Mapping of a locus for adult plant resistance to downy mildew in broccoli (Brassica oleracea convar. italica)

Farinh�, M.; Coelho, P.; Carlier, J.; Svetleva, D.; Monteiro, A.; Leit�o, J.; Leitao, J. M.; Varela, J.; Luísa Barreira

Organiza

Main Info

At present I am working as a post doctorate at the Centre of Marine Sciences (CCMAR), Portugal, in the Laboratory of Environmental Technologies for the project “Biometal demonstration plant for the biological rehabilitation of metal bearing wastewaters (BIOMETAL DEMO)” with the following main tasks: (a) batch studies to select metals-resistant Sulfate Reducing Bacteria (SRB) and low-cost organic substrates to feed SRB bioreactors, (b) optimization of continuous flow systems using Upflow Anaerobic Packed Bed (UAPB) bioreactors with SRB to treat waters contaminated with metals, (c) use of analytical techniques to monitor bacterial growth and activity, metals and organic compounds and for the characterization of the precipitates resulting from the bioremediation experiments, (d) taxonomic studies by DNA analysis to characterize bacterial communities from bioreactors, (e) support in the demonstration phase of the project: construction and evaluation of a treatment system on a pilot plant scale. Before start working in this project I visited for two months (January and February 2014) the laboratories of the Comparative Molecular Endocrinology research team of CCMAR, doing mainly bioinformatics analyses: (f) construction of phylogenetic trees based on specific DNA and protein sequences and (g) characterizing the genomic environment of specific genes in order to study the local chromosomic rearrangements occurred during evolution.

Before that, I worked for sixteen and half years (between July 1997 and December 2013) in the Laboratory of Genomics and Genetic Improvement (LGGI) at the University of Algarve, Portugal. The first six years I received grants from research projects, then I benefited of a PhD fellow for three years and the remaining seven and half years I worked as a post-doctorate, having spent six months of those six years at the Crop Centre, School of Life Sciences (former HRI), at Warwick University, United Kingdom. During these sixteen and half years I worked mainly on: (h) genetic diversity studies, (i) genetic mapping of Single Loci and Quantitative Trait Loci (QTLs), (j) constructing a genomic Bacterial Artificial Chromosome (BAC) library, (k) chromosome walking to select BAC clones from targeted mapped regions of interest, (l) preparing libraries of genomic DNA fragments for sequence by massive DNA sequencing technologies, (m) aligning the obtained sequence reads by de novo assembling and reference mapping, (n) identifying Open reading Frames (ORFs) and selecting candidate genes.

Projects

Projects Membership

	Title	Coordinator	Start	End	Funding	Budget CCMAR	Budget Total
BIOMETAL DEMO	Biometal demonstration plant for the biological rehabilitation of metal bearing- wastewaters (BIOMETAL DEMO).	Maria Clara Semedo da Silva Costa	12/2013	11/2017	Comissão Europeia	192k€

Activities

Activity type

Event

CCMAR recebe grupo de alunos da Universidade de Verão de Shou (China)

De 11 a 29 de Julho, 25 alunos da Universidade de Verão de Shou (China) vão ser acolhidos no Centro de Ciências do Mar (CCMAR) para acompanhar o trabalho dos nossos investigadores.

Segunda, 11 Julho, 2016

Bldg. 7 - Gambelas Campus

Activity type

Event

Get together CCMAR / Welcome party

Next week, join us to welcome the students from Summer School Shou (China).

We're waiting for you!

Segunda, 11 Julho, 2016

Building 7 - main hall

News

CCMAR recebe alunos de todos os graus de ensino

A política de disseminação e outreach do CCMAR é bastante alargada, de modo que esta manhã os investigadores do Centro contactaram de perto com crianças e jovens a quem explicaram um pouco do seu trabalho.

