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Della Coletta R, Fernandes SB, Monnahan PJ, Mikel MA, Bohn MO, Lipka AE, Hirsch CN. Importance of genetic architecture in marker selection decisions for genomic prediction. Theor Appl Genet 2023; 136:220. [PMID: 37819415 DOI: 10.1007/s00122-023-04469-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
KEY MESSAGE We demonstrate potential for improved multi-environment genomic prediction accuracy using structural variant markers. However, the degree of observed improvement is highly dependent on the genetic architecture of the trait. Breeders commonly use genetic markers to predict the performance of untested individuals as a way to improve the efficiency of breeding programs. These genomic prediction models have almost exclusively used single nucleotide polymorphisms (SNPs) as their source of genetic information, even though other types of markers exist, such as structural variants (SVs). Given that SVs are associated with environmental adaptation and not all of them are in linkage disequilibrium to SNPs, SVs have the potential to bring additional information to multi-environment prediction models that are not captured by SNPs alone. Here, we evaluated different marker types (SNPs and/or SVs) on prediction accuracy across a range of genetic architectures for simulated traits across multiple environments. Our results show that SVs can improve prediction accuracy, but it is highly dependent on the genetic architecture of the trait and the relative gain in accuracy is minimal. When SVs are the only causative variant type, 70% of the time SV predictors outperform SNP predictors. However, the improvement in accuracy in these instances is only 1.5% on average. Further simulations with predictors in varying degrees of LD with causative variants of different types (e.g., SNPs, SVs, SNPs and SVs) showed that prediction accuracy increased as linkage disequilibrium between causative variants and predictors increased regardless of the marker type. This study demonstrates that knowing the genetic architecture of a trait in deciding what markers to use in large-scale genomic prediction modeling in a breeding program is more important than what types of markers to use.
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Affiliation(s)
- Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Samuel B Fernandes
- Department of Crop, Soil and Environmental Sciences at University of Arkansas, Fayetteville, AR, 72701, USA
| | - Patrick J Monnahan
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Mark A Mikel
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Martin O Bohn
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
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Della Coletta R, Liese SE, Fernandes SB, Mikel MA, Bohn MO, Lipka AE, Hirsch CN. Linking genetic and environmental factors through marker effect networks to understand trait plasticity. Genetics 2023; 224:iyad103. [PMID: 37246567 DOI: 10.1093/genetics/iyad103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/19/2023] [Accepted: 05/24/2023] [Indexed: 05/30/2023] Open
Abstract
Understanding how plants adapt to specific environmental changes and identifying genetic markers associated with phenotypic plasticity can help breeders develop plant varieties adapted to a rapidly changing climate. Here, we propose the use of marker effect networks as a novel method to identify markers associated with environmental adaptability. These marker effect networks are built by adapting commonly used software for building gene coexpression networks with marker effects across growth environments as the input data into the networks. To demonstrate the utility of these networks, we built networks from the marker effects of ∼2,000 nonredundant markers from 400 maize hybrids across 9 environments. We demonstrate that networks can be generated using this approach, and that the markers that are covarying are rarely in linkage disequilibrium, thus representing higher biological relevance. Multiple covarying marker modules associated with different weather factors throughout the growing season were identified within the marker effect networks. Finally, a factorial test of analysis parameters demonstrated that marker effect networks are relatively robust to these options, with high overlap in modules associated with the same weather factors across analysis parameters. This novel application of network analysis provides unique insights into phenotypic plasticity and specific environmental factors that modulate the genome.
