Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol
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 amore »
- Authors:
-
- Cornell University, Ithaca, NY (United States)
- Cornell University, Ithaca, NY (United States); US Department of Agriculture (USDA), Ithaca, NY (United States). Agricultural Research Service
- US Department of Agriculture (USDA), Madison, WI (United States). Agricultural Research Service; University of Wisconsin, Madison, WI (United States)
- Publication Date:
- Research Org.:
- US Deptartment of Agriculture (USDA), Washington, DC (United States). Agricultural Research Service
- Sponsoring Org.:
- USDOE Office of Science (SC); National Science Foundation (NSF); US Department of Agriculture (USDA)
- OSTI Identifier:
- 1904732
- Grant/Contract Number:
- AI02-07ER64454; 0820619; 0965342
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PLoS Genetics
- Additional Journal Information:
- Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 1553-7404
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; single nucleotide polymorphisms; genomics; plant genomics; phylogeography; millet; tetraploidy; heterozygosity; ploidy
Citation Formats
Lu, Fei, Lipka, Alexander E., Glaubitz, Jeff, Elshire, Rob, Cherney, Jerome H., Casler, Michael D., Buckler, Edward S., and Costich, Denise E. Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol. United States: N. p., 2013.
Web. doi:10.1371/journal.pgen.1003215.
Lu, Fei, Lipka, Alexander E., Glaubitz, Jeff, Elshire, Rob, Cherney, Jerome H., Casler, Michael D., Buckler, Edward S., & Costich, Denise E. Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol. United States. https://doi.org/10.1371/journal.pgen.1003215
Lu, Fei, Lipka, Alexander E., Glaubitz, Jeff, Elshire, Rob, Cherney, Jerome H., Casler, Michael D., Buckler, Edward S., and Costich, Denise E. Thu .
"Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol". United States. https://doi.org/10.1371/journal.pgen.1003215. https://www.osti.gov/servlets/purl/1904732.
@article{osti_1904732,
title = {Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol},
author = {Lu, Fei and Lipka, Alexander E. and Glaubitz, Jeff and Elshire, Rob and Cherney, Jerome H. and Casler, Michael D. and Buckler, Edward S. and Costich, Denise E.},
abstractNote = {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.},
doi = {10.1371/journal.pgen.1003215},
journal = {PLoS Genetics},
number = 1,
volume = 9,
place = {United States},
year = {Thu Jan 17 00:00:00 EST 2013},
month = {Thu Jan 17 00:00:00 EST 2013}
}
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journal, December 2015
- Dodds, Ken G.; McEwan, John C.; Brauning, Rudiger
- BMC Genomics, Vol. 16, Issue 1
Association analysis for disease resistance to Fusarium oxysporum in cape gooseberry (Physalis peruviana L)
journal, March 2016
- Osorio-Guarín, Jaime A.; Enciso-Rodríguez, Felix E.; González, Carolina
- BMC Genomics, Vol. 17, Issue 1
Bioinformatic analysis of genotype by sequencing (GBS) data with NGSEP
journal, August 2016
- Perea, Claudia; De La Hoz, Juan Fernando; Cruz, Daniel Felipe
- BMC Genomics, Vol. 17, Issue S5
Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia
journal, September 2016
- Onyango, Maria G.; Aitken, Nicola C.; Jack, Cameron
- BMC Genomics, Vol. 17, Issue 1
Development of a high-density linkage map and mapping of the three-pistil gene (Pis1) in wheat using GBS markers
journal, July 2017
- Yang, Zaijun; Chen, Zhenyong; Peng, Zhengsong
- BMC Genomics, Vol. 18, Issue 1
Use of genotyping-by-sequencing to determine the genetic structure in the medicinal plant chamomile, and to identify flowering time and alpha-bisabolol associated SNP-loci by genome-wide association mapping
journal, August 2017
