SNP discovery with EST and NextGen sequencing in switchgrass (Panicum virgatum L.).

Although yield trials for switchgrass (Panicum virgatum L.), a potentially high value biofuel feedstock crop, are currently underway throughout North America, the genetic tools for crop improvement in this species are still in the early stages of development. Identification of high-density molecular...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Elhan S Ersoz, Mark H Wright, Jasmyn L Pangilinan, Moira J Sheehan, Christian Tobias, Michael D Casler, Edward S Buckler, Denise E Costich
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/bdf787ac68e94412bccaf3a77715ce35
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:bdf787ac68e94412bccaf3a77715ce35
record_format	dspace
spelling	oai:doaj.org-article:bdf787ac68e94412bccaf3a77715ce352021-11-18T08:14:16ZSNP discovery with EST and NextGen sequencing in switchgrass (Panicum virgatum L.).1932-620310.1371/journal.pone.0044112https://doaj.org/article/bdf787ac68e94412bccaf3a77715ce352012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23049744/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Although yield trials for switchgrass (Panicum virgatum L.), a potentially high value biofuel feedstock crop, are currently underway throughout North America, the genetic tools for crop improvement in this species are still in the early stages of development. Identification of high-density molecular markers, such as single nucleotide polymorphisms (SNPs), that are amenable to high-throughput genotyping approaches, is the first step in a quantitative genetics study of this model biofuel crop species. We generated and sequenced expressed sequence tag (EST) libraries from thirteen diverse switchgrass cultivars representing both upland and lowland ecotypes, as well as tetraploid and octoploid genomes. We followed this with reduced genomic library preparation and massively parallel sequencing of the same samples using the Illumina Genome Analyzer technology platform. EST libraries were used to generate unigene clusters and establish a gene-space reference sequence, thus providing a framework for assembly of the short sequence reads. SNPs were identified utilizing these scaffolds. We used a custom software program for alignment and SNP detection and identified over 149,000 SNPs across the 13 short-read sequencing libraries (SRSLs). Approximately 25,000 additional SNPs were identified from the entire EST collection available for the species. This sequencing effort generated data that are suitable for marker development and for estimation of population genetic parameters, such as nucleotide diversity and linkage disequilibrium. Based on these data, we assessed the feasibility of genome wide association mapping and genomic selection applications in switchgrass. Overall, the SNP markers discovered in this study will help facilitate quantitative genetics experiments and greatly enhance breeding efforts that target improvement of key biofuel traits and development of new switchgrass cultivars.Elhan S ErsozMark H WrightJasmyn L PangilinanMoira J SheehanChristian TobiasMichael D CaslerEdward S BucklerDenise E CostichPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 9, p e44112 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Elhan S Ersoz Mark H Wright Jasmyn L Pangilinan Moira J Sheehan Christian Tobias Michael D Casler Edward S Buckler Denise E Costich SNP discovery with EST and NextGen sequencing in switchgrass (Panicum virgatum L.).
description	Although yield trials for switchgrass (Panicum virgatum L.), a potentially high value biofuel feedstock crop, are currently underway throughout North America, the genetic tools for crop improvement in this species are still in the early stages of development. Identification of high-density molecular markers, such as single nucleotide polymorphisms (SNPs), that are amenable to high-throughput genotyping approaches, is the first step in a quantitative genetics study of this model biofuel crop species. We generated and sequenced expressed sequence tag (EST) libraries from thirteen diverse switchgrass cultivars representing both upland and lowland ecotypes, as well as tetraploid and octoploid genomes. We followed this with reduced genomic library preparation and massively parallel sequencing of the same samples using the Illumina Genome Analyzer technology platform. EST libraries were used to generate unigene clusters and establish a gene-space reference sequence, thus providing a framework for assembly of the short sequence reads. SNPs were identified utilizing these scaffolds. We used a custom software program for alignment and SNP detection and identified over 149,000 SNPs across the 13 short-read sequencing libraries (SRSLs). Approximately 25,000 additional SNPs were identified from the entire EST collection available for the species. This sequencing effort generated data that are suitable for marker development and for estimation of population genetic parameters, such as nucleotide diversity and linkage disequilibrium. Based on these data, we assessed the feasibility of genome wide association mapping and genomic selection applications in switchgrass. Overall, the SNP markers discovered in this study will help facilitate quantitative genetics experiments and greatly enhance breeding efforts that target improvement of key biofuel traits and development of new switchgrass cultivars.
format	article
author	Elhan S Ersoz Mark H Wright Jasmyn L Pangilinan Moira J Sheehan Christian Tobias Michael D Casler Edward S Buckler Denise E Costich
author_facet	Elhan S Ersoz Mark H Wright Jasmyn L Pangilinan Moira J Sheehan Christian Tobias Michael D Casler Edward S Buckler Denise E Costich
author_sort	Elhan S Ersoz
title	SNP discovery with EST and NextGen sequencing in switchgrass (Panicum virgatum L.).
title_short	SNP discovery with EST and NextGen sequencing in switchgrass (Panicum virgatum L.).
title_full	SNP discovery with EST and NextGen sequencing in switchgrass (Panicum virgatum L.).
title_fullStr	SNP discovery with EST and NextGen sequencing in switchgrass (Panicum virgatum L.).
title_full_unstemmed	SNP discovery with EST and NextGen sequencing in switchgrass (Panicum virgatum L.).
title_sort	snp discovery with est and nextgen sequencing in switchgrass (panicum virgatum l.).
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/bdf787ac68e94412bccaf3a77715ce35
work_keys_str_mv	AT elhansersoz snpdiscoverywithestandnextgensequencinginswitchgrasspanicumvirgatuml AT markhwright snpdiscoverywithestandnextgensequencinginswitchgrasspanicumvirgatuml AT jasmynlpangilinan snpdiscoverywithestandnextgensequencinginswitchgrasspanicumvirgatuml AT moirajsheehan snpdiscoverywithestandnextgensequencinginswitchgrasspanicumvirgatuml AT christiantobias snpdiscoverywithestandnextgensequencinginswitchgrasspanicumvirgatuml AT michaeldcasler snpdiscoverywithestandnextgensequencinginswitchgrasspanicumvirgatuml AT edwardsbuckler snpdiscoverywithestandnextgensequencinginswitchgrasspanicumvirgatuml AT deniseecostich snpdiscoverywithestandnextgensequencinginswitchgrasspanicumvirgatuml
_version_	1718422067159760896

SNP discovery with EST and NextGen sequencing in switchgrass (Panicum virgatum L.).

Ejemplares similares