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Publications

Year of Publication
2016	Assunção A, Costa MClara, Carlier JDias. Application of urea–agarose gel electrophoresis to select non-redundant 16S rRNAs for taxonomic studies: palladium(II) removal bacteria. Applied Microbiology and Biotechnology. 2016;100(6):2721 - 2735. doi:10.1007/s00253-015-7163-3. Ler mais acerca de Application of urea–agarose gel electrophoresis to select non-redundant 16S rRNAs for taxonomic studies: palladium(II) removal bacteria Google Scholar DOI
2016	Ballester A, Castro L, Costa MClara, et al. Design of remediation pilot plants for the treatment of industrial metal-bearing effluents (BIOMETAL DEMO project): Lab tests. Hydrometallurgy. 2016. doi:10.1016/j.hydromet.2016.10.010. Ler mais acerca de Design of remediation pilot plants for the treatment of industrial metal-bearing effluents (BIOMETAL DEMO project): Lab tests Google Scholar DOI
2016	Pereira H, Custódio L, Rodrigues MJ, et al. Profiling of antioxidant potential and phytoconstituents of Plantago coronopus. Brazilian Journal of Biology. 2016;(ahead). doi:10.1590/1519-6984.02416. Ler mais acerca de Profiling of antioxidant potential and phytoconstituents of Plantago coronopus Google Scholar DOI
2013	de Sousa N, Carlier J, Santo T, Leitão J. An integrated genetic map of pineapple (Ananas comosus (L.) Merr.). Scientia Horticulturae. 2013;157:113 - 118. doi:10.1016/j.scienta.2013.04.018. Ler mais acerca de An integrated genetic map of pineapple (Ananas comosus (L.) Merr.) Google Scholar DOI
2012	Carlier JDias, Sousa NHorta, Santo TEspírito, d’Eeckenbrugge GCoppens, Leitão JManuel. A genetic map of pineapple (Ananas comosus (L.) Merr.) including SCAR, CAPS, SSR and EST-SSR markers. Molecular Breeding. 2012;29(1):245 - 260. doi:10.1007/s11032-010-9543-9. Ler mais acerca de A genetic map of pineapple (Ananas comosus (L.) Merr.) including SCAR, CAPS, SSR and EST-SSR markers Google Scholar DOI
2012	Carlier JD, Alabaça CA, Coelho PS, Monteiro AA, Leitão JM. The downy mildew resistance locus Pp523 is located on chromosome C8 of Brassica oleracea L. Plant Breeding. 2012;131(1):170 - 175. doi:10.1111/pbr.2011.131.issue-110.1111/j.1439-0523.2011.01904.x. Ler mais acerca de The downy mildew resistance locus Pp523 is located on chromosome C8 of Brassica oleracea L. Google Scholar DOI
2011	Carlier JD, Alabaca CS, Sousa NH, et al. Physical Mapping in a Triplicated Genome: Mapping the Downy Mildew Resistance Locus Pp523 in Brassica oleracea L. G3: Genes\|Genomes\|Genetics. 2011;1(7):593 - 601. doi:10.1534/g3.111.001099. Ler mais acerca de Physical Mapping in a Triplicated Genome: Mapping the Downy Mildew Resistance Locus Pp523 in Brassica oleracea L. Google Scholar DOI
2008	Carlier J, Leitão J, FONSECA FILOMENA. Population genetic structure of Cistus ladanifer L. (Cistaceae) and genetic differentiation from co-occurring Cistus species. Plant Species Biology. 2008;23(3):141 - 151. doi:10.1111/psb.2008.23.issue-310.1111/j.1442-1984.2008.00220.x. Ler mais acerca de Population genetic structure of Cistus ladanifer L. (Cistaceae) and genetic differentiation from co-occurring Cistus species Google Scholar DOI
2006	Svetleva D, Pereira G, Carlier J, Cabrita L, Leitão J, Genchev D. Molecular characterization of Phaseolus vulgaris L. genotypes included in Bulgarian collection by ISSR and AFLP™ analyses. Scientia Horticulturae. 2006;109(3):198 - 206. doi:10.1016/j.scienta.2006.04.001. Ler mais acerca de Molecular characterization of Phaseolus vulgaris L. genotypes included in Bulgarian collection by ISSR and AFLP™ analyses Google Scholar DOI
2004	Carlier JD, Reis A, Duval MF, G. d'Eeckenbrugge C, Leitao JM. Genetic maps of RAPD, AFLP and ISSR markers in Ananas bracteatus and A. comosus using the pseudo-testcross strategy. Plant Breeding. 2004;123(2):186 - 192. doi:10.1046/j.1439-0523.2003.00924.x. Ler mais acerca de Genetic maps of RAPD, AFLP and ISSR markers in Ananas bracteatus and A. comosus using the pseudo-testcross strategy Google Scholar DOI
2004	Farinh� M, Coelho P, Carlier J, Svetleva D, Monteiro A, Leit�o J. Mapping of a locus for adult plant resistance to downy mildew in broccoli (Brassica oleracea convar. italica). Theoretical and Applied Genetics. 2004;109(7):1392 - 1398. doi:10.1007/s00122-004-1747-0. Ler mais acerca de Mapping of a locus for adult plant resistance to downy mildew in broccoli (Brassica oleracea convar. italica) Google Scholar DOI

