University of California, Berkeley | Plant & Microbial Biology
DColeman-Derr
Devin
Coleman-Derr
Abiotic stress response and plant growth promoting microbial communities
- Principal Investigator
Email:
devin.coleman-derr@ars.usda.gov
Phone:
510.559.5911
Lab Phone:
510.559.5911
Our laboratory investigates the effects of drought and other abiotic stresses on the microbiomes associated with Sorghum bicolor and other grass species. With the world population expected to reach 9 billion by 2050, it is estimated that the global food supply will need to increase by 70 percent to meet rapidly rising demand. Changes in the global climate may well compound this challenge, as predicted increases in environmental stresses, such as drought and high-salinity, are expected to reduce crop productivity. Recent studies demonstrated that microbial symbionts of crop plants are capable of enhancing the abiotic stress tolerance of their host. However, only a tiny fraction of plant microbiomes have been uncovered and evaluated. Thus, research and new tools are needed to develop a better understanding of the interrelationship between crop plant abiotic stress tolerance and crop plant microbiomes.
Additionally, the lab works on developing statistical methods and computational tools based on genome wide association studies (GWAS) that incorporate epigenomic, transcriptomic, and other data types. In addition to offering increasing the statistical power of GWAS analyses, this approach also has the potential to reveal instances where phenotypic variation is not explained by changes in nucleotide sequence, but instead by epigenetic changes (commonly referred to as “missing heritability”). Additionally, by integrating multiple ‘omics’ datasets, this strategy offers an opportunity to detect correlations among data sets and types and to directly interrogate the complex cascade of signals and forces that leads to phenotype.
Our lab is also interested in understanding the role of plant growth promoting microbes (PGPM) in improving abiotic stress response in their plant hosts. Using a variety of culture and genomics-based approaches, we are working to uncover the host machinery manipulated by several PGPM species, which in turn may serve as potential targets for direct crop improvement through conventional breeding practices.
Educational Background:
Ph.D. Plant Biology University of California at Berkeley, 2012
B.A. Natural Sciences New College of Florida, 1998
Research
Natural variaton in drought response in Sorghum bicolor and other crop species
Drought stress is arguably the most critical factor for crop production in many parts of the world and will increasingly become a greater factor with climate change; many microbial species have been shown to be capable of improving drought response in a variety of crop species. Sorghum bicolor, a crop with both feedstock and biofuels potential, is frequently grown in dry climates with frequent periods of drought. Recently, a genotype-by-sequencing (GBS) approach was used to generate a large SNP dataset for a large Sorghum association panel; these data and germplasm are publically available. Our research involves generating experimentally linked epigenetic and transcriptomic datasets using these accessions to investigate the correlation between genomic, epigenomic and transcriptomic response under drought stress. A variety of drought response phenotypes, including root morphology, biomass, and chlorophyll content are being used to detect associations between genetic variation in this broad panel of Sorghum lines and their ability to thrive in environments with limited water availability.
Sorghum as a model for drought tolerance research
Plant growth promoting microbes and abiotic stress response in crop species
A large variety of plant growth promoting microbes (PGPM) have been shown to be capable of reducing abiotic stress response in their plant hosts, though the mechanisms through which they act are still being explored and established. In addition to a number of characterized strategies of growth promotion, including improved nutrient exchange, production of phytohormones, and competition with pathogens, recent research continues to unveil novel pathways through which PGPM benefit their hosts. Using genomics-based approaches, we are working to uncover the host machinery manipulated by several PGPM species in Sorghum and other species.
Mechanisms of plant growth promotion by microbial symbionts
Recent Publications
Coleman-Derr D, Desgarennes D, Fonseca-Garcia C, Gross S, Clingenpeel S, Woyke T, North G, Visel A, Partida-Martinez LP, and Tringe SG. Plant Compartment and Biogeography Affect Microbiome Composition in Cultivated and Native Agave Species. New Phytologist. 2015 : n/a–n/a. doi:10.1111/nph.13697
Wang Y, Coleman-Derr D, Chen G, Gu YQ. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res. 2015 Jul 1;43(W1):W78-84. doi: 10.1093/nar/gkv487. Epub 2015 May 11. PubMed PMID: 25964301; PubMed Central PMCID: PMC4489293.
