|
| Status |
Public on Oct 15, 2010 |
| Title |
Pervasive gene content variation and copy number variation in both maize and its undomesticated progenitor |
| Platform organism |
Zea mays |
| Sample organisms |
Zea mays; Zea mays subsp. parviglumis |
| Experiment type |
Genome variation profiling by genome tiling array
|
| Summary |
Different 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. In order to investigate the potential contribution of CNV and PAV to genomic diversity in maize we used array comparative genomic hybridization (CGH) to compare gene content and copy number variation among 25 diverse maize inbreds 14 genotypes of the wild ancestor of maize, teosinte. The microarray included multiple probes for each of the ~32,500 stringently filtered genes identified in the B73 reference genome. We identified 479 genes exhibiting higher copy number in some genotypes (UpCNV) and 3,410 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 that are present in B73 but missing from the genome of several 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 reflect relatively old variants that are not associated with domestication or maize improvement. Many of the genes affected by CNV/PAV are either maize-specific or members of genes families suggesting that the gene loss can be tolerated through buffering by redundant functions encoded elsewhere in the genome. Many plant genomes are relatively large and contain the remnant of whole genome duplications which may provide the ability to tolerate high levels of structural variation. While this structural variation may not result in major qualitative variation due to genetic buffering, it may significantly contribute to quantitative variation.
|
| |
|
| Overall design |
1-2 replications of 25 maize inbred and 14 teosinte genotypes were hybridized to an array designed from the ~32,400 genes in the maize B73 reference genome.
|
| |
|
| Contributor(s) |
Swanson-Wagner RA, Eichten SR, Kumari S, Tiffin P, Stein JC, Ware D, Springer NM |
| Citation(s) |
21036921 |
| |
| Submission date |
Aug 23, 2010 |
| Last update date |
Mar 22, 2012 |
| Contact name |
Steve R Eichten |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Minnesota
|
| Department |
Plant Biology
|
| Lab |
Springer Lab
|
| Street address |
1445 Gortner Ave
|
| City |
St. Paul |
| State/province |
MN |
| ZIP/Postal code |
55108 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL10846 |
NimbleGen Zmays 120K CGH array [091006_NS_Zmays_CGH_exp] |
|
| Samples (58)
|
|
| Relations |
| BioProject |
PRJNA130747 |
Less...
More...