1
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Tilhou NW, Poudel HP, Lovell J, Mamidi S, Schmutz J, Daum C, Zane M, Yoshinaga Y, Lipzen A, Casler MD. Genomic prediction of switchgrass winter survivorship across diverse lowland populations. G3 (BETHESDA, MD.) 2023; 13:jkad014. [PMID: 36648238 PMCID: PMC9997553 DOI: 10.1093/g3journal/jkad014] [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: 09/08/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 01/18/2023]
Abstract
In the North-Central United States, lowland ecotype switchgrass can increase yield by up to 50% compared with locally adapted but early flowering cultivars. However, lowland ecotypes are not winter tolerant. The mechanism for winter damage is unknown but previously has been associated with late flowering time. This study investigated heading date (measured for two years) and winter survivorship (measured for three years) in a multi-generation population generated from two winter-hardy lowland individuals and diverse southern lowland populations. Sequencing data (311,776 markers) from 1,306 individuals were used to evaluate genome-wide trait prediction through cross-validation and progeny prediction (n = 52). Genetic variance for heading date and winter survivorship was additive with high narrow-sense heritability (0.64 and 0.71, respectively) and reliability (0.68 and 0.76, respectively). The initial negative correlation between winter survivorship and heading date degraded across generations (F1r = -0.43, pseudo-F2r = -0.28, pseudo-F2 progeny r = -0.15). Within-family predictive ability was moderately high for heading date and winter survivorship (0.53 and 0.52, respectively). A multi-trait model did not improve predictive ability for either trait. Progeny predictive ability was 0.71 for winter survivorship and 0.53 for heading date. These results suggest that lowland ecotype populations can obtain sufficient survival rates in the northern United States with two or three cycles of effective selection. Despite accurate genomic prediction, naturally occurring winter mortality successfully isolated winter tolerant genotypes and appears to be an efficient method to develop high-yielding, cold-tolerant switchgrass cultivars.
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Affiliation(s)
- Neal W Tilhou
- Department of Agronomy, University of Wisconsin, 1575 Linden Dr, Madison, WI 53706, USA
| | - Hari P Poudel
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, T1J 4B1 Canada
| | - John Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Sujan Mamidi
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Christopher Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA 94704, USA
| | - Matthew Zane
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA 94704, USA
| | - Yuko Yoshinaga
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA 94704, USA
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA 94704, USA
| | - Michael D Casler
- Department of Agronomy, University of Wisconsin, 1575 Linden Dr, Madison, WI 53706, USA
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2
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Tiedge K, Destremps J, Solano-Sanchez J, Arce-Rodriguez ML, Zerbe P. Foxtail mosaic virus-induced gene silencing (VIGS) in switchgrass (Panicum virgatum L.). PLANT METHODS 2022; 18:71. [PMID: 35644680 PMCID: PMC9150325 DOI: 10.1186/s13007-022-00903-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/07/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND Although the genome for the allotetraploid bioenergy crop switchgrass (Panicum virgatum) has been established, limitations in mutant resources have hampered in planta gene function studies toward crop optimization. Virus-induced gene silencing (VIGS) is a versatile technique for transient genetic studies. Here we report the implementation of foxtail mosaic virus (FoMV)-mediated gene silencing in switchgrass in above- and below-ground tissues and at different developmental stages. RESULTS The study demonstrated that leaf rub-inoculation is a suitable method for systemic gene silencing in switchgrass. For all three visual marker genes, Magnesium chelatase subunit D (ChlD) and I (ChlI) as well as phytoene desaturase (PDS), phenotypic changes were observed in leaves, albeit at different intensities. Gene silencing efficiency was verified by RT-PCR for all tested genes. Notably, systemic gene silencing was also observed in roots, although silencing efficiency was stronger in leaves (~ 63-94%) as compared to roots (~ 48-78%). Plants at a later developmental stage were moderately less amenable to VIGS than younger plants, but also less perturbed by the viral infection. CONCLUSIONS Using FoMV-mediated VIGS could be achieved in switchgrass leaves and roots, providing an alternative approach for studying gene functions and physiological traits in this important bioenergy crop.
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Affiliation(s)
- Kira Tiedge
- Department of Plant Biology, University of California, Davis, USA.
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands.
| | | | | | | | - Philipp Zerbe
- Department of Plant Biology, University of California, Davis, USA
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3
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Razar RM, Qi P, Devos KM, Missaoui AM. Genotyping-by-Sequencing and QTL Mapping of Biomass Yield in Two Switchgrass F 1 Populations (Lowland x Coastal and Coastal x Upland). FRONTIERS IN PLANT SCIENCE 2022; 13:739133. [PMID: 35665173 PMCID: PMC9162799 DOI: 10.3389/fpls.2022.739133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
The prevalence of genetic diversity in switchgrass germplasm can be exploited to capture favorable alleles that increase its range of adaptation and biomass yield. The objectives of the study were to analyze the extent of polymorphism and patterns of segregation distortion in two F1 populations and use the linkage maps to locate QTL for biomass yield. We conducted genotyping-by-sequencing on two populations derived from crosses between the allotetraploid lowland genotype AP13 (a selection from "Alamo") and coastal genotype B6 (a selection from PI 422001) with 285 progeny (AB population) and between B6 and the allotetraploid upland VS16 (a selection from "Summer") with 227 progeny (BV population). As predictable from the Euclidean distance between the parents, a higher number of raw variants was discovered in the coastal × upland BV cross (6 M) compared to the lowland × coastal AB cross (2.5 M). The final number of mapped markers was 3,107 on the BV map and 2,410 on the AB map. More segregation distortion of alleles was seen in the AB population, with 75% distorted loci compared to 11% distorted loci in the BV population. The distortion in the AB population was seen across all chromosomes in both the AP13 and B6 maps and likely resulted from zygotic or post-zygotic selection for increased levels of heterozygosity. Our results suggest lower genetic compatibility between the lowland AP13 and the coastal B6 ecotype than between B6 and the upland ecotype VS16. Four biomass QTLs were mapped in the AB population (LG 2N, 6K, 6N, and 8N) and six QTLs in the BV population [LG 1N (2), 8N (2), 9K, and 9N]. The QTL, with the largest and most consistent effect across years, explaining between 8.4 and 11.5% of the variation, was identified on 6N in the AP13 map. The cumulative effect of all the QTLs explained a sizeable portion of the phenotypic variation in both AB and BV populations and the markers associated with them may potentially be used for the marker-assisted improvement of biomass yield. Since switchgrass improvement is based on increasing favorable allele frequencies through recurrent selection, the transmission bias within individuals and loci needs to be considered as this may affect the genetic gain if the favorable alleles are distorted.
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Affiliation(s)
- Rasyidah M. Razar
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Genetic Resources and Improvement Unit, RRIM Research Station, Malaysian Rubber Board, Selangor, Malaysia
| | - Peng Qi
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Katrien M. Devos
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Ali M. Missaoui
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
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Chieppa J, Brown T, Giresi P, Juenger TE, Resco de Dios V, Tissue DT, Aspinwall MJ. Climate and stomatal traits drive covariation in nighttime stomatal conductance and daytime gas exchange rates in a widespread C 4 grass. THE NEW PHYTOLOGIST 2021; 229:2020-2034. [PMID: 33037633 DOI: 10.1111/nph.16987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
Nighttime stomatal conductance (gsn ) varies among plant functional types and species, but factors shaping the evolution of gsn remain unclear. Examinations of intraspecific variation in gsn as a function of climate and co-varying leaf traits may provide new insight into the evolution of gsn and its adaptive significance. We grew 11 genotypes of Panicum virgatum (switchgrass) representing differing home-climates in a common garden experiment and measured nighttime and daytime leaf gas exchange, as well as stomatal density (SD) and size during early-, mid-, and late-summer. We used piecewise structural equation modelling to determine direct and indirect relationships between home-climate, gas exchange, and stomatal traits. We found no direct relationship between home-climate and gsn . However, genotypes from hotter climates possessed higher SD, which resulted in higher gsn . Across genotypes, higher gsn was associated with higher daytime stomatal conductance and net photosynthesis. Our results indicate that higher gsn may arise in genotypes from hotter climates via increased SD. High SD may provide benefits to genotypes from hotter climates through enhanced daytime transpirational cooling or by permitting maximal gas exchange when conditions are suitable. These results highlight the role of climate and trait coordination in shaping genetic differentiation in gsn .
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Affiliation(s)
- Jeff Chieppa
- Department of Biology, University of North Florida, Jacksonville, FL, 32224, USA
- School of Forestry and Wildlife Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Tia Brown
- Department of Biology, Haverford College, Haverford, PA, 19041, USA
| | - Presley Giresi
- Department of Biology, University of North Florida, Jacksonville, FL, 32224, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78717, USA
| | - Víctor Resco de Dios
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Michael J Aspinwall
- Department of Biology, University of North Florida, Jacksonville, FL, 32224, USA
- School of Forestry and Wildlife Sciences, Auburn University, Auburn, AL, 36849, USA
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5
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Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. Nature 2021; 590:438-444. [PMID: 33505029 PMCID: PMC7886653 DOI: 10.1038/s41586-020-03127-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/16/2020] [Indexed: 01/30/2023]
Abstract
Long-term climate change and periodic environmental extremes threaten food and fuel security1 and global crop productivity2-4. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience5, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation6-knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate-gene-biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene-trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.
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6
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Jensen E, Shafiei R, Ma X, Serba DD, Smith DP, Slavov GT, Robson P, Farrar K, Thomas Jones S, Swaller T, Flavell R, Clifton‐Brown J, Saha MC, Donnison I. Linkage mapping evidence for a syntenic QTL associated with flowering time in perennial C 4 rhizomatous grasses Miscanthus and switchgrass. GLOBAL CHANGE BIOLOGY. BIOENERGY 2021; 13:98-111. [PMID: 33381230 PMCID: PMC7756372 DOI: 10.1111/gcbb.12755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/10/2020] [Indexed: 06/12/2023]
Abstract
Flowering in perennial species is directed via complex signalling pathways that adjust to developmental regulations and environmental cues. Synchronized flowering in certain environments is a prerequisite to commercial seed production, and so the elucidation of the genetic architecture of flowering time in Miscanthus and switchgrass could aid breeding in these underdeveloped species. In this context, we assessed a mapping population in Miscanthus and two ecologically diverse switchgrass mapping populations over 3 years from planting. Multiple flowering time quantitative trait loci (QTL) were identified in both species. Remarkably, the most significant Miscanthus and switchgrass QTL proved to be syntenic, located on linkage groups 4 and 2, with logarithm of odds scores of 17.05 and 21.8 respectively. These QTL regions contained three flowering time transcription factors: Squamosa Promoter-binding protein-Like, MADS-box SEPELLATA2 and gibberellin-responsive bHLH137. The former is emerging as a key component of the age-related flowering time pathway.
