Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.)

Bahri, Bochra A.; Daverdin, Guillaume; Xu, Xiangyang; Cheng, Jan-Fang; Barry, Kerrie W.; Brummer, E. Charles; Devos, Katrien M.

doi:10.1186/s12862-018-1193-2

Title: Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.)

Journal Article · 13 June 2018 · BMC Evolutionary Biology (Online)

DOI: https://doi.org/10.1186/s12862-018-1193-2 · OSTI ID:1544018

; Daverdin, Guillaume; Xu, Xiangyang; Cheng, Jan-Fang; Barry, Kerrie W.; Brummer, E. Charles; Devos, Katrien M.

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1544018

Journal Information:: BMC Evolutionary Biology (Online), Journal Name: BMC Evolutionary Biology (Online) Journal Issue: 1 Vol. 18; ISSN 1471-2148

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (164)

Investigation of genomic organization in switchgrass (Panicum virgatum L.) using DNA markers Missaoui, A. M.; Paterson, A. H.; Bouton, J. H. Theoretical and Applied Genetics, Vol. 110, Issue 8 https://doi.org/10.1007/s00122-005-1935-6	journal	April 2005
Mitochondrial and microsatellite data show close genetic relationships between Dibothriocephalus latus from South America (Argentina) and Europe (the Alpine lakes region) Radačovská, Alžbeta; Čisovská Bazsalovicsová, Eva; Králová-Hromadová, Ivica Parasitology Research, Vol. 121, Issue 12 https://doi.org/10.1007/s00436-022-07690-6	journal	October 2022
Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences Zhang, Yunwei; Zalapa, Juan E.; Jakubowski, Andrew R. Genetica, Vol. 139, Issue 7 https://doi.org/10.1007/s10709-011-9597-6	journal	July 2011
Molecular Markers for the Classification of Switchgrass (Panicum virgatum L.) Germplasm and to Assess Genetic Diversity in Three Synthetic Switchgrass Populations Missaoui, Ali M.; Paterson, Andrew H.; Bouton, Joseph H. Genetic Resources and Crop Evolution, Vol. 53, Issue 6 https://doi.org/10.1007/s10722-005-3878-9	journal	March 2006
Farm-Scale Production Cost of Switchgrass for Biomass Perrin, Richard; Vogel, Kenneth; Schmer, Marty BioEnergy Research, Vol. 1, Issue 1 https://doi.org/10.1007/s12155-008-9005-y	journal	March 2008
Genetic Diversity in Switchgrass Collections Assessed by EST-SSR Markers Narasimhamoorthy, B.; Saha, M. C.; Swaller, T. BioEnergy Research, Vol. 1, Issue 2 https://doi.org/10.1007/s12155-008-9011-0	journal	June 2008
Changes in Mean and Genetic Variance During Two Cycles of Within-family Selection in Switchgrass Casler, Michael D. BioEnergy Research, Vol. 3, Issue 1 https://doi.org/10.1007/s12155-009-9071-9	journal	January 2010
Genetic Diversity of Twelve Switchgrass Populations Using Molecular and Morphological Markers Cortese, Laura M.; Honig, Joshua; Miller, Chris BioEnergy Research, Vol. 3, Issue 3 https://doi.org/10.1007/s12155-010-9078-2	journal	January 2010
Development of switchgrass (Panicum virgatum) as a bioenergy feedstock in the United States McLaughlin, Samuel B.; Adams Kszos, Lynn Biomass and Bioenergy, Vol. 28, Issue 6 https://doi.org/10.1016/j.biombioe.2004.05.006	journal	June 2005
The Timing of Developmental Transitions in Plants Bäurle, Isabel; Dean, Caroline Cell, Vol. 125, Issue 4 https://doi.org/10.1016/j.cell.2006.05.005	journal	May 2006
Molecular breeding of switchgrass for use as a biofuel crop Bouton, Joseph H. Current Opinion in Genetics & Development, Vol. 17, Issue 6 https://doi.org/10.1016/j.gde.2007.08.012	journal	December 2007
Genetic Modification of Herbaceous Plants for Feed and Fuel Vogel, K. Critical Reviews in Plant Sciences, Vol. 20, Issue 1 https://doi.org/10.1016/s0735-2689(01)80011-3	journal	January 2001
Reversal of dormancy in switchgrass with low-light photoperiod extension Van Esbroeck, G. Bioresource Technology, Vol. 91, Issue 2 https://doi.org/10.1016/s0960-8524(03)00178-0	journal	January 2004
Decoupling of differentiation between traits and their underlying genes in response to divergent selection Kremer, A.; Le Corre, V. Heredity, Vol. 108, Issue 4 https://doi.org/10.1038/hdy.2011.81	journal	September 2011
An expanded library of orthogonal split inteins enables modular multi-peptide assemblies Pinto, Filipe; Thornton, Ella Lucille; Wang, Baojun Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-15272-2	journal	March 2020
Subdivision and haplotype structure in natural populations of Arabidopsis lyrata Wright, Stephen I.; Lauga, Beatrice; Charlesworth, Deborah Molecular Ecology, Vol. 12, Issue 5 https://doi.org/10.1046/j.1365-294x.2003.01743.x	journal	May 2003
Temperature-based population segregation in birch Kelly, Colleen K.; Chase, Mark W.; de Bruijn, Anette Ecology Letters, Vol. 6, Issue 2 https://doi.org/10.1046/j.1461-0248.2003.00402.x	journal	February 2003