Other Publications

Book Chapters

Coelho P, Farinhó M, Alabaça C, Sousa N, Carlier J, Leitão J, Monteiro A. (2011) Caracterização genética e molecular da resistência ao míldio na couve-brócolo. In: Santos Pereira L, de Varennes A, Oliveira C, Ferreira-Dias S (Eds.) Engenharia dos Biossistemas: Cem anos de investigação no centenário do ISA. Edições Colibri (Extra-colecção) e CEER, Lisboa. pp. 271-274

Carlier JD, Coppens d’Eeckenbrugge G, Leitão JM (2007) Pineapple. In: Kole C (ed) Genome Mapping & Molecular Breeding Vol. IV. Springer, Heidelberg, Germany. pp. 331-342

Peer-Reviewed Proceedings of International Scientific Meetings

Carlier J, Alabaça C, Rodrigues C and Leitão J (2013) On the Way to the Identification of a Downy Mildew Resistance Gene in Brassica oleracea L. Acta Horticulturae (ISHS). Acta Horticulturae (ISHS). 1005: 233-237.

Carlier J, Cabrita L, Sousa RM, Sousa AT and Leitão J (2011) ISSR and AFLP Characterization of Phomopsis amygdali ((Del.)) Tuset & Portilla Accessions. Acta Horticulturae (ISHS). 912: 645-650.

Apostolova E, Carlier J, leitão J and Svetleva D (2008) Identification of RAPD markers linked to the Fin and P loci in Phaseolus vulgaris L. Acta Horticulturae (ISHS). 830: 101-106.

Carlier JD, Nancheva D, Coppens d’Eeckenbrugge G, Leitão JM (2006) Genetic mapping of DNA markers in pineapple. Acta Horticulturae (ISHS). 702:79-86.

Coppens d´Eeckenbrugge G, Cabral JRS, de Matos AP, Carlier J, Leitão J, Duval MF, Noyer JL, Ferreira FR, Leal F, Maggioni L, Suárez Z (2005) Main results from the EU-FUNDED Project “Evaluation and utilization of pineapple genetic resources from the Amazon to breed resistant varieties”. Acta Horticulturae (ISHS). 666: 77-82.

Leitão JM, Elisiário PJ, Cabrita LF, Justo EM, Pereira GM, Carlier JD, Farinhó MJ (2000) Molecular markers in genetic variability assessment, cultivar fingerprinting and hybrid identification in fruits and vegetables. Acta Horticulturae (ISHS). 521: 185-192.

Coppens d’ Eeckenbrugge G, Cabral JRS, Carlier J, Duval MF, Ferreira FR, Leal F, Leitão J, Matos APde, Noyer JL, Suárez Z (2000) The EU-funded project “Evaluation and utilization of pineapple genetic resources from the Amazon to breed resistant varieties”. Acta Horticulturae (ISHS). 529: 169-174.

Communications

Oral Communications (as speaker)

Alexandre LM, Carlier JD, Luís AT, Costa MC (2016) Screening of industrial sub-products as alternative carbon sources to sustain the growth and activity of sulphate-reducing bacteria - Part II. 11th conference on Sustainable Development of Energy, Water and Environment Systems – SDEWES. 4-9 September. Lisbon, Portugal.

Carlier JD, Farinhó M, Alabaça C, Coelho P, Ali D, Penev R, Monteiro A, Paterson A H, Leitão J (2010) Constructing a Physical Map of the Genomic Region Encompassing the Downy Mildew Resistance Gene Pp523 in Brassica oleracea L. 28th International Horticultural Congress. 22-27 August. Lisbon, Portugal.