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Affiliation(s)
- Elaine Jensen
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Reza Shafiei
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
- University of Dundee at JHIDundeeUK
| | - Xue‐Feng Ma
- Ceres, Inc.Thousand OaksCAUSA
- Noble Research Institute, LLC.ArdmoreOKUSA
| | - Desalegn D. Serba
- Noble Research Institute, LLC.ArdmoreOKUSA
- Agricultural Research Center‐HaysKansas State UniversityHaysKSUSA
| | - Daniel P. Smith
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
- ScionRotoruaNew Zealand
| | - Gancho T. Slavov
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
- ScionRotoruaNew Zealand
| | - Paul Robson
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Kerrie Farrar
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Sian Thomas Jones
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Timothy Swaller
- Ceres, Inc.Thousand OaksCAUSA
- Genomics Institute of the Novartis Research FoundationSan DiegoCAUSA
| | - Richard Flavell
- Ceres, Inc.Thousand OaksCAUSA
- International Wheat Yield PartnershipTexas A&M UniversityCollege StationTXUSA
| | - John Clifton‐Brown
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | | | - Iain Donnison
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
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7
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Ahrens CW, James EA, Miller AD, Scott F, Aitken NC, Jones AW, Lu-Irving P, Borevitz JO, Cantrill DJ, Rymer PD. Spatial, climate and ploidy factors drive genomic diversity and resilience in the widespread grass Themeda triandra. Mol Ecol 2020; 29:3872-3888. [PMID: 32885504 DOI: 10.1111/mec.15614] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 12/27/2022]
Abstract
Global climate change poses a significant threat to natural communities around the world, with many plant species showing signs of climate stress. Grassland ecosystems are not an exception, with climate change compounding contemporary pressures such as habitat loss and fragmentation. In this study, we assess the climate resilience of Themeda triandra, a foundational species and the most widespread plant in Australia, by assessing the relative contributions of spatial, environmental and ploidy factors to contemporary genomic variation. Reduced-representation genome sequencing on 472 samples from 52 locations was used to test how the distribution of genomic variation, including ploidy polymorphism, supports adaptation to hotter and drier climates. We explicitly quantified isolation by distance (IBD) and isolation by environment (IBE) and predicted genomic vulnerability of populations to future climates based on expected deviation from current genomic composition. We found that a majority (54%) of genomic variation could be attributed to IBD, while an additional 22% (27% when including ploidy information) could be explained by two temperature and two precipitation climate variables demonstrating IBE. Ploidy polymorphisms were common within populations (31/52 populations), indicating that ploidy mixing is characteristic of T. triandra populations. Genomic vulnerabilities were found to be heterogeneously distributed throughout the landscape, and our analysis suggested that ploidy polymorphism, along with other factors linked to polyploidy, reduced vulnerability to future climates by 60% (0.25-0.10). Our data suggests that polyploidy may facilitate adaptation to hotter climates and highlight the importance of incorporating ploidy in adaptive management strategies to promote the resilience of this and other foundation species.
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Affiliation(s)
- Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia.,Royal Botanic Gardens Victoria, Melbourne, VIC, Australia
| | | | - Adam D Miller
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Warrnambool, VIC, Australia
| | - Ferguson Scott
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Nicola C Aitken
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Ashley W Jones
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Patricia Lu-Irving
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Garden, Sydney, NSW, Australia
| | - Justin O Borevitz
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | | - Paul D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
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8
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Why are tall-statured energy grasses of polyploid species complexes potentially invasive? A review of their genetic variation patterns and evolutionary plasticity. Biol Invasions 2019. [DOI: 10.1007/s10530-019-02053-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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9
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Palmer NA, Chowda-Reddy RV, Muhle AA, Tatineni S, Yuen G, Edmé SJ, Mitchell RB, Sarath G. Transcriptome divergence during leaf development in two contrasting switchgrass (Panicum virgatum L.) cultivars. PLoS One 2019; 14:e0222080. [PMID: 31513611 PMCID: PMC6742388 DOI: 10.1371/journal.pone.0222080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/21/2019] [Indexed: 01/09/2023] Open
Abstract
The genetics and responses to biotic stressors of tetraploid switchgrass (Panicum virgatum L.) lowland cultivar 'Kanlow' and upland cultivar Summer are distinct and can be exploited for trait improvement. In general, there is a paucity of data on the basal differences in transcription across tissue developmental times for switchgrass cultivars. Here, the changes in basal and temporal expression of genes related to leaf functions were evaluated for greenhouse grown 'Kanlow', and 'Summer' plants. Three biological replicates of the 4th leaf pooled from 15 plants per replicate were harvested at regular intervals beginning from leaf emergence through senescence. Increases and decreases in leaf chlorophyll and N content were similar for both cultivars. Likewise, multidimensional scaling (MDS) analysis indicated both cultivar-independent and cultivar-specific gene expression. Cultivar-independent genes and gene-networks included those associated with leaf function, such as growth/senescence, carbon/nitrogen assimilation, photosynthesis, chlorophyll biosynthesis, and chlorophyll degradation. However, many genes encoding nucleotide-binding leucine rich repeat (NB-LRRs) proteins and wall-bound kinases associated with detecting and responding to environmental signals were differentially expressed. Several of these belonged to unique cultivar-specific gene co-expression networks. Analysis of genomic resequencing data provided several examples of NB-LRRs genes that were not expressed and/or apparently absent in the genomes of Summer plants. It is plausible that cultivar (ecotype)-specific genes and gene-networks could be one of the drivers for the documented differences in responses to leaf-borne pathogens between these two cultivars. Incorporating broad resistance to plant pathogens in elite switchgrass germplasm could improve sustainability of biomass production under low-input conditions.
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Affiliation(s)
- Nathan A. Palmer
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United states of America
| | - R. V. Chowda-Reddy
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United states of America
| | - Anthony A. Muhle
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, United states of America
| | - Satyanarayana Tatineni
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United states of America
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, United states of America
| | - Gary Yuen
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, United states of America
| | - Serge J. Edmé
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United states of America
| | - Robert B. Mitchell
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United states of America
| | - Gautam Sarath
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United states of America
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10
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Weng X, Lovell JT, Schwartz SL, Cheng C, Haque T, Zhang L, Razzaque S, Juenger TE. Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C 4 grass. PLANT, CELL & ENVIRONMENT 2019; 42:2165-2182. [PMID: 30847928 DOI: 10.1111/pce.13546] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 02/26/2019] [Accepted: 02/27/2019] [Indexed: 06/09/2023]
Abstract
Photoperiod is a key environmental cue affecting flowering and biomass traits in plants. Key components of the photoperiodic flowering pathway have been identified in many species, but surprisingly few studies have globally examined the diurnal rhythm of gene expression with changes in day length. Using a cost-effective 3'-Tag RNA sequencing strategy, we characterize 9,010 photoperiod responsive genes with strict statistical testing across a diurnal time series in the C4 perennial grass, Panicum hallii. We show that the vast majority of photoperiod responses are driven by complex interactions between day length and sampling periods. A fine-scale contrast analysis at each sampling time revealed a detailed picture of the temporal reprogramming of cis-regulatory elements and biological processes under short- and long-day conditions. Phase shift analysis reveals quantitative variation among genes with photoperiod-dependent diurnal patterns. In addition, we identify three photoperiod enriched transcription factor families with key genes involved in photoperiod flowering regulatory networks. Finally, coexpression networks analysis of GIGANTEA homolog predicted 1,668 potential coincidence partners, including five well-known GI-interacting proteins. Our results not only provide a resource for understanding the mechanisms of photoperiod regulation in perennial grasses but also lay a foundation to increase biomass yield in biofuel crops.
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Affiliation(s)
- Xiaoyu Weng
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
| | - John T Lovell
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806
| | - Scott L Schwartz
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
| | - Changde Cheng
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
| | - Taslima Haque
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
| | - Li Zhang
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
| | - Samsad Razzaque
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712
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11
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Genomic Prediction for Winter Survival of Lowland Switchgrass in the Northern USA. G3-GENES GENOMES GENETICS 2019; 9:1921-1931. [PMID: 30971392 PMCID: PMC6553536 DOI: 10.1534/g3.119.400094] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The lowland ecotype of switchgrass has generated considerable interest because of its higher biomass yield and late flowering characteristics compared to the upland ecotype. However, lowland ecotypes planted in northern latitudes exhibit very low winter survival. Implementation of genomic selection could potentially enhance switchgrass breeding for winter survival by reducing generation time while eliminating the dependence on weather. The objectives of this study were to assess the potential of genomic selection for winter survival in lowland switchgrass by combining multiple populations in the training set and applying the selected model in two independent testing datasets for validation. Marker data were generated using exome capture sequencing. Validation was conducted using (1) indirect indicators of winter adaptation based on geographic and climatic variables of accessions from different source locations and (2) winter survival estimates of the phenotype. The prediction accuracies were significantly higher when the training dataset comprising all populations was used in fivefold cross validation but its application was not useful in the independent validation dataset. Nevertheless, modeling for population heterogeneity improved the prediction accuracy to some extent but the genetic relationship between the training and validation populations was found to be more influential. The predicted winter survival of lowland switchgrass indicated latitudinal and longitudinal variability, with the northeast USA the region for most cold tolerant lowland populations. Our results suggested that GS could provide valuable opportunities for improving winter survival and accelerate the lowland switchgrass breeding programs toward the development of cold tolerant cultivars suitable for northern latitudes.
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12
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Singer E, Bonnette J, Kenaley SC, Woyke T, Juenger TE. Plant compartment and genetic variation drive microbiome composition in switchgrass roots. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:185-195. [PMID: 30537406 PMCID: PMC6850097 DOI: 10.1111/1758-2229.12727] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 05/05/2023]
Abstract
Switchgrass (Panicum virgatum) is a promising biofuel crop native to the United States with genotypes that are adapted to a wide range of distinct ecosystems. Various plants have been shown to undergo symbioses with plant growth-promoting bacteria and fungi, however, plant-associated microbial communities of switchgrass have not been extensively studied to date. We present 16S ribosomal RNA gene and internal transcribed spacer (ITS) data of rhizosphere and root endosphere compartments of four switchgrass genotypes to test the hypothesis that host selection of its root microbiota prevails after transfer to non-native soil. We show that differences in bacterial, archaeal and fungal community composition and diversity are strongly driven by plant compartment and switchgrass genotypes and ecotypes. Plant-associated microbiota show an enrichment in Alphaproteobacteria and Actinobacteria as well as Sordariales and Pleosporales compared with the surrounding soil. Root associated compartments display low-complexity communities dominated and enriched in Actinobacteria, in particular Streptomyces, in the lowland genotypes, and in Alphaproteobacteria, specifically Sphingobium, in the upland genotypes. Our comprehensive root analysis serves as a snapshot of host-specific bacterial and fungal associations of switchgrass in the field and confirms that host-selected microbiomes persist after transfer to non-native soil.