Net energy of cellulosic ethanol from switchgrass Schmer, M. R.; Vogel, K. P.; Mitchell, R. B. Proceedings of the National Academy of Sciences, Vol. 105, Issue 2 https://doi.org/10.1073/pnas.0704767105	journal	January 2008
Natural selection in action during speciation Via, S. Proceedings of the National Academy of Sciences, Vol. 106, Issue Supplement_1 https://doi.org/10.1073/pnas.0901397106	journal	June 2009
Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars Cavanagh, C. R.; Chao, S.; Wang, S. Proceedings of the National Academy of Sciences, Vol. 110, Issue 20 https://doi.org/10.1073/pnas.1217133110	journal	April 2013
Recent development of the neutral theory viewed from the Wrightian tradition of theoretical population genetics. Kimura, M. Proceedings of the National Academy of Sciences, Vol. 88, Issue 14 https://doi.org/10.1073/pnas.88.14.5969	journal	July 1991
The Biology and Agronomy of Switchgrass for Biofuels Parrish, David J.; Fike, John H. Critical Reviews in Plant Sciences, Vol. 24, Issue 5-6 https://doi.org/10.1080/07352680500316433	journal	September 2005
Primer Premier 5 Lalitha, S. Biotech Software & Internet Report, Vol. 1, Issue 6 https://doi.org/10.1089/152791600459894	journal	December 2000
The Sequence Alignment/Map format and SAMtools Li, H.; Handsaker, B.; Wysoker, A. Bioinformatics, Vol. 25, Issue 16 https://doi.org/10.1093/bioinformatics/btp352	journal	June 2009
GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update Peakall, R.; Smouse, P. E. Bioinformatics, Vol. 28, Issue 19 https://doi.org/10.1093/bioinformatics/bts460	journal	July 2012
teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance. Doebley, J.; Stec, A.; Gustus, C. Genetics, Vol. 141, Issue 1 https://doi.org/10.1093/genetics/141.1.333	journal	September 1995
Inference of Population Structure Using Multilocus Genotype Data Pritchard, Jonathan K.; Stephens, Matthew; Donnelly, Peter Genetics, Vol. 155, Issue 2 https://doi.org/10.1093/genetics/155.2.945	journal	June 2000
Genetic Variability at Neutral Markers, Quantitative Trait Loci and Trait in a Subdivided Population Under Selection Le Corre, Valérie; Kremer, Antoine Genetics, Vol. 164, Issue 3 https://doi.org/10.1093/genetics/164.3.1205	journal	July 2003
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 Tamura, Koichiro; Stecher, Glen; Peterson, Daniel Molecular Biology and Evolution, Vol. 30, Issue 12 https://doi.org/10.1093/molbev/mst197	journal	October 2013
The Molecular Basis of Diversity in the Photoperiodic Flowering Responses of Arabidopsis and Rice Hayama, Ryosuke; Coupland, George Plant Physiology, Vol. 135, Issue 2 https://doi.org/10.1104/pp.104.042614	journal	June 2004
Control of Flowering Time: Interacting Pathways as a Basis for Diversity Mouradov, Aidyn; Cremer, Frédéric; Coupland, George The Plant Cell, Vol. 14, Issue suppl 1 https://doi.org/10.1105/tpc.001362	journal	May 2002
Divergent selection and heterogeneous genomic divergence Nosil, Patrik; Funk, Daniel J.; Ortiz-Barrientos, Daniel Molecular Ecology, Vol. 18, Issue 3 https://doi.org/10.1111/j.1365-294x.2008.03946.x	journal	February 2009
Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array Wang, Shichen; Wong, Debbie; Forrest, Kerrie Plant Biotechnology Journal, Vol. 12, Issue 6 https://doi.org/10.1111/pbi.12183	journal	March 2014
Diversity and population structure of northern switchgrass as revealed through exome capture sequencing Evans, Joseph; Crisovan, Emily; Barry, Kerrie The Plant Journal, Vol. 84, Issue 4 https://doi.org/10.1111/tpj.13041	journal	November 2015
SNP Markers and Their Impact on Plant Breeding Mammadov, Jafar; Aggarwal, Rajat; Buyyarapu, Ramesh International Journal of Plant Genomics, Vol. 2012 https://doi.org/10.1155/2012/728398	journal	January 2012
New genomic resources for switchgrass: a BAC library and comparative analysis of homoeologous genomic regions harboring bioenergy traits Saski, Christopher A.; Li, Zhigang; Feltus, Frank A. BMC Genomics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2164-12-369	journal	July 2011
Functional intronic polymorphisms: Buried treasure awaiting discovery within our genes Cooper, David N. Human Genomics, Vol. 4, Issue 5 https://doi.org/10.1186/1479-7364-4-5-284	journal	January 2010
Characterisation of a functional intronic polymorphism in the human growth hormone (GHI) gene Millar, David S.; Horan, Martin; Chuzhanova, Nadia A. Human Genomics, Vol. 4, Issue 5 https://doi.org/10.1186/1479-7364-4-5-289	journal	January 2010
The Pattern of Polymorphism in Arabidopsis thaliana Nordborg, Magnus; Hu, Tina T.; Ishino, Yoko PLoS Biology, Vol. 3, Issue 7 https://doi.org/10.1371/journal.pbio.0030196	journal	May 2005
Identification of Common Genetic Variation That Modulates Alternative Splicing Hull, Jeremy; Campino, Susana; Rowlands, Kate PLoS Genetics, Vol. 3, Issue 6 https://doi.org/10.1371/journal.pgen.0030099	journal	January 2007
Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol Lu, Fei; Lipka, Alexander E.; Glaubitz, Jeff PLoS Genetics, Vol. 9, Issue 1 https://doi.org/10.1371/journal.pgen.1003215	journal	January 2013
Complete Switchgrass Genetic Maps Reveal Subgenome Collinearity, Preferential Pairing and Multilocus Interactions Okada, Miki; Lanzatella, Christina; Saha, Malay C. Genetics, Vol. 185, Issue 3 https://doi.org/10.1534/genetics.110.113910	journal	April 2010
Spatial forecasting of switchgrass productivity under current and future climate change scenarios Behrman, Kathrine D.; Kiniry, James R.; Winchell, Michael Ecological Applications, Vol. 23, Issue 1 https://doi.org/10.1890/12-0436.1	journal	January 2013
Biomass Yield, Phenology, and Survival of Diverse Switchgrass Cultivars and Experimental Strains in Western North Dakota Berdahl, J. D.; Frank, A. B.; Krupinsky, J. M. Agronomy Journal, Vol. 97, Issue 2 https://doi.org/10.2134/agronj2005.0549	journal	January 2005
Biomass Production in Switchgrass across the United States: Database Description and Determinants of Yield Wullschleger, S. D.; Davis, E. B.; Borsuk, M. E. Agronomy Journal, Vol. 102, Issue 4 https://doi.org/10.2134/agronj2010.0087	journal	January 2010
Diversity among Populations of Switchgrass Based on RAPD Markers Gunter, L. E.; Tuskan, G. A.; Wullschleger, S. D. Crop Science, Vol. 36, Issue 4 https://doi.org/10.2135/cropsci1996.0011183x003600040034x	journal	January 1996
Incompatibility Systems in Switchgrass Martínez-Reyna, J. M.; Vogel, K. P. Crop Science, Vol. 42, Issue 6 https://doi.org/10.2135/cropsci2002.1800	journal	January 2002
Latitudinal Adaptation of Switchgrass Populations Casler, M. D.; Vogel, K. P.; Taliaferro, C. M. Crop Science, Vol. 44, Issue 1 https://doi.org/10.2135/cropsci2004.2930	journal	January 2004
Latitudinal and Longitudinal Adaptation of Switchgrass Populations Casler, M. D.; Vogel, K. P.; Taliaferro, C. M. Crop Science, Vol. 47, Issue 6 https://doi.org/10.2135/cropsci2006.12.0780	journal	January 2007
Genetic Diversity, Plant Adaptation Regions, and Gene Pools for Switchgrass Casler, Michael D.; Stendal, Chad A.; Kapich, Ludmila Crop Science, Vol. 47, Issue 6 https://doi.org/10.2135/cropsci2006.12.0797	journal	January 2007
Switchgrass Germplasm Resources Casler, Michael D.; Vogel, Kenneth P.; Harrison, Melanie Crop Science, Vol. 55, Issue 6 https://doi.org/10.2135/cropsci2015.02.0076	journal	January 2015
Application of Genomic Tools in Plant Breeding M. Perez-de-Castro, A.; Vilanova, S.; Canizares, J. Current Genomics, Vol. 13, Issue 3 https://doi.org/10.2174/138920212800543084	journal	April 2012
The Role of Ecotypic Variation in the Distribution of the Central Grassland of North America McMillan, Calvin Ecological Monographs, Vol. 29, Issue 4 https://doi.org/10.2307/1942132	journal	February 1959
Next-generation sequencing applications for wheat crop improvement Berkman, Paul J.; Lai, Kaitao; Lorenc, Michał T. American Journal of Botany, Vol. 99, Issue 2 https://doi.org/10.3732/ajb.1100309	journal	February 2012
SWISS-MODEL and the Swiss-Pdb Viewer: An environment for comparative protein modeling Guex, Nicolas; Peitsch, Manuel C. Electrophoresis, Vol. 18, Issue 15, p. 2714-2723 https://doi.org/10.1002/elps.1150181505	journal	January 1997
Ecotypic Differentiation Within four North American Prairie Grasses. ii. Behavioral Variation Within Transplanted Community Fractions McMillan, Calvin American Journal of Botany, Vol. 52, Issue 1 https://doi.org/10.1002/j.1537-2197.1965.tb06757.x	journal	January 1965
Investigation of genomic organization in switchgrass (Panicum virgatum L.) using DNA markers Missaoui, A. M.; Paterson, A. H.; Bouton, J. H. Theoretical and Applied Genetics, Vol. 110, Issue 8 https://doi.org/10.1007/s00122-005-1935-6	journal	April 2005
Development of highly polymorphic SNP markers from the complexity reduced portion of maize [Zea mays L.] genome for use in marker-assisted breeding Mammadov, Jafar A.; Chen, Wei; Ren, Ruihua Theoretical and Applied Genetics, Vol. 121, Issue 3 https://doi.org/10.1007/s00122-010-1331-8	journal	April 2010
Hierarchical classification of switchgrass genotypes using SSR and chloroplast sequences: ecotypes, ploidies, gene pools, and cultivars Zalapa, J. E.; Price, D. L.; Kaeppler, S. M. Theoretical and Applied Genetics, Vol. 122, Issue 4 https://doi.org/10.1007/s00122-010-1488-1	journal	November 2010
Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences Zhang, Yunwei; Zalapa, Juan E.; Jakubowski, Andrew R. Genetica, Vol. 139, Issue 7 https://doi.org/10.1007/s10709-011-9597-6	journal	July 2011
