sourdille P and Paux E (2016) Exploiting the Repetitive Fraction of the Wheat Genome for High-Throughput Single-Nucleotide Polymorphism Discovery and Genotyping. Plant Genome, 9.

Tiwari VK, Heesacker A, Riera-Lizarazu O, Gunn H, Wang S, Wang Y, Gu YQ, Paux E, Koo DH, Kumar A, Luo MC, Lazo G, Zemetra R, Akhunov E, Friebe B, Poland J, Gill BS, Kianian S and Leonard JM (2016) A whole-genome, radiation hybrid mapping resource of hexaploid wheat. Plant J, 86, 195-207.

Bassi FM, Bentley AR, Charmet G, Ortiz R and Crossa J (2016) Breeding schemes for the implementation of genomic selection in wheat (Triticum spp.). Plant Sci, 242, 23-36.

Corol DI, Ravel C, Rakszegi M, Charmet G, Bedo Z, Beale MH, Shewry PR and Ward JL (2016) (1)H-NMR screening for the high-throughput determination of genotype and environmental effects on the content of asparagine in wheat grain. Plant Biotechnol J, 14, 128-139.

Rabier CE, Barre P, Asp T, Charmet G and Mangin B (2016) On the Accuracy of Genomic Selection. PLoS One, 11, e0156086.

 2015

Bogard M, Pierre J-B, Huguenin-Bizot B, Hourcade D, Paux E, Le Bris X and Gouache D (2015) A simple approach to predict growth stages in winter wheat (Triticum aestivum L.) combining prediction of a crop model and marker based prediction of the deviation to a reference cultivar: A case study in France. Eur J Agron, 68, 57-68.

Glover NM, Daron J, Pingault L, Vandepoele K, Paux E, Feuillet C and Choulet F (2015) Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B. Genome Biol, 16, 188.

Pingault L, Choulet F, Alberti A, Glover N, Wincker P, Feuillet C and Paux E (2015) Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome. Genome Biol, 16, 29.

Oury FX, Lasme P, Michelet C, Rousset M, Abecassis J and Lullien-Pellerin V (2015) Relationships between wheat grain physical characteristics studied through near-isogenic lines with distinct puroindoline-b allele. Theor Appl Genet, 128, 913-929.

 2014

Bogard M, Ravel C, Paux E, Bordes J, Balfourier F, Chapman SC, Le Gouis J and Allard V (2014) Predictions of heading date in bread wheat (Triticum aestivum L.) using QTL-based parameters of an ecophysiological model. J Exp Bot, 65, 5849-5865.

Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, Leroy P, Mangenot S, Guilhot N, Le Gouis J, Balfourier F, Alaux M, Jamilloux V, Poulain J, Durand C, Bellec A, Gaspin C, Safar J, Dolezel J, Rogers J, Vandepoele K, Aury JM, Mayer K, Berges H, Quesneville H, Wincker P and Feuillet C (2014) Structural and functional partitioning of bread wheat chromosome 3B. Science, 345, 1249721.

Daron J, Glover N, Pingault L, Theil S, Jamilloux V, Paux E, Barbe V, Mangenot S, Alberti A, Wincker P, Quesneville H, Feuillet C and Choulet F (2014) Organization and evolution of transposable elements along the bread wheat chromosome 3B. Genome Biol, 15, 546.

Dieguez MJ, Pergolesi MF, Velasquez SM, Ingala L, Lopez M, Darino M, Paux E, Feuillet C and Sacco F (2014) Fine mapping of LrSV2, a race-specific adult plant leaf rust resistance gene on wheat chromosome 3BS. Theor Appl Genet, 127, 1133-1141.

Marcussen T, Sandve SR, Heier L, Spannagl M, The International Wheat Genome Sequencing Consortium, Pfeifer M, Jakobsen KS, Wulff BBH, Steuernagel B, Mayer KFX and Olsen O-A (2014) Ancient hybridizations among the ancestral genomes of bread wheat. Science, 345, 1250092.

Pfeifer M, Kugler KG, Sandve SR, Zhan B, Rudi H, Hvidsten TR, The International Wheat Genome Sequencing Consortium, Mayer KFX and Olsen O-A (2014) Genome interplay in the grain transcriptome of hexaploid bread wheat. Science, 345, 1250091.

Shatalina M, Messmer M, Feuillet C, Mascher F, Paux E, Choulet F, Wicker T and Keller B (2014) High-resolution analysis of a QTL for resistance to Stagonospora nodorum glume blotch in wheat reveals presence of two distinct resistance loci in the target interval. Theor Appl Genet, 127, 573-586.

The International Wheat Genome Sequencing Consortium (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science, 345, 1250091.

Thomas M, Pingault L, Poulet A, Duarte J, Throude M, Faure S, Pichon JP, Paux E, Probst AV and Tatout C (2014) Evolutionary history of Methyltransferase 1 genes in hexaploid wheat. BMC Genomics, 15, 922.

Bouguennec A, Trottet M, du Cheyron P and Lonnet P (2014) Triticale powdery mildew: population characterization and wheat gene efficiency. Commun Agric Appl Biol Sci, 79, 106-121.

Charmet G, Storlie E, Oury FX, Laurent V, Beghin D, Chevarin L, Lapierre A, Perretant MR, Rolland B, Heumez E, Duchalais L, Goudemand E, Bordes J and Robert O (2014) Genome-wide prediction of three important traits in bread wheat. Mol Breed, 34, 1843-1852.