Carlier JDD, Nancheva D, d’Eeckenbrugge GC, Leitão JM (2005) Construção de um mapa genético de marcadores moleculares em ananás baseado numa população F2. V Congresso Ibérico de Ciências Hortícolas - IV Congresso Ibero-Americano de Ciências Hortícolas. 22-27 May. Oporto, Portugal.

Carlier JD, Nancheva D, Coppens d’Eeckenbrugge G, Leitão JM (2005) Genetic mapping of DNA markers in pineapple. 5th International Pineapple Symposium. April 10-15. Port Alfred, South Africa.

Carlier JD, Fonseca F, Leitão JM (2004) Contribuição para o estudo taxonómico de Cistus palhinhae. 12º Congresso do Algarve. 28-30 October. Tavira, Portugal.

Carlier JD, Reis A, Duval MF, Coppens d´Eeckenbrugge G, Leitão JM (2002) Genetic linkage mapping of RAPD, AFLP and ISSR markers in pineapple. XXVIth International Horticultural Congress & Exhibition. August 11-17. Toronto, Canada.

Carlier JD, Duval MF, Coppens d´Eckenbrugge G, Leitão JM (1999) Resultados preliminares de mapeamento de marcadores moleculares RAPD e AFLP em ananás. 2º Workshop de Biotecnologia de Plantas. Universidade do Algarve. 6-7 May. Faro, Portugal.

Oral Communications (other speaker)

Anucha CB, Alexandre LM, Carlier JD, Luís AT, Costa MC (2016) Batch tests to access the efficiency of beetroot and orange molasses as sources of nutrients to sustain bioremediation processes for acid mine drainage. 3rd International Congress on Water, Waste and Energy Management (EWWM). 18-20 July. Rome, Italy.

Carlier JD, Costa MC (2015) “Projetos de investigação envolvendo o tratamento de águas ácidas da mina de São Domingos”. II Jornadas Interdisciplinares Mina de São Domingos / Minas, Tecnologias e Educação: Convergências. 4 December. Mina de São Domingos, Portugal,

Carlier JD, Luís AT, Costa MC (2015) Screening of industrial sub-products as alternative carbon sources to sustain the growth and activity of sulphate-reducing bacteria. 10th conference on Sustainable Development of Energy, Water and Environment Systems – SDEWES. 27 September – 2 October. Dubrovnik, Croatia.

Carlier JD, Barros RJ, Costa MC (2014) Testing Sulphate Reducing Bacteria for the bioremediation of metal-contaminated wastewaters with relatively low sulphate concentrations. International Congress on Green Chemistry and Sustainable Engineering. 29 - 31 July. Barcelona, Spain.

Leitão J, Guerreiro P, Carlier J, Alabaça C, Farinhó M, Coelho P, Monteiro A (2008) Advances in positional cloning of PpALG1 and Pp523, two linked downy mildew adult-plant resistance genes in Brassica oleracea L. Plant Genomics European Meeting, 24-27 September. Albena, Bulgaria.

Leitão JM, Farinhó M, Carlier JD, Marques AC, Alabaça CS, Gambôa C, Sousa NF, Ribeiro R, Cadima S, Formiga S e Santo TE (2007) Da genómica de plantas à genética humana: o laboratório de genómica e de melhoramento genético, FERN, UAlg. 13º Congresso do Algarve, 15-17 November. Lagos, Portugal.

Leitão JM, Elisiário PJ, Cabrita LF, Justo EM, Pereira GM, Jacob AP, Carlier JD, Farinhó MJ (1998) Molecular markers in genetic variability assessment, cultivar fingerprinting and hybrid identification in fruits and vegetables. XXV International Horticultural Congress (IHC). 2-7 August. Brussels, Belgium.

Leitão José M, Reis A, Pereira G, Carlier J, Cabrita L, Farinhó M and Talhinhas P, (2000) Molecular markers applications in production and genetic improvement of horticultural crops. International Symposium on Biotechnology Application in Horticultural Crops, 4-8 September. Beijing, China, p. 77.

