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Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

Following the domestication of maize over the past ∼10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which a...

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Autores principales: Springer, Nathan M., Ying, Kai, Fu, Yan, Ji, Tieming, Yeh, Cheng-Ting, Jia, Yi, Wu, Wei, Richmond, Todd, Kitzman, Jacob, Rosenbaum, Heidi, Iniguez, A. Leonardo, Barbazuk, W. Brad, Jeddeloh, Jeffrey A., Nettleton, Dan, Schnable, Patrick S.
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2780416/
https://www.ncbi.nlm.nih.gov/pubmed/19956538
http://dx.doi.org/10.1371/journal.pgen.1000734
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author Springer, Nathan M.
Ying, Kai
Fu, Yan
Ji, Tieming
Yeh, Cheng-Ting
Jia, Yi
Wu, Wei
Richmond, Todd
Kitzman, Jacob
Rosenbaum, Heidi
Iniguez, A. Leonardo
Barbazuk, W. Brad
Jeddeloh, Jeffrey A.
Nettleton, Dan
Schnable, Patrick S.
author_facet Springer, Nathan M.
Ying, Kai
Fu, Yan
Ji, Tieming
Yeh, Cheng-Ting
Jia, Yi
Wu, Wei
Richmond, Todd
Kitzman, Jacob
Rosenbaum, Heidi
Iniguez, A. Leonardo
Barbazuk, W. Brad
Jeddeloh, Jeffrey A.
Nettleton, Dan
Schnable, Patrick S.
author_sort Springer, Nathan M.
collection PubMed
description Following the domestication of maize over the past ∼10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level of structural diversity between the inbred lines B73 and Mo17 that is unprecedented among higher eukaryotes. A detailed analysis of altered segments of DNA conservatively estimates that there are several hundred CNV sequences among the two genotypes, as well as several thousand PAV sequences that are present in B73 but not Mo17. Haplotype-specific PAVs contain hundreds of single-copy, expressed genes that may contribute to heterosis and to the extraordinary phenotypic diversity of this important crop.
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spelling pubmed-27804162009-12-02 Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content Springer, Nathan M. Ying, Kai Fu, Yan Ji, Tieming Yeh, Cheng-Ting Jia, Yi Wu, Wei Richmond, Todd Kitzman, Jacob Rosenbaum, Heidi Iniguez, A. Leonardo Barbazuk, W. Brad Jeddeloh, Jeffrey A. Nettleton, Dan Schnable, Patrick S. PLoS Genet Research Article Following the domestication of maize over the past ∼10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level of structural diversity between the inbred lines B73 and Mo17 that is unprecedented among higher eukaryotes. A detailed analysis of altered segments of DNA conservatively estimates that there are several hundred CNV sequences among the two genotypes, as well as several thousand PAV sequences that are present in B73 but not Mo17. Haplotype-specific PAVs contain hundreds of single-copy, expressed genes that may contribute to heterosis and to the extraordinary phenotypic diversity of this important crop. Public Library of Science 2009-11-20 /pmc/articles/PMC2780416/ /pubmed/19956538 http://dx.doi.org/10.1371/journal.pgen.1000734 Text en Springer et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Springer, Nathan M.
Ying, Kai
Fu, Yan
Ji, Tieming
Yeh, Cheng-Ting
Jia, Yi
Wu, Wei
Richmond, Todd
Kitzman, Jacob
Rosenbaum, Heidi
Iniguez, A. Leonardo
Barbazuk, W. Brad
Jeddeloh, Jeffrey A.
Nettleton, Dan
Schnable, Patrick S.
Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content
title Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content
title_full Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content
title_fullStr Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content
title_full_unstemmed Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content
title_short Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content
title_sort maize inbreds exhibit high levels of copy number variation (cnv) and presence/absence variation (pav) in genome content
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2780416/
https://www.ncbi.nlm.nih.gov/pubmed/19956538
http://dx.doi.org/10.1371/journal.pgen.1000734
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