Present address: Monsanto, Leeuwenhoekweg 52, 2661 CZ Bergschenhoek, Netherlands
Changes in genome content generated via segregation of non-allelic homologs
Article first published online: 30 AUG 2012
© 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd
The Plant Journal
Volume 72, Issue 3, pages 390–399, November 2012
How to Cite
Liu, S., Ying, K., Yeh, C.-T., Yang, J., Swanson-Wagner, R., Wu, W., Richmond, T., Gerhardt, D. J., Lai, J., Springer, N., Nettleton, D., Jeddeloh, J. A. and Schnable, P. S. (2012), Changes in genome content generated via segregation of non-allelic homologs. The Plant Journal, 72: 390–399. doi: 10.1111/j.1365-313X.2012.05087.x
GenBank accession no. SRA036595.
- Issue published online: 29 OCT 2012
- Article first published online: 30 AUG 2012
- Accepted manuscript online: 25 JUN 2012 10:22AM EST
- Received 18 May 2012; revised 15 June 2012; accepted 21 June 2012; published online 30 August 2012.
- copy number variation;
- comparative genomic hybridization;
- non-allelic homologs;
- recombinant inbred line
A careful analysis of two maize recombinant inbred lines (RILs) relative to their inbred parents revealed the presence of several hundred apparently de novo copy number variants (CNVs). These changes in genome content were validated via both PCR and whole exome-array capture-and-sequencing experiments. One hundred and eighty-five genomic regions, which overlap with 38 high-confidence genes, exhibited apparently de novo copy number variation (CNV) in these two RILs and in many instances the same apparently de novo CNV events were observed in multiple RILs. Further analyses revealed that these recurrent apparently de novo CNVs were caused by segregation of single-copy homologous sequences that are located in non-allelic positions in the two parental inbred lines. F1 individuals derived from these inbred lines will be hemizygous for each of these non-allelic homologs but RIL genotypes will contain these sequences at zero, one or two genomic loci. Hence, the segregation of non-allelic homologs may contribute to transgressive segregation. Indeed, statistical associations between phenotypic quantitative trait loci and genomic losses were observed for two of 14 tested pairs of non-allelic homologs.