Changes in genome content generated via segregation of non-allelic homologs

Sanzhen Liu, Kai Ying, Cheng Ting Yeh, Jinliang Yang, Ruth Swanson-Wagner, Wei Wu, Todd Richmond, Daniel J. Gerhardt, Jinsheng Lai, Nathan Springer, Dan Nettleton, Jeffrey A. Jeddeloh, Patrick S. Schnable

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19 Scopus citations


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. F 1 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.

Original languageEnglish (US)
Pages (from-to)390-399
Number of pages10
JournalPlant Journal
Issue number3
StatePublished - Nov 2012


  • comparative genomic hybridization
  • copy number variation
  • maize
  • non-allelic homologs
  • recombinant inbred line
  • transgressive


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