PT  - JOURNAL ARTICLE
AU  - Zhi Li
AU  - Peng Zhou
AU  - Rafael Della Coletta
AU  - Tifu Zhang
AU  - Alex B. Brohammer
AU  - Brieanne Vaillancourt
AU  - Anna Lipzen
AU  - Chris Daum
AU  - Kerrie Barry
AU  - Natalia de Leon
AU  - Cory D. Hirsch
AU  - C. Robin Buell
AU  - Shawn M. Kaeppler
AU  - Nathan M. Springer
AU  - Candice N. Hirsch
TI  - Highly Genotype- and Tissue-specific Single-Parent Expression Drives Dynamic Gene Expression Complementation in Maize Hybrids
AID  - 10.1101/668681
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 668681
4099  - http://biorxiv.org/content/early/2019/06/12/668681.short
4100  - http://biorxiv.org/content/early/2019/06/12/668681.full
AB  - Maize exhibits tremendous gene expression variation between different lines. Complementation of diverse gene expression patterns in hybrids could play an important role in the manifestation of heterosis. In this study, we used transcriptome data of five different tissues from 33 maize inbreds and 89 hybrids (430 samples in total) to survey the global gene expression landscape of F1-hybrids relative to their inbred parents. Analysis of this data set revealed that single parent expression (SPE), which is defined as gene expression in only one of the two parents, while commonly observed, is highly genotype- and tissue-specific. Genes that have SPE in at least one pair of inbreds also tend to be tissue-specific. Genes with SPE caused by genomic presence/absence variation (PAV SPE) are much more frequently expressed in hybrids than genes that are present in the genome of both inbreds, but expressed in only a single-parent (non-PAV SPE) (74.7% vs. 59.7%). For non-PAV SPE genes, allele specific expression was used to investigate whether parental alleles not expressed in the inbred line (“silent allele”) can be actively transcribed in the hybrid. We found that expression of the silent allele in the hybrid is relatively rare (∼6.3% of non-PAV SPE genes), but is observed in almost all hybrids and tissues. Non-PAV SPE genes with expression of the silent allele in the hybrid are more likely to exhibit above high-parent expression level in the hybrid than those that do not express the silent allele. Finally, both PAV SPE and non-PAV SPE genes are highly enriched for being classified as non-syntenic, but depleted for curated genes with experimentally determined functions. This study provides a more comprehensive understanding of the potential role of non-PAV SPE and PAV SPE genes in heterosis.