Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents

Anja Paschold, Yi Jia, Caroline Marcon, Steve Lund, Nicholas Larson, Cheng Ting Yeh, Stephan Ossowski, Christa Lanz, Dan Nettleton, Patrick S. Schnable, Frank Hochholdinger

Research output: Contribution to journalArticle

70 Citations (Scopus)

Abstract

Typically, F1-hybrids are more vigorous than their homozygous, genetically distinct parents, a phenomenon known as heterosis. In the present study, the transcriptomes of the reciprocal maize (Zea mays L.) hybrids B73xMo17 and Mo17xB73 and their parental inbred lines B73 and Mo17 were surveyed in primary roots, early in the developmental manifestation of heterotic root traits. The application of statistical methods and a suitable experimental design established that 34,233 (i.e., 86%) of all high-confidence maize genes were expressed in at least one genotype. Nearly 70% of all expressed genes were differentially expressed between the two parents and 42%-55% of expressed genes were differentially expressed between one of the parents and one of the hybrids. In both hybrids, ~10% of expressed genes exhibited nonadditive gene expression. Consistent with the dominance model (i.e., complementation) for heterosis, 1124 genes that were expressed in the hybrids were expressed in only one of the two parents. For 65 genes, it could be shown that this was a consequence of complementation of genomic presence/absence variation. For dozens of other genes, alleles from the inactive inbred were activated in the hybrid, presumably via interactions with regulatory factors from the active inbred. As a consequence of these types of complementation, both hybrids expressed more genes than did either parental inbred. Finally, in hybrids, ∼14% of expressed genes exhibited allele-specific expression (ASE) levels that differed significantly from the parental-inbred expression ratios, providing further evidence for interactions of regulatory factors from one parental genome with target genes from the other parental genome.

Original languageEnglish (US)
Pages (from-to)2445-2454
Number of pages10
JournalGenome Research
Volume22
Issue number12
DOIs
StatePublished - Dec 1 2012
Externally publishedYes

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Transcriptome
Zea mays
Genes
Hybrid Vigor
Alleles
Genome
Research Design
Genotype
Gene Expression

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents. / Paschold, Anja; Jia, Yi; Marcon, Caroline; Lund, Steve; Larson, Nicholas; Yeh, Cheng Ting; Ossowski, Stephan; Lanz, Christa; Nettleton, Dan; Schnable, Patrick S.; Hochholdinger, Frank.

In: Genome Research, Vol. 22, No. 12, 01.12.2012, p. 2445-2454.

Research output: Contribution to journalArticle

Paschold, A, Jia, Y, Marcon, C, Lund, S, Larson, N, Yeh, CT, Ossowski, S, Lanz, C, Nettleton, D, Schnable, PS & Hochholdinger, F 2012, 'Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents', Genome Research, vol. 22, no. 12, pp. 2445-2454. https://doi.org/10.1101/gr.138461.112
Paschold, Anja ; Jia, Yi ; Marcon, Caroline ; Lund, Steve ; Larson, Nicholas ; Yeh, Cheng Ting ; Ossowski, Stephan ; Lanz, Christa ; Nettleton, Dan ; Schnable, Patrick S. ; Hochholdinger, Frank. / Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents. In: Genome Research. 2012 ; Vol. 22, No. 12. pp. 2445-2454.
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