Genome sequencing to
support germplasm
analysis and utilization
Robert Henry
New sequencing technologies
Illumina
PacBio
Life Technologies
Brozynska M, Furtado A and Henry RJ (2014) Direct Chloroplast
Sequencing: Comparison of Sequencing Platforms and Analysis
Tools for Whole Chloroplast Barcoding. Plos One 9 e110387
Genomics Technology
2013
2014
2008
2001
Domestication of New Crops
Henry RJ (2012) Next generation
sequencing for understanding and
accelerating crop domestication. Briefings
in Functional Genomics 11: 51-56.
Microlaena domestication
Shapter FM, Cross M, Ablett G,
Malory S, Chivers IH, King GJ and
Henry RJ (2013) High-throughput
sequencing and mutagenesis to
accelerate the domestication of
Microlaena stipoides as a new food
crop. PLOS ONE 8(12) e82641.
doi:10.1371/journal.pone.0082641
Crop wild relatives
Characterization of domestication genes in
wild relatives
Malory S, Shapter FM, Elphinstone MS, Chivers IH and Henry RJ (2011)
Characterizing homologues of crop domestication genes in poorly described
wild relatives by high-throughput sequencing of whole genomes.
Plant Biotechnology Journal 9: 1131-1140.
Rice wild relatives
Kasem S, Waters DLE, Rice N,
Shapter FM, Henry RJ (2010)
Whole grain morphology of
Australian rice species. Plant
Genetic Resources:
Characterization and Utilization
8:74-81.
Kasem S, Waters DLE,
Rice N, Shapter FM, and
Henry RJ ( 2011) The
endosperm morphology of
rice and its wild relatives as
observed by scanning
electron microscopy. Rice
4: 12-13.
New Diversity for Rice
Waters DLE, Nock CJ, Ishikawa R, Rice N and Henry RJ (2012) Chloroplast genome sequence confirms
distinctness of Australian and Asian wild rice. Ecology and Evolution 2: 211-217
Large wild rice populations
Photo Marta Brozynska
Rice
South America/
Africa
Australia
Africa
Asia
Wambugu PW, Brozynska M, Furtado A, Waters D and Henry RJ (2014)
Relationships of wild and domesticated rice species based on whole chloroplast
genome sequences.
Wild Australian Rice
(Photos Marta Brozynska)
Genome deserts in domesticated rice
Krishnan S G, Waters DLE, Katiyar SK, Sadananda AR, Satyadev V and Henry
R (2012) Genome-wide DNA polymorphisms in elite indica rice inbreds
discovered by whole-genome sequencing. Plant Biotechnology Journal 10:
623-634.
Cereal Starches
Wheat relative
A and B type Granules
A: <10µM
B: 10-50µM
Sorghum granules
10-30µM
Spherical to
non-uniform polyhedral
Rice like Granules
Rigid dodecahedrons
2-5µM
Compound granules
Health Starch and Plant Genetics
 Starch digestibility
 Starch chemistry
 Plant genetics
Bread genes in wheat
Wheat quality a constraint on productivity gains
Understanding why we have been successful in the past
Henry RJ (2014) Wheat genomics for grain quality improvement. Cereal Foods World 59, 22-24
Novel alleles in high quality
Queensland wheat genotypes
Photo Terry Taylor and Glen Fox
Gillies S, Furtado A, Henry RJ
(2012) Gene expression in the
developing aleurone and
starchy endosperm of wheat.
Plant Biotechnology Journal
10; 668-679.
Prime Hard
Wheat
Predicting Hybrid Performance
Yield
Genetic distance SNP
Novel high value horticultural products
Whole genome comparative analysis for crop improvement
Koepke T, Schaeffer S, Harper A, Dicenta F, Henry RJ, Moller BL, Sanchez-Perez R, Dhingra A
(2013) Comparative Genomics Analysis in Prunoideae to Identify Biologically Relevant
Polymorphisms. Plant Biotechnology Journal 11, 883-893.
Macadamia
Coffee Consortium
UMR DIADE:
Alexandre de Kochko
Romain Guyot
Christine Tranchant
Valérie Poncet
Perla Hamon
Serge Hamon
Claudine Campa
Stéphane Dussert
Thierry Joët
UMR RPB:
Philippe Lashermes
Benoît Bertrand
Marie-Christine Combes
François Anthony
Università di Trieste:
University of Queensland:
Giorgio Graziosi
Alberto Pallavicini
Robert Henry
ENEA:
Giovanni Giuliano
Gaetano Perrotta
David SANKOFF
EMBRAPA:
Alan C. Andrade
QuickTime™ et un
décompresseur
sont requis pour visionner cette image.
