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2019

18/11/19

Aguirre‐Liguori J. A., Gaut B. S., Jaramillo‐Correa J. P., Tenaillon M. I., Montes‐Hernández S., García‐Oliva F., Hearne S. J., Eguiarte L. E. (2019) Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies (Zea mays parviglumis and Zea mays mexicana ). Molecular Ecology, 28 (11) 2814-2830. doi:10.1111/mec.15098

Allier A., Moreau L., Charcosset A., Teyssèdre S., Lehermeier C. (2019a) Usefulness Criterion and Post-selection Parental Contributions in Multi-parental Crosses: Application to Polygenic Trait Introgression. G3 Genes|Genomes|Genetics, 9 (5) 1469–1479. doi:10.1534/g3.119.400129

Allier A, Teyssèdre S, Lehermeier C, Charcosset A, Moreau L (2019b) Genomic prediction with a maize collaborative panel: identification of genetic resources to enrich elite breeding programs. Theor Appl Genet, https://doi.org/10.1007/s00122-019-03451-9

Allier A., Teyssèdre S., Lehermeier C., Claustres B., Maltese S., Melkior S., Moreau L., Charcosset A. (2019c) Assessment of breeding programs sustainability: application of phenotypic and genomic indicators to a North European grain maize program. Theor Appl Genet, 132 (5) 1321–1334. doi:10.1007/s00122-019-03280-w

Bancel E., Bonnot T., Davanture M., Alvarez D., Zivy M., Martre P., Déjean S. and Ravel C. (2019) Proteomic Data Integration Highlights Central Actors Involved in Einkorn (Triticum monococcum ssp. monococcum) Grain Filling in Relation to Grain Storage Protein Composition. Front Plant Sci, 10 832. doi:10.3389/fpls.2019.00832

Belouah I., Blein-Nicolas M., Balliau T., Gibon Y., Zivy M., Colombie S. (2019) Peptide filtering differently affects the performances of XIC-based quantification methods. J Proteomics, 193 131–141. doi:10.1016/j.jprot.2018.10.003

Belouah I., Nazaret C., Pétriacq P., Prigent S., Bénard C., Mengin V., Blein-Nicolas M., Denton A. K., Balliau T., Augé S., Bouchez O., Mazat J.-P., Stitt M., Usadel B., Zivy M., Beauvoit B., Gibon Y., Colombié S. (2019) Modeling protein destiny in developing fruit. Plant Physiol, 180 (3) 1709–1724. doi:10.1104/pp.19.00086

Blein-Nicolas M., Negro S.S., Balliau T.,  Welcker C., Cabrera Bosquet L., Nicolas S.D., Charcosset A. and Zivy M. (2019) Integrating proteomics and genomics into systems genetics provides novel insights into the mechanisms of drought tolerance in maize. Under consideration at Nature Communications, available at bioRxiv https://doi.org/10.1101/636514

Boussardon C., Martin-Magniette M.-L., Godin B., Benamar A., Vittrant B., Citerne S., Mary-Huard T., Macherel D., Rajjou L., Budar F. (2019) Novel Cytonuclear Combinations Modify Arabidopsis thaliana Seed Physiology and Vigor. Front Plant Sci, 10 32. doi:10.3389/fpls.2019.00032

Carreté L., Ksiezopolska E., Gómez-Molero E., Angoulvant A., Bader O., Fairhead C., Gabaldón T. (2019) Genome Comparisons of Candida glabrata Serial Clinical Isolates Reveal Patterns of Genetic Variation in Infecting Clonal Populations. Front Microbiol, 10 112. doi:10.3389/fmicb.2019.00112

Chauffour F., Bailly M., Perreau F., Cueff G., Suzuki H., Collet B., Frey A., Clément G., Soubigou-Taconnat L., Balliau T., Krieger-Liszkay A., Rajjou L., Marion-Poll A. (2019) Multi-omics analysis reveals sequential roles for ABA during seed maturation. Plant Physiol, 180 (2) 1198–1218. doi:10.1104/pp.19.00338

Cornille A., Antolin F., Garcia E., Vernesi C., Fietta A., Brinkkemper O., Kirleis W., Schlumbaum A., Roldán-Ruiz I. (2019) A Multifaceted Overview of Apple Tree Domestication. Trends in Plant Science, 24 (8) 770-782. doi: https://doi.org/10.1016/j.tplants.2019.05.007

Courret C., Gérard P. R., Ogereau D., Falque M., Moreau L., Montchamp-Moreau C. (2019) X-chromosome meiotic drive in Drosophila simulans: a QTL approach reveals the complex polygenic determinism of Paris drive suppression. Heredity, 122 (6) 906–915. doi:10.1038/s41437-018-0163-1

Cui J., Davanture M., Zivy M., Lamade E., Tcherkez G. (2019) Metabolic responses to potassium availability and waterlogging reshape respiration and carbon use efficiency in oil palm. New Phytol, 223 (1) 310-322. doi:10.1111/nph.15751