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Affiliation(s)
- Esther Singer
- Department of Energy Joint Genome InstituteWalnut CreekCAUSA
| | - Jason Bonnette
- Department of Integrative Biology, University of Texas AustinAustinTXUSA
| | - Shawn C. Kenaley
- School of Integrative Plant Science, Cornell UniversityIthacaNYUSA
| | - Tanja Woyke
- Department of Energy Joint Genome InstituteWalnut CreekCAUSA
| | - Thomas E. Juenger
- Department of Integrative Biology, University of Texas AustinAustinTXUSA
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13
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Poudel HP, Sanciangco MD, Kaeppler SM, Buell CR, Casler MD. Quantitative Trait Loci for Freezing Tolerance in a Lowland x Upland Switchgrass Population. FRONTIERS IN PLANT SCIENCE 2019; 10:372. [PMID: 30984223 PMCID: PMC6450214 DOI: 10.3389/fpls.2019.00372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/11/2019] [Indexed: 05/20/2023]
Abstract
Low-temperature related abiotic stress is an important factor affecting winter survival in lowland switchgrass when grown in northern latitudes in the United States. A better understanding of the genetic architecture of freezing tolerance in switchgrass will aid the development of lowland switchgrass cultivars with improved winter survival. The objectives of this study were to conduct a freezing tolerance assessment, generate a genetic map using single nucleotide polymorphism (SNP) markers, and identify QTL (quantitative trait loci) associated with freezing tolerance in a lowland × upland switchgrass population. A pseudo-F2 mapping population was generated from an initial cross between the lowland population Ellsworth and the upland cultivar Summer. The segregating progenies were screened for freezing tolerance in a controlled-environment facility. Two clonal replicates of each genotype were tested at six different treatment temperatures ranging from -15 to -5°C at an interval of 2°C for two time periods. Tiller emergence (days) and tiller number were recorded following the recovery of each genotype with the hypothesis that upland genotype is the source for higher tiller number and early tiller emergence. Survivorship of the pseudo-F2 population ranged from 89% at -5°C to 5% at -15°C with an average LT50 of -9.7°C. Genotype had a significant effect on all traits except tiller number at -15°C. A linkage map was constructed from bi-allelic single nucleotide polymorphism markers generated using exome capture sequencing. The final map consisted of 1618 markers and 2626 cM, with an average inter-marker distance of 1.8 cM. Six significant QTL were identified, one each on chromosomes 1K, 5K, 5N, 6K, 6N, and 9K, for the following traits: tiller number, tiller emergence days and LT50. A comparative genomics study revealed important freezing tolerance genes/proteins, such as COR47, DREB2B, zinc finger-CCCH, WRKY, GIGANTEA, HSP70, and NRT2, among others that reside within the 1.5 LOD confidence interval of the identified QTL.
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Affiliation(s)
- Hari P. Poudel
- Department of Agronomy, University of Wisconsin–Madison, Madison, WI, United States
| | - Millicent D. Sanciangco
- Department of Plant Biology, Plant Resilience Institute, and MSU AgBioResearch, Michigan State University, East Lansing, MI, United States
| | - Shawn M. Kaeppler
- Department of Agronomy, University of Wisconsin–Madison, Madison, WI, United States
| | - C. Robin Buell
- Department of Plant Biology, Plant Resilience Institute, and MSU AgBioResearch, Michigan State University, East Lansing, MI, United States
| | - Michael D. Casler
- U.S. Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service, Madison, WI, United States
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14
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Clifton‐Brown J, Harfouche A, Casler MD, Dylan Jones H, Macalpine WJ, Murphy‐Bokern D, Smart LB, Adler A, Ashman C, Awty‐Carroll D, Bastien C, Bopper S, Botnari V, Brancourt‐Hulmel M, Chen Z, Clark LV, Cosentino S, Dalton S, Davey C, Dolstra O, Donnison I, Flavell R, Greef J, Hanley S, Hastings A, Hertzberg M, Hsu T, Huang LS, Iurato A, Jensen E, Jin X, Jørgensen U, Kiesel A, Kim D, Liu J, McCalmont JP, McMahon BG, Mos M, Robson P, Sacks EJ, Sandu A, Scalici G, Schwarz K, Scordia D, Shafiei R, Shield I, Slavov G, Stanton BJ, Swaminathan K, Taylor G, Torres AF, Trindade LM, Tschaplinski T, Tuskan GA, Yamada T, Yeon Yu C, Zalesny RS, Zong J, Lewandowski I. Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar. GLOBAL CHANGE BIOLOGY. BIOENERGY 2019; 11:118-151. [PMID: 30854028 PMCID: PMC6392185 DOI: 10.1111/gcbb.12566] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/18/2018] [Indexed: 05/07/2023]
Abstract
Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output-input energy ratios: namely Panicum virgatum (switchgrass), species of the genera Miscanthus (miscanthus), Salix (willow) and Populus (poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed-based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5 years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass-scale deployment of PBCs.
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Affiliation(s)
- John Clifton‐Brown
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Antoine Harfouche
- Department for Innovation in Biological, Agrofood and Forest systemsUniversity of TusciaViterboItaly
| | | | - Huw Dylan Jones
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | | | | | - Lawrence B. Smart
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityGenevaNew York
| | - Anneli Adler
- SweTree Technologies ABUmeåSweden
- Institute of Crop Production EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Chris Ashman
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Danny Awty‐Carroll
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | | | - Sebastian Bopper
- Department of Seed Science and Technology, Institute of Plant Breeding, Seed Science and Population GeneticsUniversity of HohenheimStuttgartGermany
| | - Vasile Botnari
- Institute of Genetics, Physiology and Plant Protection (IGFPP) of Academy of Sciences of MoldovaChisinauMoldova
| | | | - Zhiyong Chen
- Insitute of MiscanthusHunan Agricultural UniversityHunan ChangshaChina
| | - Lindsay V. Clark
- Department of Crop Sciences & Center for Advanced Bioenergy and Bioproducts Innovation, 279 Edward R Madigan LaboratoryUniversity of IllinoisUrbanaIllinois
| | - Salvatore Cosentino
- Dipartimento di Agricoltura Alimentazione e AmbienteUniversità degli Studi di CataniaCataniaItaly
| | - Sue Dalton
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Chris Davey
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Oene Dolstra
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Iain Donnison
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | | | - Joerg Greef
- Julius Kuhn‐Institut (JKI)Bundesforschungsinstitut fur KulturpflanzenBraunschweigGermany
| | | | - Astley Hastings
- Institute of Biological and Environmental ScienceUniversity of AberdeenAberdeenUK
| | | | - Tsai‐Wen Hsu
- Taiwan Endemic Species Research Institute (TESRI)Nantou CountyTaiwan
| | - Lin S. Huang
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Antonella Iurato
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Elaine Jensen
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Xiaoli Jin
- Department of Agronomy & The Key Laboratory of Crop Germplasm Resource of Zhejiang ProvinceZhejiang UniversityHangzhouChina
| | - Uffe Jørgensen
- Department of AgroecologyAarhus University Centre for Circular BioeconomyTjeleDenmark
| | - Andreas Kiesel
- Department of Biobased Products and Energy Crops, Institute of Crop ScienceUniversity of HohenheimStuttgartGermany
| | - Do‐Soon Kim
- Department of Plant Sciences, Research Institute of Agriculture & Life Sciences, CALSSeoul National UniversitySeoulKorea
| | - Jianxiu Liu
- Institute of BotanyJiangsu Province and Chinese Academy of SciencesNanjingChina
| | - Jon P. McCalmont
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Bernard G. McMahon
- Natural Resources Research InstituteUniversity of Minnesota – DuluthDuluthMinnesota
| | | | - Paul Robson
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Erik J. Sacks
- Department of Crop Sciences & Center for Advanced Bioenergy and Bioproducts Innovation, 279 Edward R Madigan LaboratoryUniversity of IllinoisUrbanaIllinois
| | - Anatolii Sandu
- Institute of Genetics, Physiology and Plant Protection (IGFPP) of Academy of Sciences of MoldovaChisinauMoldova
| | - Giovanni Scalici
- Dipartimento di Agricoltura Alimentazione e AmbienteUniversità degli Studi di CataniaCataniaItaly
| | - Kai Schwarz
- Julius Kuhn‐Institut (JKI)Bundesforschungsinstitut fur KulturpflanzenBraunschweigGermany
| | - Danilo Scordia
- Dipartimento di Agricoltura Alimentazione e AmbienteUniversità degli Studi di CataniaCataniaItaly
| | - Reza Shafiei
- James Hutton InstituteUniversity of DundeeDundeeUK
| | | | | | | | | | - Gail Taylor
- Biological SciencesUniversity of SouthamptonSouthamptonUK
| | - Andres F. Torres
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Luisa M. Trindade
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Timothy Tschaplinski
- The Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTennessee
| | - Gerald A. Tuskan
- The Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTennessee
| | - Toshihiko Yamada
- Field Science Centre for the Northern BiosphereHokkaido UniversitySapporoJapan
| | - Chang Yeon Yu
- College of Agriculture and Life Sciences 2Kangwon National UniversityChuncheonSouth Korea
| | | | - Junqin Zong
- Institute of BotanyJiangsu Province and Chinese Academy of SciencesNanjingChina
| | - Iris Lewandowski
- Department of Biobased Products and Energy Crops, Institute of Crop ScienceUniversity of HohenheimStuttgartGermany
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15
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Ramstein GP, Evans J, Nandety A, Saha MC, Brummer EC, Kaeppler SM, Buell CR, Casler MD. Candidate Variants for Additive and Interactive Effects on Bioenergy Traits in Switchgrass ( Panicum virgatum L.) Identified by Genome-Wide Association Analyses. THE PLANT GENOME 2018; 11:180002. [PMID: 30512032 DOI: 10.3835/plantgenome2018.01.0002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Switchgrass ( L.) is a promising herbaceous energy crop, but further gains in biomass yield and quality must be achieved to enable a viable bioenergy industry. Developing DNA markers can contribute to such progress, but depiction of genetic bases should be reliable, involving simple additive marker effects and also interactions with genetic backgrounds (e.g., ecotypes) or synergies with other markers. We analyzed plant height, C content, N content, and mineral concentration in a diverse panel consisting of 512 genotypes of upland and lowland ecotypes. We performed association analyses based on exome capture sequencing and tested 439,170 markers for marginal effects, 83,290 markers for marker × ecotype interactions, and up to 311,445 marker pairs for pairwise interactions. Analyses of pairwise interactions focused on subsets of marker pairs preselected on the basis of marginal marker effects, gene ontology annotation, and pairwise marker associations. Our tests identified 12 significant effects. Homology and gene expression information corroborated seven effects and indicated plausible causal pathways: flowering time and lignin synthesis for plant height; plant growth and senescence for C content and mineral concentration. Four pairwise interactions were detected, including three interactions preselected on the basis of pairwise marker correlations. Furthermore, a marker × ecotype interaction and a pairwise interaction were confirmed in an independent switchgrass panel. Our analyses identified reliable candidate variants for important bioenergy traits. Moreover, they exemplified the importance of interactive effects for depicting genetic bases and illustrated the usefulness of preselecting marker pairs for identifying pairwise marker interactions in association studies.