Molecular Markers for the Classification of Switchgrass (Panicum virgatum L.) Germplasm and to Assess Genetic Diversity in Three Synthetic Switchgrass Populations Missaoui, Ali M.; Paterson, Andrew H.; Bouton, Joseph H. Genetic Resources and Crop Evolution, Vol. 53, Issue 6 https://doi.org/10.1007/s10722-005-3878-9	journal	March 2006
Single-locus EST-SSR markers for characterization of population genetic diversity and structure across ploidy levels in switchgrass (Panicum virgatum L.) Okada, Miki; Lanzatella, Christina; Tobias, Christian M. Genetic Resources and Crop Evolution, Vol. 58, Issue 6 https://doi.org/10.1007/s10722-010-9631-z	journal	November 2010
A comparative analysis of population structure of a forest tree, Eucalyptus globulus (Myrtaceae), using microsatellite markers and quantitative traits Steane, Dorothy A.; Conod, Natalie; Jones, Rebecca C. Tree Genetics & Genomes, Vol. 2, Issue 1 https://doi.org/10.1007/s11295-005-0028-7	journal	January 2006
Farm-Scale Production Cost of Switchgrass for Biomass Perrin, Richard; Vogel, Kenneth; Schmer, Marty BioEnergy Research, Vol. 1, Issue 1 https://doi.org/10.1007/s12155-008-9005-y	journal	March 2008
Genetic Diversity in Switchgrass Collections Assessed by EST-SSR Markers Narasimhamoorthy, B.; Saha, M. C.; Swaller, T. BioEnergy Research, Vol. 1, Issue 2 https://doi.org/10.1007/s12155-008-9011-0	journal	June 2008
Changes in Mean and Genetic Variance During Two Cycles of Within-family Selection in Switchgrass Casler, Michael D. BioEnergy Research, Vol. 3, Issue 1 https://doi.org/10.1007/s12155-009-9071-9	journal	January 2010
Genetic Diversity of Twelve Switchgrass Populations Using Molecular and Morphological Markers Cortese, Laura M.; Honig, Joshua; Miller, Chris BioEnergy Research, Vol. 3, Issue 3 https://doi.org/10.1007/s12155-010-9078-2	journal	January 2010
Perennial Biomass Grasses and the Mason–Dixon Line: Comparative Productivity across Latitudes in the Southern Great Plains Kiniry, J. R.; Anderson, L. C.; Johnson, M. -V. V. BioEnergy Research, Vol. 6, Issue 1 https://doi.org/10.1007/s12155-012-9254-7	journal	September 2012
Linkage Maps of Lowland and Upland Tetraploid Switchgrass Ecotypes Serba, Desalegn; Wu, Limin; Daverdin, Guillaume BioEnergy Research, Vol. 6, Issue 3 https://doi.org/10.1007/s12155-013-9315-6	journal	March 2013
Evolution of switchgrass (Panicum virgatum L.) based on sequences of the nuclear gene encoding plastid acetyl-CoA carboxylase Huang, Shaoxing; Su, Xiujuan; Haselkorn, Robert Plant Science, Vol. 164, Issue 1 https://doi.org/10.1016/S0168-9452(02)00327-8	journal	January 2003
Reversal of dormancy in switchgrass with low-light photoperiod extension Van Esbroeck, G. Bioresource Technology, Vol. 91, Issue 2 https://doi.org/10.1016/S0960-8524(03)00178-0	journal	January 2004
Switchgrass cultivars and germplasm for biomass feedstock production in Texas Sanderson, M. A.; Reed, R. L.; Ocumpaugh, W. R. Bioresource Technology, Vol. 67, Issue 3 https://doi.org/10.1016/S0960-8524(98)00132-1	journal	March 1999
The development and current status of perennial rhizomatous grasses as energy crops in the US and Europe Lewandowski, Iris; Scurlock, Jonathan M. O.; Lindvall, Eva Biomass and Bioenergy, Vol. 25, Issue 4 https://doi.org/10.1016/S0961-9534(03)00030-8	journal	October 2003
Development of switchgrass (Panicum virgatum) as a bioenergy feedstock in the United States McLaughlin, Samuel B.; Adams Kszos, Lynn Biomass and Bioenergy, Vol. 28, Issue 6 https://doi.org/10.1016/j.biombioe.2004.05.006	journal	June 2005
The Timing of Developmental Transitions in Plants Bäurle, Isabel; Dean, Caroline Cell, Vol. 125, Issue 4 https://doi.org/10.1016/j.cell.2006.05.005	journal	May 2006
Molecular breeding of switchgrass for use as a biofuel crop Bouton, Joseph H. Current Opinion in Genetics & Development, Vol. 17, Issue 6 https://doi.org/10.1016/j.gde.2007.08.012	journal	December 2007
A common intronic variant of CXCR3 is functionally associated with gene expression levels and the polymorphic immune cell responses to stimuli Choi, Jung-Won; Park, Choon-Sik; Hwang, Minyoung Journal of Allergy and Clinical Immunology, Vol. 122, Issue 6 https://doi.org/10.1016/j.jaci.2008.09.026	journal	December 2008
Genetic Modification of Herbaceous Plants for Feed and Fuel Vogel, K. Critical Reviews in Plant Sciences, Vol. 20, Issue 1 https://doi.org/10.1016/s0735-2689(01)80011-3	journal	January 2001
CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis Suárez-López, Paula; Wheatley, Kay; Robson, Frances Nature, Vol. 410, Issue 6832 https://doi.org/10.1038/35074138	journal	April 2001
Adaptive protein evolution at the Adh locus in Drosophila McDonald, John H.; Kreitman, Martin Nature, Vol. 351, Issue 6328 https://doi.org/10.1038/351652a0	journal	June 1991
Decoupling of differentiation between traits and their underlying genes in response to divergent selection Kremer, A.; Le Corre, V. Heredity, Vol. 108, Issue 4 https://doi.org/10.1038/hdy.2011.81	journal	September 2011