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Affiliation(s)
- Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Sharon E Liese
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Samuel B Fernandes
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Mark A Mikel
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Martin O Bohn
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
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Mehl KM, Mikel MA, Bradley CA. Evaluation of Corn Germplasm Accessions for Resistance to Clavibacter nebraskensis, Causal Agent of Goss's Bacterial Wilt and Leaf Blight. Plant Dis 2021; 105:156-163. [PMID: 33118875 DOI: 10.1094/pdis-11-19-2394-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Goss's bacterial wilt and leaf blight of corn (Zea mays), caused by Clavibacter nebraskensis, is a reemerging disease in the Midwestern United States. From 2011 to 2013, field studies and a greenhouse study were conducted to assess the University of Illinois maize inbred collection for putative sources of resistance to Goss's bacterial wilt and leaf blight. This inbred collection consisted of over 2,000 diverse inbred corn lines that have been collected from all over the world. An initial field screen of over 1,000 inbred lines from the collection was conducted in Urbana, IL in 2011. These lines were inoculated with a C. nebraskensis cell suspension and rated for Goss's bacterial wilt and leaf blight severity using a 1-to-9 scale, with a score of 1 being most resistant. Means for Goss's bacterial wilt and leaf blight ratings ranged from 1 to 8.5. The initial screen identified over 150 lines that had high levels of resistance (severity score of ≤2.5). In total, 177 lines were used in the second stage of field screening. In the second stage, average Goss's bacterial wilt and leaf blight severity ranged from 1.1 to 7.4. Nine lines with high levels of resistance in 2011 and 2012 were advanced to the third stage of field screening. The mean Goss's bacterial wilt and leaf blight severity rating of the resistant lines in the last stage was 1.9, while the susceptible check had a mean score of 6.4. These nine lines were also used in the greenhouse to assess whether resistance varied based on inoculating roots, stems, or leaves. Disease severity was significantly (P ≤ 0.05) less when roots were inoculated compared with both leaf and stem inoculations, which were not significantly different from each other. Lines having high levels of field resistance were also found to be resistant in greenhouse screening regardless of inoculation method. Clustering of pedigree distance of the 34 resistant lines (severity score of ≤2.5) with known pedigree information found that 21 clustered with the Lancaster heterotic family, 4 were related to the Iowa Stiff Stalk Synthetic family, and 9 did not cluster with an identifiable heterotic family. These results show that the Lancaster family is an excellent source of Goss's wilt resistance, and that fewer sources of resistance were found in other families. The most resistant lines identified from this research are potential sources of resistance to Goss's bacterial wilt and leaf blight, and their lineage can be used in corn breeding programs to develop resistant hybrids.
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Affiliation(s)
- Kelsey M Mehl
- Department of Plant Pathology, University of Kentucky Research and Education Center, Princeton, KY 42445, U.S.A
| | - Mark A Mikel
- Roy J. Carver Biotechnology Center and Department of Crop Sciences, University of Illinois, Urbana, IL 61801, U.S.A
| | - Carl A Bradley
- Department of Plant Pathology, University of Kentucky Research and Education Center, Princeton, KY 42445, U.S.A
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Gage JL, Vaillancourt B, Hamilton JP, Manrique-Carpintero NC, Gustafson TJ, Barry K, Lipzen A, Tracy WF, Mikel MA, Kaeppler SM, Buell CR, de Leon N. Multiple Maize Reference Genomes Impact the Identification of Variants by Genome-Wide Association Study in a Diverse Inbred Panel. Plant Genome 2019; 12:180069. [PMID: 31290926 DOI: 10.3835/plantgenome2018.09.0069] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Use of a single reference genome for genome-wide association studies (GWAS) limits the gene space represented to that of a single accession. This limitation can complicate identification and characterization of genes located within presence-absence variations (PAVs). In this study, we present the draft de novo genome assembly of 'PHJ89', an 'Oh43'-type inbred line of maize ( L.). From three separate reference genome assemblies ('B73', 'PH207', and PHJ89) that represent the predominant germplasm groups of maize, we generated three separate whole-seedling gene expression profiles and single nucleotide polymorphism (SNP) matrices from a panel of 942 diverse inbred lines. We identified 34,447 (B73), 39,672 (PH207), and 37,436 (PHJ89) transcripts that are not present in the respective reference genome assemblies. Genome-wide association studies were conducted in the 942 inbred panel with both the SNP and expression data values to map (SCMV) resistance. Highlighting the impact of alternative reference genomes in gene discovery, the GWAS results for SCMV resistance with expression values as a surrogate measure of PAV resulted in robust detection of the physical location of a known resistance gene when the B73 reference that contains the gene was used, but not the PH207 reference. This study provides the valuable resource of the Oh43-type PHJ89 genome assembly as well as SNP and expression data for 942 individuals generated from three different reference genomes.
