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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.

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Presentation on theme: "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."— Presentation transcript:

1 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

2 The Devos lab: Post-docs: Xiangyang Xu ( ) 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

3 Graduate Students: MSc Sandra Odonkor (MSc: 2012 – current) - IPBGG PhD Rajiv Parvathaneni (PhD: 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 The Devos lab: Funding: Total funding to KMD Lab: 2.5 M Funding sources: NSF, USDA, DOE, BESC BioInnovate, ICRISAT

4 Pearl millet Switchgrass Wheat Foxtail millet Seashore Paspalum finger millet Research Overview:

5 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)

6 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)

7 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)*

8 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; ) 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)

9 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)

10 Seashore paspalum – Mapping salt tolerance Objectives: -Germplasm characterization -Mapping of salt tolerance -Effects of salt on gene expression Funding: -NSF-GRFP to Doug Eudy ( )

11 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 ( )

12 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

13 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

14 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 ( ) -Program reviews (2)

15 Doug Guillaume Dagne Bochra Trudi Sandra Rajiv Stephan Victoria


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