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16
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Bahri BA, Daverdin G, Xu X, Cheng JF, Barry KW, Brummer EC, Devos KM. Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.). BMC Evol Biol 2018; 18:91. [PMID: 29898656 PMCID: PMC6000970 DOI: 10.1186/s12862-018-1193-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 05/15/2018] [Indexed: 11/24/2022] Open
Abstract
Background Advances in genomic technologies have expanded our ability to accurately and exhaustively detect natural genomic variants that can be applied in crop improvement and to increase our knowledge of plant evolution and adaptation. Switchgrass (Panicum virgatum L.), an allotetraploid (2n = 4× = 36) perennial C4 grass (Poaceae family) native to North America and a feedstock crop for cellulosic biofuel production, has a large potential for genetic improvement due to its high genotypic and phenotypic variation. In this study, we analyzed single nucleotide polymorphism (SNP) variation in 372 switchgrass genotypes belonging to 36 accessions for 12 genes putatively involved in biomass production to investigate signatures of selection that could have led to ecotype differentiation and to population adaptation to geographic zones. Results A total of 11,682 SNPs were mined from ~ 15 Gb of sequence data, out of which 251 SNPs were retained after filtering. Population structure analysis largely grouped upland accessions into one subpopulation and lowland accessions into two additional subpopulations. The most frequent SNPs were in homozygous state within accessions. Sixty percent of the exonic SNPs were non-synonymous and, of these, 45% led to non-conservative amino acid changes. The non-conservative SNPs were largely in linkage disequilibrium with one haplotype being predominantly present in upland accessions while the other haplotype was commonly present in lowland accessions. Tajima’s test of neutrality indicated that PHYB, a gene involved in photoperiod response, was under positive selection in the switchgrass population. PHYB carried a SNP leading to a non-conservative amino acid change in the PAS domain, a region that acts as a sensor for light and oxygen in signal transduction. Conclusions Several non-conservative SNPs in genes potentially involved in plant architecture and adaptation have been identified and led to population structure and genetic differentiation of ecotypes in switchgrass. We suggest here that PHYB is a key gene involved in switchgrass natural selection. Further analyses are needed to determine whether any of the non-conservative SNPs identified play a role in the differential adaptation of upland and lowland switchgrass. Electronic supplementary material The online version of this article (10.1186/s12862-018-1193-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bochra A Bahri
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), and Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA. .,Laboratory of Bioaggressors and Integrated Protection in Agriculture, The National Agronomic Institute of Tunisia, University of Carthage, 43 Avenue Charles-Nicolle, 1082, Tunis, Tunisia.
| | - Guillaume Daverdin
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), and Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.,Present address: Vinson Edward Ltd, Faversham, ME13 8UP, UK
| | - Xiangyang Xu
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), and Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.,Present address: USDA-ARS, Wheat, Peanut and Other Field Crops Research Unit, Stillwater, OK, 74075, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, CA, 94598, USA
| | - Kerrie W Barry
- DOE Joint Genome Institute, Walnut Creek, California, CA, 94598, USA
| | - E Charles Brummer
- Plant Breeding Center, Plant Sciences Department, University of California, Davis, CA, 95616, USA
| | - Katrien M Devos
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), and Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
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Evans J, Sanciangco MD, Lau KH, Crisovan E, Barry K, Daum C, Hundley H, Jenkins J, Kennedy M, Kunde-Ramamoorthy G, Vaillancourt B, Acharya A, Schmutz J, Saha M, Kaeppler SM, Brummer EC, Casler MD, Buell CR. Extensive Genetic Diversity is Present within North American Switchgrass Germplasm. THE PLANT GENOME 2018; 11. [PMID: 29505643 DOI: 10.3835/plantgenome2017.06.0055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Switchgrass ( is a perennial native North American grass present in two ecotypes: upland, found primarily in the northern range of switchgrass habitats, and lowland, found largely in the southern reaches of switchgrass habitats. Previous studies focused on a diversity panel of primarily northern switchgrass, so to expand our knowledge of genetic diversity in a broader set of North American switchgrass, exome capture sequence data were generated for 632 additional, primarily lowland individuals. In total, over 37 million single nucleotide polymorphisms (SNPs) were identified and a set of 1.9 million high-confidence SNPs were obtained from 1169 individuals from 140 populations (67 upland, 65 lowland, 8 admixed) were used in downstream analyses of genetic diversity and population structure. Seven separate population groups were identified with moderate genetic differentiation [mean fixation index (Fst) estimate of 0.06] between the lowland and the upland populations. Ecotype-specific and population-specific SNPs were identified for use in germplasm evaluations. Relative to rice ( L.), maize ( L.), soybean [ (L.) Merr.], and Gaertn., analyses of nucleotide diversity revealed a high degree of genetic diversity (0.0135) across all individuals, consistent with the outcrossing mode of reproduction and the polyploidy of switchgrass. This study supports the hypothesis that repeated glaciation events, ploidy barriers, and restricted gene flow caused by flowering time differences have resulted in distinct gene pools across ecotypes and geographic regions. These data provide a resource to associate alleles with traits of interest for forage, restoration, and biofuel feedstock efforts in switchgrass.
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18
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Milano ER, Payne CE, Wolfrum E, Lovell J, Jenkins J, Schmutz J, Juenger TE. Quantitative trait loci for cell wall composition traits measured using near-infrared spectroscopy in the model C4 perennial grass Panicum hallii. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:25. [PMID: 29434668 PMCID: PMC5797396 DOI: 10.1186/s13068-018-1033-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 01/27/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND Biofuels derived from lignocellulosic plant material are an important component of current renewable energy strategies. Improvement efforts in biofuel feedstock crops have been primarily focused on increasing biomass yield with less consideration for tissue quality or composition. Four primary components found in the plant cell wall contribute to the overall quality of plant tissue and conversion characteristics, cellulose and hemicellulose polysaccharides are the primary targets for fuel conversion, while lignin and ash provide structure and defense. We explore the genetic architecture of tissue characteristics using a quantitative trait loci (QTL) mapping approach in Panicum hallii, a model lignocellulosic grass system. Diversity in the mapping population was generated by crossing xeric and mesic varietals, comparative to northern upland and southern lowland ecotypes in switchgrass. We use near-infrared spectroscopy with a primary analytical method to create a P. hallii specific calibration model to quickly quantify cell wall components. RESULTS Ash, lignin, glucan, and xylan comprise 68% of total dry biomass in P. hallii: comparable to other feedstocks. We identified 14 QTL and one epistatic interaction across these four cell wall traits and found almost half of the QTL to localize to a single linkage group. CONCLUSIONS Panicum hallii serves as the genomic model for its close relative and emerging biofuel crop, switchgrass (P. virgatum). We used high throughput phenotyping to map genomic regions that impact natural variation in leaf tissue composition. Understanding the genetic architecture of tissue traits in a tractable model grass system will lead to a better understanding of cell wall structure as well as provide genomic resources for bioenergy crop breeding programs.
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Affiliation(s)
- Elizabeth R. Milano
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712 USA
| | - Courtney E. Payne
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Ed Wolfrum
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - John Lovell
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712 USA
| | - Jerry Jenkins
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Thomas E. Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712 USA
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19
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Chen G, Zhang W, Fang J, Dong L. Identification of massive molecular markers in Echinochloa phyllopogon using a restriction-site associated DNA approach. PLANT DIVERSITY 2017; 39:287-293. [PMID: 30159521 PMCID: PMC6112297 DOI: 10.1016/j.pld.2017.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 08/23/2017] [Accepted: 08/28/2017] [Indexed: 06/08/2023]
Abstract
Echinochloa phyllopogon proliferation seriously threatens rice production worldwide. We combined a restriction-site associated DNA (RAD) approach with Illumina DNA sequencing for rapid and mass discovery of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for E. phyllopogon. RAD tags were generated from the genomic DNA of two E. phyllopogon plants, and sequenced to produce 5197.7 Mb and 5242.9 Mb high quality sequences, respectively. The GC content of E. phyllopogon was 45.8%, which is high for monocots. In total, 4710 putative SSRs were identified in 4132 contigs, which permitted the design of PCR primers for E. phyllopogon. Most repeat motifs among the SSRs identified were dinucleotide (>82%), and most of these SSRs were four motif-repeats (>75%). The most frequent motif was AT, accounting for 36.3%-37.2%, followed by AG and AC. In total, 78 putative polymorphic SSR loci were found. A total of 49,179 SNPs were discovered between the two samples of E. phyllopogon, 67.1% of which were transversions and 32.9% were transitions. We used eight SSRs to study the genetic diversity of four E. phyllopogon populations collected from rice fields in China and all eight loci tested were polymorphic.
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Affiliation(s)
- Guoqi Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China (Nanjing Agricultural University), Ministry of Agriculture, Nanjing 210095, China
| | - Wei Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China (Nanjing Agricultural University), Ministry of Agriculture, Nanjing 210095, China
| | - Jiapeng Fang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China (Nanjing Agricultural University), Ministry of Agriculture, Nanjing 210095, China
| | - Liyao Dong
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China (Nanjing Agricultural University), Ministry of Agriculture, Nanjing 210095, China
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20
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Chen S, Kaeppler SM, Vogel KP, Casler MD. Selection Signatures in Four Lignin Genes from Switchgrass Populations Divergently Selected for In Vitro Dry Matter Digestibility. PLoS One 2016; 11:e0167005. [PMID: 27893787 PMCID: PMC5125650 DOI: 10.1371/journal.pone.0167005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/07/2016] [Indexed: 12/28/2022] Open
Abstract
Switchgrass is undergoing development as a dedicated cellulosic bioenergy crop. Fermentation of lignocellulosic biomass to ethanol in a bioenergy system or to volatile fatty acids in a livestock production system is strongly and negatively influenced by lignification of cell walls. This study detects specific loci that exhibit selection signatures across switchgrass breeding populations that differ in in vitro dry matter digestibility (IVDMD), ethanol yield, and lignin concentration. Allele frequency changes in candidate genes were used to detect loci under selection. Out of the 183 polymorphisms identified in the four candidate genes, twenty-five loci in the intron regions and four loci in coding regions were found to display a selection signature. All loci in the coding regions are synonymous substitutions. Selection in both directions were observed on polymorphisms that appeared to be under selection. Genetic diversity and linkage disequilibrium within the candidate genes were low. The recurrent divergent selection caused excessive moderate allele frequencies in the cycle 3 reduced lignin population as compared to the base population. This study provides valuable insight on genetic changes occurring in short-term selection in the polyploid populations, and discovered potential markers for breeding switchgrass with improved biomass quality.
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Affiliation(s)
- Shiyu Chen
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Shawn M. Kaeppler
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Energy, Great Lakes Bioenergy Research Center, Madison, Wisconsin, United States of America
| | - Kenneth P. Vogel
- USDA-ARS, Grain, Forage, and Bioenergy Research Unit, Lincoln, Nebraska, United States of America
- Department of Agronomy & Horticulture, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Michael D. Casler
- Department of Energy, Great Lakes Bioenergy Research Center, Madison, Wisconsin, United States of America
- USDA-ARS, U.S. Dairy Forage Research Center, Madison, Wisconsin, United States of America
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21
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Milano ER, Lowry DB, Juenger TE. The Genetic Basis of Upland/Lowland Ecotype Divergence in Switchgrass ( Panicum virgatum). G3 (BETHESDA, MD.) 2016; 6:3561-3570. [PMID: 27613751 PMCID: PMC5100855 DOI: 10.1534/g3.116.032763] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/30/2016] [Indexed: 12/29/2022]
Abstract
The evolution of locally adapted ecotypes is a common phenomenon that generates diversity within plant species. However, we know surprisingly little about the genetic mechanisms underlying the locally adapted traits involved in ecotype formation. The genetic architecture underlying locally adapted traits dictates how an organism will respond to environmental selection pressures, and has major implications for evolutionary ecology, conservation, and crop breeding. To understand the genetic architecture underlying the divergence of switchgrass (Panicum virgatum) ecotypes, we constructed a genetic mapping population through a four-way outbred cross between two northern upland and two southern lowland accessions. Trait segregation in this mapping population was largely consistent with multiple independent loci controlling the suite of traits that characterizes ecotype divergence. We assembled a joint linkage map using ddRADseq, and mapped quantitative trait loci (QTL) for traits that are divergent between ecotypes, including flowering time, plant size, physiological processes, and disease resistance. Overall, we found that most QTL had small to intermediate effects. While we identified colocalizing QTL for multiple traits, we did not find any large-effect QTL that clearly controlled multiple traits through pleiotropy or tight physical linkage. These results indicate that ecologically important traits in switchgrass have a complex genetic basis, and that similar loci may underlie divergence across the geographic range of the ecotypes.
