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Tilhou NW, Bonnette J, Boe AR, Fay PA, Fritschi FB, Mitchell RB, Rouquette FM, Wu Y, Jastrow JD, Ricketts M, Maher SD, Juenger TE, Lowry DB. Genomic prediction of regional-scale performance in switchgrass (Panicum virgatum) by accounting for genotype-by-environment variation and yield surrogate traits. G3 (BETHESDA, MD.) 2024; 14:jkae159. [PMID: 39028116 PMCID: PMC11457067 DOI: 10.1093/g3journal/jkae159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 01/30/2024] [Accepted: 06/24/2024] [Indexed: 07/20/2024]
Abstract
Switchgrass is a potential crop for bioenergy or carbon capture schemes, but further yield improvements through selective breeding are needed to encourage commercialization. To identify promising switchgrass germplasm for future breeding efforts, we conducted multisite and multitrait genomic prediction with a diversity panel of 630 genotypes from 4 switchgrass subpopulations (Gulf, Midwest, Coastal, and Texas), which were measured for spaced plant biomass yield across 10 sites. Our study focused on the use of genomic prediction to share information among traits and environments. Specifically, we evaluated the predictive ability of cross-validation (CV) schemes using only genetic data and the training set (cross-validation 1: CV1), a subset of the sites (cross-validation 2: CV2), and/or with 2 yield surrogates (flowering time and fall plant height). We found that genotype-by-environment interactions were largely due to the north-south distribution of sites. The genetic correlations between the yield surrogates and the biomass yield were generally positive (mean height r = 0.85; mean flowering time r = 0.45) and did not vary due to subpopulation or growing region (North, Middle, or South). Genomic prediction models had CV predictive abilities of -0.02 for individuals using only genetic data (CV1), but 0.55, 0.69, 0.76, 0.81, and 0.84 for individuals with biomass performance data from 1, 2, 3, 4, and 5 sites included in the training data (CV2), respectively. To simulate a resource-limited breeding program, we determined the predictive ability of models provided with the following: 1 site observation of flowering time (0.39); 1 site observation of flowering time and fall height (0.51); 1 site observation of fall height (0.52); 1 site observation of biomass (0.55); and 5 site observations of biomass yield (0.84). The ability to share information at a regional scale is very encouraging, but further research is required to accurately translate spaced plant biomass to commercial-scale sward biomass performance.
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Affiliation(s)
- Neal W Tilhou
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jason Bonnette
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Arvid R Boe
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57006, USA
| | - Philip A Fay
- Grassland, Soil and Water Research Laboratory, USDA-ARS, Temple, TX 76502, USA
| | - Felix B Fritschi
- Division of Plant Science & Technology, University of Missouri, Columbia, MO 65201, USA
| | - Robert B Mitchell
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, NE 68583, USA
| | - Francis M Rouquette
- Texas A&M AgriLife Research and Extension Center, Texas A&M University, Overton, TX 75682, USA
| | - Yanqi Wu
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74075, USA
| | - Julie D Jastrow
- Environmental Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Michael Ricketts
- Environmental Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Shelley D Maher
- USDA-NRCS, E. “Kika” de la Garza Plant Materials Center, Kingsville, TX 78363, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- Great Lake Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
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Heckman RW, Pereira CG, Aspinwall MJ, Juenger TE. Physiological Responses of C 4 Perennial Bioenergy Grasses to Climate Change: Causes, Consequences, and Constraints. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:737-769. [PMID: 38424068 DOI: 10.1146/annurev-arplant-070623-093952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
C4 perennial bioenergy grasses are an economically and ecologically important group whose responses to climate change will be important to the future bioeconomy. These grasses are highly productive and frequently possess large geographic ranges and broad environmental tolerances, which may contribute to the evolution of ecotypes that differ in physiological acclimation capacity and the evolution of distinct functional strategies. C4 perennial bioenergy grasses are predicted to thrive under climate change-C4 photosynthesis likely evolved to enhance photosynthetic efficiency under stressful conditions of low [CO2], high temperature, and drought-although few studies have examined how these species will respond to combined stresses or to extremes of temperature and precipitation. Important targets for C4 perennial bioenergy production in a changing world, such as sustainability and resilience, can benefit from combining knowledge of C4 physiology with recent advances in crop improvement, especially genomic selection.