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Gage JL, Vaillancourt B, Hamilton JP, Manrique-Carpintero NC, Gustafson TJ, Barry K, Lipzen A, Tracy WF, Mikel MA, Kaeppler SM, Buell CR, de Leon N. Multiple Maize Reference Genomes Impact the Identification of Variants by Genome-Wide Association Study in a Diverse Inbred Panel. Plant Genome 2019; 12. [PMID: 31290926 DOI: 10.3835/plantgenome2018.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Use of a single reference genome for genome-wide association studies (GWAS) limits the gene space represented to that of a single accession. This limitation can complicate identification and characterization of genes located within presence-absence variations (PAVs). In this study, we present the draft de novo genome assembly of 'PHJ89', an 'Oh43'-type inbred line of maize ( L.). From three separate reference genome assemblies ('B73', 'PH207', and PHJ89) that represent the predominant germplasm groups of maize, we generated three separate whole-seedling gene expression profiles and single nucleotide polymorphism (SNP) matrices from a panel of 942 diverse inbred lines. We identified 34,447 (B73), 39,672 (PH207), and 37,436 (PHJ89) transcripts that are not present in the respective reference genome assemblies. Genome-wide association studies were conducted in the 942 inbred panel with both the SNP and expression data values to map (SCMV) resistance. Highlighting the impact of alternative reference genomes in gene discovery, the GWAS results for SCMV resistance with expression values as a surrogate measure of PAV resulted in robust detection of the physical location of a known resistance gene when the B73 reference that contains the gene was used, but not the PH207 reference. This study provides the valuable resource of the Oh43-type PHJ89 genome assembly as well as SNP and expression data for 942 individuals generated from three different reference genomes.
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Avni R, Nave M, Barad O, Baruch K, Twardziok SO, Gundlach H, Hale I, Mascher M, Spannagl M, Wiebe K, Jordan KW, Golan G, Deek J, Ben-Zvi B, Ben-Zvi G, Himmelbach A, MacLachlan RP, Sharpe AG, Fritz A, Ben-David R, Budak H, Fahima T, Korol A, Faris JD, Hernandez A, Mikel MA, Levy AA, Steffenson B, Maccaferri M, Tuberosa R, Cattivelli L, Faccioli P, Ceriotti A, Kashkush K, Pourkheirandish M, Komatsuda T, Eilam T, Sela H, Sharon A, Ohad N, Chamovitz DA, Mayer KFX, Stein N, Ronen G, Peleg Z, Pozniak CJ, Akhunov ED, Distelfeld A. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science 2018; 357:93-97. [PMID: 28684525 DOI: 10.1126/science.aan0032] [Citation(s) in RCA: 465] [Impact Index Per Article: 77.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/08/2017] [Indexed: 01/07/2023]
Abstract
Wheat (Triticum spp.) is one of the founder crops that likely drove the Neolithic transition to sedentary agrarian societies in the Fertile Crescent more than 10,000 years ago. Identifying genetic modifications underlying wheat's domestication requires knowledge about the genome of its allo-tetraploid progenitor, wild emmer (T. turgidum ssp. dicoccoides). We report a 10.1-gigabase assembly of the 14 chromosomes of wild tetraploid wheat, as well as analyses of gene content, genome architecture, and genetic diversity. With this fully assembled polyploid wheat genome, we identified the causal mutations in Brittle Rachis 1 (TtBtr1) genes controlling shattering, a key domestication trait. A study of genomic diversity among wild and domesticated accessions revealed genomic regions bearing the signature of selection under domestication. This reference assembly will serve as a resource for accelerating the genome-assisted improvement of modern wheat varieties.