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Affiliation(s)
- Elizabeth R Milano
- Department of Integrative Biology, The University of Texas at Austin, Texas 78712
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Texas 78712
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22
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Morris GP, Hu Z, Grabowski PP, Borevitz JO, de Graaff M, Miller RM, Jastrow JD. Genotypic diversity effects on biomass production in native perennial bioenergy cropping systems. GLOBAL CHANGE BIOLOGY. BIOENERGY 2016; 8:1000-1014. [PMID: 27668013 PMCID: PMC5019262 DOI: 10.1111/gcbb.12309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 08/20/2015] [Indexed: 05/07/2023]
Abstract
The perennial grass species that are being developed as biomass feedstock crops harbor extensive genotypic diversity, but the effects of this diversity on biomass production are not well understood. We investigated the effects of genotypic diversity in switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii) on perennial biomass cropping systems in two experiments conducted over 2008-2014 at a 5.4-ha fertile field site in northeastern Illinois, USA. We varied levels of switchgrass and big bluestem genotypic diversity using various local and nonlocal cultivars - under low or high species diversity, with or without nitrogen inputs - and quantified establishment, biomass yield, and biomass composition. In one experiment ('agronomic trial'), we compared three switchgrass cultivars in monoculture to a switchgrass cultivar mixture and three different species mixtures, with or without N fertilization. In another experiment ('diversity gradient'), we varied diversity levels in switchgrass and big bluestem (1, 2, 4, or 6 cultivars per plot), with one or two species per plot. In both experiments, cultivar mixtures produced yields equivalent to or greater than the best cultivars. In the agronomic trial, the three switchgrass mixture showed the highest production overall, though not significantly different than best cultivar monoculture. In the diversity gradient, genotypic mixtures had one-third higher biomass production than the average monoculture, and none of the monocultures were significantly higher yielding than the average mixture. Year-to-year variation in yields was lowest in the three-cultivar switchgrass mixtures and Cave-In-Rock (the southern Illinois cultivar) and also reduced in the mixture of switchgrass and big bluestem relative to the species monocultures. The effects of genotypic diversity on biomass composition were modest relative to the differences among species and genotypes. Our findings suggest that local genotypes can be included in biomass cropping systems without compromising yields and that genotypic mixtures could help provide high, stable yields of high-quality biomass feedstocks.
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Affiliation(s)
| | - Zhenbin Hu
- Department of AgronomyKansas State UniversityManhattanKS66506USA
| | | | - Justin O. Borevitz
- Research School of BiologyAustralian National UniversityActonACT2601Australia
| | | | | | - Julie D. Jastrow
- Biosciences DivisionArgonne National LaboratoryArgonneIL60439USA
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23
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Palik DJ, Snow AA, Stottlemyer AL, Miriti MN, Heaton EA. Relative Performance of Non-Local Cultivars and Local, Wild Populations of Switchgrass (Panicum virgatum) in Competition Experiments. PLoS One 2016; 11:e0154444. [PMID: 27120201 PMCID: PMC4847931 DOI: 10.1371/journal.pone.0154444] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 04/13/2016] [Indexed: 11/18/2022] Open
Abstract
The possibility of increased invasiveness in cultivated varieties of native perennial species is a question of interest in biofuel risk assessment. Competitive success is a key factor in the fitness and invasive potential of perennial plants, and thus the large-scale release of high-yielding biomass cultivars warrants empirical comparisons with local conspecifics in the presence of competitors. We evaluated the performance of non-local cultivars and local wild biotypes of the tallgrass species Panicum virgatum L. (switchgrass) in competition experiments during two growing seasons in Ohio and Iowa. At each location, we measured growth and reproductive traits (plant height, tiller number, flowering time, aboveground biomass, and seed production) of four non-locally sourced cultivars and two locally collected wild biotypes. Plants were grown in common garden experiments under three types of competition, referred to as none, moderate (with Schizachyrium scoparium), and high (with Bromus inermis). In both states, the two “lowland” cultivars grew taller, flowered later, and produced between 2x and 7.5x more biomass and between 3x and 34x more seeds per plant than local wild biotypes, while the other two cultivars were comparable to wild biotypes in these traits. Competition did not affect relative differences among biotypes, with the exception of shoot number, which was more similar among biotypes under high competition. Insights into functional differences between cultivars and wild biotypes are crucial for developing biomass crops while mitigating the potential for invasiveness. Here, two of the four cultivars generally performed better than wild biotypes, indicating that these biotypes may pose more of a risk in terms of their ability to establish vigorous feral populations in new regions outside of their area of origin. Our results support an ongoing assessment of switchgrass cultivars developed for large-scale planting for biofuels.
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Affiliation(s)
- D. J. Palik
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
| | - A. A. Snow
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - A. L. Stottlemyer
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - M. N. Miriti
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - E. A. Heaton
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
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Accuracy of Genomic Prediction in Switchgrass (Panicum virgatum L.) Improved by Accounting for Linkage Disequilibrium. G3-GENES GENOMES GENETICS 2016; 6:1049-62. [PMID: 26869619 PMCID: PMC4825640 DOI: 10.1534/g3.115.024950] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Switchgrass is a relatively high-yielding and environmentally sustainable biomass crop, but further genetic gains in biomass yield must be achieved to make it an economically viable bioenergy feedstock. Genomic selection (GS) is an attractive technology to generate rapid genetic gains in switchgrass, and meet the goals of a substantial displacement of petroleum use with biofuels in the near future. In this study, we empirically assessed prediction procedures for genomic selection in two different populations, consisting of 137 and 110 half-sib families of switchgrass, tested in two locations in the United States for three agronomic traits: dry matter yield, plant height, and heading date. Marker data were produced for the families’ parents by exome capture sequencing, generating up to 141,030 polymorphic markers with available genomic-location and annotation information. We evaluated prediction procedures that varied not only by learning schemes and prediction models, but also by the way the data were preprocessed to account for redundancy in marker information. More complex genomic prediction procedures were generally not significantly more accurate than the simplest procedure, likely due to limited population sizes. Nevertheless, a highly significant gain in prediction accuracy was achieved by transforming the marker data through a marker correlation matrix. Our results suggest that marker-data transformations and, more generally, the account of linkage disequilibrium among markers, offer valuable opportunities for improving prediction procedures in GS. Some of the achieved prediction accuracies should motivate implementation of GS in switchgrass breeding programs.
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25
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Evans J, Crisovan E, Barry K, Daum C, Jenkins J, Kunde-Ramamoorthy G, Nandety A, Ngan CY, Vaillancourt B, Wei CL, Schmutz J, Kaeppler SM, Casler MD, Buell CR. Diversity and population structure of northern switchgrass as revealed through exome capture sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:800-15. [PMID: 26426343 DOI: 10.1111/tpj.13041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/31/2015] [Accepted: 09/03/2015] [Indexed: 05/11/2023]
Abstract
Panicum virgatum L. (switchgrass) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuel feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype, composed of tetraploid and octoploid accessions, and a southern lowland ecotype, composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single-nucleotide polymorphisms (SNPs), of which 1 590 653 high-confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype-restricted, non-synonymous SNPs that are predicted to affect the protein function of CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering, which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near-reference Kanlow population, 17 228 genes present in more copies than in the reference genome (up-CNVs), 112 630 genes present in fewer copies than in the reference genome (down-CNVs) and 14 430 presence/absence variants (PAVs), affecting a total of 9979 genes, including two upland-specific CNV clusters. In total, 45 719 genes were affected by an SNP, CNV, or PAV across the panel, providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.
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Affiliation(s)
- Joseph Evans
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Emily Crisovan
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Kerrie Barry
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Chris Daum
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - Aruna Nandety
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Chew Yee Ngan
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Brieanne Vaillancourt
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Chia-Lin Wei
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Shawn M Kaeppler
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Michael D Casler
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- USDA-ARS, U.S. Dairy Forage Research Center, 1925 Linden Dr., Madison, WI, 53706-1108, USA
| | - Carol Robin Buell
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
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26
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Ecker G, Zalapa J, Auer C. Switchgrass (Panicum virgatum L.) Genotypes Differ between Coastal Sites and Inland Road Corridors in the Northeastern US. PLoS One 2015; 10:e0130414. [PMID: 26125564 PMCID: PMC4488425 DOI: 10.1371/journal.pone.0130414] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/20/2015] [Indexed: 11/18/2022] Open
Abstract
Switchgrass (Panicum virgatum L.) is a North American grass that exhibits vast genetic diversity across its geographic range. In the Northeastern US, local switchgrass populations were restricted to a narrow coastal zone before European settlement, but current populations inhabit inland road verges raising questions about their origin and genetics. These questions are important because switchgrass lines with novel traits are being cultivated as a biofuel feedstock, and gene flow could impact the genetic integrity and distribution of local populations. This study was designed to determine if: 1) switchgrass plants collected in the Long Island Sound Coastal Lowland coastal Level IV ecoregion represented local populations, and 2) switchgrass plants collected from road verges in the adjacent inland regions were most closely related to local coastal populations or switchgrass from other geographic regions. The study used 18 microsatellite markers to infer the genetic relationships between 122 collected switchgrass plants and a reference dataset consisting of 28 cultivars representing ecotypes, ploidy levels, and lineages from North America. Results showed that 84% of 88 plants collected in the coastal plants were most closely aligned with the Lowland tetraploid genetic pool. Among this group, 61 coastal plants were similar to, but distinct from, all Lowland tetraploid cultivars in the reference dataset leading to the designation of a genetic sub-population called the Southern New England Lowland Tetraploids. In contrast, 67% of 34 plants collected in road verges in the inland ecoregions were most similar to two Upland octoploid cultivars; only 24% of roadside plants were Lowland tetraploid. These results suggest that cryptic, non-local genotypes exist in road verges and that gene flow from biofuels plantations could contribute to further changes in switchgrass population genetics in the Northeast.