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Affiliation(s)
- Robert W Heckman
- Rocky Mountain Research Station, US Department of Agriculture Forest Service, Cedar City, Utah, USA;
| | - Caio Guilherme Pereira
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA;
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA;
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Headrick KC, Juenger TE, Heckman RW. Plant physical defenses contribute to a latitudinal gradient in resistance to insect herbivory within a widespread perennial grass. AMERICAN JOURNAL OF BOTANY 2024; 111:e16260. [PMID: 38031482 DOI: 10.1002/ajb2.16260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
PREMISE Herbivore pressure can vary across the range of a species, resulting in different defensive strategies. If herbivory is greater at lower latitudes, plants may be better defended there, potentially driving a latitudinal gradient in defense. However, relationships that manifest across the entire range of a species may be confounded by differences within genetic subpopulations, which may obscure the drivers of these latitudinal gradients. METHODS We grew plants of the widespread perennial grass Panicum virgatum in a common garden that included genotypes from three genetic subpopulations spanning an 18.5° latitudinal gradient. We then assessed defensive strategies of these plants by measuring two physical resistance traits-leaf mass per area (LMA) and leaf ash, a proxy for silica-and multiple measures of herbivory by caterpillars of the generalist herbivore fall armyworm (Spodoptera frugiperda). RESULTS Across all genetic subpopulations, low-latitude plants experienced less herbivory than high-latitude plants. Within genetic subpopulations, however, this relationship was inconsistent-the most widely distributed and phenotypically variable subpopulation (Atlantic) exhibited more consistent latitudinal trends than either of the other two subpopulations. The two physical resistance traits, LMA and leaf ash, were both highly heritable and positively associated with resistance to different measures of herbivory across all subpopulations, indicating their importance in defense against herbivores. Again, however, these relationships were inconsistent within subpopulations. CONCLUSIONS Defensive gradients that occur across the entire species range may not arise within localized subpopulations. Thus, identifying the drivers of latitudinal gradients in herbivory defense may depend on adequately sampling the diversity within a species.
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Affiliation(s)
- Kevin C Headrick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Robert W Heckman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
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Palmer NA, Alvarez S, Naldrett MJ, Muhle A, Sarath G, Edmé SJ, Tatineni S, Mitchell RB, Yuen G. Dynamic Reconfiguration of Switchgrass Proteomes in Response to Rust ( Puccinia novopanici) Infection. Int J Mol Sci 2023; 24:14630. [PMID: 37834079 PMCID: PMC10572835 DOI: 10.3390/ijms241914630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Switchgrass (Panicum virgatum L.) can be infected by the rust pathogen (Puccinia novopanici) and results in lowering biomass yields and quality. Label-free quantitative proteomics was conducted on leaf extracts harvested from non-infected and infected plants from a susceptible cultivar (Summer) at 7, 11, and 18 days after inoculation (DAI) to follow the progression of disease and evaluate any plant compensatory mechanisms to infection. Some pustules were evident at 7 DAI, and their numbers increased with time. However, fungal DNA loads did not appreciably change over the course of this experiment in the infected plants. In total, 3830 proteins were identified at 1% false discovery rate, with 3632 mapped to the switchgrass proteome and 198 proteins mapped to different Puccinia proteomes. Across all comparisons, 1825 differentially accumulated switchgrass proteins were identified and subjected to a STRING analysis using Arabidopsis (A. thaliana L.) orthologs to deduce switchgrass cellular pathways impacted by rust infection. Proteins associated with plastid functions and primary metabolism were diminished in infected Summer plants at all harvest dates, whereas proteins associated with immunity, chaperone functions, and phenylpropanoid biosynthesis were significantly enriched. At 18 DAI, 1105 and 151 proteins were significantly enriched or diminished, respectively. Many of the enriched proteins were associated with mitigation of cellular stress and defense.