Damerval C., Citerne H., Conde E. S. N., Deveaux Y., Delannoy E., Joets J., Simonnet F., Staedler Y., Schonenberger J., Yansouni J., Le Guilloux M., Sauquet H., Nadot S. (2019) Unraveling the Developmental and Genetic Mechanisms Underpinning Floral Architecture in Proteaceae. Front Plant Sci, 10 18. doi:10.3389/fpls.2019.00018

Fairhead C., Fischer G., Liti G., Neuveglise C., Schacherer J. (2019) Andre Goffeau’s imprinting on second generation yeast ‘genomologists’. Yeast, 36 (4) 167-175. doi:10.1002/yea.3377

Gabaldon T., Fairhead C. (2019) Genomes shed light on the secret life of Candida glabrata: not so asexual, not so commensal. Curr Genet, 65 (1) 93–98. doi:10.1007/s00294-018-0867-z

Hartmann F. E., Rodríguez de la Vega R. C., Carpentier F., Gladieux P., Cornille A., Hood M. E. and Giraud T. (2019) Understanding Adaptation, Coevolution, Host Specialization, and Mating System in Castrating Anther-Smut Fungi by Combining Population and Comparative Genomics. Annu Rev Phytopathol, 57 (1), annurev-phyto-082718-095947. doi:10.1146/annurev-phyto-082718-095947

Havé M., Luo J., Tellier F., Balliau T., Cueff G., Chardon F., Zivy M., Rajjou L., Cacas J., Masclaux‐Daubresse C. (2019) Proteomic and lipidomic analyses of the Arabidopsis atg5 autophagy mutant reveal major changes in ER and peroxisome metabolisms and in lipid composition. New Phytologist, 223 (3) 1461-1477. doi:10.1111/nph.15913

Henry C., Haller L., Blein-Nicolas M., Zivy M., Canette A., Verbrugghe M., Mézange C., Boulay M., Gardan R., Samson S., Martin V., André-Leroux G. and Monnet V. (2019) Identification of Hanks-Type Kinase PknB-Specific Targets in the Streptococcus thermophilus Phosphoproteome. Front Microbiol, 10 1329. doi:10.3389/fmicb.2019.01329

Kreplak J, ... Falque M, ... Wincker P, Burstin J (2019) A reference genome for pea provides insight into legume genome evolution. Nat Genet, 51 (9) 1411–1422. https://doi.org/10.1038/s41588-019-0480-1

Lecarpentier C., Barillot R., Blanc E., Abichou M., Goldringer I., Barbillon P., Enjalbert J., Andrieu B. (2019) WALTer: a three-dimensional wheat model to study competition for light through the prediction of tillering dynamics. Ann Bot, 123 (6) 961-975. doi:10.1093/aob/mcy226

Liu S.*, Cornille A.*, Decroocq S., Tricon D., Chague A., Eyquard J.-P., Liu W.S., Giraud T., Decroocq V. (2019) The complex evolutionary history of apricots: species divergence, gene flow and multiple domestication events. Mol Ecol, https://doi.org/10.1111/mec.15296. * Co-first authors: these authors have contributed equally to this work.

Mabire C., Duarte J., Darracq A., Pirani A., Rimbert H., Madur D., Combes V., Vitte C., Praud S., Rivière N., Joets J., Pichon J.-P., Nicolas S.D. (2019) High throughput genotyping of structural variations in a complex plant genome using an original Affymetrix® axiom® array. BMC Genomics, 20 (1) 848. https://doi.org/10.1186/s12864-019-6136-9

Mangin B., Rincent R., Rabier C.-E., Moreau L., Goudemand-Dugue E. (2019) Training set optimization of genomic prediction by means of EthAcc. PLOS ONE, 14 (2) e0205629. doi:10.1371/journal.pone.0205629

Marchadier E., Hanemian M., Tisné S., Bach L., Bazakos C., Gilbault E., Haddadi P., Virlouvet L., Loudet O. (2019) The complex genetic architecture of shoot growth natural variation in Arabidopsis thaliana. PLOS Genetics, 15 (4) e1007954. doi:10.1371/journal.pgen.1007954

Maroc L, Fairhead C (2019) A new inducible CRISPR‐Cas9 system useful for genome editing and study of double‐strand break repair in Candida glabrata. Yeast, yea.3440. https://doi.org/10.1002/yea.3440

Martinez Palacios P., Jacquemot M.-P., Tapie M., Rousselet A., Diop M., Remoué C., Falque M., Lloyd A., Jenczewski E., Lassalle G., Chévre A.-M., Lelandais C., Crespi M., Brabant P., Joets J., Alix K. (2019) Assessing the Response of Small RNA Populations to Allopolyploidy Using Resynthesized Brassica napus Allotetraploids. Molecular Biology and Evolution, 36 (4) 709–726. doi:10.1093/molbev/msz007

Millet E. J., Kruijer W., Coupel-Ledru A., Alvarez Prado S., Cabrera-Bosquet L., Lacube S., Charcosset A., Welcker C., Eeuwijk F. van, Tardieu F. (2019) Genomic prediction of maize yield across European environmental conditions. Nature Genetics, 51 (6) 952-956. doi:10.1038/s41588-019-0414-y