The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana Balasubramanian, Sureshkumar; Sureshkumar, Sridevi; Agrawal, Mitesh Nature Genetics, Vol. 38, Issue 6 https://doi.org/10.1038/ng1818	journal	May 2006
Ancient genomes reveal social and genetic structure of Late Neolithic Switzerland Furtwängler, Anja; Rohrlach, A. B.; Lamnidis, Thiseas C. Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-15560-x	journal	April 2020
SPOCD1 is an essential executor of piRNA-directed de novo DNA methylation Zoch, Ansgar; Auchynnikava, Tania; Berrens, Rebecca V. Nature, Vol. 584, Issue 7822 https://doi.org/10.1038/s41586-020-2557-5	journal	July 2020
Subdivision and haplotype structure in natural populations of Arabidopsis lyrata Wright, Stephen I.; Lauga, Beatrice; Charlesworth, Deborah Molecular Ecology, Vol. 12, Issue 5 https://doi.org/10.1046/j.1365-294X.2003.01743.x	journal	May 2003
Temperature-based population segregation in birch Kelly, Colleen K.; Chase, Mark W.; de Bruijn, Anette Ecology Letters, Vol. 6, Issue 2 https://doi.org/10.1046/j.1461-0248.2003.00402.x	journal	February 2003
Net energy of cellulosic ethanol from switchgrass Schmer, M. R.; Vogel, K. P.; Mitchell, R. B. Proceedings of the National Academy of Sciences, Vol. 105, Issue 2 https://doi.org/10.1073/pnas.0704767105	journal	January 2008
Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light Filiault, D. L.; Wessinger, C. A.; Dinneny, J. R. Proceedings of the National Academy of Sciences, Vol. 105, Issue 8 https://doi.org/10.1073/pnas.0712174105	journal	February 2008
Natural selection in action during speciation Via, S. Proceedings of the National Academy of Sciences, Vol. 106, Issue Supplement_1 https://doi.org/10.1073/pnas.0901397106	journal	June 2009
Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars Cavanagh, C. R.; Chao, S.; Wang, S. Proceedings of the National Academy of Sciences, Vol. 110, Issue 20 https://doi.org/10.1073/pnas.1217133110	journal	April 2013
Recent development of the neutral theory viewed from the Wrightian tradition of theoretical population genetics. Kimura, M. Proceedings of the National Academy of Sciences, Vol. 88, Issue 14 https://doi.org/10.1073/pnas.88.14.5969	journal	July 1991
Evidence for adaptive evolution of the G6pd gene in the Drosophila melanogaster and Drosophila simulans lineages. Eanes, W. F.; Kirchner, M.; Yoon, J. Proceedings of the National Academy of Sciences, Vol. 90, Issue 16 https://doi.org/10.1073/pnas.90.16.7475	journal	August 1993
The Biology and Agronomy of Switchgrass for Biofuels Parrish, David J.; Fike, John H. Critical Reviews in Plant Sciences, Vol. 24, Issue 5-6 https://doi.org/10.1080/07352680500316433	journal	September 2005
Genetic Modification of Herbaceous Plants for Feed and Fuel Vogel, Kenneth P.; Jung, Hans-Joachim G. Critical Reviews in Plant Sciences, Vol. 20, Issue 1 https://doi.org/10.1080/20013591099173	journal	January 2001
A Comparison of Bayesian Methods for Haplotype Reconstruction from Population Genotype Data Stephens, Matthew; Donnelly, Peter The American Journal of Human Genetics, Vol. 73, Issue 5 https://doi.org/10.1086/379378	journal	November 2003
Adaptations between Ecotypes and along Environmental Gradients in Panicum virgatum Lowry, David B.; Behrman, Kathrine D.; Grabowski, Paul The American Naturalist, Vol. 183, Issue 5 https://doi.org/10.1086/675760	journal	May 2014
Primer Premier 5 Lalitha, S. Biotech Software & Internet Report, Vol. 1, Issue 6 https://doi.org/10.1089/152791600459894	journal	December 2000
The Sequence Alignment/Map format and SAMtools Li, H.; Handsaker, B.; Wysoker, A. Bioinformatics, Vol. 25, Issue 16 https://doi.org/10.1093/bioinformatics/btp352	journal	June 2009
GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update Peakall, R.; Smouse, P. E. Bioinformatics, Vol. 28, Issue 19 https://doi.org/10.1093/bioinformatics/bts460	journal	July 2012
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Tajima, F. Genetics, Vol. 123, Issue 3 https://doi.org/10.1093/genetics/123.3.585	journal	November 1989
teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance. Doebley, J.; Stec, A.; Gustus, C. Genetics, Vol. 141, Issue 1 https://doi.org/10.1093/genetics/141.1.333	journal	September 1995
The Molecular Evolution of terminal ear1, a Regulatory Gene in the Genus Zea White, Shawn E.; Doebley, John F. Genetics, Vol. 153, Issue 3 https://doi.org/10.1093/genetics/153.3.1455	journal	November 1999
Inference of Population Structure Using Multilocus Genotype Data Pritchard, Jonathan K.; Stephens, Matthew; Donnelly, Peter Genetics, Vol. 155, Issue 2 https://doi.org/10.1093/genetics/155.2.945	journal	June 2000
