Rapid genomic characterization of the genus vitis.

Next-generation sequencing technologies promise to dramatically accelerate the use of genetic information for crop improvement by facilitating the genetic mapping of agriculturally important phenotypes. The first step in optimizing the design of genetic mapping studies involves large-scale polymorph...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Sean Myles, Jer-Ming Chia, Bonnie Hurwitz, Charles Simon, Gan Yuan Zhong, Edward Buckler, Doreen Ware
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8d9ad1bb05d84189abf97a9e904cd413
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:8d9ad1bb05d84189abf97a9e904cd413
record_format	dspace
spelling	oai:doaj.org-article:8d9ad1bb05d84189abf97a9e904cd4132021-11-25T06:26:45ZRapid genomic characterization of the genus vitis.1932-620310.1371/journal.pone.0008219https://doaj.org/article/8d9ad1bb05d84189abf97a9e904cd4132010-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20084295/?tool=EBIhttps://doaj.org/toc/1932-6203Next-generation sequencing technologies promise to dramatically accelerate the use of genetic information for crop improvement by facilitating the genetic mapping of agriculturally important phenotypes. The first step in optimizing the design of genetic mapping studies involves large-scale polymorphism discovery and a subsequent genome-wide assessment of the population structure and pattern of linkage disequilibrium (LD) in the species of interest. In the present study, we provide such an assessment for the grapevine (genus Vitis), the world's most economically important fruit crop. Reduced representation libraries (RRLs) from 17 grape DNA samples (10 cultivated V. vinifera and 7 wild Vitis species) were sequenced with sequencing-by-synthesis technology. We developed heuristic approaches for SNP calling, identified hundreds of thousands of SNPs and validated a subset of these SNPs on a 9K genotyping array. We demonstrate that the 9K SNP array provides sufficient resolution to distinguish among V. vinifera cultivars, between V. vinifera and wild Vitis species, and even among diverse wild Vitis species. We show that there is substantial sharing of polymorphism between V. vinifera and wild Vitis species and find that genetic relationships among V. vinifera cultivars agree well with their proposed geographic origins using principal components analysis (PCA). Levels of LD in the domesticated grapevine are low even at short ranges, but LD persists above background levels to 3 kb. While genotyping arrays are useful for assessing population structure and the decay of LD across large numbers of samples, we suggest that whole-genome sequencing will become the genotyping method of choice for genome-wide genetic mapping studies in high-diversity plant species. This study demonstrates that we can move quickly towards genome-wide studies of crop species using next-generation sequencing. Our study sets the stage for future work in other high diversity crop species, and provides a significant enhancement to current genetic resources available to the grapevine genetic community.Sean MylesJer-Ming ChiaBonnie HurwitzCharles SimonGan Yuan ZhongEdward BucklerDoreen WarePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 1, p e8219 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sean Myles Jer-Ming Chia Bonnie Hurwitz Charles Simon Gan Yuan Zhong Edward Buckler Doreen Ware Rapid genomic characterization of the genus vitis.
description	Next-generation sequencing technologies promise to dramatically accelerate the use of genetic information for crop improvement by facilitating the genetic mapping of agriculturally important phenotypes. The first step in optimizing the design of genetic mapping studies involves large-scale polymorphism discovery and a subsequent genome-wide assessment of the population structure and pattern of linkage disequilibrium (LD) in the species of interest. In the present study, we provide such an assessment for the grapevine (genus Vitis), the world's most economically important fruit crop. Reduced representation libraries (RRLs) from 17 grape DNA samples (10 cultivated V. vinifera and 7 wild Vitis species) were sequenced with sequencing-by-synthesis technology. We developed heuristic approaches for SNP calling, identified hundreds of thousands of SNPs and validated a subset of these SNPs on a 9K genotyping array. We demonstrate that the 9K SNP array provides sufficient resolution to distinguish among V. vinifera cultivars, between V. vinifera and wild Vitis species, and even among diverse wild Vitis species. We show that there is substantial sharing of polymorphism between V. vinifera and wild Vitis species and find that genetic relationships among V. vinifera cultivars agree well with their proposed geographic origins using principal components analysis (PCA). Levels of LD in the domesticated grapevine are low even at short ranges, but LD persists above background levels to 3 kb. While genotyping arrays are useful for assessing population structure and the decay of LD across large numbers of samples, we suggest that whole-genome sequencing will become the genotyping method of choice for genome-wide genetic mapping studies in high-diversity plant species. This study demonstrates that we can move quickly towards genome-wide studies of crop species using next-generation sequencing. Our study sets the stage for future work in other high diversity crop species, and provides a significant enhancement to current genetic resources available to the grapevine genetic community.
format	article
author	Sean Myles Jer-Ming Chia Bonnie Hurwitz Charles Simon Gan Yuan Zhong Edward Buckler Doreen Ware
author_facet	Sean Myles Jer-Ming Chia Bonnie Hurwitz Charles Simon Gan Yuan Zhong Edward Buckler Doreen Ware
author_sort	Sean Myles
title	Rapid genomic characterization of the genus vitis.
title_short	Rapid genomic characterization of the genus vitis.
title_full	Rapid genomic characterization of the genus vitis.
title_fullStr	Rapid genomic characterization of the genus vitis.
title_full_unstemmed	Rapid genomic characterization of the genus vitis.
title_sort	rapid genomic characterization of the genus vitis.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/8d9ad1bb05d84189abf97a9e904cd413
work_keys_str_mv	AT seanmyles rapidgenomiccharacterizationofthegenusvitis AT jermingchia rapidgenomiccharacterizationofthegenusvitis AT bonniehurwitz rapidgenomiccharacterizationofthegenusvitis AT charlessimon rapidgenomiccharacterizationofthegenusvitis AT ganyuanzhong rapidgenomiccharacterizationofthegenusvitis AT edwardbuckler rapidgenomiccharacterizationofthegenusvitis AT doreenware rapidgenomiccharacterizationofthegenusvitis
_version_	1718413692763111424

Rapid genomic characterization of the genus vitis.

Ejemplares similares