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Affiliation(s)
- Raz Avni
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Moran Nave
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | | | | | - Sven O Twardziok
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Neuherberg, Germany
| | - Heidrun Gundlach
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Neuherberg, Germany
| | - Iago Hale
- University of New Hampshire, Durham, NH, USA
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, Germany. .,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Manuel Spannagl
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Neuherberg, Germany
| | | | | | - Guy Golan
- The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jasline Deek
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Batsheva Ben-Zvi
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | | | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, Germany
| | | | - Andrew G Sharpe
- University of Saskatchewan, Saskatoon, Canada.,Global Institute for Food Security, Saskatoon, SK, Canada
| | | | - Roi Ben-David
- Agricultural Research Organization (ARO), Bet Dagan, Israel
| | | | | | | | - Justin D Faris
- U.S. Department of Agriculture (USDA)-Agricultural Research Service, Fargo, ND, USA
| | | | | | | | | | | | | | - Luigi Cattivelli
- Council of Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Primetta Faccioli
- Council of Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Aldo Ceriotti
- CNR-National Research Council, Institute of Agricultural Biology and Biotechnology, Milano, Italy
| | | | | | - Takao Komatsuda
- National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Tamar Eilam
- The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, Israel
| | - Hanan Sela
- The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.,The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, Israel
| | - Nir Ohad
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Daniel A Chamovitz
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Klaus F X Mayer
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Neuherberg, Germany.,School of Life Sciences Weihenstephan, Technical University of Munich, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, Germany
| | | | - Zvi Peleg
- The Hebrew University of Jerusalem, Rehovot, Israel
| | | | | | - Assaf Distelfeld
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.,The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, Israel
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Doğramaci M, Anderson JV, Chao WS, Horvath DP, Hernandez AG, Mikel MA, Foley ME. Foliar Glyphosate Treatment Alters Transcript and Hormone Profiles in Crown Buds of Leafy Spurge and Induces Dwarfed and Bushy Phenotypes throughout its Perennial Lifecycle. Plant Genome 2017; 10. [PMID: 29293817 DOI: 10.3835/plantgenome2016.09.0098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 04/25/2017] [Indexed: 06/07/2023]
Abstract
Leafy spurge ( L.) is an invasive weed of North America and its perennial nature attributed to underground adventitious buds (UABs) that undergo seasonal cycles of para-, endo-, and ecodormancy. Recommended rates of glyphosate (∼1 kg ha) destroy aboveground shoots but plants still regenerate vegetatively; therefore, it is considered glyphosate-tolerant. However, foliar application of glyphosate at higher rates (2.2-6.7 kg ha) causes sublethal effects that induce UABs to produce stunted, bushy phenotypes. We investigated the effects of glyphosate treatment (±2.24 kg ha) on vegetative growth, phytohormone, and transcript profiles in UABs under controlled environments during one simulated seasonal cycle. Because shoots derived from UABs of foliar glyphosate-treated plants produced stunted, bushy phenotypes, we could not directly determine if these UABs transitioned through seasonally induced endo- and ecodormancy. However, transcript abundance for leafy spurge dormancy marker genes and principal component analyses suggested that UABs of foliar glyphosate-treated plants transitioned through endo- and ecodormancy. Glyphosate treatment increased shikimate abundance in UABs 7 d after treatment; however, the abundance of shikimate gradually decreased as UABs transitioned through endo- and ecodormancy. The dissipation of shikimate over time suggests that glyphosate's target site was no longer affected, but these changes did not reverse the altered phenotypes observed from UABs of foliar glyphosate-treated leafy spurge. Transcript profiles further indicated that foliar glyphosate treatment significantly affected phytohormone biosynthesis and signaling, particularly auxin transport; gibberellic acid, abscisic acid and jasmonic acid biosynthesis; ethylene responses; and detoxification and cell cycle processes in UABs. These results correlated well with the available phytohormone profiles and altered phenotypes.
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Hirsch CN, Hirsch CD, Brohammer AB, Bowman MJ, Soifer I, Barad O, Shem-Tov D, Baruch K, Lu F, Hernandez AG, Fields CJ, Wright CL, Koehler K, Springer NM, Buckler E, Buell CR, de Leon N, Kaeppler SM, Childs KL, Mikel MA. Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. Plant Cell 2016; 28:2700-2714. [PMID: 27803309 PMCID: PMC5155341 DOI: 10.1105/tpc.16.00353] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 10/19/2016] [Accepted: 10/31/2016] [Indexed: 05/18/2023]
Abstract
Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison of these two assemblies revealed over 2500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools.
