Transcript Katrien Devos - Department of Crop and Soil Sciences

Katrien M. Devos
Dept. of Crop and Soil Sciences
Institute of Plant Breeding, Genetics and Genomics
Dept. of Plant Biology
0.5 EFT Research
0.25 EFT Teaching
Adjunct status
Dept. of Genetics
Institute of Bioinformatics
The Devos lab: 2009 - 2014
Post-docs:
Xiangyang Xu (2006-2010)
Xuewen Wang (2008 – 2012)
Xiaomei Wu (2009 – 2011)
Bochra Bahri (2009 – 2010)
Stephan Schröder (2011 – 2013)
Guillaume Daverdin (2011 – 2014)
Currently 3 post-doc positions open
Visiting Scientists:
Bochra Bahri (2010 – current: several months each year) - Tunisia
Ignatius Angarawai (2010: 3 months) – Nigeria
Dipnarayan Saha (2013– 2014: 8 months) – India
Visiting Graduate Students:
Anabelle Grimm (2012: 6 months) - Germany
Dagnachew Lule (2013: 8 months) – Ethiopia
Davis Gimode (2014: 2.5 months) - Kenya
The Devos lab: 2009 - 2014
Graduate Students:
MSc
Sandra Odonkor (MSc: 2012 – current) - IPBGG
PhD
Rajiv Parvathaneni (PhD: 2009- current) - IPBGG
Doug Eudy (PhD: 2009 – current) – IPBGG
Alex Johnson (PhD: 2013 – current) – Plant biology
Christian Schwoyer (PhD: 2013 – current) – Genetics
Debkanta Chakraborty (PhD: 2013 – current) – IOB
Technicians:
Trudi Thomas
Funding:
Total funding to KMD Lab: 2.5 M
Funding sources: NSF, USDA, DOE, BESC
BioInnovate, ICRISAT
Research Overview: 2009 - 2014
Pearl millet
finger millet
Seashore Paspalum
Foxtail millet
Switchgrass
Wheat
Switchgrass for Bioenergy
Objectives:
-
Upland
Lowland
Resource development
Trait mapping
- Biomass yield
- Biomass quality
- Cold tolerance
- Colonization by AMF
- Identification of the A and B genomes
Funding:
Publications:
-
USDA (2007 – 2011)
BESC/DOE (2007 – 2017)
DOE (2014 – 2017)
- Linkage Maps of Lowland and Upland Tetraploid Switchgrass Ecotypes
(BioEnergy Research 2013)*
- Comparative relationships and chromosome evolution in switchgrass
(Panicum virgatum) and its genomic model, foxtail millet (Setaria italica)
(BioEnergy Research 2014)*
- Quantitative trait loci (QTL) underlying biomass yield and plant height in
switchgrass (BioEnergy Research – Under revision)
Setaria: A Model for Switchgrass
Objectives:
-
Sequencing of the Setaria genome
Comparative analysis with switchgrass
Trait mapping
- Biomass yield
- Biomass quality
- Domestication traits
Funding:
-
USDA (2008 – 2013)
JGI Community Sequencing Program
Publications:
- Foxtail millet (Setaria italica): a sequence-driven grass model system
(Plant Physiology 2009)
- Sequencing and analysis of a reference genome for the model plant
Setaria (Nature Biotechnology 2012)*
- Genetic control and comparative genomic analysis of flowering time in
Setaria (Poaceae) (G3 2013)
Setaria viridis: A Ubiquitous Weed
Objectives:
-
Population structure analysis of US and
global S. viridis collection
Effects of herbicide resistance on linkage
disequilibrium
Funding:
-
NSF (2010 – 2015)
Publications:
- Population genetics of Setaria viridis, a new model system (Molecular
Ecology – Submitted)*
Aegilops tauschii – A Model for Wheat
Objectives:
-
Ae. tauschii
Wheat
(AABBDD)
(DD)
Sequencing of the Ae. tauschii genome
Understanding the structure and evolution
of large genomes
- Genome size is correlated with gene
space – Implications?
- What drives the formation of gene
islands?
Funding:
-
NSF (2007 – 2010; 2013 - 2017)
Publications:
during the evolution of Aegilops tauschii,
Brachypodium distachyon, Oryza sativa, and Sorghum bicolor genomes
(Molecular Biology and Evolution 2011)*
- The insular organization of gene space in grass genomes and its evolution
(PLoS One 2013)*
- Gene
space
dynamics
Pearl millet – Characterization of d2
Objectives:
-
Isolation of the d2 dwarfing gene
Characterization of ABCB1
-
Studying
prevalence
and
behind recurrent intron loss
mechanisms
Funding:
-
USDA (2008 – 2012)
NSF-DDIG (2013 – 2014)
Publications:
- Fine-mapping and identification of a candidate gene underlying the d2
dwarfing phenotype in pearl millet, Cenchrus americanus (L.) Morrone
(G3 2013)*
- Recurrent loss of specific introns during angiosperm evolution (2014)
PLoS Genetics (under revision)
Seashore paspalum – Mapping salt tolerance
Objectives:
-
Germplasm characterization
Mapping of salt tolerance
Effects of salt on gene expression
Funding:
-
NSF-GRFP to Doug Eudy (2010 - 2014)
Finger Millet – Germplasm characterization
Objectives:
-
Assist finger millet breeders/scientists in
East Africa with research and training
Genotype mainly East African finger millet
collection
Sequencing of the finger millet genome
Funding:
-
BioInnovate (2013 - 2014)
Program Impact (2009 – 2014)
- Publications: 14
- Number of citations: 167
- Overall H-index: 39
- Provided genetic and genomic tools for breeders and the
scientific community (e.g. markers, genetic maps, genome
sequences)
- Contributed to the overall knowledge on the structure, function
and evolution of genes and genomes
- Trained graduate students and international scientist
Future Goals
- Move from trait loci to genes underlying those traits and
their functional characterization
- Exploit sequence/resequencing data to study natural variation
and their phenotypic effects
- Move beyond the genome to the mRNA and small RNA
transcriptomes and their effect on phenotypes
- Continue to enhance our understanding on genome structure,
function and evolution
Teaching
- 2 credit hours per semester
- Essential skills for graduate students (PBIO 8020) Fall
- Grant writing (PBIO 8840) – Spring/uneven years
- Genetic mapping (PBGG 8871) – Spring/even years
- Graduate seminar (PBIO 8820) – Spring/even years
- Training of graduate students
Service
- Editorial Board of 3 journals
- Chair-elect, Chair, Past-chair of C-7 division of CSSA
(2009-2011)
- Program reviews (2)
Rajiv
Bochra
Dagne
Sandra
Trudi
Stephan
Victoria
Doug
Guillaume