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Affiliation(s)
- Nathan A. Palmer
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Sophie Alvarez
- Proteomics and Metabolomics Core Facility, Center for Biotechnology, University of Nebraska at Lincoln, Lincoln, NE 68588-0664, USA; (S.A.); (M.J.N.)
| | - Michael J. Naldrett
- Proteomics and Metabolomics Core Facility, Center for Biotechnology, University of Nebraska at Lincoln, Lincoln, NE 68588-0664, USA; (S.A.); (M.J.N.)
| | - Anthony Muhle
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Gautam Sarath
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Serge J. Edmé
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Satyanarayana Tatineni
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
- Department of Plant Pathology, University of Nebraska at Lincoln, Lincoln, NE 68583-0722, USA;
| | - Robert B. Mitchell
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Gary Yuen
- Department of Plant Pathology, University of Nebraska at Lincoln, Lincoln, NE 68583-0722, USA;
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Host genotype controls ecological change in the leaf fungal microbiome. PLoS Biol 2022; 20:e3001681. [PMID: 35951523 PMCID: PMC9371330 DOI: 10.1371/journal.pbio.3001681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/18/2022] [Indexed: 11/19/2022] Open
Abstract
Leaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass (Panicum virgatum). We also sampled a replicated subset of genotypes across 3 additional sites to compare the importance of time, space, ecology, and genetics. We found a strong successional pattern in the microbiome shaped both by host genetics and environmental factors. Further, we used genome-wide association (GWA) mapping and RNA sequencing to show that 3 cysteine-rich receptor-like kinases (crRLKs) were linked to a genetic locus associated with microbiome structure. We confirmed GWAS results in an independent set of genotypes for both the internal transcribed spacer (ITS) and large subunit (LSU) ribosomal DNA markers. Fungal pathogens were central to microbial covariance networks, and genotypes susceptible to pathogens differed in their expression of the 3 crRLKs, suggesting that host immune genes are a principal means of controlling the entire leaf microbiome. Leaf fungal microbiomes can strongly influence host plant success. Monitoring the leaf fungal microbiome of switchgrass over time shows microbial ecological succession, and reveals the host plant genes that influence community-wide changes.
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VanWallendael A, Lowry DB, Hamilton JA. One hundred years into the study of ecotypes, new advances are being made through large-scale field experiments in perennial plant systems. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102152. [PMID: 35065527 DOI: 10.1016/j.pbi.2021.102152] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/31/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
A hundred years after Turesson first clearly described how locally adaptive variation is distributed within species, plant biologists are making major breakthroughs in our understanding of mechanisms underlying adaptation from local populations to the scale of continents. Although the genetics of local adaptation has typically been studied in smaller reciprocal transplant experiments, it is now being evaluated with whole genomes in large-scale networks of common garden experiments with perennial switchgrass and poplar trees. These studies support the hypothesis that a complex combination of loci, both with and without adaptive trade-offs, underlies local adaptation and that hybridization and adaptive introgression play a key role in the evolution of these species. Future studies incorporating high-throughput phenotyping, gene expression, and modeling will be used to predict responses of these species to climate change.
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Affiliation(s)
- Acer VanWallendael
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA; Program in Ecology, Evolution, and Behaviour, Michigan State University, East Lansing, MI, 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA; Program in Ecology, Evolution, and Behaviour, Michigan State University, East Lansing, MI, 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA.
| | - Jill A Hamilton
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16801, USA
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7
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Muhle AA, Palmer NA, Edme SJ, Sarath G, Yuen G, Mitchell RB, Tatineni S. Effect of cultivar and temperature on the synergistic interaction between panicum mosaic virus and satellite panicum mosaic virus in switchgrass. Arch Virol 2022; 167:1247-1256. [PMID: 35344095 DOI: 10.1007/s00705-022-05412-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 01/27/2022] [Indexed: 11/02/2022]
Abstract
Panicum mosaic virus (PMV), the type member of the genus Panicovirus in the family Tombusviridae, naturally infects switchgrass (Panicum virgatum L.). PMV and its molecular partner, satellite panicum mosaic virus (SPMV), interact synergistically in coinfected millets to exacerbate the disease phenotype and increase the accumulation of PMV compared to plants infected with PMV alone. In this study, we examined the reaction of switchgrass cvs. Summer and Kanlow to PMV and PMV+SPMV infections at 24°C and 32°C. Switchgrass cv. Summer was susceptible to PMV at both temperatures. In contrast, cv. Kanlow was tolerant to PMV at 24°C, but not at 32°C, suggesting that Kanlow harbors temperature-sensitive resistance to PMV. At 24°C, PMV was readily detected in inoculated leaves, but not in upper uninoculated leaves of Kanlow, suggesting that resistance to PMV was likely mediated by abrogation of long-distance virus transport. Coinfection by PMV and SPMV at 24°C and 32°C in cv. Summer, but not in Kanlow, caused increased symptomatic systemic infection and mild disease synergism with slightly increased PMV accumulation compared to plants infected with PMV alone. These data suggest that the interaction between PMV and SPMV in switchgrass is cultivar-dependent, manifested in Summer but not in Kanlow. However, co-inoculation of cv. Kanlow with PMV+SPMV caused an enhanced asymptomatic infection, suggesting a role of SPMV in enhancement of symptomless infection in a tolerant cultivar. These data suggest that enhanced asymptomatic infections in a virus-tolerant switchgrass cultivar could serve as a source of virus spread and play an important role in panicum mosaic disease epidemiology under field conditions. Our data reveal that the cultivar, coinfection with SPMV, and temperature influence the severity of symptoms elicited by PMV in switchgrass.
