Jeffrey L Bennetzen

University of Georgia, Атина, Georgia, United States

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Publications (200)1606.18 Total impact

  • Hao Wang, Katrien M Devos, Jeffrey L Bennetzen
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    ABSTRACT: Numerous instances of presence/absence variations for introns have been documented in eukaryotes, and some cases of recurrent loss of the same intron have been suggested. However, there has been no comprehensive or phylogenetically deep analysis of recurrent intron loss. Of 883 cases of intron presence/absence variation that we detected in five sequenced grass genomes, 93 were confirmed as recurrent losses and the rest could be explained by single losses (652) or single gains (118). No case of recurrent intron gain was observed. Deep phylogenetic analysis often indicated that apparent intron gains were actually numerous independent losses of the same intron. Recurrent loss exhibited extreme non-randomness, in that some introns were removed independently in many lineages. The two larger genomes, maize and sorghum, were found to have a higher rate of both recurrent loss and overall loss and/or gain than foxtail millet, rice or Brachypodium. Adjacent introns and small introns were found to be preferentially lost. Intron loss genes exhibited a high frequency of germ line or early embryogenesis expression. In addition, flanking exon A+T-richness and intron TG/CG ratios were higher in retained introns. This last result suggests that epigenetic status, as evidenced by a loss of methylated CG dinucleotides, may play a role in the process of intron loss. This study provides the first comprehensive analysis of recurrent intron loss, makes a series of novel findings on the patterns of recurrent intron loss during the evolution of the grass family, and provides insight into the molecular mechanism(s) underlying intron loss.
    PLoS Genetics 12/2014; 10(12):e1004843. · 8.52 Impact Factor
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    ABSTRACT: Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.
    Proceedings of the National Academy of Sciences 11/2014; 111:E4954-E4962. · 9.81 Impact Factor
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    ABSTRACT: Plants from the Zingiberaceae family are a key source of spices and herbal medicines. Species identification within this group is critical in the search for known and possibly novel bioactive compounds. To facilitate precise characterization of this group, we have sequenced chloroplast genomes from species representing five major groups within Zingiberaceae. Generally, the structure of these genomes is similar to the basal angiosperm excepting an expansion of 3 kb associated with the inverted repeat A region. Portions of this expansion appear to be shared across the entire Zingiberales order, which includes gingers and bananas. We used whole plastome alignment information to develop DNA barcodes that would maximize the ability to differentiate species within the Zingiberaceae. Our computation pipeline identified regions of high variability that were flanked by highly conserved regions used for primer design. This approach yielded hitherto unexploited regions of variability. These theoretically optimal barcodes were tested on a range of species throughout the family and were found to amplify and differentiate genera and, in some cases, species. Still, though these barcodes were specifically optimized for the Zingiberaceae, our data support the emerging consensus that whole plastome sequences are needed for robust species identification and phylogenetics within this family. Copyright: ß 2014 Vaughn et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability: The authors confirm that all data underlying the findings are fully available without restriction. The information available from NCBI. The raw DNA sequence reads for the project are available with the bioproject ID PRJNA2536794 and the Zingiber officinale plastome sequence and annotation are available at NCBI accession no KM213122./0809/38). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist.
    PLoS ONE 10/2014; · 3.53 Impact Factor
  • Justin N Vaughn, Jeffrey L Bennetzen
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    ABSTRACT: The insertion of DNA into a genome can result in the duplication and dispersal of functional sequences through the genome. In addition, a deeper understanding of insertion mechanisms will inform methods of genetic engineering and plant transformation. Exploiting structural variations in numerous rice accessions, we have inferred and analyzed intermediate length (10-1,000 bp) insertions in plants. Insertions in this size class were found to be approximately equal in frequency to deletions, and compound insertion-deletions comprised only 0.1% of all events. Our findings indicate that, as observed in humans, tandem or partially tandem duplications are the dominant form of insertion (48%), although short duplications from ectopic donors account for a sizable fraction of insertions in rice (38%). Many nontandem duplications contain insertions from nearby DNA (within 200 bp) and can contain multiple donor sources-some distant-in single events. Although replication slippage is a plausible explanation for tandem duplications, the end homology required in such a model is most often absent and rarely is >5 bp. However, end homology is commonly longer than expected by chance. Such findings lead us to favor a model of patch-mediated double-strand-break creation followed by nonhomologous end-joining. Additionally, a striking bias toward 31-bp partially tandem duplications suggests that errors in nucleotide excision repair may be resolved via a similar, but distinct, pathway. In summary, the analysis of recent insertions in rice suggests multiple underappreciated causes of structural variation in eukaryotes.
