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Title: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing

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 genomemore » (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.« less

Authors:
 [1];  [1];  [2];  [2];  [3];  [2];  [4];  [2];  [1];  [2];  [5];  [6];  [7];  [1]
  1. Michigan State Univ., East Lansing, MI (United States). DOE Great Lakes Bioenergy Research Center. Dept. of Plant Biology
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
  4. Univ. of Oklahoma, Norman, OK (United States). Dept. of Microbiology and Plant Biology
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
  6. Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center. Dept. of Agronomy
  7. Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center; USDA-ARS Dairy Forage Research Center, Madison, WI (United States)
Publication Date:
Research Org.:
Univ. of Wisconsin, Madison, WI (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Michigan State Univ., East Lansing, MI (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1438259
Alternate Identifier(s):
OSTI ID: 1616044
Grant/Contract Number:  
FC02-07ER64494; AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
The Plant Journal
Additional Journal Information:
Journal Volume: 84; Journal Issue: 4; Journal ID: ISSN 0960-7412
Publisher:
Society for Experimental Biology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 09 BIOMASS FUELS; Panicum virgatum; exome capture; switchgrass; polyploid; genomics; PRJNA280418

Citation Formats

Evans, Joseph, Crisovan, Emily, Barry, Kerrie, Daum, Chris, Jenkins, Jerry, Kunde-Ramamoorthy, Govindarajan, Nandety, Aruna, Ngan, Chew Yee, Vaillancourt, Brieanne, Wei, Chia-Lin, Schmutz, Jeremy, Kaeppler, Shawn M., Casler, Michael D., and Buell, Carol Robin. Diversity and population structure of northern switchgrass as revealed through exome capture sequencing. United States: N. p., 2015. Web. doi:10.1111/tpj.13041.
Evans, Joseph, Crisovan, Emily, Barry, Kerrie, Daum, Chris, Jenkins, Jerry, Kunde-Ramamoorthy, Govindarajan, Nandety, Aruna, Ngan, Chew Yee, Vaillancourt, Brieanne, Wei, Chia-Lin, Schmutz, Jeremy, Kaeppler, Shawn M., Casler, Michael D., & Buell, Carol Robin. Diversity and population structure of northern switchgrass as revealed through exome capture sequencing. United States. doi:10.1111/tpj.13041.
Evans, Joseph, Crisovan, Emily, Barry, Kerrie, Daum, Chris, Jenkins, Jerry, Kunde-Ramamoorthy, Govindarajan, Nandety, Aruna, Ngan, Chew Yee, Vaillancourt, Brieanne, Wei, Chia-Lin, Schmutz, Jeremy, Kaeppler, Shawn M., Casler, Michael D., and Buell, Carol Robin. Thu . "Diversity and population structure of northern switchgrass as revealed through exome capture sequencing". United States. doi:10.1111/tpj.13041. https://www.osti.gov/servlets/purl/1438259.
@article{osti_1438259,
title = {Diversity and population structure of northern switchgrass as revealed through exome capture sequencing},
author = {Evans, Joseph and Crisovan, Emily and Barry, Kerrie and Daum, Chris and Jenkins, Jerry and Kunde-Ramamoorthy, Govindarajan and Nandety, Aruna and Ngan, Chew Yee and Vaillancourt, Brieanne and Wei, Chia-Lin and Schmutz, Jeremy and Kaeppler, Shawn M. and Casler, Michael D. and Buell, Carol Robin},
abstractNote = {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.},
doi = {10.1111/tpj.13041},
journal = {The Plant Journal},
number = 4,
volume = 84,
place = {United States},
year = {2015},
month = {10}
}

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Cited by: 20 works
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    Works referencing / citing this record:

    Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing
    dataset, December 2015

    • Evans, Joseph; Crisovan, Emily; Barry, Kerrie
    • Dryad Digital Repository-Supplementary information for journal article at DOI: 10.1111/tpj.13041, 10 files
    • DOI: 10.5061/dryad.nh8ph.2

    Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing
    dataset, October 2015

    • Evans, Joseph; Crisovan, Emily; Barry, Kerrie
    • Dryad Digital Repository-Supplementary information for journal article at DOI: 10.1111/tpj.13041, 10 files
    • DOI: 10.5061/dryad.nh8ph.1

    Mechanisms of Floral Induction in Grasses: Something Borrowed, Something New: Figure 1.
    journal, January 2009


    Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics.
    journal, December 1984

    • Saghai-Maroof, M. A.; Soliman, K. M.; Jorgensen, R. A.
    • Proceedings of the National Academy of Sciences, Vol. 81, Issue 24
    • DOI: 10.1073/pnas.81.24.8014

    Easyfig: a genome comparison visualizer
    journal, January 2011


    Net energy of cellulosic ethanol from switchgrass
    journal, January 2008

    • Schmer, M. R.; Vogel, K. P.; Mitchell, R. B.
    • Proceedings of the National Academy of Sciences, Vol. 105, Issue 2
    • DOI: 10.1073/pnas.0704767105

    The Switchgrass Genome: Tools and Strategies
    journal, January 2011


    Chloroplast DNA and Nuclear DNA Content Variations among Cultivars of Switchgrass, Panicum virgatum L.
    journal, January 1996


    Identification of a Selfing Compatible Genotype and Mode of Inheritance in Switchgrass
    journal, December 2011


    The genetic legacy of the Quaternary ice ages
    journal, June 2000


    Latitudinal and Longitudinal Adaptation of Switchgrass Populations
    journal, January 2007


    Leaf Appearance Rate and Final Leaf Number of Switchgrass Cultivars
    journal, January 1997


    Efficient Genome-Wide Detection and Cataloging of EMS-Induced Mutations Using Exome Capture and Next-Generation Sequencing
    journal, April 2014

    • Henry, Isabelle M.; Nagalakshmi, Ugrappa; Lieberman, Meric C.
    • The Plant Cell, Vol. 26, Issue 4
    • DOI: 10.1105/tpc.113.121590

    Sources of Sediment in Lake Pepin on the Upper Mississippi River in Response to Holocene Climatic Changes
    journal, January 2006

    • Kelley, David W.; Brachfeld, Stefanie A.; Nater, Edward A.
    • Journal of Paleolimnology, Vol. 35, Issue 1
    • DOI: 10.1007/s10933-005-8686-x

    CONSTANS and the evolutionary origin of photoperiodic timing of flowering
    journal, January 2011


    The B73 Maize Genome: Complexity, Diversity, and Dynamics
    journal, November 2009

    • Schnable, P. S.; Ware, D.; Fulton, R. S.
    • Science, Vol. 326, Issue 5956, p. 1112-1115
    • DOI: 10.1126/science.1178534

    Regulation and Identity of Florigen: FLOWERING LOCUS T Moves Center Stage
    journal, June 2008


    Chromosome Number and Nuclear DNA Content of Several Switchgrass Populations
    journal, January 1996


    Genetics in geographically structured populations: defining, estimating and interpreting FST
    journal, September 2009

    • Holsinger, Kent E.; Weir, Bruce S.
    • Nature Reviews Genetics, Vol. 10, Issue 9
    • DOI: 10.1038/nrg2611

    Latitudinal Adaptation of Switchgrass Populations
    journal, January 2004


    Predicting Deleterious Amino Acid Substitutions
    journal, May 2001


    The Sequence Alignment/Map format and SAMtools
    journal, June 2009


    Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice
    journal, August 2006


    Estimates of Genetic Parameters in Switchgrass1
    journal, January 1983


    ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
    journal, July 2010

    • Wang, K.; Li, M.; Hakonarson, H.
    • Nucleic Acids Research, Vol. 38, Issue 16
    • DOI: 10.1093/nar/gkq603

    Hd1 , a Major Photoperiod Sensitivity Quantitative Trait Locus in Rice, Is Closely Related to the Arabidopsis Flowering Time Gene CONSTANS
    journal, December 2000