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Affiliation(s)
- Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Alex B Brohammer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Megan J Bowman
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Ilya Soifer
- Calico Labs, San Francisco, California 94080
| | | | | | | | - Fei Lu
- Instiute for Genome Diversity, Cornell University, Ithaca, New York 14850
| | - Alvaro G Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
| | - Christopher J Fields
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
| | - Chris L Wright
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
| | | | - Nathan M Springer
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Edward Buckler
- Instiute for Genome Diversity, Cornell University, Ithaca, New York 14850
- U.S. Department of Agriculture/Agricultural Research Services, Ithaca, New York 14850
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- DOE Great Lakes Bioenergy Research Center, East Lansing, Michigan 48824
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin 53706
- DOE Great Lakes Bioenergy Research Center, Madison, Wisconsin 53706
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin 53706
- DOE Great Lakes Bioenergy Research Center, Madison, Wisconsin 53706
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Center for Genomics-Enabled Plant Sciences, Michigan State University, East Lansing, Michigan 48824
| | - Mark A Mikel
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
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Doğramacı M, Foley ME, Horvath DP, Hernandez AG, Khetani RS, Fields CJ, Keating KM, Mikel MA, Anderson JV. Glyphosate's impact on vegetative growth in leafy spurge identifies molecular processes and hormone cross-talk associated with increased branching. BMC Genomics 2015; 16:395. [PMID: 25986459 PMCID: PMC4437557 DOI: 10.1186/s12864-015-1627-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 05/11/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Leafy spurge (Euphorbia esula) is a perennial weed that is considered glyphosate tolerant, which is partially attributed to escape through establishment of new vegetative shoots from an abundance of underground adventitious buds. Leafy spurge plants treated with sub-lethal concentrations of foliar-applied glyphosate produce new vegetative shoots with reduced main stem elongation and increased branching. Processes associated with the glyphosate-induced phenotype were determined by RNAseq using aerial shoots derived from crown buds of glyphosate-treated and -untreated plants. Comparison between transcript abundance and accumulation of shikimate or phytohormones (abscisic acid, auxin, cytokinins, and gibberellins) from these same samples was also done to reveal correlations. RESULTS Transcriptome assembly and analyses confirmed differential abundance among 12,918 transcripts (FDR ≤ 0.05) and highlighted numerous processes associated with shoot apical meristem maintenance and stem growth, which is consistent with the increased number of actively growing meristems in response to glyphosate. Foliar applied glyphosate increased shikimate abundance in crown buds prior to decapitation of aboveground shoots, which induces growth from these buds, indicating that 5-enolpyruvylshikimate 3-phosphate (EPSPS) the target site of glyphosate was inhibited. However, abundance of shikimate was similar in a subsequent generation of aerial shoots derived from crown buds of treated and untreated plants, suggesting EPSPS is no longer inhibited or abundance of shikimate initially observed in crown buds dissipated over time. Overall, auxins, gibberellins (precursors and catabolites of bioactive gibberellins), and cytokinins (precursors and bioactive cytokinins) were more abundant in the aboveground shoots derived from glyphosate-treated plants. CONCLUSION Based on the overall data, we propose that the glyphosate-induced phenotype resulted from complex interactions involving shoot apical meristem maintenance, hormone biosynthesis and signaling (auxin, cytokinins, gibberellins, and strigolactones), cellular transport, and detoxification mechanisms.
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Affiliation(s)
- Münevver Doğramacı
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - Michael E Foley
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - David P Horvath
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - Alvaro G Hernandez
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Radhika S Khetani
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Christopher J Fields
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Kathleen M Keating
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Mark A Mikel
- Department of Crop Sciences, 2608 Institute for Genomic Biology, and Roy J. Carver Biotechnology Center, University of Illinois, Urbana, IL, 61801, USA.