    Proceedings of the National Academy of Sciences 04/2014; · 9.81 Impact Factor
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    ABSTRACT: Gene expression is a complex process, requiring precise spatial and temporal regulation of transcription factor activity; however, modifications of individual cis- and trans-acting modules can be molded by natural selection to create a sizeable number of novel phenotypes. Results from decades of research indicate that developmental and phenotypic divergence among eukaryotic organisms is driven primarily by variation in levels of gene expression that are dictated by mutations either in structural or regulatory regions of genes. The relative contributions and interplay of cis- and trans-acting regulatory factors to this evolutionary process, however, remain poorly understood. Analysis of 8 genes in the Bz1-Sh1 interval of maize indicates significant allele-specific expression biases in at least one tissue for all genes, ranging from 1.3-fold to 36-fold. All detected effects were cis-regulatory in nature, although genetic background may also influence the level of expression bias and tissue specificity for some allelic combinations. Most allelic pairs exhibited the same direction and approximate intensity of bias across all four tissues; however, a subset of allelic pairs show alternating dominance across different tissue types or variation in the degree of bias in different tissues. In addition, the genes showing the most striking levels of allelic bias co-localize with a previously described recombination hotspot in this region, suggesting a naturally occurring genetic mechanism for creating regulatory variability for a subset of plant genes that may ultimately lead to evolutionary diversification.This article is protected by copyright. All rights reserved.
    The Plant Journal 04/2014; · 6.58 Impact Factor
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    ABSTRACT: Date palm (Phoenix dactylifera) has been cultivated since ancient times, but little is known about its genetic diversity and population structure. Examination of 80 date palm accessions grown in the United Arab Emirates, including a collection of varieties from around the world, using 21 microsatellite markers, indicated extensive genetic diversity, with many accessions heterozygous for most markers. The average number of alleles per locus (19), expected heterozygosity (0.7), observed heterozygosity (0.25) and fixation indices (Fst = 0.6, Rst = 0.72) demonstrated significant population structure. Analysis with a model-based Baysian method, STRUCTURE 2.4.1, indicated that the 80 accessions could be broadly divided into nine groups. Independent samples of genotypes with the same name, collected from different experimental stations, usually clustered together. The study was enriched for germplasm from the United Arab Emirates (UAE), and one STRUCTURE-derived grouping consisted mainly of UAE accessions. In a few other clusters, several genotypes from the UAE, Iraq and Oman grouped together. Two clusters included accessions from both North Africa and the Middle East. Many accessions in the STRUCTURE-derived populations appeared to be genetic admixtures. The results indicated a broad dissemination of related germplasms across date-palm growing regions of the world, with very few alleles that still correlate with particular regional germplasms.
    Tropical Plant Biology 03/2014; 7(1):31.
  • Jeffrey L Bennetzen, Hao Wang
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    ABSTRACT: Transposable elements (TEs) are the key players in generating genomic novelty by a combination of the chromosome rearrangements they cause and the genes that come under their regulatory sway. Genome size, gene content, gene order, centromere function, and numerous other aspects of nuclear biology are driven by TE activity. Although the origins and attitudes of TEs have the hallmarks of selfish DNA, there are numerous cases where TE components have been co-opted by the host to create new genes or modify gene regulation. In particular, epigenetic regulation has been transformed from a process to silence invading TEs and viruses into a key strategy for regulating plant genes. Most, perhaps all, of this epigenetic regulation is derived from TE insertions near genes or TE-encoded factors that act in trans. Enormous pools of genome data and new technologies for reverse genetics will lead to a powerful new era of TE analysis in plants. Expected final online publication date for the Annual Review of Plant Biology Volume 65 is April 29, 2014. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.