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Affiliation(s)
- Geoffrey Ecker
- Department of Plant Science and Landscape Architecture, 1390 Storrs Road, U-4163, University of Connecticut, Storrs, Connecticut, 06269, United States of America
- * E-mail:
| | - Juan Zalapa
- USDA, Agricultural Research Service, Vegetable Crops Research Unit, Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin, 53706, United States of America
| | - Carol Auer
- Department of Plant Science and Landscape Architecture, 1390 Storrs Road, U-4163, University of Connecticut, Storrs, Connecticut, 06269, United States of America
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Wang Y, Yang C, Jin Q, Zhou D, Wang S, Yu Y, Yang L. Genome-wide distribution comparative and composition analysis of the SSRs in Poaceae. BMC Genet 2015; 16:18. [PMID: 25886726 PMCID: PMC4333251 DOI: 10.1186/s12863-015-0178-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 02/05/2015] [Indexed: 11/21/2022] Open
Abstract
Background The Poaceae family is of great importance to human beings since it comprises the cereal grasses which are the main sources for human food and animal feed. With the rapid growth of genomic data from Poaceae members, comparative genomics becomes a convinent method to study genetics of diffierent species. The SSRs (Simple Sequence Repeats) are widely used markers in the studies of Poaceae for their high abundance and stability. Results In this study, using the genomic sequences of 9 Poaceae species, we detected 11,993,943 SSR loci and developed 6,799,910 SSR primer pairs. The results show that SSRs are distributed on all the genomic elements in grass. Hexamer is the most frequent motif and AT/TA is the most frequent motif in dimer. The abundance of the SSRs has a positive linear relationship with the recombination rate. SSR sequences in the coding regions involve a higher GC content in the Poaceae than that in the other species. SSRs of 70-80 bp in length showed the highest AT/GC base ratio among all of these loci. The result shows the highest polymorphism rate belongs to the SSRs ranged from 30 bp to 40 bp. Using all the SSR primers of Japonica, nineteen universal primers were selected and located on the genome of the grass family. The information of SSR loci, the SSR primers and the tools of mining and analyzing SSR are provided in the PSSRD (Poaceae SSR Database, http://biodb.sdau.edu.cn/pssrd/). Conclusions Our study and the PSSRD database provide a foundation for the comparative study in the Poaceae and it will accelerate the study on markers application, gene mapping and molecular breeding.
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Affiliation(s)
- Yi Wang
- Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018, China.
| | - Chao Yang
- Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018, China.
| | - Qiaojun Jin
- College of Plant Protection, Northwest Agriculture and Forestry University, Yangling, 712100, China.
| | - Dongjie Zhou
- Agricultural Big-Data Research Center, Shandong Agricultural University, Taian, 271018, China.
| | - Shuangshuang Wang
- Agricultural Big-Data Research Center, Shandong Agricultural University, Taian, 271018, China.
| | - Yuanjie Yu
- Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018, China.
| | - Long Yang
- Key Laboratory of Crop Biology of China, Shandong Agricultural University, Taian, 271018, China. .,Agricultural Big-Data Research Center, Shandong Agricultural University, Taian, 271018, China.
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28
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Liu Y, Zhang X, Tran H, Shan L, Kim J, Childs K, Ervin EH, Frazier T, Zhao B. Assessment of drought tolerance of 49 switchgrass (Panicum virgatum) genotypes using physiological and morphological parameters. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:152. [PMID: 26396590 PMCID: PMC4578271 DOI: 10.1186/s13068-015-0342-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 09/10/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.) is a warm-season C4 grass that is a target lignocellulosic biofuel species. In many regions, drought stress is one of the major limiting factors for switchgrass growth. The objective of this study was to evaluate the drought tolerance of 49 switchgrass genotypes. The relative drought stress tolerance was determined based on a set of parameters including plant height, leaf length, leaf width, leaf sheath length, leaf relative water content (RWC), electrolyte leakage (EL), photosynthetic rate (Pn), stomatal conductance (g s), transpiration rate (Tr), intercellular CO2 concentration (Ci), and water use efficiency (WUE). RESULTS SRAP marker analysis determined that the selected 49 switchgrass genotypes represent a diverse genetic pool of switchgrass germplasm. Principal component analysis (PCA) and drought stress indexes (DSI) of each physiological parameter showed significant differences in the drought stress tolerance among the 49 genotypes. Heatmap and PCA data revealed that physiological parameters are more sensitive than morphological parameters in distinguishing the control and drought treatments. Metabolite profiling data found that under drought stress, the five best drought-tolerant genotypes tended to have higher levels of abscisic acid (ABA), spermine, trehalose, and fructose in comparison to the five most drought-sensitive genotypes. CONCLUSION Based on PCA ranking value, the genotypes TEM-SEC, TEM-LoDorm, BN-13645-64, Alamo, BN-10860-61, BN-12323-69, TEM-SLC, T-2086, T-2100, T-2101, Caddo, and Blackwell-1 had relatively higher ranking values, indicating that they are more tolerant to drought. In contrast, the genotypes Grif Nebraska 28, Grenville-2, Central Iowa Germplasm, Cave-in-Rock, Dacotah, and Nebraska 28 were found to be relatively sensitive to drought stress. By analyzing physiological response parameters and different metabolic profiles, the methods utilized in this study identified drought-tolerant and drought-sensitive switchgrass genotypes. These results provide a foundation for future research directed at understanding the molecular mechanisms underlying switchgrass tolerance to drought.
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Affiliation(s)
- Yiming Liu
- />Department of Crop and Soil Environmental Science, Virginia Tech, 367 Smyth Hall, 185 Ag Quad Ln, Blacksburg, VA 24061 USA
| | - Xunzhong Zhang
- />Department of Crop and Soil Environmental Science, Virginia Tech, 367 Smyth Hall, 185 Ag Quad Ln, Blacksburg, VA 24061 USA
| | - Hong Tran
- />Department of Statistics, Virginia Tech, Blacksburg, VA USA
| | - Liang Shan
- />Department of Statistics, Virginia Tech, Blacksburg, VA USA
| | - Jeongwoon Kim
- />Department of Plant Biology, Michigan State University, East Lansing, MI USA
| | - Kevin Childs
- />Department of Plant Biology, Michigan State University, East Lansing, MI USA
- />Center for Genomics-Enabled Plant Science, Michigan State University, East Lansing, MI USA
| | - Erik H. Ervin
- />Department of Crop and Soil Environmental Science, Virginia Tech, 367 Smyth Hall, 185 Ag Quad Ln, Blacksburg, VA 24061 USA
| | - Taylor Frazier
- />Department of Horticulture, Virginia Tech, 407 Latham Hall, 220 Ag Quad Ln, Blacksburg, VA 24061 USA
| | - Bingyu Zhao
- />Department of Horticulture, Virginia Tech, 407 Latham Hall, 220 Ag Quad Ln, Blacksburg, VA 24061 USA
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Lowry DB, Hernandez K, Taylor SH, Meyer E, Logan TL, Barry KW, Chapman JA, Rokhsar DS, Schmutz J, Juenger TE. The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii. THE NEW PHYTOLOGIST 2015; 205:402-14. [PMID: 25252269 PMCID: PMC4265272 DOI: 10.1111/nph.13027] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 07/31/2014] [Indexed: 05/08/2023]
Abstract
The process of plant speciation often involves the evolution of divergent ecotypes in response to differences in soil water availability between habitats. While the same set of traits is frequently associated with xeric/mesic ecotype divergence, it is unknown whether those traits evolve independently or if they evolve in tandem as a result of genetic colocalization either by pleiotropy or genetic linkage. The self-fertilizing C4 grass species Panicum hallii includes two major ecotypes found in xeric (var. hallii) or mesic (var. filipes) habitats. We constructed the first linkage map for P. hallii by genotyping a reduced representation genomic library of an F2 population derived from an intercross of var. hallii and filipes. We then evaluated the genetic architecture of divergence between these ecotypes through quantitative trait locus (QTL) mapping. Overall, we mapped QTLs for nine morphological traits that are involved in the divergence between the ecotypes. QTLs for five key ecotype-differentiating traits all colocalized to the same region of linkage group five. Leaf physiological traits were less divergent between ecotypes, but we still mapped five physiological QTLs. We also discovered a two-locus Dobzhansky-Muller hybrid incompatibility. Our study suggests that ecotype-differentiating traits may evolve in tandem as a result of genetic colocalization.
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Affiliation(s)
- David B Lowry
- Department of Integrative Biology and Institute for Cellular and Molecular Biology, University of Texas at Austin, 1 University Station C0990, Austin, TX, 78712, USA; Division of Science and Environmental Policy, California State University, Monterey Bay, 100 Campus Center, Seaside, CA, 93955, USA
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Lipka AE, Lu F, Cherney JH, Buckler ES, Casler MD, Costich DE. Accelerating the switchgrass (Panicum virgatum L.) breeding cycle using genomic selection approaches. PLoS One 2014; 9:e112227. [PMID: 25390940 PMCID: PMC4229143 DOI: 10.1371/journal.pone.0112227] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 09/30/2014] [Indexed: 11/28/2022] Open
Abstract
Switchgrass (Panicum virgatum L.) is a perennial grass undergoing development as a biofuel feedstock. One of the most important factors hindering breeding efforts in this species is the need for accurate measurement of biomass yield on a per-hectare basis. Genomic selection on simple-to-measure traits that approximate biomass yield has the potential to significantly speed up the breeding cycle. Recent advances in switchgrass genomic and phenotypic resources are now making it possible to evaluate the potential of genomic selection of such traits. We leveraged these resources to study the ability of three widely-used genomic selection models to predict phenotypic values of morphological and biomass quality traits in an association panel consisting of predominantly northern adapted upland germplasm. High prediction accuracies were obtained for most of the traits, with standability having the highest ten-fold cross validation prediction accuracy (0.52). Moreover, the morphological traits generally had higher prediction accuracies than the biomass quality traits. Nevertheless, our results suggest that the quality of current genomic and phenotypic resources available for switchgrass is sufficiently high for genomic selection to significantly impact breeding efforts for biomass yield.
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Affiliation(s)
- Alexander E. Lipka
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
- * E-mail:
| | - Fei Lu
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
| | - Jerome H. Cherney
- Department of Crop and Soil Sciences, Cornell University, Ithaca, New York, United States of America
| | - Edward S. Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
- Agricultural Research Service, United States Department of Agriculture, Ithaca, New York, United States of America
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Michael D. Casler
- Agricultural Research Service, United States Department of Agriculture, Madison, Wisconsin, United States of America
- Department of Agronomy, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Denise E. Costich
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
- Agricultural Research Service, United States Department of Agriculture, Ithaca, New York, United States of America
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Ahrens CW, Meyer TH, Auer CA. Distribution models for Panicum virgatum (Poaceae) reveal an expanded range in present and future climate regimes in the northeastern United States. AMERICAN JOURNAL OF BOTANY 2014; 101:1886-1894. [PMID: 25366854 DOI: 10.3732/ajb.1400047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY Expanded area cultivated with the bioenergy crop Panicum virgatum (switchgrass) could alter the genetics of native populations through gene flow, so understanding current and future species distribution is a first step toward estimating ecological impacts. We surveyed switchgrass distribution in the northeastern United States and generated statistical models to address hypotheses about current distribution relative to historical records and responses to climate change. METHODS Surveys were conducted on 1600 km of road verges along environmental gradients. Switchgrass abundance became the training data for two multivariate generalized linear models that generated maps representing the probability of switchgrass in road verges. Models were evaluated and the superior model was used with variables from three climate change scenarios for 2050 and 2099. KEY RESULTS Switchgrass populations were found in 41% of roadside plots and up to 188 km from the coast. The environmental variables temperature, urban areas, and sandy soils were positively correlated with switchgrass presence, while elevation, soil pH, and distance to the coast were negatively correlated. The model without spatial autocorrelation performed better. Models and maps incorporating climate change predictions showed a sharp northward shift in suitable habitat. CONCLUSIONS Switchgrass populations in the northeastern United States occur on inland road verges, supporting the idea that species distribution has expanded relative to historical descriptions of a restricted coastal habitat. The optimal model showed that mean temperature, elevation, and urban development were important in switchgrass distribution today, and climate change will increase suitable habitat for future bioenergy production and wild populations.