O'Connor RM, Fung JM, Sharp KH, Benner JS, McClung C, Cushing S, Lamkin ER, Fomenkov AI, Henrissat B, Londer YY, Scholz MB, Posfai J, Malfatti S, Tringe SG, Woyke T, Malmstrom RR, Coleman-Derr D, Altamia MA, Dedrick S, Kaluziak ST, Haygood MG, Distel DL. Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk. Proc Natl Acad Sci U S A. 2014 Nov 25;111(47):E5096-104. doi: 10.1073/pnas.1413110111. Epub 2014 Nov 10. PubMed PMID: 25385629; PubMed Central PMCID: PMC4250168.
Coleman-Derr D, Tringe SG. Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance. Front Microbiol. 2014 Jun 6;5:283. doi: 10.3389/fmicb.2014.00283. eCollection 2014. PubMed PMID: 24936202; PubMed Central PMCID: PMC4047557.
Wagner MR, Lundberg DS, Coleman-Derr D, Tringe SG, Dangl JL, Mitchell-Olds T. Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol Lett. 2014 Jun;17(6):717-26. doi: 10.1111/ele.12276. Epub 2014 Apr 4. Erratum in: Ecol Lett. 2015 Feb;18(2):218-20. PubMed PMID: 24698177; PubMed Central PMCID: PMC4048358.
Martin JA, Johnson NV, Gross SM, Schnable J, Meng X, Wang M, Coleman-Derr D, Lindquist E, Wei CL, Kaeppler S, Chen F, Wang Z. A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing. Sci Rep. 2014 Mar 31;4:4519. doi: 10.1038/srep04519. PubMed PMID: 24682209; PubMed Central PMCID: PMC3970191.
Zemach A, Kim MY, Hsieh PH, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 2013 Mar 28;153(1):193-205. doi: 10.1016/j.cell.2013.02.033. PubMed PMID: 23540698; PubMed Central PMCID: PMC4035305.
Coleman-Derr D, Zilberman D. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harb Symp Quant Biol. 2012;77:147-54. doi: 10.1101/sqb.2012.77.014944. Epub 2012 Dec 18. Review. PubMed PMID: 23250988.
Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genet. 2012;8(10):e1002988. doi: 10.1371/journal.pgen.1002988. Epub 2012 Oct 11. PubMed PMID: 23071449; PubMed Central PMCID: PMC3469445.
Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, Blake N, Clegg MT, Coleman-Derr D, Conley EJ, Crossman CC, Deal KR, Dubcovsky J, Gill BS, Gu YQ, Hadam J, Heo H, Huo N, Lazo GR, Luo MC, Ma YQ, Matthews DE, McGuire PE, Morrell PL, Qualset CO, Renfro J, Tabanao D, Talbert LE, Tian C, Toleno DM, Warburton ML, You FM, Zhang W, Dvorak J. Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes. BMC Genomics. 2010 Dec 14;11:702. doi: 10.1186/1471-2164-11-702. PubMed PMID: 21156062; PubMed Central PMCID: PMC3022916.
Anderson OD, Coleman-Derr D, Gu YQ, Heath S. Structural and transcriptional analysis of plant genes encoding the bifunctional lysine ketoglutarate reductase saccharopine dehydrogenase enzyme. BMC Plant Biol. 2010 Jun 16;10:113. doi: 10.1186/1471-2229-10-113. PubMed PMID: 20565711; PubMed Central PMCID: PMC3017810.
Luo MC, Deal KR, Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, Blake N, Clegg MT, Coleman-Derr D, Conley EJ, Crossman CC, Dubcovsky J, Gill BS, Gu YQ, Hadam J, Heo HY, Huo N, Lazo G, Ma Y, Matthews DE, McGuire PE, Morrell PL, Qualset CO, Renfro J, Tabanao D, Talbert LE, Tian C, Toleno DM, Warburton ML, You FM, Zhang W, Dvorak J. Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae. Proc Natl Acad Sci U S A. 2009 Sep 15;106(37):15780-5. doi: 10.1073/pnas.0908195106. Epub 2009 Aug 26. PubMed PMID: 19717446; PubMed Central PMCID: PMC2747195.