    Annual Review of Plant Biology 02/2014; · 18.71 Impact Factor
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    ABSTRACT: Caldicellulosiruptor bescii is an anaerobic thermophilic bacterium of special interest for use in the consolidated bioprocessing of plant biomass to biofuels. In the course of experiments to engineer pyruvate metabolism in C. bescii, we isolated a mutant of C. bescii that contained an insertion in the L-lactate dehydrogenase gene (ldh). PCR amplification and sequencing of the ldh gene from this mutant revealed a 1,609-bp insertion that contained a single open reading frame of 479 amino acids (1,440 bp) annotated as a hypothetical protein with unknown function. The ORF is flanked by an 8-base direct repeat sequence. Bioinformatic analysis indicated that this ORF is part of a novel transposable element, ISCbe4, which is only intact in the genus Caldicellulosiruptor, but has ancient relatives that are present in degraded (and previously unrecognized) forms across many bacterial and archaeal clades.
    Journal of Industrial Microbiology 10/2013; · 1.80 Impact Factor
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    ABSTRACT: Maize is one of the most important food crops and a key model for genetics and developmental biology. A genetically anchored and high-quality draft genome sequence of maize inbred B73 has been obtained to serve as a reference sequence. To facilitate evolutionary studies in maize and its close relatives, much like the OMAP (www.OMAP.org) BAC resource did for the rice community, we constructed BAC libraries for maize inbred lines Zheng58, Chang7-2 and Mo17 and maize wild relatives Zea mays ssp. parviglumis and Tripsacum dactyloides. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed BIBAC libraries for the maize inbred B73 and the sorghum land race Nengsi-1. The BAC/BIBAC vectors facilitate transfer of large intact DNA inserts from BAC clones to the BIBAC vector and functional complementation of large DNA fragments. These seven ZMAP BAC/BIBAC libraries have average insert sizes ranging from 92kb to 148kb, organellar DNA from 0.17% to 2.3%, empty vector rates between 0.35% and 5.56%, and genome equivalents of 4.7- to 8.4-fold. The usefulness of the Parviglumis and Tripsacum BAC libraries was demonstrated by mapping clones to the reference genome. Novel genes and alleles present in these ZMAP libraries can now be used for functional complementation studies and positional or homology-based cloning of genes for translational genomics.
    Genetics 09/2013; · 4.39 Impact Factor
  • C Vitte, M C Estep, J Leebens-Mack, J L Bennetzen
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    ABSTRACT: Background and AimsAlthough monocotyledonous plants comprise one of the two major groups of angiosperms and include >65 000 species, comprehensive genome analysis has been focused mainly on the Poaceae (grass) family. Due to this bias, most of the conclusions that have been drawn for monocot genome evolution are based on grasses. It is not known whether these conclusions apply to many other monocots.Methods To extend our understanding of genome evolution in the monocots, Asparagales genomic sequence data were acquired and the structural properties of asparagus and onion genomes were analysed. Specifically, several available onion and asparagus bacterial artificial chromosomes (BACs) with contig sizes >35 kb were annotated and analysed, with a particular focus on the characterization of long terminal repeat (LTR) retrotransposons.Key ResultsThe results reveal that LTR retrotransposons are the major components of the onion and garden asparagus genomes. These elements are mostly intact (i.e. with two LTRs), have mainly inserted within the past 6 million years and are piled up into nested structures. Analysis of shotgun genomic sequence data and the observation of two copies for some transposable elements (TEs) in annotated BACs indicates that some families have become particularly abundant, as high as 4-5 % (asparagus) or 3-4 % (onion) of the genome for the most abundant families, as also seen in large grass genomes such as wheat and maize.Conclusions Although previous annotations of contiguous genomic sequences have suggested that LTR retrotransposons were highly fragmented in these two Asparagales genomes, the results presented here show that this was largely due to the methodology used. In contrast, this current work indicates an ensemble of genomic features similar to those observed in the Poaceae.