 2013

Bassi FM, Kumar A, Zhang Q, Paux E, Huttner E, Kilian A, Dizon R, Feuillet C, Xu SS and Kianian SF (2013) Radiation hybrid QTL mapping of Tdes2 involved in the first meiotic division of wheat. Theor Appl Genet, 126, 1977-1990.

Breen J, Wicker T, Shatalina M, Frenkel Z, Bertin I, Philippe R, Spielmeyer W, Simkova H, Safar J, Cattonaro F, Scalabrin S, Magni F, Vautrin S, Berges H, International Wheat Genome Sequencing C, Paux E, Fahima T, Dolezel J, Korol A, Feuillet C and Keller B (2013) A physical map of the short arm of wheat chromosome 1A. PLoS One, 8, e80272.

Li B, Choulet F, Heng Y, Hao W, Paux E, Liu Z, Yue W, Jin W, Feuillet C and Zhang X (2013) Wheat centromeric retrotransposons: the new ones take a major role in centromeric structure. Plant J, 73, 952-965.

Philippe R, Paux E, Bertin I, Sourdille P, Choulet F, Laugier C, Simkova H, Safar J, Bellec A, Vautrin S, Frenkel Z, Cattonaro F, Magni F, Scalabrin S, Martis MM, Mayer KF, Korol A, Berges H, Dolezel J and Feuillet C (2013) A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat. Genome Biol, 14, R64.

Raats D, Frenkel Z, Krugman T, Dodek I, Sela H, Simkova H, Magni F, Cattonaro F, Vautrin S, Berges H, Wicker T, Keller B, Leroy P, Philippe R, Paux E, Dolezel J, Feuillet C, Korol A and Fahima T (2013) The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution. Genome Biol, 14, R138.

Bordes J, Ravel C, Jaubertie JP, Duperrier B, Gardet O, Heumez E, Pissavy AL, Charmet G, Le Gouis J and Balfourier F (2013) Genomic regions associated with the nitrogen limitation response revealed in a global wheat core collection. Theor Appl Genet, 126, 805-822.

Plessis A, Ravel C, Bordes J, Balfourier F and Martre P (2013) Association study of wheat grain protein composition reveals that gliadin and glutenin composition are trans-regulated by different chromosome regions. J Exp Bot, 64, 3627-3644.

Wilhelm EP, Boulton MI, Al-Kaff N, Balfourier F, Bordes J, Greenland AJ, Powell W and Mackay IJ (2013) Rht-1 and Ppd-D1 associations with height, GA sensitivity, and days to heading in a worldwide bread wheat collection. Theor Appl Genet, 126, 2233-2243.

Wilhelm EP, Mackay IJ, Saville RJ, Korolev AV, Balfourier F, Greenland AJ, Boulton MI and Powell W (2013) Haplotype dictionary for the Rht-1 loci in wheat. Theor Appl Genet, 126, 1733-1747.

 2012

Capron D, Mouzeyar S, Boulaflous A, Girousse C, Rustenholz C, Laugier C, Paux E and Bouzidi MF (2012) Transcriptional profile analysis of E3 ligase and hormone-related genes expressed during wheat grain development. BMC Plant Biol, 12, 35.

Kumar A, Bassi FM, Paux E, Al-Azzam O, de Jimenez MM, Denton AM, Gu YQ, Huttner E, Kilian A, Kumar S, Goyal A, Iqbal MJ, Tiwari VK, Dogramaci M, Balyan HS, Dhaliwal HS, Gupta PK, Randhawa GS, Feuillet C, Pawlowski WP and Kianian SF (2012) DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum. BMC Genomics, 13, 339.

Paux E, Sourdille P, Mackay I and Feuillet C (2012) Sequence-based marker development in wheat: advances and applications to breeding. Biotechnol Adv, 30, 1071-1088.

Philippe R, Choulet F, Paux E, van Oeveren J, Tang J, Wittenberg AH, Janssen A, van Eijk MJ, Stormo K, Alberti A, Wincker P, Akhunov E, van der Vossen E and Feuillet C (2012) Whole Genome Profiling provides a robust framework for physical mapping and sequencing in the highly complex and repetitive wheat genome. BMC Genomics, 13, 47.

Schulman AH, Flavell AJ, Paux E and Ellis TH (2012) The application of LTR retrotransposons as molecular markers in plants. Methods Mol Biol, 859, 115-153.

Corol DI, Ravel C, Raksegi M, Bedo Z, Charmet G, Beale MH, Shewry PR and Ward JL (2012) Effects of genotype and environment on the contents of betaine, choline, and trigonelline in cereal grains. J Agric Food Chem, 60, 5471-5481.

Hagenblad J, Asplund L, Balfourier F, Ravel C and Leino MW (2012) Strong presence of the high grain protein content allele of NAM-B1 in Fennoscandian wheat. Theor Appl Genet, 125, 1677-1686.

Hao C, Wang Y, Hou J, Feuillet C, Balfourier F and Zhang X (2012) Association mapping and haplotype analysis of a 3.1-Mb genomic region involved in Fusarium head blight resistance on wheat chromosome 3BS. PLoS One, 7, e46444.

Jaillais B, Boulet JC, Roger JM, Balfourier F, Berbezy P and Bertrand D (2012) Application of direct calibration in multivariate image analysis of heterogeneous materials. Anal Chim Acta, 734, 45-53.

Le Gouis J, Bordes J, Ravel C, Heumez E, Faure S, Praud S, Galic N, Remoue C, Balfourier F, Allard V and Rousset M (2012) Genome-wide association analysis to identify chromosomal regions determining components of earliness in wheat. Theor Appl Genet, 124, 597-611.