SNP discovery and development of a high-density genotyping array for sunflower.

Recent advances in next-generation DNA sequencing technologies have made possible the development of high-throughput SNP genotyping platforms that allow for the simultaneous interrogation of thousands of single-nucleotide polymorphisms (SNPs). Such resources have the potential to facilitate the rapi...

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Autores principales:	Eleni Bachlava, Christopher A Taylor, Shunxue Tang, John E Bowers, Jennifer R Mandel, John M Burke, Steven J Knapp
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/66986d2142fa4b38b43cb0f05993c63e
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spelling	oai:doaj.org-article:66986d2142fa4b38b43cb0f05993c63e2021-11-18T07:30:56ZSNP discovery and development of a high-density genotyping array for sunflower.1932-620310.1371/journal.pone.0029814https://doaj.org/article/66986d2142fa4b38b43cb0f05993c63e2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22238659/?tool=EBIhttps://doaj.org/toc/1932-6203Recent advances in next-generation DNA sequencing technologies have made possible the development of high-throughput SNP genotyping platforms that allow for the simultaneous interrogation of thousands of single-nucleotide polymorphisms (SNPs). Such resources have the potential to facilitate the rapid development of high-density genetic maps, and to enable genome-wide association studies as well as molecular breeding approaches in a variety of taxa. Herein, we describe the development of a SNP genotyping resource for use in sunflower (Helianthus annuus L.). This work involved the development of a reference transcriptome assembly for sunflower, the discovery of thousands of high quality SNPs based on the generation and analysis of ca. 6 Gb of transcriptome re-sequencing data derived from multiple genotypes, the selection of 10,640 SNPs for inclusion in the genotyping array, and the use of the resulting array to screen a diverse panel of sunflower accessions as well as related wild species. The results of this work revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, greater than 95% of successful SNP assays revealed polymorphism, and more than 90% of these assays could be successfully transferred to related wild species. Analysis of the polymorphism data revealed patterns of genetic differentiation that were largely congruent with the evolutionary history of sunflower, though the large number of markers allowed for finer resolution than has previously been possible.Eleni BachlavaChristopher A TaylorShunxue TangJohn E BowersJennifer R MandelJohn M BurkeSteven J KnappPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 1, p e29814 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Eleni Bachlava Christopher A Taylor Shunxue Tang John E Bowers Jennifer R Mandel John M Burke Steven J Knapp SNP discovery and development of a high-density genotyping array for sunflower.
description	Recent advances in next-generation DNA sequencing technologies have made possible the development of high-throughput SNP genotyping platforms that allow for the simultaneous interrogation of thousands of single-nucleotide polymorphisms (SNPs). Such resources have the potential to facilitate the rapid development of high-density genetic maps, and to enable genome-wide association studies as well as molecular breeding approaches in a variety of taxa. Herein, we describe the development of a SNP genotyping resource for use in sunflower (Helianthus annuus L.). This work involved the development of a reference transcriptome assembly for sunflower, the discovery of thousands of high quality SNPs based on the generation and analysis of ca. 6 Gb of transcriptome re-sequencing data derived from multiple genotypes, the selection of 10,640 SNPs for inclusion in the genotyping array, and the use of the resulting array to screen a diverse panel of sunflower accessions as well as related wild species. The results of this work revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, greater than 95% of successful SNP assays revealed polymorphism, and more than 90% of these assays could be successfully transferred to related wild species. Analysis of the polymorphism data revealed patterns of genetic differentiation that were largely congruent with the evolutionary history of sunflower, though the large number of markers allowed for finer resolution than has previously been possible.
format	article
author	Eleni Bachlava Christopher A Taylor Shunxue Tang John E Bowers Jennifer R Mandel John M Burke Steven J Knapp
author_facet	Eleni Bachlava Christopher A Taylor Shunxue Tang John E Bowers Jennifer R Mandel John M Burke Steven J Knapp
author_sort	Eleni Bachlava
title	SNP discovery and development of a high-density genotyping array for sunflower.
title_short	SNP discovery and development of a high-density genotyping array for sunflower.
title_full	SNP discovery and development of a high-density genotyping array for sunflower.
title_fullStr	SNP discovery and development of a high-density genotyping array for sunflower.
title_full_unstemmed	SNP discovery and development of a high-density genotyping array for sunflower.
title_sort	snp discovery and development of a high-density genotyping array for sunflower.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/66986d2142fa4b38b43cb0f05993c63e
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SNP discovery and development of a high-density genotyping array for sunflower.

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