    Annals of Botany 07/2013; · 3.45 Impact Factor
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    Qihui Zhu, Jeffrey L Bennetzen, Shavannor M Smith
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    ABSTRACT: Resistance Gene Homologues (RGHs) were isolated from the switchgrass variety Alamo by a combination of PCR and expressed sequence tag (EST) database mining. Fifty-eight RGHs were isolated by PCR and 295 RGHs were identified in 424,545 switchgrass ESTs. Four NBS-LRR RGHs were selected to investigate RGH haplotypic diversity in seven switchgrass varieties chosen for their representation of a broad range of the switchgrass germplasm. Lowland and upland ecotypes were found to be less similar, even from nearby populations, than were more distant populations with similar growth environments. A majority (83.5%) of the variability in these four RGHs was found to be attributable to the within-population component. The difference in nucleotide diversity between and within populations was observed to be small, while this diversity is maintained to similar degrees at both population and ecotype levels. The results also revealed that the analyzed RGHs were under positive selection in the studied switchgrass accessions. Intragenic recombination was detected in switchgrass RGHs, thereby demonstrating an active genetic process that has the potential to generate new resistance genes with new specificities that might act against newly-arising pathogen races.
    G3-Genes Genomes Genetics 04/2013; · 1.79 Impact Factor
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    ABSTRACT: The microsatellite library was developed for Greenhouse Whitefly (Trialeurodes vaporariorum). The citation of this journal include all research studies published at this particular issue of the journal. Our study could be found at: tomato.biol.trinity.edu/manuscripts/13-2/mer-12-0390.pdf‎
    Molecular Ecology Resources 03/2013; 13(2):341-343. · 7.43 Impact Factor
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    ABSTRACT: Pearl millet is one of the most important subsistence crops grown in India and sub-Saharan Africa. In many cereal crops, reduced height is a key trait for enhancing yield, and dwarf mutants have been extensively used in breeding to reduce yield loss due to lodging under intense management. In pearl millet, the recessive dwarfing gene has been deployed widely in commercial germplasm grown in India, the United States, and Australia. Despite its importance, very little research has gone into determining the identity of the gene. We used comparative information, genetic mapping in two F populations representing a total of some 1500 progeny, and haplotype analysis of three tall and three dwarf inbred lines to delineate the region by two genetic markers that, in sorghum, define a region of 410 kb with 40 annotated genes. One of the sorghum genes annotated within this region is , which encodes a P-glycoprotein involved in auxin transport. This gene had previously been shown to underlie the economically important dwarf mutation in sorghum. The cosegregation of with the phenotype, its differential expression in the tall inbred ICMP 451 and the dwarf inbred Tift 23DB, and the similar phenotype of stacked lower internodes in the sorghum and pearl millet mutants suggest that is a likely candidate for .
    G3-Genes Genomes Genetics 03/2013; 3(3):563-72. · 1.79 Impact Factor
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    M C Estep, J D Debarry, J L Bennetzen
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    ABSTRACT: Sample sequence analysis was employed to investigate the repetitive DNAs that were most responsible for the evolved variation in genome content across seven panicoid grasses with >5-fold variation in genome size and different histories of polyploidy. In all cases, the most abundant repeats were LTR retrotransposons, but the particular families that had become dominant were found to be different in the Pennisetum, Saccharum, Sorghum and Zea lineages. One element family, Huck, has been very active in all of the studied species over the last few million years. This suggests the transmittal of an active or quiescent autonomous set of Huck elements to this lineage at the founding of the panicoids. Similarly, independent recent activity of Ji and Opie elements in Zea and of Leviathan elements in Sorghum and Saccharum species suggests that members of these families with exceptional activation potential were present in the genome(s) of the founders of these lineages. In a detailed analysis of the Zea lineage, the combined action of several families of LTR retrotransposons were observed to have approximately doubled the genome size of Zea luxurians relative to Zea mays and Zea diploperennis in just the last few million years. One of the LTR retrotransposon amplification bursts in Zea may have been initiated by polyploidy, but the great majority of transposable element activations are not. Instead, the results suggest random activation of a few or many LTR retrotransposons families in particular lineages over evolutionary time, with some families especially prone to future activation and hyper-amplification.Heredity (2013) 110, 194-204; doi:10.1038/hdy.2012.99.