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Affiliation(s)
- Collin W Ahrens
- Royal Botanic Gardens Melbourne, Birdwood Avenue, Private Bag 2000, South Yarra, VIC 3141, Australia
| | - Thomas H Meyer
- University of Connecticut, Department of Natural Resources and the Environment, 1376 Storrs Road, Unit 4087, Storrs, Connecticut 06269 USA
| | - Carol A Auer
- University of Connecticut, Department of Plant Science, Agricultural Biotechnology Laboratory, 1390 Storrs Road, Unit 4163, Storrs, Connecticut 06269 USA
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32
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Grabowski PP, Morris GP, Casler MD, Borevitz JO. Population genomic variation reveals roles of history, adaptation and ploidy in switchgrass. Mol Ecol 2014; 23:4059-73. [PMID: 24962137 PMCID: PMC4142443 DOI: 10.1111/mec.12845] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 06/19/2014] [Accepted: 06/20/2014] [Indexed: 01/09/2023]
Abstract
Geographic patterns of genetic variation are shaped by multiple evolutionary processes, including genetic drift, migration and natural selection. Switchgrass (Panicum virgatum L.) has strong genetic and adaptive differentiation despite life history characteristics that promote high levels of gene flow and can homogenize intraspecific differences, such as wind-pollination and self-incompatibility. To better understand how historical and contemporary factors shape variation in switchgrass, we use genotyping-by-sequencing to characterize switchgrass from across its range at 98 042 SNPs. Population structuring reflects biogeographic and ploidy differences within and between switchgrass ecotypes and indicates that biogeographic history, ploidy incompatibilities and differential adaptation each have important roles in shaping ecotypic differentiation in switchgrass. At one extreme, we determine that two Panicum taxa are not separate species but are actually conspecific, ecologically divergent types of switchgrass adapted to the extreme conditions of coastal sand dune habitats. Conversely, we identify natural hybrids among lowland and upland ecotypes and visualize their genome-wide patterns of admixture. Furthermore, we determine that genetic differentiation between primarily tetraploid and octoploid lineages is not caused solely by ploidy differences. Rather, genetic diversity in primarily octoploid lineages is consistent with a history of admixture. This suggests that polyploidy in switchgrass is promoted by admixture of diverged lineages, which may be important for maintaining genetic differentiation between switchgrass ecotypes where they are sympatric. These results provide new insights into the mechanisms shaping variation in widespread species and provide a foundation for dissecting the genetic basis of adaptation in switchgrass.
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Affiliation(s)
- Paul P Grabowski
- U.S. Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI 53706, USA; Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
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Clark LV, Brummer JE, Głowacka K, Hall MC, Heo K, Peng J, Yamada T, Yoo JH, Yu CY, Zhao H, Long SP, Sacks EJ. A footprint of past climate change on the diversity and population structure of Miscanthus sinensis. ANNALS OF BOTANY 2014; 114:97-107. [PMID: 24918203 PMCID: PMC4071102 DOI: 10.1093/aob/mcu084] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Miscanthus is a perennial C4 grass that is a leading potential feedstock crop for the emerging bioenergy industry in North America, Europe and China. However, only a single, sterile genotype of M. × giganteus (M×g), a nothospecies derived from diploid M. sinensis (Msi) and tetraploid M. sacchariflorus (Msa), is currently available to farmers for biomass production. To facilitate breeding of Miscanthus, this study characterized genetic diversity and population structure of Msi in its native range of East Asia. METHODS A total of 767 accessions were studied, including 617 Msi from most of its native range in China, Japan and South Korea, and 77 ornamental cultivars and 43 naturalized individuals from the USA. Accessions were evaluated with 21 207 restriction site-associated DNA sequencing single nucleotide polymorphism (SNP) markers, 424 GoldenGate SNPs and ten plastid microsatellite markers. KEY RESULTS Six genetic clusters of Msi from geographically distinct regions in Asia were identified. Genetic data indicated that (1) south-eastern China was the origin of Msi populations found in temperate eastern Asia, which is consistent with this area probably having been a refugium during the last glacial maximum (LGM); (2) Msi migrated directly from south-eastern China to Japan before migrating to the same latitudes in China and Korea, which is consistent with the known sequence of warming post-LGM; (3) ornamental Msi cultivars were derived from the southern Japan population, and US naturalized populations were derived from a sub-set of the ornamental cultivars; and (4) many ornamental cultivars previously described as Msi have hybrid ancestry from Msa and Msi, whereas US naturalized populations of Msi do not. CONCLUSIONS Population structure of Msi was driven by patterns of warming since the LGM, and secondarily by geographical barriers. This study will facilitate germplasm conservation, association analyses and identification of potential heterotic groups for the improvement of Miscanthus as a bioenergy crop.
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Affiliation(s)
- Lindsay V Clark
- University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Joe E Brummer
- Colorado State University, Fort Collins, CO 80523, USA
| | - Katarzyna Głowacka
- University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland
| | | | - Kweon Heo
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Junhua Peng
- Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | | | - Ji Hye Yoo
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Chang Yeon Yu
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Hua Zhao
- Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Stephen P Long
- University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Erik J Sacks
- University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
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Lowry DB, Behrman KD, Grabowski P, Morris GP, Kiniry JR, Juenger TE. Adaptations between ecotypes and along environmental gradients in Panicum virgatum. Am Nat 2014; 183:682-92. [PMID: 24739200 DOI: 10.1086/675760] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Determining the patterns and mechanisms of natural selection in the wild is of fundamental importance to understanding the differentiation of populations and the evolution of new species. However, it is often unknown the extent to which adaptive genetic variation is distributed among ecotypes between distinct habitats versus along large-scale geographic environmental gradients, such as those that track latitude. Classic studies of selection in the wild in switchgrass, Panicum virgatum, tested for adaptation at both of these levels of natural variation. Here we review what these field experiments and modern agronomic field trials have taught us about natural variation and selection at both the ecotype and environmental gradient levels in P. virgatum. With recent genome sequencing efforts in P. virgatum, it is poised to become an excellent system for understanding the adaptation of grassland species across the eastern half of North America. The identification of genetic loci involved in different types of adaptations will help to understand the evolutionary mechanisms of diversification within P. virgatum and provide useful information for the breeding of high-yielding cultivars for different ecoregions.
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Affiliation(s)
- David B Lowry
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
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Casler MD, Vogel KP. Selection for Biomass Yield in Upland, Lowland, and Hybrid Switchgrass. CROP SCIENCE 2014. [PMID: 0 DOI: 10.2135/cropsci2013.04.0239] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Affiliation(s)
- Michael D. Casler
- USDA‐ARSU.S. Dairy Forage Research Center1925 Linden Dr.MadisonWI53706‐1108
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Mutegi E, Stottlemyer AL, Snow AA, Sweeney PM. Genetic Structure of Remnant Populations and Cultivars of Switchgrass (Panicum virgatum) in the Context of Prairie Conservation and Restoration. Restor Ecol 2013. [DOI: 10.1111/rec.12070] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Evans Mutegi
- Department of Evolution, Ecology and Organismal Biology; Ohio State University; Columbus OH 43210 U.S.A
| | - Amy L. Stottlemyer
- Department of Evolution, Ecology and Organismal Biology; Ohio State University; Columbus OH 43210 U.S.A
| | - Allison A. Snow
- Department of Evolution, Ecology and Organismal Biology; Ohio State University; Columbus OH 43210 U.S.A
| | - Patricia M. Sweeney
- Department of Evolution, Ecology and Organismal Biology; Ohio State University; Columbus OH 43210 U.S.A
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Lowry DB, Purmal CT, Juenger TE. A population genetic transect of Panicum hallii (Poaceae). AMERICAN JOURNAL OF BOTANY 2013; 100:592-601. [PMID: 23425558 DOI: 10.3732/ajb.1200379] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
PREMISE OF STUDY Understanding the relationship between climate, adaptation, and population structure is of fundamental importance to botanists because these factors are crucial for the evolution of biodiversity and the response of species to future climate change. Panicum hallii is an emerging model system for perennial grass and bioenergy research, yet very little is known about the relationship between climate and population structure in this system. • METHODS We analyzed geographic population differentiation across 39 populations of P. hallii along a longitudinal transect from the savannas of central Texas through the deserts of Arizona and New Mexico. A combination of morphological and genetic (microsatellite) analysis was used to explore patterns of population structure. • KEY RESULTS We found strong differentiation between high elevation western desert populations and lower elevation eastern populations of P. hallii, with a pronounced break in structure occurring in western Texas. In addition, we confirmed that there are high levels of morphological and genetic structure between previous recognized varieties (var. hallii and var. filipes) within this species. • CONCLUSIONS The results of this study suggest that patterns of population structure within P. hallii may be driven by climatic variation over space. Overall, this study lays the groundwork for future studies on the genetics of local adaptation and reproductive isolation in this system.
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Affiliation(s)
- David B Lowry
- Section of Integrative Biology, The University of Texas at Austin, 1 University Station C0930, Austin, TX 78712, USA.
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Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genet 2013; 9:e1003215. [PMID: 23349638 PMCID: PMC3547862 DOI: 10.1371/journal.pgen.1003215] [Citation(s) in RCA: 399] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 11/19/2012] [Indexed: 01/01/2023] Open
Abstract
Switchgrass (Panicum virgatum L.) is a perennial grass that has been designated as an herbaceous model biofuel crop for the United States of America. To facilitate accelerated breeding programs of switchgrass, we developed both an association panel and linkage populations for genome-wide association study (GWAS) and genomic selection (GS). All of the 840 individuals were then genotyped using genotyping by sequencing (GBS), generating 350 GB of sequence in total. As a highly heterozygous polyploid (tetraploid and octoploid) species lacking a reference genome, switchgrass is highly intractable with earlier methodologies of single nucleotide polymorphism (SNP) discovery. To access the genetic diversity of species like switchgrass, we developed a SNP discovery pipeline based on a network approach called the Universal Network-Enabled Analysis Kit (UNEAK). Complexities that hinder single nucleotide polymorphism discovery, such as repeats, paralogs, and sequencing errors, are easily resolved with UNEAK. Here, 1.2 million putative SNPs were discovered in a diverse collection of primarily upland, northern-adapted switchgrass populations. Further analysis of this data set revealed the fundamentally diploid nature of tetraploid switchgrass. Taking advantage of the high conservation of genome structure between switchgrass and foxtail millet (Setaria italica (L.) P. Beauv.), two parent-specific, synteny-based, ultra high-density linkage maps containing a total of 88,217 SNPs were constructed. Also, our results showed clear patterns of isolation-by-distance and isolation-by-ploidy in natural populations of switchgrass. Phylogenetic analysis supported a general south-to-north migration path of switchgrass. In addition, this analysis suggested that upland tetraploid arose from upland octoploid. All together, this study provides unparalleled insights into the diversity, genomic complexity, population structure, phylogeny, phylogeography, ploidy, and evolutionary dynamics of switchgrass. Recent advances in sequencing technologies have enabled large-scale surveys of genetic diversity in model species with a wholly or partly sequenced reference genome. However, thousands of key species, which are essential for food, health, energy, and ecology, do not have reference genomes. To accelerate their breeding cycle via marker assisted selection, high-throughput genotyping is required for these valuable species, in spite of the absence of reference genomes. Based on genotyping by sequencing (GBS) technology, we developed a new single nucleotide polymorphism (SNP) discovery protocol, the Universal Network-Enabled Analysis Kit (UNEAK), which can be widely used in any species, regardless of genome complexity or the availability of a reference genome. Here we test this protocol on switchgrass, currently the prime energy crop species in the United States of America. In addition to the discovery of over a million SNPs and construction of high-density linkage maps, we provide novel insights into the genome complexity, ploidy, phylogeny, and evolution of switchgrass. This is only the beginning: we believe UNEAK offers the key to the exploration and exploitation of the genetic diversity of thousands of non-model species.