Gu YQ, Wanjugi H, Coleman-Derr D, Kong X, Anderson OD. Conserved globulin gene across eight grass genomes identify fundamental units of the loci encoding seed storage proteins. Funct Integr Genomics. 2010 Mar;10(1):111-22. doi: 10.1007/s10142-009-0135-x. Epub 2009 Aug 26. PubMed PMID: 19707805.
Wanjugi H, Coleman-Derr D, Huo N, Kianian SF, Luo MC, Wu J, Anderson O, Gu YQ. Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat. Genome. 2009 Jun;52(6):576-87. doi: 10.1139/g09-033. PubMed PMID: 19483776.
Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature. 2008 Nov 6;456(7218):125-9. doi: 10.1038/nature07324. Epub 2008 Sep 24. PubMed PMID: 18815594; PubMed Central PMCID: PMC2877514.
Bortiri E, Coleman-Derr D, Lazo GR, Anderson OD, Gu YQ. The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes. BMC Res Notes. 2008 Jul 31;1:61. doi: 10.1186/1756-0500-1-61. PubMed PMID: 18710514; PubMed Central PMCID: PMC2527572.
Huo N, Lazo GR, Vogel JP, You FM, Ma Y, Hayden DM, Coleman-Derr D, Hill TA, Dvorak J, Anderson OD, Luo MC, Gu YQ. The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences. Funct Integr Genomics. 2008 May;8(2):135-47. Epub 2007 Nov 6. PubMed PMID: 17985162.
Gao S, Gu YQ, Wu J, Coleman-Derr D, Huo N, Crossman C, Jia J, Zuo Q, Ren Z, Anderson OD, Kong X. Rapid evolution and complex structural organization in genomic regions harboring multiple prolamin genes in the polyploid wheat genome. Plant Mol Biol. 2007 Sep;65(1-2):189-203. Epub 2007 Jul 16. PubMed PMID: 17629796.
Zhang S, Gu YQ, Singh J, Coleman-Derr D, Brar DS, Jiang N, Lemaux PG. New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification. Plant Mol Biol. 2007 Jul;64(5):589-600. Epub 2007 May 30. PubMed PMID: 17534720.
Huo N, Gu YQ, Lazo GR, Vogel JP, Coleman-Derr D, Luo MC, Thilmony R, Garvin DF, Anderson OD. Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome. 2006 Sep;49(9):1099-108. PubMed PMID: 17110990.
Gu YQ, Salse J, Coleman-Derr D, Dupin A, Crossman C, Lazo GR, Huo N, Belcram H, Ravel C, Charmet G, Charles M, Anderson OD, Chalhoub B. Types and rates of sequence evolution at the high-molecular-weight glutenin locus in hexaploid wheat and its ancestral genomes. Genetics. 2006 Nov;174(3):1493-504. Epub 2006 Oct 8. PubMed PMID: 17028342; PubMed Central PMCID: PMC1667099.
Vogel JP, Gu YQ, Twigg P, Lazo GR, Laudencia-Chingcuanco D, Hayden DM, Donze TJ, Vivian LA, Stamova B, Coleman-Derr D. EST sequencing and phylogenetic analysis of the model grass Brachypodium distachyon. Theor Appl Genet. 2006 Jul;113(2):186-95. Epub 2006 May 18. PubMed PMID: 16791686.
Lazo GR, Lui N, Gu YQ, Kong X, Coleman-Derr D, Anderson OD. Hybsweeper: a resource for detecting high-density plate gridding coordinates. Biotechniques. 2005 Sep;39(3):320, 322, 324. PubMed PMID: 16206904.
Gu YQ, Coleman-Derr D, Kong X, Anderson OD. Rapid genome evolution revealed by comparative sequence analysis of orthologous regions from four triticeae genomes. Plant Physiol. 2004 May;135(1):459-70. Epub 2004 Apr 30. PubMed PMID: 15122014; PubMed Central PMCID: PMC429398.
Gu YQ, Crossman C, Kong X, Luo M, You FM, Coleman-Derr D, Dubcovsky J, Anderson OD. Genomic organization of the complex alpha-gliadin gene loci in wheat. Theor Appl Genet. 2004 Aug;109(3):648-57. Epub 2004 Apr 22. PubMed PMID: 15103408.
Lab photo 2016
