Andrade conilon-2012
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Transcript of Andrade conilon-2012
The importance of C. canephora:
2n=2x=22
Allogamous species2n=4x=44
Autogamous species
Challenges
Growers and Industry
• Climate changes
• Competition with other commodities (Bioenergy)
• Sustainable production systems
• Preservation of natural resources (minerals, water, etc.)
• Quality (Competition with other beverages)
• Socio-economic aspects
http://www.lge.ibi.unicamp.br/cafe/
https://alanine.cenargen.embrapa.br/
Functional Genomics
Functional Genomics
Coffee ESTs
Espécie BP > 20 BP Total Reads
250 BP
Phred≥20
Reads Total Qualidade
(%)
Coffea arabica 83.368.331 181.429.319 131.718 187.078 71,10
Coffea canephora 8.074.170 14.735.317 12.359 15.322 80,66
Coffea racemosa 8.475.698 14.530.379 12.097 15.546 77,81
Total 99.918.199 210.695.015 156.174 217.946 71,66
Unigene Set
• Contigs: 19.031
• Singlets: 13.928
• Unigene: 33.000
% of Unigene
12%
75%
13%
dbEST Brazil-ESTs Common
Coffea sp. : 246,541 ESTs
71.1%
28.9%
no hits found
hits
71.1%No hitsHits
28.9%
Lin et al., 2005Vieira et al., 2006Poncet et al., 2006
Cost:
Service, R.F. Science, 2006
• Gouveia et al. 2005
• Ferreira et al. 2007
• Nunes et al. 2007
• RAPD, AFLP
NGS technologies
Improvements in the rate of DNA sequencing over the past 30 years and into the future. From slab gels to capillary sequencing and second-generation sequencingtechnologies, there has been a more than a million-fold improvement in the rate ofsequence generation over this time scale.
Stratton, MR. Nature, 2009
Stratton, MR. Nature, 2009
Output still increasing!
Pareek et al., 2011
Metzker, ML. Nature, 2010
Cost reduction:
Morrell et al, Nature, Feb. 2012
Crop genome size. Genome size of published crop genomes (green) andunpublished (blue).
Plant genomes
Plant genomes
Plant genomes
Coffee Genomics
International Coffee Genome Network
Founding meeting
Paris – 4 & 5 April 2005
(http://www.coffeegenome.org )
Coffee GenomicsPatrick Wincker, Benoit Bertrand, Xavier Argout, Alexandre de Kochko,
Philippe Lashermes
Ray Ming, Victor A. Albert, Steve Rounsley,
Chifumi Nagai
Alan C. Andrade
Giorgio Graziosi, Giovanni Giuliano
Robert Henry
David Sankoff
Jayarama
Coffee Genomics
Genotype: Double-haploid
HD 200-94 - IRD
Genome estimated size: 710 Mb
Coffee GenomicsFinal status – Sequencing Completed!Total coverage for assembly: 29 X - 454: 28.8 X
single end : 14,83 X long single end: 8,24 X mate paired reads : 5,8 X (2,2X de 8kb, 3,6X de 20kb)
- Sanger sequencing (BAC ends ): 0.2X- For assembly correction and gap closure :
Solexa : 69,7 X - single end : 7,3X - paired end reads : 62,4X
Coffee Genomics
Final Assembly statistics scaffold statistics:N50 size= 1260636 number= 108N80 size= 65268 number= 635N90 size= 21947 number= 2191Assembly size= 568577705 number= 13345 minSize= 1995 maxSize= 9027918 averageSize= 42606
Applied Coffee Genomics
Applied Coffee Genomics
Applied Coffee Genomics
Applied Coffee Genomics
Applied Coffee Genomics
The basics is the same:Comparisons!
Diferences Similarities
Sequences
Phenotype
Phenotyping
Phenotyping...
Germplasm Collection
Experimental field of Embrapa
Real Data from the neighbours...
CBH: circunference at breast height; HG: height growth; WSG: wood specific gravity; PY: Pulp Yield
Eucalyptus grandis
Resende et al., New Phytologist 2012
Real Data from the neighbours...
CBH: circunference at breast height; HG: height growth; WSG: wood specific gravity; PY: Pulp Yield
Resende et al., New Phytologist 2012
Eucalyptus grandis
Real Data from the neighbours...
CBH: circunference at breast height; HG: height growth; WSG: wood specific gravity; PY: Pulp Yield
Resende et al., New Phytologist 2012
Partners:
Thank you!
The new variety “Genoma” is coming…