Genetic Variability at Neutral Markers, Quantitative Trait Loci and Trait in a Subdivided Population Under Selection Le Corre, Valérie; Kremer, Antoine Genetics, Vol. 164, Issue 3 https://doi.org/10.1093/genetics/164.3.1205	journal	July 2003
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 Tamura, Koichiro; Stecher, Glen; Peterson, Daniel Molecular Biology and Evolution, Vol. 30, Issue 12 https://doi.org/10.1093/molbev/mst197	journal	October 2013
Keeping It Local: Evidence for Positive Selection in Swedish Arabidopsis thaliana Huber, Christian D.; Nordborg, Magnus; Hermisson, Joachim Molecular Biology and Evolution, Vol. 31, Issue 11 https://doi.org/10.1093/molbev/msu247	journal	August 2014
DNA Polymorphism at the FRIGIDA Gene in Arabidopsis thaliana: Extensive Nonsynonymous Variation Is Consistent with Local Selection for Flowering Time Le Corre, Valérie; Roux, Fabrice; Reboud, Xavier Molecular Biology and Evolution, Vol. 19, Issue 8 https://doi.org/10.1093/oxfordjournals.molbev.a004187	journal	August 2002
Temperature signals contribute to the timing of photoperiodic growth cessation and bud set in poplar Rohde, A.; Bastien, C.; Boerjan, W. Tree Physiology, Vol. 31, Issue 5 https://doi.org/10.1093/treephys/tpr038	journal	May 2011
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data McKenna, A.; Hanna, M.; Banks, E. Genome Research, Vol. 20, Issue 9 https://doi.org/10.1101/gr.107524.110	journal	July 2010
The Molecular Basis of Diversity in the Photoperiodic Flowering Responses of Arabidopsis and Rice Hayama, Ryosuke; Coupland, George Plant Physiology, Vol. 135, Issue 2 https://doi.org/10.1104/pp.104.042614	journal	June 2004
Role of FRIGIDA and FLOWERING LOCUS C in Determining Variation in Flowering Time of Arabidopsis Shindo, Chikako; Aranzana, Maria Jose; Lister, Clare Plant Physiology, Vol. 138, Issue 2 https://doi.org/10.1104/pp.105.061309	journal	May 2005
Control of Flowering Time: Interacting Pathways as a Basis for Diversity Mouradov, Aidyn; Cremer, Frédéric; Coupland, George The Plant Cell, Vol. 14, Issue suppl 1 https://doi.org/10.1105/tpc.001362	journal	May 2002
cis -Regulatory Elements and Chromatin State Coordinately Control Temporal and Spatial Expression of FLOWERING LOCUS T in Arabidopsis Adrian, Jessika; Farrona, Sara; Reimer, Julia J. The Plant Cell, Vol. 22, Issue 5 https://doi.org/10.1105/tpc.110.074682	journal	May 2010
The age of the grasses and clusters of origins of C ₄ photosynthesis Vicentini, Alberto; Barber, Janet C.; Aliscioni, Sandra S. Global Change Biology, Vol. 14, Issue 12 https://doi.org/10.1111/j.1365-2486.2008.01688.x	journal	December 2008
Divergent selection and heterogeneous genomic divergence Nosil, Patrik; Funk, Daniel J.; Ortiz-Barrientos, Daniel Molecular Ecology, Vol. 18, Issue 3 https://doi.org/10.1111/j.1365-294X.2008.03946.x	journal	February 2009
Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape: GENOMIC DIVERSITY IN SWITCHGRASS Morris, Geoffrey P.; Grabowski, Paul P.; Borevitz, Justin O. Molecular Ecology, Vol. 20, Issue 23 https://doi.org/10.1111/j.1365-294X.2011.05335.x	journal	November 2011
Genetic basis of local adaptation and flowering time variation in Arabidopsis lyrata : GENETIC BASIS OF LOCAL ADAPTATION IN Leinonen, PÄIvi H.; Remington, David L.; LeppÄLÄ, Johanna Molecular Ecology, Vol. 22, Issue 3 https://doi.org/10.1111/j.1365-294X.2012.05678.x	journal	June 2012
Adaptive Population Differentiation in Phenology Across a Latitudinal Gradient in European Aspen (Populus Tremula, l.): a Comparison of Neutral Markers, Candidate Genes and Phenotypic Traits Hall, David; Luquez, Virginia; Garcia, Victoria M. Evolution, Vol. 61, Issue 12 https://doi.org/10.1111/j.1558-5646.2007.00230.x	journal	December 2007
Landscape genomics and a common garden trial reveal adaptive differentiation to temperature across Europe in the tree species Alnus glutinosa De Kort, Hanne; Vandepitte, Katrien; Bruun, Hans Henrik Molecular Ecology, Vol. 23, Issue 19 https://doi.org/10.1111/mec.12813	journal	June 2014
Association genetics, geography and ecophysiology link stomatal patterning in Populus trichocarpa with carbon gain and disease resistance trade-offs McKown, Athena D.; Guy, Robert D.; Quamme, Linda Molecular Ecology, Vol. 23, Issue 23 https://doi.org/10.1111/mec.12969	journal	November 2014
Genetic architecture of flowering time differentiation between locally adapted populations of Arabidopsis thaliana Grillo, Michael A.; Li, Changbao; Hammond, Mark New Phytologist, Vol. 197, Issue 4 https://doi.org/10.1111/nph.12109	journal	January 2013
Major QTLs for critical photoperiod and vernalization underlie extensive variation in flowering in the Mimulus guttatus species complex Friedman, Jannice; Willis, John H. New Phytologist, Vol. 199, Issue 2 https://doi.org/10.1111/nph.12260	journal	April 2013