| | - James V Anderson
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
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10
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Doğramacı M, Foley ME, Horvath DP, Hernandez AG, Khetani RS, Fields CJ, Keating KM, Mikel MA, Anderson JV. Glyphosate's impact on vegetative growth in leafy spurge identifies molecular processes and hormone cross-talk associated with increased branching. BMC Genomics 2015. [PMID: 25986459 DOI: 10.1186/s12864‐015‐1627‐9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Leafy spurge (Euphorbia esula) is a perennial weed that is considered glyphosate tolerant, which is partially attributed to escape through establishment of new vegetative shoots from an abundance of underground adventitious buds. Leafy spurge plants treated with sub-lethal concentrations of foliar-applied glyphosate produce new vegetative shoots with reduced main stem elongation and increased branching. Processes associated with the glyphosate-induced phenotype were determined by RNAseq using aerial shoots derived from crown buds of glyphosate-treated and -untreated plants. Comparison between transcript abundance and accumulation of shikimate or phytohormones (abscisic acid, auxin, cytokinins, and gibberellins) from these same samples was also done to reveal correlations. RESULTS Transcriptome assembly and analyses confirmed differential abundance among 12,918 transcripts (FDR ≤ 0.05) and highlighted numerous processes associated with shoot apical meristem maintenance and stem growth, which is consistent with the increased number of actively growing meristems in response to glyphosate. Foliar applied glyphosate increased shikimate abundance in crown buds prior to decapitation of aboveground shoots, which induces growth from these buds, indicating that 5-enolpyruvylshikimate 3-phosphate (EPSPS) the target site of glyphosate was inhibited. However, abundance of shikimate was similar in a subsequent generation of aerial shoots derived from crown buds of treated and untreated plants, suggesting EPSPS is no longer inhibited or abundance of shikimate initially observed in crown buds dissipated over time. Overall, auxins, gibberellins (precursors and catabolites of bioactive gibberellins), and cytokinins (precursors and bioactive cytokinins) were more abundant in the aboveground shoots derived from glyphosate-treated plants. CONCLUSION Based on the overall data, we propose that the glyphosate-induced phenotype resulted from complex interactions involving shoot apical meristem maintenance, hormone biosynthesis and signaling (auxin, cytokinins, gibberellins, and strigolactones), cellular transport, and detoxification mechanisms.
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Affiliation(s)
- Münevver Doğramacı
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - Michael E Foley
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - David P Horvath
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - Alvaro G Hernandez
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Radhika S Khetani
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Christopher J Fields
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Kathleen M Keating
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Mark A Mikel
- Department of Crop Sciences, 2608 Institute for Genomic Biology, and Roy J. Carver Biotechnology Center, University of Illinois, Urbana, IL, 61801, USA.
| | - James V Anderson
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
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Dong Y, Kumar CG, Chia N, Kim PJ, Miller PA, Price ND, Cann IKO, Flynn TM, Sanford RA, Krapac IG, Locke RA, Hong PY, Tamaki H, Liu WT, Mackie RI, Hernandez AG, Wright CL, Mikel MA, Walker JL, Sivaguru M, Fried G, Yannarell AC, Fouke BW. Halomonas sulfidaeris-dominated microbial community inhabits a 1.8 km-deep subsurface Cambrian Sandstone reservoir. Environ Microbiol 2013; 16:1695-708. [PMID: 24238218 DOI: 10.1111/1462-2920.12325] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 10/31/2013] [Indexed: 01/12/2023]
Abstract
A low-diversity microbial community, dominated by the γ-proteobacterium Halomonas sulfidaeris, was detected in samples of warm saline formation porewater collected from the Cambrian Mt. Simon Sandstone in the Illinois Basin of the North American Midcontinent (1.8 km/5872 ft burial depth, 50°C, pH 8, 181 bars pressure). These highly porous and permeable quartz arenite sandstones are directly analogous to reservoirs around the world targeted for large-scale hydrocarbon extraction, as well as subsurface gas and carbon storage. A new downhole low-contamination subsurface sampling probe was used to collect in situ formation water samples for microbial environmental metagenomic analyses. Multiple lines of evidence suggest that this H. sulfidaeris-dominated subsurface microbial community is indigenous and not derived from drilling mud microbial contamination. Data to support this includes V1-V3 pyrosequencing of formation water and drilling mud, as well as comparison with previously published microbial analyses of drilling muds in other sites. Metabolic pathway reconstruction, constrained by the geology, geochemistry and present-day environmental conditions of the Mt. Simon Sandstone, implies that H. sulfidaeris-dominated subsurface microbial community may utilize iron and nitrogen metabolisms and extensively recycle indigenous nutrients and substrates. The presence of aromatic compound metabolic pathways suggests this microbial community can readily adapt to and survive subsurface hydrocarbon migration.
