Cocoa

Collection of native Theobroma cacao L. accessions from the Ecuadorian Amazon highlights a hotspot of cocoa diversity. Fouet Olivier, Loor Rey Gaston, Rhone Bénédicte, Subia Cristian, Calderón Darío, Fernández Fabián, Sotomayor Ignacio, Rivallan Ronan, Colonges Kelly, Vignes Hélène, Angamarca Freddy, Yaguana Byron, Costet Pierre, Argout Xavier, Lanaud Claire. 2022. Plants, People, Planet, 4 (6) : 605-617. https://doi.org/10.1002/ppp3.10282

Variability and genetic determinants of cocoa aromas in trees native to South Ecuadorian Amazonia. Colonges Kelly, Loor Solorzano Rey Gaston, Jimenez Juan Carlos, Lahon Marie-Christine, Seguine Edward, Calderón Darío, Subia Cristian, Sotomayor Ignacio, Fernández Fabián, Lebrun Marc, Fouet Olivier, Rhone Bénédicte, Argout Xavier, Costet Pierre, Lanaud Claire, Boulanger Renaud. 2022. Plants, People, Planet, 4 (6) : 618-637. https://doi.org/10.1002/ppp3.10268

Identification and distribution of novel badnaviral sequences integrated in the genome of cacao (Theobroma cacao). Muller Emmanuelle, Ullah Ihsa, Dunwell Jim M., Daymond Andrew J., Richardson Megan, Allainguillaume Joel, Wetten Andrew. 2021. Scientific Reports, 11:8270, 13 p.https://doi.org/10.1038/s41598-021-87690-1

Evaluation of adaptation and yield stability of cocoa progenies in marginal conditions: Results from an on farm cocoa trial set up in a forest-savannah transition area in Cameroon. Feumba De Tchoua Le Blanc, Sounigo Olivier, Bourgoing Raymond, Efombagn Mousseni Ives Bruno, Abolo Dieudonné, Ambang Zachée, Cilas Christian. 2021. Crops, 1 (1) : 20-29. https://doi.org/10.3390/crops1010004

Cacao breeding in Colombia, past, present and future. Rodriguez-Medina Caren, Caicedo Arana Alvaro, Sounigo Olivier, Argout Xavier, Alvarado Alvarado Gabriel, Yockteng Roxana. 2020. Breeding Science, 69 (3) : 373-382. https://doi.org/10.1270/jsbbs.19011The use and domestication of Theobroma cacao during the mid-Holocene in the upper Amazon. Zarrillo Sonia, Gaikwad Nilesh, Lanaud Claire, Powis Terry, Viot Christopher, Lesur Isabelle, Fouet Olivier, Argout Xavier, Guichoux Erwan, Salin Franck, Loor Solorzano Rey Gaston,

Bouchez Olivier, Vignes Hélène, Severts Patrick, Hurtado Julio, Yepez Alexandra, Grivetti Louis, Blake Michael, Valdez Francisco. 2018. Nature Ecology and Evolution, 2 : 1879-1888. https://doi.org/10.1038/s41559-018-0697-xDeciphering the Theobroma cacao self-incompatibility system: from genomics to diagnostic markers for self-compatibility. Lanaud Claire, Fouet Olivier, Legavre Thierry, Lopes Uilson Vanderlei, Sounigo Olivier, Eyango Marie Claire, Mermaz Benoit, da Silva Marcos Ramos, Loor

Solorzano Rey Gaston, Argout Xavier, Gyapay Gabor, Ebaiarrey Herman Ebai, Colonges Kelly, Sanier Christine, Rivallan Ronan, Mastin Géraldine, Cryer Nicholas, Boccara Michel, Verdeil Jean-Luc, Efombagn Mousseni Ives Bruno, Peres Gramacho Karina, Clément Didier. 2017. Journal of Experimental Botany, 68 (17) : 4775-4790. https://doi.org/10.1093/jxb/erx293

The cacao Criollo genome v2.0: An improved version of the genome for genetic and functional genomic studies. Argout Xavier, Martin Guillaume, Droc Gaëtan, Fouet Olivier, Labadie Karine, Rivals Eric, Aury Jean-Marc, Lanaud Claire. 2017. BMC Genomics, 18:730, 9 p.
https://doi.org/10.1186/s12864-017-4120-9

Legavre T., Ducamp M., Sabau X., Argout X., Fouet O., Dedieu F., Surujdeo-Maharaj S., Garcia D., Paulin L., Lanaud C. (2015) Identification of Theobroma cacao genes differentially expressed during Phytophthora megakarya infection. Physiological and Molecular Plant Pathology, 92 : p. 1-13.

