Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content

Nathan M. Springer; Kai Ying; Yan Fu; Tieming Ji; Cheng Ting Yeh; Yi Jia; Wei Wu; Todd Richmond; Jacob Kitzman; Heidi Rosenbaum; A. Leonardo Iniguez; W. Brad Barbazuk; Jeffrey A. Jeddeloh; Dan Nettleton; Patrick S. Schnable

doi:10.1371/journal.pgen.1000734

Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content

Nathan M. Springer, Kai Ying, Yan Fu, Tieming Ji, Cheng Ting Yeh, Yi Jia, Wei Wu, Todd Richmond, Jacob Kitzman, Heidi Rosenbaum, A. Leonardo Iniguez, W. Brad Barbazuk, Jeffrey A. Jeddeloh, Dan Nettleton, Patrick S. Schnable

Research output: Contribution to journal › Article › peer-review

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Abstract

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.

Original language	English (US)
Article number	e1000734
Journal	PLoS genetics
Volume	5
Issue number	11
DOIs	https://doi.org/10.1371/journal.pgen.1000734
State	Published - Nov 2009
Externally published	Yes

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Springer, N. M., Ying, K., Fu, Y., Ji, T., Yeh, C. T., Jia, Y., Wu, W., Richmond, T., Kitzman, J., Rosenbaum, H., Iniguez, A. L., Barbazuk, W. B., Jeddeloh, J. A., Nettleton, D., & Schnable, P. S. (2009). Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS genetics, 5(11), Article e1000734. https://doi.org/10.1371/journal.pgen.1000734

Springer, NM, Ying, K, Fu, Y, Ji, T, Yeh, CT, Jia, Y, Wu, W, Richmond, T, Kitzman, J, Rosenbaum, H, Iniguez, AL, Barbazuk, WB, Jeddeloh, JA, Nettleton, D & Schnable, PS 2009, 'Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content', PLoS genetics, vol. 5, no. 11, e1000734. https://doi.org/10.1371/journal.pgen.1000734

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title = "Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content",

abstract = "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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AU - Wu, Wei

AU - Richmond, Todd

AU - Kitzman, Jacob

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AU - Iniguez, A. Leonardo

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AU - Schnable, Patrick S.

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Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content

Abstract

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