TY - JOUR
T1 - Changes in genome content generated via segregation of non-allelic homologs
AU - Liu, Sanzhen
AU - Ying, Kai
AU - Yeh, Cheng Ting
AU - Yang, Jinliang
AU - Swanson-Wagner, Ruth
AU - Wu, Wei
AU - Richmond, Todd
AU - Gerhardt, Daniel J.
AU - Lai, Jinsheng
AU - Springer, Nathan
AU - Nettleton, Dan
AU - Jeddeloh, Jeffrey A.
AU - Schnable, Patrick S.
N1 - Copyright:
Copyright 2013 Elsevier B.V., All rights reserved.
PY - 2012/11
Y1 - 2012/11
N2 - 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.
AB - 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.
KW - comparative genomic hybridization
KW - copy number variation
KW - maize
KW - non-allelic homologs
KW - recombinant inbred line
KW - transgressive
UR - http://www.scopus.com/inward/record.url?scp=84868213317&partnerID=8YFLogxK
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U2 - 10.1111/j.1365-313X.2012.05087.x
DO - 10.1111/j.1365-313X.2012.05087.x
M3 - Article
C2 - 22731681
AN - SCOPUS:84868213317
SN - 0960-7412
VL - 72
SP - 390
EP - 399
JO - Plant Journal
JF - Plant Journal
IS - 3
ER -