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Affiliation(s)
- Anthony A Muhle
- United States Department of Agriculture-Agricultural Research Service, University of Nebraska-Lincoln, Lincoln, USA.,Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Nathan A Palmer
- United States Department of Agriculture-Agricultural Research Service, University of Nebraska-Lincoln, Lincoln, USA
| | - Serge J Edme
- United States Department of Agriculture-Agricultural Research Service, University of Nebraska-Lincoln, Lincoln, USA.,Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Gautam Sarath
- United States Department of Agriculture-Agricultural Research Service, University of Nebraska-Lincoln, Lincoln, USA.,Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Gary Yuen
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Robert B Mitchell
- United States Department of Agriculture-Agricultural Research Service, University of Nebraska-Lincoln, Lincoln, USA.,Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Satyanarayana Tatineni
- United States Department of Agriculture-Agricultural Research Service, University of Nebraska-Lincoln, Lincoln, USA. .,Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
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8
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Xu Y, Shrestha V, Piasecki C, Wolfe B, Hamilton L, Millwood RJ, Mazarei M, Stewart CN. Sustainability Trait Modeling of Field-Grown Switchgrass ( Panicum virgatum) Using UAV-Based Imagery. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122726. [PMID: 34961199 PMCID: PMC8709265 DOI: 10.3390/plants10122726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/29/2021] [Accepted: 12/07/2021] [Indexed: 05/17/2023]
Abstract
Unmanned aerial vehicles (UAVs) provide an intermediate scale of spatial and spectral data collection that yields increased accuracy and consistency in data collection for morphological and physiological traits than satellites and expanded flexibility and high-throughput compared to ground-based data collection. In this study, we used UAV-based remote sensing for automated phenotyping of field-grown switchgrass (Panicum virgatum), a leading bioenergy feedstock. Using vegetation indices calculated from a UAV-based multispectral camera, statistical models were developed for rust disease caused by Puccinia novopanici, leaf chlorophyll, nitrogen, and lignin contents. For the first time, UAV remote sensing technology was used to explore the potentials for multiple traits associated with sustainable production of switchgrass, and one statistical model was developed for each individual trait based on the statistical correlation between vegetation indices and the corresponding trait. Also, for the first time, lignin content was estimated in switchgrass shoots via UAV-based multispectral image analysis and statistical analysis. The UAV-based models were verified by ground-truthing via correlation analysis between the traits measured manually on the ground-based with UAV-based data. The normalized difference red edge (NDRE) vegetation index outperformed the normalized difference vegetation index (NDVI) for rust disease and nitrogen content, while NDVI performed better than NDRE for chlorophyll and lignin content. Overall, linear models were sufficient for rust disease and chlorophyll analysis, but for nitrogen and lignin contents, nonlinear models achieved better results. As the first comprehensive study to model switchgrass sustainability traits from UAV-based remote sensing, these results suggest that this methodology can be utilized for switchgrass high-throughput phenotyping in the field.
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Affiliation(s)
- Yaping Xu
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (Y.X.); (V.S.); (C.P.); (B.W.); (L.H.)
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Vivek Shrestha
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (Y.X.); (V.S.); (C.P.); (B.W.); (L.H.)
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Cristiano Piasecki
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (Y.X.); (V.S.); (C.P.); (B.W.); (L.H.)
