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cis dominantly explains regulatory divergence between two indica rice genotypes; drought further enhances regulatory differences

View ORCID ProfileNelzo C. Ereful, Li-Yu Liu, Shu-Min Kao, Eric Tsai, Antonio Laurena, Michael Thomson, Andy Greenland, Wayne Powell, Ian Mackay, Hei Leung
doi: https://doi.org/10.1101/714907
Nelzo C. Ereful
The John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge, CB3 0LE UKInternational Rice Research Institute (IRRI), Los Baños, Laguna 4031 Philippines
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  • ORCID record for Nelzo C. Ereful
  • For correspondence: nelzo.ereful@niab.com
Li-Yu Liu
Department of Agronomy, National Taiwan University (NTU), Taipei City 100, Taiwan
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Shu-Min Kao
Center for Plant Systems Biology, VIB, Ghent B-9052, BelgiumDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
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Eric Tsai
Department of Agronomy, National Taiwan University (NTU), Taipei City 100, Taiwan
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Antonio Laurena
Philippine Genome Center – Agriculture, University of the Philippines, Los Baños, Laguna 4031 Philippines
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Michael Thomson
Texas A &M, Department of Soil and Crop Sciences 2474 TAMU, College Station, TX, 77843-2474, USA
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Andy Greenland
The John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge, CB3 0LE UK
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Wayne Powell
SRUC, Peter Wilson Building, West Mains Road, Edinburgh, EH9 3JG UK
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Ian Mackay
The John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge, CB3 0LE UKSRUC, Peter Wilson Building, West Mains Road, Edinburgh, EH9 3JG UK
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Hei Leung
International Rice Research Institute (IRRI), Los Baños, Laguna 4031 Philippines
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Abstract

Background cis and/or trans regulatory divergence within or between related taxa on a genome-wide scale has been largely unexamined in crops, more so, the effect of stress on cis/trans architecture. In this study, the indica genotypes IR64, an elite drought-susceptible lowland variety, and Apo (IR55423-01 or NSIC RC9), a moderate drought-tolerant upland genotype together with their hybrid (IR64 × Apo) were exposed to non- and water-stress conditions. Evidence of cis and/or trans regulatory differences was tested between these two indica rice genotypes.

Results By sequencing (RNA-seq) the parents and their hybrid, we are able to map genes diverging in cis and/or trans factors between the two genotypes. Under non-stress conditions, cis dominantly explains (11.2%) regulatory differences, followed by trans (8.9%). Further analysis showed that water-limiting conditions largely affect trans and cis + trans factors. Between the two inbred lines, Apo appears to exhibit higher expression fold change of genes enriched in “response to stress” and “photosynthesis” under non- and water-stress conditions. On the molecular level, cis and/or trans regulatory divergence explains their genotypic differences and differential drought response.

Conclusions Parent–hybrid RNA-seq has the potential to identify genes diverging in cis and/or trans factors even between intra-sub-specifically related genotypes. By comparing cis/trans landscape under stressed and unstressed conditions, this approach has the ability to assess the impact of drought on gene expression. Computational analysis and association of several drought-yield QTL markers with cis- and/or trans-diverging genes provide converging evidences suggestive of a potential approach to identify trait-associated candidate genes using hybrids and their parents alone.

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  • Updated mailing addresses of two authors.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 30, 2019.
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cis dominantly explains regulatory divergence between two indica rice genotypes; drought further enhances regulatory differences
Nelzo C. Ereful, Li-Yu Liu, Shu-Min Kao, Eric Tsai, Antonio Laurena, Michael Thomson, Andy Greenland, Wayne Powell, Ian Mackay, Hei Leung
bioRxiv 714907; doi: https://doi.org/10.1101/714907
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cis dominantly explains regulatory divergence between two indica rice genotypes; drought further enhances regulatory differences
Nelzo C. Ereful, Li-Yu Liu, Shu-Min Kao, Eric Tsai, Antonio Laurena, Michael Thomson, Andy Greenland, Wayne Powell, Ian Mackay, Hei Leung
bioRxiv 714907; doi: https://doi.org/10.1101/714907

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