Prediction of environmental response in field-grown rice using expression-dynamics-QTL

Makoto Kashima, Ryota L. Sakamoto, Hiroki Saito, Satoshi Ohkubo, Ayumi Tezuka, Ayumi Deguchi, Yoichi Hashida, Yuko Kurita & Atsushi J. Nagano

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Jan 14, 2019
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Received Date: 22nd December 18

How genetic variations affect environmental responses of field-grown plants throughout their lives remains unclear. Using large-scale time-series RNA sequencing of field-grown rice from chromosome segment substitution lines (CSSLs), we identified 1675 expression dynamics quantitative trait loci (edQTLs), which cause differences in gene expression dynamics (GED) under field conditions. Based on the edQTLs, we predicted GED under environments different from training environments, and in rice cultivars with more complex genotypes than the CSSLs. The results demonstrated that integrating genotype (G) and environment (E) information can help predict the environmental response of GED under field conditions throughout the life of an organism. We anticipate that edQTLs identification help understand the G×E of organisms under natural environments, which is difficult to assess with laboratory equipment. As transcriptome-based trait prediction functions effectively3,4, the prediction of GED based on  G×E will contribute to crop breeding by increasing the accuracy of trait prediction under diverse conditions.

Read in full at bioRxiv.

This is an abstract of a preprint hosted on an independent third party site. It has not been peer reviewed but is currently under consideration at Nature Communications.

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