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
- ATSI Brasil Pesquisa e Consultoria, Passo Fundo 99054-328, RS, Brazil
| | - Benjamin Wolfe
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (Y.X.); (V.S.); (C.P.); (B.W.); (L.H.)
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Lance Hamilton
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (Y.X.); (V.S.); (C.P.); (B.W.); (L.H.)
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Reginald J. Millwood
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (Y.X.); (V.S.); (C.P.); (B.W.); (L.H.)
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
- Correspondence: (R.J.M.); (M.M.); (C.N.S.J.)
| | - Mitra Mazarei
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (Y.X.); (V.S.); (C.P.); (B.W.); (L.H.)
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
- Correspondence: (R.J.M.); (M.M.); (C.N.S.J.)
| | - Charles Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (Y.X.); (V.S.); (C.P.); (B.W.); (L.H.)
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
- Correspondence: (R.J.M.); (M.M.); (C.N.S.J.)
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9
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Hamann E, Denney D, Day S, Lombardi E, Jameel MI, MacTavish R, Anderson JT. Review: Plant eco-evolutionary responses to climate change: Emerging directions. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 304:110737. [PMID: 33568289 DOI: 10.1016/j.plantsci.2020.110737] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 05/14/2023]
Abstract
Contemporary climate change is exposing plant populations to novel combinations of temperatures, drought stress, [CO2] and other abiotic and biotic conditions. These changes are rapidly disrupting the evolutionary dynamics of plants. Despite the multifactorial nature of climate change, most studies typically manipulate only one climatic factor. In this opinion piece, we explore how climate change factors interact with each other and with biotic pressures to alter evolutionary processes. We evaluate the ramifications of climate change across life history stages,and examine how mating system variation influences population persistence under rapid environmental change. Furthermore, we discuss how spatial and temporal mismatches between plants and their mutualists and antagonists could affect adaptive responses to climate change. For example, plant-virus interactions vary from highly pathogenic to mildly facilitative, and are partly mediated by temperature, moisture availability and [CO2]. Will host plants exposed to novel, stressful abiotic conditions be more susceptible to viral pathogens? Finally, we propose novel experimental approaches that could illuminate how plants will cope with unprecedented global change, such as resurrection studies combined with experimental evolution, genomics or epigenetics.
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Affiliation(s)
- Elena Hamann
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
| | - Derek Denney
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
| | - Samantha Day
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
| | - Elizabeth Lombardi
- Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - M Inam Jameel
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
| | - Rachel MacTavish
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
| | - Jill T Anderson
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA 30602, USA.
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10
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Roth C, Murray D, Scott A, Fu C, Averette AF, Sun S, Heitman J, Magwene PM. Pleiotropy and epistasis within and between signaling pathways defines the genetic architecture of fungal virulence. PLoS Genet 2021; 17:e1009313. [PMID: 33493169 PMCID: PMC7861560 DOI: 10.1371/journal.pgen.1009313] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 02/04/2021] [Accepted: 12/17/2020] [Indexed: 01/11/2023] Open
Abstract
Cryptococcal disease is estimated to affect nearly a quarter of a million people annually. Environmental isolates of Cryptococcus deneoformans, which make up 15 to 30% of clinical infections in temperate climates such as Europe, vary in their pathogenicity, ranging from benign to hyper-virulent. Key traits that contribute to virulence, such as the production of the pigment melanin, an extracellular polysaccharide capsule, and the ability to grow at human body temperature have been identified, yet little is known about the genetic basis of variation in such traits. Here we investigate the genetic basis of melanization, capsule size, thermal tolerance, oxidative stress resistance, and antifungal drug sensitivity using quantitative trait locus (QTL) mapping in progeny derived from a cross between two divergent C. deneoformans strains. Using a "function-valued" QTL analysis framework that exploits both time-series information and growth differences across multiple environments, we identified QTL for each of these virulence traits and drug susceptibility. For three QTL we identified the underlying genes and nucleotide differences that govern variation in virulence traits. One of these genes, RIC8, which encodes a regulator of cAMP-PKA signaling, contributes to variation in four virulence traits: melanization, capsule size, thermal tolerance, and resistance to oxidative stress. Two major effect QTL for amphotericin B resistance map to the genes SSK1 and SSK2, which encode key components of the HOG pathway, a fungal-specific signal transduction network that orchestrates cellular responses to osmotic and other stresses. We also discovered complex epistatic interactions within and between genes in the HOG and cAMP-PKA pathways that regulate antifungal drug resistance and resistance to oxidative stress. Our findings advance the understanding of virulence traits among diverse lineages of Cryptococcus, and highlight the role of genetic variation in key stress-responsive signaling pathways as a major contributor to phenotypic variation.