Lachenaud P., Fouet O., Couturier C., Lanaud C. (2015) Cacao trees (Theobroma cacao L.) of the Guiana genetic group: Tanpok 2012 survey. Genetic Resources and Crop Evolution : 10 p.

Cardoso T.H.S., Oliveira Freitas A.C., Andrade B.S., Oliveira de Sousa A., Da Silva Santiago A., Koop D.M., Gramacho K.P., Alvim F.C., Micheli F., Pirovani C.P. (2015) TcCYPR04, a cacao papain-like cysteine-protease detected in senescent and necrotic tissues interacts with a cystatin TcCYS4. PloS One, 10 (12) : e0144440 (20 p.).

Argout, X., Salse, J., Aury, J.M., Guiltinan, M.J., Droc, G., Gouzy, J., Allègre, M., Chaparro, C., Legavre, T., Maximova, S.N., Abrouk, M., Murat, F., Fouet, O., Poulain, J., Ruiz, M., Roguet, Y., Rodier Goud, M., Barbosa Neto, J.F., Sabot, F., Kudrna, D., Ammiraju, J.S.S., Schuster, S.C., Carlson, J.E., Sallet, E., Schiex, T., Dievart, A., Kramer, M., Gelley, L., Shi, Z., Bérard, A., Viot, C., Boccara, M., Risterucci, A.M., Guignon, V., Sabau, X., Axtell, M.J., Ma, Z., Zhang, Y., Brown, S., Bourge, M., Golser, W., Song, X., Clément, D., Rivallan, R., Tahi, G.M., Akaza, J.M., Pitollat, B., Gramacho, K.P., D'Hont, A., Brunel, D., Infante, D., Kébé, I., Costet, P., Wing, R., Mc Combie, W.R., Guiderdoni, E., Quetier, F., Panaud, O., Wincker, P., Bocs, S., Lanaud, C. (2011) The genome of Theobroma cacao. Nature Genetics, 43 (2): 101-108. http://dx.doi.org/10.1038/ng.736

Coffee

Dos Santos Scholz M.B., Good-Kitzberger C.S., Pagiatto N.F., Protasio Pereira L.F., Davrieux F., Pot D., Charmetant P., Leroy T. (2016) Chemical composition in wild ethiopian Arabica coffee accessions. Euphytica : 10 p. http://dx.doi.org/10.1007/s10681-016-1653-y. 

Yuyama P.M., Reis Júnior O., Ivamoto S.T., Domingues D.S., Carazzolle M.F., Pereira G.A.G., Charmetant P., Leroy T., Pereira L.F.P. (2016) Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits. Molecular Genetics and Genomics, 291 (1): p. 323-336.http://dx.doi.org/10.1007/s00438-015-1111-x.

Perthuis B., Vassal J.M., Fenouillet C., Leroy T. (2015) Cry1Ac insecticidal protein levels in genetically modified Coffea canephora Pierre coffee plants were negatively correlated with the growth speed in a field experiment. Euphytica, 202 (3) : p. 373-383.

Denoeud F., Carretero-Paulet L., Dereeper A., Droc G., Guyot R., Pietrella M., Chunfang Zheng, Alberti A., Anthony F., Aprea G., Aury J.M., Bento P., Bernard M., Bocs S., Campa C., Cenci A., Combes M.C., Crouzillat D., Da Silva C., Daddiego L., De Bellis F., Dussert S., Garsmeur O., Gayraud T., Guignon V., Jahn K., Jamilloux V., Joët T., Labadie K., Tianying Lan, Leclercq J., Lepelley M., Leroy T., Lei-Ting Li, Librado P., Lopez L., Muñoz A., Noël B., Pallavicini A., Perrotta G., Poncet V., Pot D., Priyono, Rigoreau M., Rouard M., Rozas J., Tranchant-Dubreuil C., VanBuren R., Qiong Zhang, Andrade A.A., Argout X., Bertrand B., De Kochko A., Graziosi G., Henry R., Jayarama, Ming R., Nagai C., Rounsley S., Sankoff D., Giuliano G., Albert V.A., Wincker P., Lashermes P. (2014) The coffee genome provides insight into the convergent evolution of caffeine biosynthesis Science, 345 (6201) : p. 1181-1184.

Rubber

Moura De Souza L., Le Guen V., Cerqueira-Silva C.B.M., Silva C.C., Mantello C.C., Conson A.R.O., Gomes Vianna J.P., Zucchi M.I., Scaloppi Junior E.J., De Freitas Fialho J., Teixeira de Moraes M.L., De Souza Gonçalves P., Pereira de Souza A. (2015) Genetic diversity strategy for the management and use of rubber genetic resources: more than 1,000 wild and cultivated accessions in a 100-genotype core collection. PloS One, 10 (7) : e0134607 (20 p.).

