Allelic genome structural variations in maize detected by array comparative genome hybridization |
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Authors: | André Beló Mary K Beatty David Hondred Kevin A Fengler Bailin Li Antoni Rafalski |
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Institution: | (1) DuPont Crop Genetics, Route 141, Henry Clay Road, Wilmington, DE 19803, USA;(2) Department of Plant and Soil Sciences, University of Delaware, 152 Townsend Hall, Newark, DE 19716, USA;(3) Pioneer Hi-Bred International, 7300 NW 62nd Avenue, Johnston, IA 50131, USA |
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Abstract: | DNA polymorphisms such as insertion/deletions and duplications affecting genome segments larger than 1 kb are known as copy-number
variations (CNVs) or structural variations (SVs). They have been recently studied in animals and humans by using array-comparative
genome hybridization (aCGH), and have been associated with several human diseases. Their presence and phenotypic effects in
plants have not been investigated on a genomic scale, although individual structural variations affecting traits have been
described. We used aCGH to investigate the presence of CNVs in maize by comparing the genome of 13 maize inbred lines to B73.
Analysis of hybridization signal ratios of 60,472 60-mer oligonucleotide probes between inbreds in relation to their location
in the reference genome (B73) allowed us to identify clusters of probes that deviated from the ratio expected for equal copy-numbers.
We found CNVs distributed along the maize genome in all chromosome arms. They occur with appreciable frequency in different
germplasm subgroups, suggesting ancient origin. Validation of several CNV regions showed both insertion/deletions and copy-number
differences. The nature of CNVs detected suggests CNVs might have a considerable impact on plant phenotypes, including disease
response and heterosis. |
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