- Otto, Lars-Gernot; Mondal, Prodyut; Brassac, Jonathan
- BMC Genomics, Vol. 18, Issue 1
QTL mapping and candidate genes for resistance to Fusarium ear rot and fumonisin contamination in maize
journal, January 2017
- Maschietto, Valentina; Colombi, Cinzia; Pirona, Raul
- BMC Plant Biology, Vol. 17, Issue 1
UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study
journal, June 2018
- Qi, Peng; Gimode, Davis; Saha, Dipnarayan
- BMC Plant Biology, Vol. 18, Issue 1
High-density linkage map construction and mapping QTL for yield and yield components in autotetraploid alfalfa using RAD-seq
journal, April 2019
- Zhang, Fan; Kang, Junmei; Long, Ruicai
- BMC Plant Biology, Vol. 19, Issue 1
Simple SNP-based minimal marker genotyping for Humulus lupulus L. identification and variety validation
journal, October 2015
- Henning, John A.; Coggins, Jamie; Peterson, Matthew
- BMC Research Notes, Vol. 8, Issue 1
Genotyping by Genome Reducing and Sequencing for Outbred Animals
journal, July 2013
- Chen, Qiang; Ma, Yufang; Yang, Yumei
- PLoS ONE, Vol. 8, Issue 7
TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline
journal, February 2014
- Glaubitz, Jeffrey C.; Casstevens, Terry M.; Lu, Fei
- PLoS ONE, Vol. 9, Issue 2
Classification and Characterization of Species within the Genus Lens Using Genotyping-by-Sequencing (GBS)
journal, March 2015
- Wong, Melissa M. L.; Gujaria-Verma, Neha; Ramsay, Larissa
- PLOS ONE, Vol. 10, Issue 3
Genotyping-By-Sequencing (GBS) Detects Genetic Structure and Confirms Behavioral QTL in Tame and Aggressive Foxes (Vulpes vulpes)
journal, June 2015
- Johnson, Jennifer L.; Wittgenstein, Helena; Mitchell, Sharon E.
- PLOS ONE, Vol. 10, Issue 6
Validation of Genotyping-By-Sequencing Analysis in Populations of Tetraploid Alfalfa by 454 Sequencing
journal, June 2015
- Rocher, Solen; Jean, Martine; Castonguay, Yves
- PLOS ONE, Vol. 10, Issue 6
Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine
journal, August 2015
- Hyma, Katie E.; Barba, Paola; Wang, Minghui
- PLOS ONE, Vol. 10, Issue 8
Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies
journal, July 2016
- Gimode, Davis; Odeny, Damaris A.; de Villiers, Etienne P.
- PLOS ONE, Vol. 11, Issue 7
Genetic Variation within Clonal Lineages of Phytophthora infestans Revealed through Genotyping-By-Sequencing, and Implications for Late Blight Epidemiology
journal, November 2016
- Hansen, Zachariah R.; Everts, Kathryne L.; Fry, William E.
- PLOS ONE, Vol. 11, Issue 11
Comparative analysis of genetic diversity and differentiation of cauliflower (Brassica oleracea var. botrytis) accessions from two ex situ genebanks
journal, February 2018
- Yousef, Eltohamy A. A.; Müller, Thomas; Börner, Andreas
- PLOS ONE, Vol. 13, Issue 2
Genotyping-by-sequencing highlights patterns of genetic structure and domestication in artichoke and cardoon
journal, October 2018
- Pavan, Stefano; Curci, Pasquale L.; Zuluaga, Diana L.
- PLOS ONE, Vol. 13, Issue 10
Transcriptome analysis and annotation: SNPs identified from single copy annotated unigenes of three polyploid blueberry crops
journal, April 2019
- Wang, Yunsheng; Shahid, Muhammad Qasim; Ghouri, Fozia
- PLOS ONE, Vol. 14, Issue 4
Diatraea saccharalis history of colonization in the Americas. The case for human-mediated dispersal
journal, July 2019
- Francischini, Fabricio J. B.; Cordeiro, Erick M. G.; de Campos, Jaqueline B.
- PLOS ONE, Vol. 14, Issue 7
Genetic Diversity Analysis of Highly Incomplete SNP Genotype Data with Imputations: An Empirical Assessment
journal, March 2014
- Fu, Yong-Bi
- G3: Genes|Genomes|Genetics, Vol. 4, Issue 5
Fast and Cost-Effective Genetic Mapping in Apple Using Next-Generation Sequencing
journal, September 2014
- Gardner, Kyle M.; Brown, Patrick; Cooke, Thomas F.
