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Katrien M. Devos Dept . 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:

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Katrien M. Devos Dept . of Crop and Soil Sciences

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  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: 2009 - 2014 Post-docs: Xiangyang Xu (2006-2010) Xuewen Wang (2008 – 2012) Xiaomei Wu (2009 – 2011) BochraBahri (2009 – 2010) Stephan Schröder (2011 – 2013) Guillaume Daverdin (2011 – 2014) Currently 3 post-doc positions open Visiting Scientists: BochraBahri (2010 – current: several months each year) - Tunisia Ignatius Angarawai (2010: 3 months) – Nigeria DipnarayanSaha (2013– 2014: 8 months) – India Visiting Graduate Students: Anabelle Grimm (2012: 6 months) - Germany DagnachewLule (2013: 8 months) – Ethiopia Davis Gimode (2014: 2.5 months) - Kenya

  3. 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

  4. Research Overview: 2009 - 2014 Pearl millet finger millet Seashore Paspalum Foxtail millet Wheat Switchgrass

  5. Switchgrass for Bioenergy • Objectives: • Resource development • Trait mapping • Biomass yield • Biomass quality • Cold tolerance • Colonization by AMF • - Identification of the A and B genomes Upland Lowland • Funding: • USDA (2007 – 2011) • BESC/DOE(2007 – 2017) • DOE (2014 – 2017) • Publications: • Linkage Maps of Lowland and Upland TetraploidSwitchgrassEcotypes (BioEnergy Research 2013)* • Comparative relationships and chromosome evolution in switchgrass (Panicumvirgatum) and its genomic model, foxtail millet (Setariaitalica) (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 (Setariaitalica): 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. Setariaviridis: 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 Setariaviridis, a new model system (Molecular Ecology – Submitted)*

  8. Aegilopstauschii– A Model for Wheat • Objectives: • Sequencing of the Ae. tauschiigenome • Understanding the structure and evolution of large genomes • Genome size is correlated with gene space – Implications? • What drives the formation of gene islands? Ae. tauschii (DD) Wheat (AABBDD) • Funding: • NSF (2007 – 2010; 2013 - 2017) • Publications: • Gene space dynamics during the evolution of Aegilopstauschii, Brachypodiumdistachyon, 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)*

  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, Cenchrusamericanus (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 (2010 - 2014)

  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 (2013 - 2014)

  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 (2009-2011) • Program reviews (2)

  15. Sandra Stephan Rajiv Victoria Trudi Bochra Doug Guillaume Dagne

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