Déon M., Fumanal B., Gimenez S., Bieysse D., Oliveira R.R., Shuib S.S., Breton F., Elumalai S., Vida J.B., Seguin M., Leroy T., Roeckel-Drevet P., Pujade-Renaud V. (2014) Diversity of the cassiicolin gene in Corynespora cassiicola and relation with the pathogenicity in Hevea brasiliensis. Fungal Biology, 118 (1) : p. 32-47.

Rippel Salgado L., Martins Koop D., Guariz Pinheiro D., Rivallan R., Le Guen V., Nicolás M.F., De Almeida L.G.P., Ribeiro Rocha V., Magalhaes M., Gerber A.L., Figueira A., De Mattos Cascardo J.C., Ribeiro de Vasconcelos A.T., Araújo Silva W., Coutinho L.L., Garcia D. (2014) De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers. BMC Genomics, 15 (236) : 15 p.

Cubry P., Pujade-Renaud V., Garcia D., Espeout S., Le Guen V., Granet F., Seguin M. (2014) Development and characterization of a new set of 164 polymorphic EST-SSR markers for diversity and breeding studies in rubber tree (Hevea brasiliensis Müll. Arg.). Plant Breeding, 133 (3) : p. 419-426.

Plantation trees (genera: Eucalyptus, Pinus, Acacia, Tectona)

Plomion C., Bartholomé J., Lesur I., Boury C., Rodríguez-Quilón I., Lagraulet H., Ehrenmann F., Bouffier L., Gion J.M., Grivet D., de Miguel M., de Maria N., Cervera M.T., Bagnoli F., Isik F., Vendramin G.G., González-Martínez S.C. (2016) High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster). Molecular Ecology Resources, 16 : p. 574-587.

Bartholomé J., Mandrou E., Mabiala A., Jenkins J., Nabihoudine I., Klopp C., Schmutz J., Plomion C., Gion J.M. (2015) High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly. New Phytologist, 206 (4) : p. 1283-1296.

de Miguel M., Bartholomé J., Ehrenmann F., Murat F., Moriguchi Y., Uchiyama K., Ueno S., Tsumura Y., Lagraulet H., de Maria N., Cabezas J.A., Cervera M.T., Gion J.M., Salse J., Plomion C. (2015) Evidence of intense chromosomal shuffling during conifer evolution. Genome Biology and Evolution, 7 (1) : p. 2799-2809.

Monteuuis O., Goh D.K.S. (2015) Field growth performances of teak genotypes of different ages clonally produced by rooted cuttings, in vitro microcuttings, and meristem culture. Canadian Journal of Forest Research, 45 (1) : p. 9-14.

Oil palm

Improving the accuracy of genomic predictions in an outcrossing species with hybrid cultivars between heterozygote parents: a case study of oil palm (Elaeis guineensis Jacq.) Achille Nyouma, Joseph Martin Bell, Florence Jacob, Virginie Riou, Aurore Manez, Virginie Pomiès, Hubert Domonhedo, Deni Arifiyanto, Benoit Cochard, Tristan Durand-Gasselin, David Cros Molecular Genetics and Genomics 297 (2), 523-533, 2022

Genomic predictions improve clonal selection in oil palm (Elaeis guineensis Jacq.) hybrids Achille Nyouma, Joseph Martin Bell, Florence Jacob, Virginie Riou, Aurore Manez, Virginie Pomiès, Leifi Nodichao, Indra Syahputra, Dadang Affandi, Benoit Cochard, Tristan Durand-Gasselin, David Cros Plant Science 299, 110547, 2020

Merciere M., Laybats A., Carasco-Lacombe C., Tan J.S., Klopp C., Durand-Gasselin T., Alwee S.S.R.S., Camus-Kulandaivelu L., Breton F. (2015) Identification and development of new polymorphic microsatellite markers using genome assembly for Ganoderma boninense, causal agent of oil palm basal stem rot disease. Mycological Progress, 14 (103) : 11 p..

Cros D., Denis M., Sanchez L., Cochard B., Flori A., Durand-Gasselin T., Nouy B., Omoré A., Pomies V., Riou V., Suryana E., Bouvet J.M. (2015) Genomic selection prediction accuracy in a perennial crop: case study of oil palm (Elaeis guineensis Jacq.). Theoretical and Applied Genetics, 128 (3) : p. 397-410.

Tisne S., Denis M., Cros D., Pomies V., Riou V., Syahputra I., Omoré A., Durand-Gasselin T., Bouvet J.M., Cochard B. (2015) Mixed model approach for IBD-based QTL mapping in a complex oil palm pedigree. BMC Genomics, 16 (798) : 12 p.