- G3 Genes|Genomes|Genetics, Vol. 4, Issue 9
A High-Density Linkage Map for Astyanax mexicanus Using Genotyping-by-Sequencing Technology
journal, February 2015
- Carlson, Brian M.; Onusko, Samuel W.; Gross, Joshua B.
- G3 Genes|Genomes|Genetics, Vol. 5, Issue 2
Genotyping by Sequencing in Almond: SNP Discovery, Linkage Mapping, and Marker Design
journal, January 2018
- Goonetilleke, Shashi N.; March, Timothy J.; Wirthensohn, Michelle G.
- G3 Genes|Genomes|Genetics, Vol. 8, Issue 1
Extensions of BLUP Models for Genomic Prediction in Heterogeneous Populations: Application in a Diverse Switchgrass Sample
journal, March 2019
- Ramstein, Guillaume P.; Casler, Michael D.
- G3 Genes|Genomes|Genetics, Vol. 9, Issue 3
Genomic Prediction for Winter Survival of Lowland Switchgrass in the Northern USA
journal, June 2019
- Poudel, Hari P.; Sanciangco, Millicent D.; Kaeppler, Shawn M.
- G3 Genes|Genomes|Genetics, Vol. 9, Issue 6
Linkage Disequilibrium Estimation in Low Coverage High-Throughput Sequencing Data
journal, March 2018
- Bilton, Timothy P.; McEwan, John C.; Clarke, Shannon M.
- Genetics, Vol. 209, Issue 2
Genetic Diversity, Population Structure, and Linkage Disequilibrium of a Core Collection of Ziziphus jujuba Assessed with Genome-wide SNPs Developed by Genotyping-by-sequencing and SSR Markers
journal, April 2017
- Chen, Wu; Hou, Lu; Zhang, Zhiyong
- Frontiers in Plant Science, Vol. 8
Genotyping-by-Sequencing and Its Exploitation for Forage and Cool-Season Grain Legume Breeding
journal, May 2017
- Annicchiarico, Paolo; Nazzicari, Nelson; Wei, Yanling
- Frontiers in Plant Science, Vol. 8
Discovery of Putative Herbicide Resistance Genes and Its Regulatory Network in Chickpea Using Transcriptome Sequencing
journal, June 2017
- Iquebal, Mir A.; Soren, Khela R.; Gangwar, Priyanka
- Frontiers in Plant Science, Vol. 8
Genome-Wide Association Study Reveals Natural Variations Contributing to Drought Resistance in Crops
journal, June 2017
- Wang, Hongwei; Qin, Feng
- Frontiers in Plant Science, Vol. 8
Genome Scans Reveal Homogenization and Local Adaptations in Populations of the Soybean Cyst Nematode
journal, July 2018
- Gendron St-Marseille, Anne-Frédérique; Lord, Etienne; Véronneau, Pierre-Yves
- Frontiers in Plant Science, Vol. 9
Genomic Prediction for 25 Agronomic and Quality Traits in Alfalfa (Medicago sativa)
journal, August 2018
- Jia, Congjun; Zhao, Fuping; Wang, Xuemin
- Frontiers in Plant Science, Vol. 9
Genomic Selection for Ascochyta Blight Resistance in Pea
journal, December 2018
- Carpenter, Margaret A.; Goulden, David S.; Woods, Carmel J.
- Frontiers in Plant Science, Vol. 9
Genetic Diversity of Northern Wheatgrass (Elymus lanceolatus ssp. lanceolatus) as Revealed by Genotyping-by-Sequencing
journal, April 2018
- Li, Pingchuan; Bhattarai, Surendra; Peterson, Gregory
- Diversity, Vol. 10, Issue 2
Evaluation of Switchgrass Genotypes for Cold-Tolerant Seed Germination from Native Populations in the Northeast USA
journal, October 2019
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- Plants, Vol. 8, Issue 10
Next-Generation Sampling: Pairing Genomics with Herbarium Specimens Provides Species-Level Signal in Solidago (Asteraceae)
journal, June 2015
- Beck, James B.; Semple, John C.
- Applications in Plant Sciences, Vol. 3, Issue 6