Ferreira FR, Duval M-F, Bernasconi B, Cabral JRS, Carlier J, Ferreira ME, Leal F, Leitão J, de Matos AP, Suarez Z and G. Coppens d'Eeckenbrugge (1999) Avaliação e uso de germoplasma de abacaxi para obtenção de variedades melhoradas. Segundo Simpósio de Recursos Genéticos para América Latina e Caribe. Novembro 21-26. Brasilia, Brasil Abstract 249.

Posters

Donaldben MN, CarlierJD, Costa MC (2016) Investigating the Biodegradation of Acetaminophen by Bacteria communities. 11th conference on Sustainable Development of Energy, Water and Environment Systems – SDEWES. September 4-9. Lisbon, Portugal.

Goossens G, Carlier JD, Assunção A, Costa MC (2016) Investigating the biotechnological potential of filamentous algae from extreme environments. 3rd International Congress on Water, Waste and Energy Management (EWWM). July 18-20. Rome, Italy.

Fazenda P, Carlier J, Jacinto R and Leitão J (2013) Identificação de marcadores SSR em medronheiro (Arbutus unedo L.) por sequenciação massiva paralela. Encontro Nacional do Medronho. December 13. Silves, Portugal.

Carlier J, Alabaça C, Rodrigues C and Leitão J (2012) On the Way to the Identification of a Downy Mildew Resistance Gene in Brassica oleracea L. 6th International Symposium on Brassica and 18th Crucifer Genetic Workshop. November 12 – 16. Catania, Italy.

Carlier J, Farinhó M, Alabaça C, Coelho P, Monteiro A and José Leitão (2011) Genomic mapping of a downy mildew resistance gene in Brassica oleracea L. XXXVI Jornadas Portuguesas de Genética. May 30 - June 1. Coimbra, Portugal.

Alabaça C, Sousa N, Coelho P, Monteiro A, Carlier J and José Leitão (2011) QTL mapping of downy mildew resistance in couve Algarvia. XXXVI Jornadas Portuguesas de Genética. May 30 - June 1. Coimbra, Portugal.

Carlier J, Coelho P, Monteiro A and José Leitão (2009) Assigning the linkage groups of a Brassica oleracea L. map to physical chromosomes. Plant Genomics European Meeting, October 7-10. Lisbon, Portugal.

Carlier J, Farinhó M, Alabaça C, Coelho P, Monteiro A and José Leitão (2009) Exploiting the Brassica/Arabidopsis genomic synteny for BAC contig construction. Plant Genomics European Meeting, October 7-10. Lisbon, Portugal.

Santo T, Sousa N, Carlier J and José Leitão (2009) A new genetic map of pineapple (Ananas comosus L.) integrates data from an F1 and an F2 population. Plant Genomics European Meeting, October 7-10. Lisbon, Portugal.

Carlier J, Cabrita L, Sousa RM, Sousa AT and Leitão J (2009) ISSR and AFLP Characterization of Phomopsis amygdale (Del.) Tuset & Portilla Accessions. 5th International Symposium on Pistachios & Almonds, October 6 – 10, Sanliurfa – Turkey

Carlier J, Santo T, Sousa N and José Leitão (2008) An Integrated Genetic Map of Pineapple (Ananas comosus (L.) Merrill). Plant Genomics European Meeting, September 24-27. Albena, Bulgaria.

Santo T, Carlier J and José Leitão (2008) A Genetic Map of Pineapple (Ananas comosus L.) Constructed Using an F2 Population. Plant Genomics European Meeting, September 24-27. Albena, Bulgaria.

Farinhó M, Carlier J, Alabaça C, Guerreiro P, Coelho P, Monteiro A and José Leitão (2008) Progressing Towards the Map-Based Cloning of Downy Mildew Resistance Genes in Brassica oleracea L. 5th ISHS International Symposium on Brassicas and the 16thCrucifer Genetics Workshop. September 8 – 12. Lillehammer, Norway.

Apostolova E, Carlier J, Leitão J and Diana Svetleva (2008) Identification of RAPD markers linked to the Fin and P loci in Phaseolus vulgaris L. IVth Balkan Symposium on Vegetables and Potatoes, September 9 – 12. Plovdiv, Bulgaria.

