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Changes in genome content generated via segregation of non‐allelic homologs
Author(s) -
Liu Sanzhen,
Ying Kai,
Yeh ChengTing,
Yang Jinliang,
SwansonWagner Ruth,
Wu Wei,
Richmond Todd,
Gerhardt Daniel J.,
Lai Jinsheng,
Springer Nathan,
Nettleton Dan,
Jeddeloh Jeffrey A.,
Schnable Patrick S.
Publication year - 2012
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/j.1365-313x.2012.05087.x
Subject(s) - genetics , biology , inbred strain , homologous chromosome , allele , genome , copy number variation , quantitative trait locus , gene , transgressive segregation , genotype
Summary 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.