Genotypic variation in traits linked to climate and aboveground productivity in a widespread C ₄ grass: evidence for a functional trait syndrome Aspinwall, Michael J.; Lowry, David B.; Taylor, Samuel H. New Phytologist, Vol. 199, Issue 4 https://doi.org/10.1111/nph.12341	journal	May 2013
Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data Grabowski, Paul P.; Evans, Joseph; Daum, Chris New Phytologist, Vol. 213, Issue 1 https://doi.org/10.1111/nph.14101	journal	July 2016
Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array Wang, Shichen; Wong, Debbie; Forrest, Kerrie Plant Biotechnology Journal, Vol. 12, Issue 6 https://doi.org/10.1111/pbi.12183	journal	March 2014
Diversity and population structure of northern switchgrass as revealed through exome capture sequencing Evans, Joseph; Crisovan, Emily; Barry, Kerrie The Plant Journal, Vol. 84, Issue 4 https://doi.org/10.1111/tpj.13041	journal	November 2015
FT Protein Movement Contributes to Long-Distance Signaling in Floral Induction of Arabidopsis Corbesier, L.; Vincent, C.; Jang, S. Science, Vol. 316, Issue 5827 https://doi.org/10.1126/science.1141752	journal	May 2007
Arabidopsis, the Rosetta Stone of Flowering Time? Simpson, G. G. Science, Vol. 296, Issue 5566 https://doi.org/10.1126/science.296.5566.285	journal	April 2002
New genomic resources for switchgrass: a BAC library and comparative analysis of homoeologous genomic regions harboring bioenergy traits Saski, Christopher A.; Li, Zhigang; Feltus, Frank A. BMC Genomics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2164-12-369	journal	July 2011
Functional intronic polymorphisms: Buried treasure awaiting discovery within our genes Cooper, David N. Human Genomics, Vol. 4, Issue 5 https://doi.org/10.1186/1479-7364-4-5-284	journal	January 2010
Characterisation of a functional intronic polymorphism in the human growth hormone (GHI) gene Millar, David S.; Horan, Martin; Chuzhanova, Nadia A. Human Genomics, Vol. 4, Issue 5 https://doi.org/10.1186/1479-7364-4-5-289	journal	January 2010
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Langmead, Ben; Trapnell, Cole; Pop, Mihai Genome Biology, Vol. 10, Issue 3 https://doi.org/10.1186/gb-2009-10-3-r25	journal	January 2009
Genomics reveals new landscapes for crop improvement Bevan, Michael W.; Uauy, Cristobal Genome Biology, Vol. 14, Issue 6 https://doi.org/10.1186/gb-2013-14-6-206	journal	June 2013
Application of next-generation sequencing technology to study genetic diversity and identify unique SNP markers in bread wheat from Kazakhstan Shavrukov, Yuri; Suchecki, Radoslaw; Eliby, Serik BMC Plant Biology, Vol. 14, Issue 1 https://doi.org/10.1186/s12870-014-0258-7	journal	September 2014
The Pattern of Polymorphism in Arabidopsis thaliana Nordborg, Magnus; Hu, Tina T.; Ishino, Yoko PLoS Biology, Vol. 3, Issue 7 https://doi.org/10.1371/journal.pbio.0030196	journal	May 2005
Identification of Common Genetic Variation That Modulates Alternative Splicing Hull, Jeremy; Campino, Susana; Rowlands, Kate PLoS Genetics, Vol. 3, Issue 6 https://doi.org/10.1371/journal.pgen.0030099	journal	January 2007
Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol Lu, Fei; Lipka, Alexander E.; Glaubitz, Jeff PLoS Genetics, Vol. 9, Issue 1 https://doi.org/10.1371/journal.pgen.1003215	journal	January 2013
Chloroplast Genome Variation in Upland and Lowland Switchgrass Young, Hugh A.; Lanzatella, Christina L.; Sarath, Gautam PLoS ONE, Vol. 6, Issue 8 https://doi.org/10.1371/journal.pone.0023980	journal	August 2011
Five Nuclear Loci Resolve the Polyploid History of Switchgrass (Panicum virgatum L.) and Relatives Triplett, Jimmy K.; Wang, Yunjing; Zhong, Jinshun PLoS ONE, Vol. 7, Issue 6 https://doi.org/10.1371/journal.pone.0038702	journal	June 2012
Elevated Levels of MYB30 in the Phloem Accelerate Flowering in Arabidopsis through the Regulation of FLOWERING LOCUS T Liu, Liangyu; Zhang, Jian; Adrian, Jessika PLoS ONE, Vol. 9, Issue 2 https://doi.org/10.1371/journal.pone.0089799	journal	February 2014
A Multilocus Sequence Survey in Arabidopsis thaliana Reveals a Genome-Wide Departure From a Neutral Model of DNA Sequence Polymorphism Schmid, Karl J.; Ramos-Onsins, Sebastian; Ringys-Beckstein, Henriette Genetics, Vol. 169, Issue 3 https://doi.org/10.1534/genetics.104.033795	journal	January 2005
Cis -regulatory Changes at FLOWERING LOCUS T Mediate Natural Variation in Flowering Responses of Arabidopsis thaliana Schwartz, Christopher; Balasubramanian, Sureshkumar; Warthmann, Norman Genetics, Vol. 183, Issue 2 https://doi.org/10.1534/genetics.109.104984	journal	August 2009
Complete Switchgrass Genetic Maps Reveal Subgenome Collinearity, Preferential Pairing and Multilocus Interactions Okada, Miki; Lanzatella, Christina; Saha, Malay C. Genetics, Vol. 185, Issue 3 https://doi.org/10.1534/genetics.110.113910	journal	April 2010
