katrien m. devos dept . of crop and soil sciences

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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

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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: - PowerPoint PPT Presentation

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Page 1: Katrien M. Devos Dept . of Crop and Soil  Sciences

Katrien M. Devos

Dept. of Crop and Soil SciencesInstitute of Plant Breeding, Genetics and Genomics

Dept. of Plant Biology

0.5 EFT Research0.25 EFT Teaching

Adjunct statusDept. of Genetics

Institute of Bioinformatics

Page 2: Katrien M. Devos Dept . of Crop and Soil  Sciences

The Devos lab: 2009 - 2014Post-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) - TunisiaIgnatius Angarawai (2010: 3 months) – NigeriaDipnarayan Saha (2013– 2014: 8 months) – India

Visiting Graduate Students:

Anabelle Grimm (2012: 6 months) - GermanyDagnachew Lule (2013: 8 months) – EthiopiaDavis Gimode (2014: 2.5 months) - Kenya

Page 3: Katrien M. Devos Dept . of Crop and Soil  Sciences

Graduate Students:

MScSandra Odonkor (MSc: 2012 – current) - IPBGG

PhDRajiv Parvathaneni (PhD: 2009- current) - IPBGGDoug Eudy (PhD: 2009 – current) – IPBGGAlex Johnson (PhD: 2013 – current) – Plant biologyChristian Schwoyer (PhD: 2013 – current) – GeneticsDebkanta Chakraborty (PhD: 2013 – current) – IOB

Technicians:

Trudi Thomas

The Devos lab: 2009 - 2014

Funding:

Total funding to KMD Lab: 2.5 M

Funding sources: NSF, USDA, DOE, BESC

BioInnovate, ICRISAT

Page 4: Katrien M. Devos Dept . of Crop and Soil  Sciences

Pearl millet

Switchgrass

WheatFoxtail millet

Seashore Paspalum

finger millet

Research Overview: 2009 - 2014

Page 5: Katrien M. Devos Dept . of Crop and Soil  Sciences

Switchgrass for Bioenergy

Lowland

Upland

Objectives:- Resource development- Trait mapping

- Biomass yield- Biomass quality- Cold tolerance- Colonization by AMF

- Identification of the A and B genomes

Funding:- USDA (2007 – 2011)- BESC/DOE (2007 – 2017)- DOE (2014 – 2017)

Publications:- 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)

Page 6: Katrien M. Devos Dept . of Crop and Soil  Sciences

Setaria: A Model for SwitchgrassObjectives:- 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)

Page 7: Katrien M. Devos Dept . of Crop and Soil  Sciences

Setaria viridis: A Ubiquitous WeedObjectives:- 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)*

Page 8: Katrien M. Devos Dept . of Crop and Soil  Sciences

Aegilops tauschii – A Model for Wheat

Objectives:- 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:- Gene space dynamics 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)*

Ae. tauschii(DD)

Wheat (AABBDD)

Page 9: Katrien M. Devos Dept . of Crop and Soil  Sciences

Pearl millet – Characterization of d2

Objectives:- Isolation of the d2 dwarfing gene- Characterization of ABCB1

- Studying prevalence and mechanisms behind recurrent intron loss

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)

Page 10: Katrien M. Devos Dept . of Crop and Soil  Sciences

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)

Page 11: Katrien M. Devos Dept . of Crop and Soil  Sciences

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)

Page 12: Katrien M. Devos Dept . of Crop and Soil  Sciences

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

Page 13: Katrien M. Devos Dept . of Crop and Soil  Sciences

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

Page 14: Katrien M. Devos Dept . of Crop and Soil  Sciences

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)

Page 15: Katrien M. Devos Dept . of Crop and Soil  Sciences

DougGuillaume

Dagne

BochraTrudi

SandraRajiv

StephanVictoria