A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species.

Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS) is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restric...

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Autores principales:	Robert J Elshire, Jeffrey C Glaubitz, Qi Sun, Jesse A Poland, Ken Kawamoto, Edward S Buckler, Sharon E Mitchell
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/31116166343f4707945429a3dd822f8b
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spelling	oai:doaj.org-article:31116166343f4707945429a3dd822f8b2021-11-18T06:54:27ZA robust, simple genotyping-by-sequencing (GBS) approach for high diversity species.1932-620310.1371/journal.pone.0019379https://doaj.org/article/31116166343f4707945429a3dd822f8b2011-05-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21573248/?tool=EBIhttps://doaj.org/toc/1932-6203Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS) is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs). This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM) and barley (Oregon Wolfe Barley) recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.Robert J ElshireJeffrey C GlaubitzQi SunJesse A PolandKen KawamotoEdward S BucklerSharon E MitchellPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 5, p e19379 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Robert J Elshire Jeffrey C Glaubitz Qi Sun Jesse A Poland Ken Kawamoto Edward S Buckler Sharon E Mitchell A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species.
description	Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS) is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs). This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM) and barley (Oregon Wolfe Barley) recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.
format	article
author	Robert J Elshire Jeffrey C Glaubitz Qi Sun Jesse A Poland Ken Kawamoto Edward S Buckler Sharon E Mitchell
author_facet	Robert J Elshire Jeffrey C Glaubitz Qi Sun Jesse A Poland Ken Kawamoto Edward S Buckler Sharon E Mitchell
author_sort	Robert J Elshire
title	A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species.
title_short	A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species.
title_full	A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species.
title_fullStr	A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species.
title_full_unstemmed	A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species.
title_sort	robust, simple genotyping-by-sequencing (gbs) approach for high diversity species.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/31116166343f4707945429a3dd822f8b
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A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species.

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