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Liu L, Wu Y. Development of a genome-wide multiple duplex-SSR protocol and its applications for the identification of selfed progeny in switchgrass. BMC Genomics 2012; 13:522. [PMID: 23031617 PMCID: PMC3533973 DOI: 10.1186/1471-2164-13-522] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 10/01/2012] [Indexed: 12/01/2022] Open
Abstract
Background Switchgrass (Panicum virgatum) is a herbaceous crop for the cellulosic biofuel feedstock development in the USA and Europe. As switchgrass is a naturally outcrossing species, accurate identification of selfed progeny is important to producing inbreds, which can be used in the production of heterotic hybrids. Development of a technically reliable, time-saving and easily used marker system is needed to quantify and characterize breeding origin of progeny plants of targeted parents. Results Genome-wide screening of 915 mapped microsatellite (simple sequence repeat, SSR) markers was conducted, and 842 (92.0%) produced clear and scorable bands on a pooled DNA sample of eight switchgrass varieties. A total of 166 primer pairs were selected on the basis of their relatively even distribution in switchgrass genome and PCR amplification quality on 16 tetraploid genotypes. Mean polymorphic information content value for the 166 markers was 0.810 ranging from 0.116 to 0.959. From them, a core set of 48 loci, which had been mapped on 17 linkage groups, was further tested and optimized to develop 24 sets of duplex markers. Most of (up to 87.5%) targeted, but non-allelic amplicons within each duplex were separated by more than 10-bp. Using the established duplex PCR protocol, selfing ratio (i.e., selfed/all progeny x100%) was identified as 0% for a randomly selected open-pollinated ‘Kanlow’ genotype grown in the field, 15.4% for 22 field-grown plants of bagged inflorescences, and 77.3% for a selected plant grown in a growth chamber. Conclusions The study developed a duplex SSR-based PCR protocol consisting of 48 markers, providing ample choices of non-tightly-linked loci in switchgrass whole genome, and representing a powerful, time-saving and easily used method for the identification of selfed progeny in switchgrass. The protocol should be a valuable tool in switchgrass breeding efforts.
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Affiliation(s)
- Linglong Liu
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, 74078-6028, USA
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Young HA, Sarath G, Tobias CM. Karyotype variation is indicative of subgenomic and ecotypic differentiation in switchgrass. BMC PLANT BIOLOGY 2012; 12:117. [PMID: 22834676 PMCID: PMC3492167 DOI: 10.1186/1471-2229-12-117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 07/11/2012] [Indexed: 05/07/2023]
Abstract
BACKGROUND Karyotypes can provide information about taxonomic relationships, genetic aberrations, and the evolutionary origins of species. However, differentiation of the tiny chromosomes of switchgrass (Panicum virgatum L.) and creation of a standard karyotype for this bioenergy crop has not been accomplished due to lack of distinguishing features and polyploidy. RESULTS A cytogenetic study was conducted on a dihaploid individual (2n = 2X = 18) of switchgrass to establish a chromosome karyotype. Size differences, condensation patterns, and arm-length ratios were used as identifying features and fluorescence in-situ hybridization (FISH) assigned 5S and 45S rDNA loci to chromosomes 7 and 2 respectively. Both a maize CentC and a native switchgrass centromeric repeat (PviCentC) that shared 73% sequence identity demonstrated a strong signal on chromosome 3. However, only the PviCentC probe labeled the centromeres of all chromosomes. Unexpected PviCentC and 5S rDNA hybidization patterns were consistent with severe reduction or total deletion of these repeats in one subgenome. These patterns were maintained in tetraploid and octoploid individuals. The 45S rDNA repeat produced the expected number of loci in dihaploid, tetraploid and octoploid individuals. Differences observed at the 5S rDNA loci between the upland and lowland ecotypes of switchgrass provided a basis for distinguishing these subpopulations. CONCLUSION Collectively, these results provide a quantitative karyotype of switchgrass chromosomes. FISH analyses indicate genetic divergence between subgenomes and allow for the classification of switchgrass plants belonging to divergent genetic pools. Furthermore, the karyotype structure and cytogenetic analysis of switchgrass provides a framework for future genetic and genomic studies.
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Affiliation(s)
- Hugh A Young
- Genomics and Gene Discovery Research Unit, USDA-Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Gautam Sarath
- USDA Central-East Regional Biomass Center, 137 Keim Hall, East Campus, UNL, Lincoln, NE, 68583, USA
| | - Christian M Tobias
- Genomics and Gene Discovery Research Unit, USDA-Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
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Meyer E, Logan TL, Juenger TE. Transcriptome analysis and gene expression atlas for Panicum hallii var. filipes, a diploid model for biofuel research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:879-90. [PMID: 22324449 DOI: 10.1111/j.1365-313x.2012.04938.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Panicum hallii is an emerging model for genetic studies of agronomic traits in Panicum, presenting a tractable diploid alternative study system to the tetra- or octaploid biofuel crop switchgrass (Panicum virgatum). To characterize the gene complement in P. hallii var. filipes and enable gene expression analysis in this system we sequenced, assembled, and annotated the transcriptome. Over 300 Mb of normalized cDNA prepared from multiple tissues and treatments was sequenced using 454-Titanium, producing an annotated assembly including 15 422 unique gene names. Comparison with other grass genomes identified putative P. hallii homologs for >14 000 previously characterized genes. We also developed an atlas of gene expression across tissues and stages using RNA-Seq (the quantitative analysis of short cDNA reads). SOLiD sequencing and quantitative analysis of more than 40 million cDNA tags identified substantial variation in expression profiles among tissues, consistent with known functional differences. Putative homologs were found for all enzymes in the phenylpropanoid pathway leading to lignin biosynthesis, including genes with known effects on biomass conversion efficiency. The resources developed here will enable studies of the genes underlying variation in cell wall composition, drought tolerance, and biomass production in Panicum.
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Affiliation(s)
- Eli Meyer
- Section of Integrative Biology, University of Texas - Austin, 1 University Station, Austin, TX 78712, USA.
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Liu L, Wu Y, Wang Y, Samuels T. A high-density simple sequence repeat-based genetic linkage map of switchgrass. G3 (BETHESDA, MD.) 2012; 2:357-70. [PMID: 22413090 PMCID: PMC3291506 DOI: 10.1534/g3.111.001503] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Accepted: 01/16/2012] [Indexed: 11/18/2022]
Abstract
Switchgrass (Panicum virgatum) has been identified as a promising cellulosic biofuel crop in the United States. Construction of a genetic linkage map is fundamental for switchgrass molecular breeding and the elucidation of its genetic mechanisms for economically important traits. In this study, a novel population consisting of 139 selfed progeny of a northern lowland genotype, NL 94 LYE 16X13, was used to construct a linkage map. A total of 2493 simple sequence repeat markers were screened for polymorphism. Of 506 polymorphic loci, 80.8% showed a goodness-of-fit of 1:2:1 segregation ratio. Among 469 linked loci on the framework map, 241 coupling vs. 228 repulsion phase linkages were detected that conformed to a 1:1 ratio, confirming disomic inheritance. A total of 499 loci were mapped to 18 linkage groups (LG), of which the cumulative length was 2085.2 cM, with an average marker interval of 4.2 cM. Nine homeologous LG pairs were identified based on multi-allele markers and comparative genomic analysis. Two clusters of segregation-distorted loci were identified on LG 5b and 9b, respectively. Comparative analysis indicated a one-to-one relationship between nine switchgrass homeologous groups and nine foxtail millet (Setaria italica) chromosomes, suggesting strong homology between the two species. The linkage map derived from selfing a heterozygous parent, instead of two separate maps usually constructed for a cross-fertilized species, provides a new genetic framework to facilitate genomics research, quantitative trait locus (QTL) mapping, and marker-assisted breeding.
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Affiliation(s)
- Linglong Liu
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, Oklahoma 74078
| | - Yanqi Wu
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, Oklahoma 74078
| | | | - Tim Samuels
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, Oklahoma 74078
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Morris GP, Grabowski PP, Borevitz JO. Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape. Mol Ecol 2011; 20:4938-52. [PMID: 22060816 DOI: 10.1111/j.1365-294x.2011.05335.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Connecting broad-scale patterns of genetic variation and population structure to genetic diversity on a landscape is a key step towards understanding historical processes of migration and adaptation. New genomic approaches can be used to increase the resolution of phylogeographic studies while reducing locus sampling effects and circumventing ascertainment bias. Here, we use a novel approach based on high-throughput sequencing to characterize genetic diversity in complete chloroplast genomes and >10,000 nuclear loci in switchgrass, at continental and landscape scales. Switchgrass is a North American tallgrass species, which is widely used in conservation and perennial biomass production, and shows strong ecotypic adaptation and population structure across the continental range. We sequenced 40.9 billion base pairs from 24 individuals from across the species' range and 20 individuals from the Indiana Dunes. Analysis of plastome sequence revealed 203 variable SNP sites that define eight haplogroups, which are differentiated by 4-127 SNPs and confirmed by patterns of indel variation. These include three deeply divergent haplogroups, which correspond to the previously described lowland-upland ecotypic split and a novel upland haplogroup split that dates to the mid-Pleistocene. Most of the plastome haplogroup diversity present in the northern switchgrass range, including in the Indiana Dunes, originated in the mid- or upper Pleistocene prior to the most recent postglacial recolonization. Furthermore, a recently colonized landscape feature (approximately 150 ya) in the Indiana Dunes contains several deeply divergent upland haplogroups. Nuclear markers also support a deep lowland-upland split, followed by limited gene flow, and show extensive gene flow in the local population of the Indiana Dunes.
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Affiliation(s)
- Geoffrey P Morris
- Department of Ecology and Evolution, University of Chicago, 1101 East 57th St., Chicago, IL 60637, USA.
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