Negro S. S., Millet E. J., Madur D., Bauland C., Combes V., Welcker C., Tardieu F., Welcker C. Tardieu F., Charcosset A. and Nicolas S. D. (2019) Genotyping-by-sequencing and SNP-arrays are complementary for detecting quantitative trait loci by tagging different haplotypes in association studies. BMC Plant Biol 19 (1), 318. doi:10.1186/s12870-019-1926-4

Peace C. P., ..., Cornille A., ..., Jung S., Vanderzande S. (2019) Apple whole genome sequences: recent advances and new prospects. Horticulture Research, 6 (1) 59. doi:10.1038/s41438-019-0141-7

Petrizzelli M., Vienne D. de, Dillmann C. (2019) Decoupling the Variances of Heterosis and Inbreeding Effects Is Evidenced in Yeast’s Life-History and Proteomic Traits. Genetics, 211 (2) 741–756. doi:10.1534/genetics.118.301635

Rio S., Mary-Huard T., Moreau L., Charcosset A. (2019) Genomic selection efficiency and a priori estimation of accuracy in a structured dent maize panel. Theor Appl Genet, 132 (1) 81–96. doi:10.1007/s00122-018-3196-1

Rusconi F. (2019) mineXpert : Biological Mass Spectrometry Data Visualization and Mining with Full JavaScript Ability. J Proteome Res, 18 (5) 2254–2259. doi:10.1021/acs.jproteome.9b00099

Scarcelli N., Cubry P., Akakpo R., Thuillet A.-C., Obidiegwu J., Baco M. N., Otoo E., Sonké B., Dansi A., Djedatin G., Mariac C., Couderc M., Causse S., Alix K., Chaïr H., François O., Vigouroux Y. (2019) Yam genomics supports West Africa as a major cradle of crop domestication. Science Advances, 5 (5) eaaw1947. doi:10.1126/sciadv.aaw1947

Seye A. I., Bauland C., Giraud H., Mechin V., Reymond M., Charcosset A., Moreau L. (2019) Quantitative trait loci mapping in hybrids between Dent and Flint maize multiparental populations reveals group-specific QTL for silage quality traits with variable pleiotropic effects on yield. Theor Appl Genet, 132 (5) 1523–1542. doi:10.1007/s00122-019-03296-2

Srisuwan S., Sihachakr D., Martin J., Valles J., Ressayre A., Brown S. C., Siljak-Yakovlev S. (2019) Change in nuclear DNA content and pollen size with polyploidisation in the sweet potato (Ipomoea batatas, Convolvulaceae) complex. Plant Biol (Stuttg), 21 (2) 237–247. doi:10.1111/plb.12945

Tenaillon M. I., Seddiki K., Mollion M., Le Guilloux M., Marchadier E., Ressayre A. and Dillmann C. (2019) Transcriptomic response to divergent selection for flowering times reveals convergence and key players of the underlying gene regulatory network (preprint). bioRxiv, 461947. http://biorxiv.org/lookup/doi/10.1101/461947. Recommendation on PCI Evol Biol

Termolino P, Falque M, Aiese Cigliano R, Cremona G, Paparo R, Ederveen A, Martin OC, Consiglio FM, Conicella C (2019) Recombination suppression in heterozygotes for a pericentric inversion induces the interchromosomal effect on crossovers in Arabidopsis. Plant J, tpj.14505. https://doi.org/10.1111/tpj.14505

Tourrette E, Bernardo R, Falque M, Martin OC (2019) Assessing by Modeling the Consequences of Increased Recombination in Recurrent Selection of Oryza sativa and Brassica rapa. G3, Epub ahead of print. https://doi.org/10.1534/g3.119.400545

Urien C., Legrand J., Montalent P., Casaregola S., Sicard D. (2019) Fungal Species Diversity in French Bread Sourdoughs Made of Organic Wheat Flour. Front Microbiol, 10 201. doi:10.3389/fmicb.2019.00201

Vasseur F., Fouqueau L., Vienne D. de, Nidelet T., Violle C., Weigel D. (2019) Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana. PLOS Biology, 17 (4) e3000214. doi:10.1371/journal.pbio.3000214

Virlouvet L., El Hage F., Griveau Y., Jacquemot M.-P., Gineau E., Baldy A., Legay S., Horlow C., Combes V., Bauland C., Palafre C., Falque M., Moreau L., Coursol S., Méchin V., Reymond M. (2019) Water Deficit-Responsive QTLs for Cell Wall Degradability and Composition in Maize at Silage Stage. Front Plant Sci, 10 488. doi:10.3389/fpls.2019.00488

Volk G.M., Cornille A. (2019) Genetic Diversity and Domestication History in Pyrus. In: Korban S. (eds) The Pear Genome. Compendium of Plant Genomes. Springer, Cham. p 51-62. doi: https://doi.org/10.1007/978-3-030-11048-2_3