Spatial forecasting of switchgrass productivity under current and future climate change scenarios Behrman, Kathrine D.; Kiniry, James R.; Winchell, Michael Ecological Applications, Vol. 23, Issue 1 https://doi.org/10.1890/12-0436.1	journal	January 2013
Biomass Yield, Phenology, and Survival of Diverse Switchgrass Cultivars and Experimental Strains in Western North Dakota Berdahl, J. D.; Frank, A. B.; Krupinsky, J. M. Agronomy Journal, Vol. 97, Issue 2 https://doi.org/10.2134/agronj2005.0549	journal	January 2005
Biomass Production in Switchgrass across the United States: Database Description and Determinants of Yield Wullschleger, S. D.; Davis, E. B.; Borsuk, M. E. Agronomy Journal, Vol. 102, Issue 4 https://doi.org/10.2134/agronj2010.0087	journal	January 2010
Estimates of Genetic Parameters in Switchgrass1 Talbert, L. E.; Timothy, D. H.; Burns, J. C. Crop Science, Vol. 23, Issue 4 https://doi.org/10.2135/cropsci1983.0011183X002300040029x	journal	January 1983
Diversity among Populations of Switchgrass Based on RAPD Markers Gunter, L. E.; Tuskan, G. A.; Wullschleger, S. D. Crop Science, Vol. 36, Issue 4 https://doi.org/10.2135/cropsci1996.0011183X003600040034x	journal	January 1996
Chloroplast DNA and Nuclear DNA Content Variations among Cultivars of Switchgrass, Panicum virgatum L. Hultquist, Sherry J.; Vogel, K. P.; Lee, D. J. Crop Science, Vol. 36, Issue 4 https://doi.org/10.2135/cropsci1996.0011183X003600040039x	journal	January 1996
Incompatibility Systems in Switchgrass Martínez-Reyna, J. M.; Vogel, K. P. Crop Science, Vol. 42, Issue 6 https://doi.org/10.2135/cropsci2002.1800	journal	January 2002
Variation between Alamo and Cave‐in‐Rock Switchgrass in Response to Photoperiod Extension van Esbroeck, G. A.; Hussey, M. A.; Sanderson, M. A. Crop Science, Vol. 43, Issue 2 https://doi.org/10.2135/cropsci2003.6390	journal	March 2003
Latitudinal Adaptation of Switchgrass Populations Casler, M. D.; Vogel, K. P.; Taliaferro, C. M. Crop Science, Vol. 44, Issue 1 https://doi.org/10.2135/cropsci2004.2930	journal	January 2004
Latitudinal and Longitudinal Adaptation of Switchgrass Populations Casler, M. D.; Vogel, K. P.; Taliaferro, C. M. Crop Science, Vol. 47, Issue 6 https://doi.org/10.2135/cropsci2006.12.0780	journal	January 2007
Genetic Diversity, Plant Adaptation Regions, and Gene Pools for Switchgrass Casler, Michael D.; Stendal, Chad A.; Kapich, Ludmila Crop Science, Vol. 47, Issue 6 https://doi.org/10.2135/cropsci2006.12.0797	journal	January 2007
Natural Hybrids and Gene Flow between Upland and Lowland Switchgrass Zhang, Yunwei; Zalapa, Juan; Jakubowski, Andrew R. Crop Science, Vol. 51, Issue 6 https://doi.org/10.2135/cropsci2011.02.0104	journal	January 2011
Switchgrass Germplasm Resources Casler, Michael D.; Vogel, Kenneth P.; Harrison, Melanie Crop Science, Vol. 55, Issue 6 https://doi.org/10.2135/cropsci2015.02.0076	journal	January 2015
Application of Genomic Tools in Plant Breeding M. Perez-de-Castro, A.; Vilanova, S.; Canizares, J. Current Genomics, Vol. 13, Issue 3 https://doi.org/10.2174/138920212800543084	journal	April 2012
An Analysis of Variation Between Upland and Lowland Switchgrass, Panicum Virgatum L., in Central Oklahoma Porter, Clyde L. Ecology, Vol. 47, Issue 6 https://doi.org/10.2307/1935646	journal	November 1966
The Role of Ecotypic Variation in the Distribution of the Central Grassland of North America McMillan, Calvin Ecological Monographs, Vol. 29, Issue 4 https://doi.org/10.2307/1942132	journal	February 1959
Ecotypic Differentiation Within Four North American Prairie Grasses. II. Behavioral Variation Within Transplanted Community Fractions McMillan, Calvin American Journal of Botany, Vol. 52, Issue 1 https://doi.org/10.2307/2439975	journal	January 1965
Next-generation sequencing applications for wheat crop improvement Berkman, Paul J.; Lai, Kaitao; Lorenc, Michał T. American Journal of Botany, Vol. 99, Issue 2 https://doi.org/10.3732/ajb.1100309	journal	February 2012
Comparative Genomics in Switchgrass Using 61,585 High-Quality Expressed Sequence Tags Tobias, Christian M.; Sarath, Gautam; Twigg, Paul The Plant Genome Journal, Vol. 1, Issue 2 https://doi.org/10.3835/plantgenome2008.08.0003	journal	January 2008
The Switchgrass Genome: Tools and Strategies Casler, Michael D.; Tobias, Christian M.; Kaeppler, Shawn M. The Plant Genome Journal, Vol. 4, Issue 3 https://doi.org/10.3835/plantgenome2011.10.0026	journal	January 2011
Spatial forecasting of switchgrass productivity under current and future climate change scenarios Behrman, Kathrine D.; Kiniry, James R.; Winchell, Michael Figshare https://doi.org/10.6084/m9.figshare.c.3295646.v1	collection	January 2016

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