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United States Department of Agriculture

Agricultural Research Service

Research Project: BIOINFORMATIC METHODS AND TOOLS TO PREDICT SMALL GRAIN FIELD PERFORMANCE

Location: Plant, Soil and Nutrition Research

Title: Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor

Authors
item Swanson-Wagner, Ruth -
item Eichten, Steve -
item Kumari, Sunita -
item Tiffin, Peter -
item Stein, Joshua -
item Ware, Doreen
item Springer, Nathan -

Submitted to: Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 1, 2010
Publication Date: October 29, 2010
Citation: Swanson-Wagner, R.A., Eichten, S.R., Kumari, S., Tiffin, P., Stein, J.C., Ware, D., Springer, N.M. 2010. Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Research. 20(12):1689-1699.

Interpretive Summary: Variation in gene copy number was examined in 34 diverse maize inbreds and teosinte in comparison to the B73 reference genome sequence of maize. About 3800 of the ~32,500 annotated maize genes showed variation in copy number in at least one genotype, and most of these (~88%) displayed reduction in copy number. Many of these genes are either maize-specific (e.g. absent in other grass species) or members of large gene families, suggesting that the gene loss can be tolerated through buffering by redundant functions encoded elsewhere in the genome. The high levels of heterosis observed in maize may involve complementation within gene families where individual members of the gene family are missing within the inbred parents but hybrids have all members of the gene family and full functionality.

Technical Abstract: 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. 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 20 diverse maize inbreds and 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 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 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 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. The high levels of heterosis observed in maize may involve complementation within gene families where individual members of the gene family are missing within the inbred parents but hybrids have all members of the gene family and full functionality.

Last Modified: 4/16/2014
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