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Affiliation(s)
- Cullen Roth
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
| | - Debra Murray
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Alexandria Scott
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Ci Fu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Anna F. Averette
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Paul M. Magwene
- Department of Biology, Duke University, Durham, North Carolina, United States of America
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11
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Pingault L, Palmer NA, Koch KG, Heng-Moss T, Bradshaw JD, Seravalli J, Twigg P, Louis J, Sarath G. Differential Defense Responses of Upland and Lowland Switchgrass Cultivars to a Cereal Aphid Pest. Int J Mol Sci 2020; 21:ijms21217966. [PMID: 33120946 PMCID: PMC7672581 DOI: 10.3390/ijms21217966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 02/01/2023] Open
Abstract
Yellow sugarcane aphid (YSA) (Sipha flava, Forbes) is a damaging pest on many grasses. Switchgrass (Panicum virgatum L.), a perennial C4 grass, has been selected as a bioenergy feedstock because of its perceived resilience to abiotic and biotic stresses. Aphid infestation on switchgrass has the potential to reduce the yields and biomass quantity. Here, the global defense response of switchgrass cultivars Summer and Kanlow to YSA feeding was analyzed by RNA-seq and metabolite analysis at 5, 10, and 15 days after infestation. Genes upregulated by infestation were more common in both cultivars compared to downregulated genes. In total, a higher number of differentially expressed genes (DEGs) were found in the YSA susceptible cultivar (Summer), and fewer DEGs were observed in the YSA resistant cultivar (Kanlow). Interestingly, no downregulated genes were found in common between each time point or between the two switchgrass cultivars. Gene co-expression analysis revealed upregulated genes in Kanlow were associated with functions such as flavonoid, oxidation-response to chemical, or wax composition. Downregulated genes for the cultivar Summer were found in co-expression modules with gene functions related to plant defense mechanisms or cell wall composition. Global analysis of defense networks of the two cultivars uncovered differential mechanisms associated with resistance or susceptibility of switchgrass in response to YSA infestation. Several gene co-expression modules and transcription factors correlated with these differential defense responses. Overall, the YSA-resistant Kanlow plants have an enhanced defense even under aphid uninfested conditions.
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Affiliation(s)
- Lise Pingault
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (L.P.); (K.G.K.); (T.H.-M.); (J.D.B.)
| | - Nathan A. Palmer
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, NE 68583, USA;
| | - Kyle G. Koch
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (L.P.); (K.G.K.); (T.H.-M.); (J.D.B.)
| | - Tiffany Heng-Moss
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (L.P.); (K.G.K.); (T.H.-M.); (J.D.B.)
| | - Jeffrey D. Bradshaw
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (L.P.); (K.G.K.); (T.H.-M.); (J.D.B.)
| | - Javier Seravalli
- Redox Biology Center, Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Paul Twigg
- Biology Department, University of Nebraska-Kearney, Kearney, NE 68849, USA;
| | - Joe Louis
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (L.P.); (K.G.K.); (T.H.-M.); (J.D.B.)
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
- Correspondence: (J.L.); (G.S.); Tel.: +1-402-472-8098 (J.L.); +1-402-472-4204 (G.S.)
| | - Gautam Sarath
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (L.P.); (K.G.K.); (T.H.-M.); (J.D.B.)
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, NE 68583, USA;
- Correspondence: (J.L.); (G.S.); Tel.: +1-402-472-8098 (J.L.); +1-402-472-4204 (G.S.)
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12
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Catalán P, Vogel JP. Advances on genomics, biology, ecology and evolution of Brachypodium, a bridging model grass system for cereals and biofuel grasses. THE NEW PHYTOLOGIST 2020; 227:1587-1590. [PMID: 33439505 DOI: 10.1111/nph.16831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Pilar Catalán
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, 22071, Huesca, Spain
| | - John P Vogel
- United States Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
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