Carlier JD, Santo TE and José Leitão (2007) A linkage map of pineapple (Ananas comosus L.) constructed using an F2 progeny. 1º Encontro da Plataforma Nacional de Genómica Funcional de Plantas. Universidade do Algarve, FERN. July 12-13. Faro, Portugal.

Carlier J and José Leitão (2006) Constructing an integrated map of DNA markers in Pineapple. Plant & Animal Genomes XIV Conference. January 14-18. San Diego, CA, USA.

Handaji N, Carlier J, Cabrita L and José Leitão (2005) Molecular characterization of the Morocco mandarin “Nadorcott” using isozymes, ISSR, RAPD and AFLP. 7th International Congress of Citrus Nuresrymen. September 17–21. Cairo, Egypt.

Handaji N, Carlier J, Cabrita L, Yahia B and José Leitão (2005) Assessement of genetic diversity among mandarins germplasm from INRA Morocco using ISSR and AFLP. 7th International Congress of Citrus Nuresrymen. September 17–21. Cairo, Egypt.

Handaji N, Carlier J, Cabrita L, Ben Yahia H and Leitão JM (2005) Evaluation of genetic diversity among mandarins germplasm in INRA Morocco by molecular markers. 12th European Congress on Biotechnology. August 21-25. Copenhagen, Denmark.

Handaji N, Carlier J, Cabrita L, Ben Yahia H and Leitão JM (2005) Identification of Morocco hybrid mandarin "Nadorcott" using isozymes, ISSR, RAPD and AFLP. 12th European Congress on Biotechnology. August 21-25. Copenhagen, Denmark.

Handaji N, Carlier J and José Leitão (2004) DNA analysis of citrus cultivars from INRA Morocco germplasm with inter simple sequence repeat markers. 10Th International Society of Citriculture (ISC) Congress. February 15-20. Agadir, Morocco.

Carlier JD, Nancheva D, Reis A and José Leitão (2004) Preliminary Results of Mapping DNA markers in Pineapple using a F2 Population. XXXI Jornadas Portuguesas de Genética. February 5-6. Oeiras, Portugal.

Farinhó M, Carlier J, Coelho P, Svetleva D, Monteiro A and José Leitão (2004) Mapping a Downy Mildew Resistance Gene in Broccoli. XXXI Jornadas Portuguesas de Genética. February 5-6. Oeiras, Portugal.

Farinhó M, Carlier J, Svetleva D, Monteiro A and José Leitão (2002) Genetic linkage map of Broccoli based on AFLP, RAPD, SSR and ISSR markers linked to resistance against the Downy Mildew. XXVIth International Horticultural Congress & Exhibition. August 11-17. Toronto, Canada.

Reis A, Carlier JD, Duval MF, Coppens d´Eckenbrugge G and José Leitão (2000) Mapeamento genético de marcadores RAPD, AFLP e ISSR em Ananas spp. 4º Workshop de Biotecnologia de Plantas. April 27-28. Evora, Portugal.

Leitão J, Reis A, Pereira G, Fernandes J, Carlier J, Cabrita L and Mario Farinhó (1999) Use of molecular markers for selection, genotyping, genetic relatedness assessment and genome mapping in fruit and vegetable species. International symposium on plant genetics engineering. Centre for genetic engineering and biotechnology. December 6-10. Havana, Cuba.

Miguel G, Reis A, Carlier J, Venâncio F, Tavares A, Martins A, Duarte F and José Leitão (1999) Preliminary studies on genetic polymorphisms between two chemotypes of Thymus mastichina subsp. mastichina. 30th International Symposium on Essential Oils. September 5-8. Leipzig, Germany.

Carlier JD, Duval MF, Coppens d´Eckenbrugge G and José Leitão (1999) Preliminary results of mapping RAPD and AFLP markers in pineapple. The 9th European Congress on Biotechnology. July 11-15. Brussels, Belgium.

Coppens d’ Eeckenbrugge G, Cabral JRS, Carlier J, Duval MF, Ferreira FR, Leal F, Leitão J, Matos APde, Noyer JL and Zoraida Suárez (1998) The EU-funded project “Evaluation and utilization of pineapple genetic resources from the Amazon to breed resistant varieties”. Third International pineapple Symposium. November 20-24. Pattaya, Thailand.

Supervising