    Heredity 02/2013; 110(2):194-204. · 4.11 Impact Factor
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    ABSTRACT: Phrynops geoffroanus is a freshwater turtle species, with a wide distribution in South America, living in many types of habitats, including polluted urban rivers. However, the lack of knowledge hinders broader approaches to various ecological and evolutionary aspects of this species. In this study eight polymorphic microsatellite markers were isolated and characterized in 48 individuals from two natural populations. In the Piracicaba river population, the number of alleles for the eight loci ranged from 4 to 15, whereas the observed and expected heterozygosities per locus varied from 0.29 to 0.87 and from 0.31 to 0.90, respectively. In Piracicamirim stream population, the number of alleles ranged from 4 to 13, and the observed and expected heterozygosities per locus varied from 0.46 to 0.75 and from 0.53 to 0.88, respectively. These microsatellites provide efficient genetic markers for population structure, species relationships and phylogeography studies.
    Molecular Ecology Resources 01/2013; · 7.43 Impact Factor
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    Hao Wang, Jeffrey L Bennetzen
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    ABSTRACT: Although centromere function is highly conserved in eukaryotes, centromere sequences are highly variable. Only a few centromeres have been sequenced in higher eukaryotes because of their repetitive nature, thus hindering study of their structure and evolution. Conserved single-copy sequences in pericentromeres (CSCPs) of sorghum and maize were found to be diagnostic characteristics of adjacent centromeres. By analyzing comparative map data and CSCP sequences of sorghum, maize, and rice, the major evolutionary events related to centromere dynamics were discovered for the maize lineage after its divergence from a common ancestor with sorghum. (i) Remnants of ancient CSCP regions were found for the 10 lost ancestral centromeres, indicating that two ancient homeologous chromosome pairs did not contribute any centromeres to the current maize genome, whereas two other pairs contributed both of their centromeres. (ii) Five cases of long-distance, intrachromosome movement of CSCPs were detected in the retained centromeres, with inversion the major process involved. (iii) The 12 major chromosomal rearrangements that led to maize chromosome number reduction from 20 to 10 were uncovered. (iv) In addition to whole chromosome insertion near (but not always into) other centromeres, translocation and fusion were found to be important mechanisms underlying grass chromosome number reduction. (v) Comparison of chromosome structures confirms the polyploid event that led to the tetraploid ancestor of modern maize.
    Proceedings of the National Academy of Sciences 11/2012; · 9.81 Impact Factor
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    ABSTRACT: The draft genome of pear (Pyrus bretschneideri) using a combination of BAC-by-BAC and next generation sequencing is reported. A 512.0 Mb sequence corresponding to 97.1% of the estimated genome size of this highly heterozygous species is assembled with 194x coverage. High-density genetic maps comprising of 2,005 SNP markers anchored 75.5% of the sequence to all 17 chromosomes. The pear genome encodes 42,812 protein-coding genes, and of these, ~28.5% encode multiple isoforms. High quality of the assembly and annotation is assessed and confirmed using Sanger-derived BAC sequences along with transcriptome sequences of different tissues. Repetitive sequences of 271.9 Mb in length, accounting for 53.1% of the pear genome, are identified. Simulation of eudicots to the ancestor of Rosaceae has re-constructed nine ancestral chromosomes. Pear and apple have diverged from each other ~5.4 to 21.5 MYA, and a recent whole-genome duplication (WGD) event must have occurred 30-45 MYA prior to their divergence, but following divergence from strawberry. When compared with the apple genome sequence, size differences between apple and pear genomes are confirmed mainly due to presence of repetitive sequences predominantly contributed by transposable elements (TEs), while genic regions are similar in both species. Genes critical for self-incompatibility, lignified stone cells (a unique feature of pear fruit), sorbitol metabolism and volatile compounds of fruit have also been identified. Multiple candidate SFB genes appear as tandem repeats in the S-locus region of pear; while, lignin synthesis-related gene family expansion and highly expressed gene families of HCT, C3'H, and CCOMT contribute to high accumulation of both G-lignin and S-lignin. Expansion of S6PDH, SDH, and SOT along with evolutionary relationships of pear and apple have demonstrated their divergence from a common ancestor. Moreover, α-linolenic acid metabolism is a key pathway for aroma in pear fruit.
