RT Journal
A1 Swanson-Wagner, Ruth A.
A1 Eichten, Steven R.
A1 Kumari, Sunita
A1 Tiffin, Peter
A1 Stein, Joshua C.
A1 Ware, Doreen
A1 Springer, Nathan M.
T1 Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor
JF Genome Research 
JO Genome Research 
YR 2010 
FD December 01 
VO 20 
IS 12 
SP 1689 
OP 1699 
DO 10.1101/gr.109165.110 
UL http://genome.cshlp.org/content/20/12/1689.abstract 
AB Individuals of the same species are generally thought to have very similar genomes. However, there is growing evidence that structural variation in the form of copy number variation (CNV) and presence–absence variation (PAV) can lead to variation in the genome content of individuals within a species. Array comparative genomic hybridization (CGH) was used to compare gene content and copy number variation among 19 diverse maize inbreds and 14 genotypes of the wild ancestor of maize, teosinte. We identified 479 genes exhibiting higher copy number in some genotypes (UpCNV) and 3410 genes that have either fewer copies or are missing in the genome of at least one genotype relative to B73 (DownCNV/PAV). Many of these DownCNV/PAV are examples of genes present in B73, but missing from other genotypes. Over 70% of the CNV/PAV examples are identified in multiple genotypes, and the majority of events are observed in both maize and teosinte, suggesting that these variants predate domestication and that there is not strong selection acting against them. Many of the genes affected by CNV/PAV are either maize specific (thus possible annotation artifacts) or members of large gene families, suggesting that the gene loss can be tolerated through buffering by redundant functions encoded elsewhere in the genome. While this structural variation may not result in major qualitative variation due to genetic buffering, it may significantly contribute to quantitative variation.