    • Yano, Masahiro; Katayose, Yuichi; Ashikari, Motoyuki
    • The Plant Cell, Vol. 12, Issue 12
    • DOI: 10.1105/tpc.12.12.2473

    Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean
    journal, October 2012


    Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences
    journal, July 2011


    Distinct Copy Number, Coding Sequence, and Locus Methylation Patterns Underlie Rhg1 -Mediated Soybean Resistance to Soybean Cyst Nematode
    journal, April 2014

    • Cook, David E.; Bayless, Adam M.; Wang, Kai
    • Plant Physiology, Vol. 165, Issue 2
    • DOI: 10.1104/pp.114.235952

    HTSeq--a Python framework to work with high-throughput sequencing data
    journal, September 2014


    Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing
    dataset, October 2015

    • Evans, Joseph; Crisovan, Emily; Barry, Kerrie
    • Dryad Digital Repository-Supplementary information for journal article at DOI: 10.1111/tpj.13041, 10 files
    • DOI: 10.5061/dryad.nh8ph.1

    Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing
    dataset, December 2015

    • Evans, Joseph; Crisovan, Emily; Barry, Kerrie
    • Dryad Digital Repository-Supplementary information for journal article at DOI: 10.1111/tpj.13041, 10 files
    • DOI: 10.5061/dryad.nh8ph.2

    A Papaver somniferum 10-Gene Cluster for Synthesis of the Anticancer Alkaloid Noscapine
    journal, May 2012


    Molecular Markers for the Classification of Switchgrass (Panicum virgatum L.) Germplasm and to Assess Genetic Diversity in Three Synthetic Switchgrass Populations
    journal, March 2006

    • Missaoui, Ali M.; Paterson, Andrew H.; Bouton, Joseph H.
    • Genetic Resources and Crop Evolution, Vol. 53, Issue 6
    • DOI: 10.1007/s10722-005-3878-9

    Basic local alignment search tool
    journal, October 1990

    • Altschul, Stephen F.; Gish, Warren; Miller, Webb
    • Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
    • DOI: 10.1016/s0022-2836(05)80360-2

    Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
    journal, August 2013

    • Anders, Simon; McCarthy, Davis J.; Chen, Yunshun
    • Nature Protocols, Vol. 8, Issue 9
    • DOI: 10.1038/nprot.2013.099

    Synergy in a medicinal plant: Antimicrobial action of berberine potentiated by 5'-methoxyhydnocarpin, a multidrug pump inhibitor
    journal, February 2000

    • Stermitz, F. R.; Lorenz, P.; Tawara, J. N.
    • Proceedings of the National Academy of Sciences, Vol. 97, Issue 4
    • DOI: 10.1073/pnas.030540597

    Plant responses to photoperiod
    journal, November 2008


    Biomass yield and quality of 20 switchgrass populations in southern Iowa, USA
    journal, December 2002


    A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato
    journal, May 2013


    Genetic Diversity, Plant Adaptation Regions, and Gene Pools for Switchgrass
    journal, January 2007


    A Genome-Wide Survey of Switchgrass Genome Structure and Organization
    journal, April 2012


    Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor
    journal, October 2010

    • Swanson-Wagner, R. A.; Eichten, S. R.; Kumari, S.
    • Genome Research, Vol. 20, Issue 12
    • DOI: 10.1101/gr.109165.110

    edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    journal, November 2009


    Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum
    journal, September 2011

    • Murphy, R. L.; Klein, R. R.; Morishige, D. T.
    • Proceedings of the National Academy of Sciences, Vol. 108, Issue 39, p. 16469-16474
    • DOI: 10.1073/pnas.1106212108

    Plant essential oils for pest and disease management
    journal, September 2000


    Aluminum tolerance in maize is associated with higher MATE1 gene copy number
    journal, March 2013

    • Maron, L. G.; Guimaraes, C. T.; Kirst, M.
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