    Genome Research 11/2012; · 14.40 Impact Factor
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    ABSTRACT: Tef (Eragrostis tef) is a major cereal crop in Ethiopia. Lodging is the primary constraint to increasing productivity in this allotetraploid species, accounting for losses of ~15-45% in yield each year. As a first step toward identifying semi-dwarf varieties that might have improved lodging resistance, an ~6X fosmid library was constructed and used to identify both homoeologues of the dw3 semi-dwarfing gene of Sorghum bicolor. An EMS mutagenized population, consisting of ~21,210 tef plants, was planted and leaf materials were collected into 23 superpools. Two dwarfing candidate genes, homoeologues of dw3 of sorghum and rht1 of wheat, were sequenced directly from each superpool with 454 technology, and 120 candidate mutations were identified. Out of ten candidates tested, six independent mutations were validated by Sanger sequencing, including two predicted detrimental mutations in both dw3 homoeologues with a potential to improve lodging resistance in tef through further breeding. This study demonstrates that high throughput sequencing can identify potentially valuable mutations in under-studied plant species like tef, and has provided mutant lines that can now be combined and tested in breeding programs for improved lodging resistance.
    Genetics 08/2012; · 4.39 Impact Factor

Publication Stats

14k Citations
1,606.18 Total Impact Points

Institutions

  • 2004–2014
    • University of Georgia
      • Department of Genetics
      Атина, Georgia, United States
    • University of Missouri - St. Louis
      • Department of Biology
      Saint Louis, MI, United States
  • 2004–2012
    • Rutgers, The State University of New Jersey
      New Brunswick, New Jersey, United States
  • 2011
    • University of California, Berkeley
      • Department of Plant and Microbial Biology
      Berkeley, MO, United States
  • 1984–2011
    • Purdue University
      • • Department of Horticulture and Landscape Architecture
      • • Department of Biological Sciences
      West Lafayette, Indiana, United States
  • 2008–2010
    • The University of Arizona
      • School of Plant Sciences
      Tucson, AZ, United States
    • Maseno University
      Winam, Kisumu, Kenya
    • University of California, Riverside
      • Department of Botany and Plant Sciences
      Riverside, California, United States
  • 2009
    • Oklahoma State University - Stillwater
      • Department of Botany
      Stillwater, OK, United States
  • 1987–2009
    • Iowa State University
      Ames, Iowa, United States
  • 2001–2007
    • John Innes Centre
      • Department of Crop Genetics
      Norwich, England, United Kingdom
    • University of California, Davis
      • Department of Plant Sciences
      Davis, CA, United States
  • 2006
    • Biomedical Research Institute, Rockville
      Maryland, United States
  • 2002
    • University of Hyderabad
      • Department of Plant Sciences
      Hyderābād, State of Andhra Pradesh, India
  • 1999–2001
    • Scottish Crop Research Institute
      Aberdeen, Scotland, United Kingdom
  • 1996
    • Missouri State University
      Springfield, Missouri, United States
  • 1993–1995
    • Kansas State University
      • Department of Plant Pathology
      Manhattan, KS, United States