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PMID: 19756477 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't

Allelic genome structural variations in maize detected by array comparative genome hybridization.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik ·Vol. 120 ·No. 2 ·2010-01-00 ·Pages 355-67

Beló A, Beatty MK, Hondred D, Fengler KA, Li B, Rafalski A

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.

MeSH Terms
Alleles Comparative Genomic Hybridization Gene Dosage Genome, Plant Inbreeding Oligonucleotide Array Sequence Analysis Zea mays/genetics
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Beló André
DuPont Crop Genetics, Route 141, Henry Clay Road, Wilmington, DE 19803, USA. [email protected]
Beatty Mary K
Hondred David
Fengler Kevin A
Li Bailin
Rafalski Antoni
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Article Info
Journal
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Abbr.
Theor Appl Genet
ISSN
1432-2242
DOI
10.1007/s00122-009-1128-9
Email
[email protected]
Published
2010-01-00
Epub
2009-00-19
Pages
355-67
Language
English
Region
Germany
NLM ID
0145600
Subset
IM
External Links
PubMed source DOI: 10.1007/s00122-009-1128-9 View journal details
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