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Affiliation(s)
- Yiran Dong
- Energy Biosciences Institute, University of Illinois Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA; Institute for Genomic Biology, University of Illinois Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA; Department of Geology, University of Illinois Urbana-Champaign, 1301 W. Green Street, Urbana, IL, 61801, USA
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12
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Bushman BS, Larson SR, Mott IW, Cliften PF, Wang RRC, Chatterton NJ, Hernandez AG, Ali S, Kim RW, Thimmapuram J, Gong G, Liu L, Mikel MA. Development and annotation of perennial Triticeae ESTs and SSR markers. Genome 2008; 51:779-88. [DOI: 10.1139/g08-062] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Triticeae contains hundreds of species of both annual and perennial types. Although substantial genomic tools are available for annual Triticeae cereals such as wheat and barley, the perennial Triticeae lack sufficient genomic resources for genetic mapping or diversity research. To increase the amount of sequence information available in the perennial Triticeae, three expressed sequence tag (EST) libraries were developed and annotated for Pseudoroegneria spicata , a mixture of both Elymus wawawaiensis and E. lanceolatus , and a Leymus cinereus × L. triticoides interspecific hybrid. The ESTs were combined into unigene sets of 8 780 unigenes for P. spicata, 11 281 unigenes for Leymus, and 7 212 unigenes for Elymus. Unigenes were annotated based on putative orthology to genes from rice, wheat, barley, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Simple sequence repeat (SSR) markers were developed, tested for amplification and polymorphism, and aligned to the rice genome. Leymus EST markers homologous to rice chromosome 2 genes were syntenous on Leymus homeologous groups 6a and 6b (previously 1b), demonstrating promise for in silico comparative mapping. All ESTs and SSR markers are available on an EST information management and annotation database ( http://titan.biotec.uiuc.edu/triticeae/ ).
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Affiliation(s)
- B. Shaun Bushman
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Steve R. Larson
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ivan W. Mott
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paul F. Cliften
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Richard R.-C. Wang
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - N. Jerry Chatterton
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alvaro G. Hernandez
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shahjahan Ali
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ryan W. Kim
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jyothi Thimmapuram
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - George Gong
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lei Liu
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mark A. Mikel
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Lokko Y, Anderson JV, Rudd S, Raji A, Horvath D, Mikel MA, Kim R, Liu L, Hernandez A, Dixon AGO, Ingelbrecht IL. Characterization of an 18,166 EST dataset for cassava (Manihot esculenta Crantz) enriched for drought-responsive genes. Plant Cell Rep 2007; 26:1605-18. [PMID: 17541599 DOI: 10.1007/s00299-007-0378-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2007] [Revised: 05/03/2007] [Accepted: 05/04/2007] [Indexed: 05/15/2023]
Abstract
Cassava (Manihot esculenta Crantz) is a staple food for over 600 million people in the tropics and subtropics and is increasingly used as an industrial crop for starch production. Cassava has a high growth rate under optimal conditions but also performs well in drought-prone areas and on marginal soils. To increase the tools for understanding and manipulating drought tolerance in cassava, we generated expressed sequence tags (ESTs) from normalized cDNA libraries prepared from dehydration-stressed and control well-watered tissues. Analysis of a total of 18,166 ESTs resulted in the identification of 8,577 unique gene clusters (5,383 singletons and 3,194 clusters). Functional categories could be assigned to 63% of the unigenes, while another approximately 11% were homologous to hypothetical genes with unclear functions. The remaining approximately 26% were not significantly homologous to sequences in public databases suggesting that some may be novel and putatively specific to cassava. The dehydration-stressed library uncovered numerous ESTs with recognized roles in drought-responses, including those that encode late-embryogenesis-abundant proteins thought to confer osmoprotective functions during water stress, transcription factors, heat-shock proteins as well as proteins involved in signal transduction and oxidative stress. The unigene clusters were screened for short tandem repeats for further development as microsatellite markers. A total of 592 clusters contained 646 repeats, representing 3.3% of the ESTs queried. The ESTs presented here are the first dehydration stress transcriptome of cassava and can be utilized for the development of microarrays and gene-derived molecular markers to further dissect the molecular basis of drought tolerance in cassava.
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Affiliation(s)
- Y Lokko
- Central Biotechnology Laboratory, International Institute of Tropical Agriculture, Oyo Road, Ibadan, Nigeria
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