Victor Albert
University of Illinois at Urbana Champaign:
Ray Ming
Xavier Argout
Thierry Leroy
Hawaii Agriculture Research Center:
Patrick Wincker
Coffee Bord of India:
Jayarama
University at Buffalo:
UMR AGAP:
GENOSCOPE:
University of Ottawa:
QuickTime™ et un
décompresseur
sont requis pour visionner cette image.
ICCRI:
Priyono
Chifumi Nagai
Ming-Li Wang
University of Arizona:
Steve Rounsley
Nestlé R&D:
Dominique Crouzillat
Michel Rigoreau
XIX PAG 2011
Why sequence Coffee?
Coffee is one the most traded commodities worldwide and is the second commodity exported
by developing countries.
More than 75 million families, almost exclusively in Southern countries, rely on coffee
production.
Out of the more than 100 Coffea species, only 2 are widely cultivated, C. arabica (75% of the
market) and C. canephora (25%).
Improvement is still necessary to better tolerate biotic (fungi, bacteria, nematodes, insects…)
and abiotic (drought) stresses.
XIX PAG 2011
Caffeine
Denoeud et al (2014) The Coffee Genome Provides Insight into the Convergent Evolution of Caffeine
Biosynthesis. Science
Coffee species
Wild Australian coffee relative
Coffea brassii
Photo: Australian Tropical Herbarium
13 genomes consortium
Victor Albert
Lorenzo Carretero-Paulet
Emmanuel Couturon
Romain Guyot
Alexandre de Kochko
Perla Hamon
Serge Hamon
Dominique Crouzillat
Michel Rigoreau
Ray Ming
Vimel Rattina
Lukas Muller
Suzy Strickler
Douglas Silva Domingues
Giuseppe Aprea
Giovanni Giuliano
Marco Pietrella
Jean-Jacques Rakotomalala
Agnelo Furtado
Robert Henry
Hue Tran
Filipe Perreira
Hosahalli Sreenath
Alexandre Rossi Paschoal
Coffee species
Hue Tran 13 genomes consortium
Peanut
Selection for quality and disease resistance
Dan O’Connor
Energy crops
• Sugarcane
• Eucalypts
Biofuel from non food plants
Biomass
(cellulose)
PreEnzymes
treatment
Sugars
Ethanol
Biodiesel
Aviation Fuel
Sugarcane sequencing consortium
Souza GM, Berges H, Bocs S, Casu R, D’Hont A, Ferreira JE, Henry R, Ming R
Potier B, Van Sluys MA, Vincentz M and Paterson AH (2011) The sugarcane
genome challenges: Strategies for sequencing a highly complex genome. Tropical
Plant Biology 4: 145-156.
Sugarcane genome
Eucalypts
Shepherd M, Bartle, J, Lee DJ, Brawner J, Bush D, Turnbull P, Macdonell P, Brown TR, Simmons B
and Henry R (2011) Eucalypts as a biofuel feedstock. Biofuels 2: 639-657.
Eucalypt relationships Adam Healey
Corymbia henryii
Information Technology
Rossetto M and Henry RJ (2014) Escape
from the laboratory: new horizons for plant
genetics. Trends in Plant Science
Plant relationships
TropAg 2015
Acknowledgements
Tal Cooper
Ernnie Omar Syafika
Thi Phuong Thuy Mai
Jeremie Touze
Orawan Bunyatang
Yuwei Luo
Parimalan Rangan
Frikkie Botha
Andrew Geering
Nageswararao Rao(RCN)Rachaputi
Bob Gilbert
Maurizio Rossetto
Kemal Kazan
Ratnakar Thengane
Daniel Waters
Slade Lee
Roger Shivas
Graeme Wright
Glen Fox
Heather Smyth
Tim Fitzgerald
Marta Brozynska
Jonathan James Powell
Abhijeet Raosaheb Survase
Peterson Weru Wambugu
Ravi Chandrabhan Nirmal
Adam Healey
Thi Minh Hue Tran
Van Nam Hoang
Wanporn Khemmuk
Daniel John O’Connor
Kai Wang
Tiparat Tikapunya Tikapunya
Bing Cheng
Hayba Qayssar Younan Badro
Patrick Mason
Annelie Marquardt
Ali Imad Mohammad Moner
Samantha Yap
Agnelo Furtado
Jason Lupoi