EQTLs Regulating Transcript Variations Associated with Rapid Internode Elongation in Deepwater Rice.

Takeshi Kuroha,Miyako Kusano,Motoyuki Ashikari,Yusuke Kurokawa,Keisuke Nagai,Hideshi Yasui,Atsushi Fukushima,Yoshiaki Nagamura

doi:10.3389/fpls.2017.01753

Abstract

To avoid low oxygen, oxygen deficiency or oxygen deprivation, deepwater rice cultivated in flood planes can develop elongated internodes in response to submergence. Knowledge of the gene regulatory networks underlying rapid internode elongation is important for an understanding of the evolution and adaptation of major crops in response to flooding. To elucidate the genetic and molecular basis controlling their deepwater response we used microarrays and performed expression quantitative trait loci (eQTL) and phenotypic QTL (phQTL) analyses of internode samples of 85 recombinant inbred line (RIL) populations of non-deepwater (Taichung 65)- and deepwater rice (Bhadua). After evaluating the phenotypic response of the RILs exposed to submergence, confirming the genotypes of the populations, and generating 188 genetic markers, we identified 10,047 significant eQTLs comprised of 2,902 cis-eQTLs and 7,145 trans-eQTLs and three significant eQTL hotspots on chromosomes 1, 4, and 12 that affect the expression of many genes. The hotspots on chromosomes 1 and 4 located at different position from phQTLs detected in this study and other previous studies. We then regarded the eQTL hotspots as key regulatory points to infer causal regulatory networks of deepwater response including rapid internode elongation. Our results suggest that the downstream regulation of the eQTL hotspots on chromosomes 1 and 4 is independent, and that the target genes are partially regulated by SNORKEL1 and SNORKEL2 genes (SK1/2), key ethylene response factors. Subsequent bioinformatic analyses, including gene ontology-based annotation and functional enrichment analysis and promoter enrichment analysis, contribute to enhance our understanding of SK1/2-dependent and independent pathways. One remarkable observation is that the functional categories related to photosynthesis and light signaling are significantly over-represented in the candidate target genes of SK1/2. The combined results of these investigations together with genetical genomics approaches using structured populations with a deepwater response are also discussed in the context of current molecular models concerning the rapid internode elongation in deepwater rice. This study provides new insights into the underlying genetic architecture of gene expression regulating the response to flooding in deepwater rice and will be an important community resource for analyses on the genetic basis of deepwater responses.

Highlights

Flooding, an environmental stress, affects the growth and development of most plants by limiting the exchange of gases such as oxygen and carbonic dioxide and reducing the light intensity; this reduces yield around the world
Two significant phQTLs for number of elongated internodes (NEI) were located at marker position “P0770_1” on chromosome 1; on chromosome 12 they were at the same position for total internode length (TIL) and plant height (PH) (Supplementary Figure S5C)
The location of these two phQTLs for all phenotypic traits was consistent with the quantitative trait loci (QTL) with respect to the internode elongation previously detected by mapping with Taichung 65 (T65)/Bhadua (Kawano et al, 2008) and T65/C9285 (Hattori et al, 2007, 2008)

Summary

Introduction

An environmental stress, affects the growth and development of most plants by limiting the exchange of gases such as oxygen and carbonic dioxide and reducing the light intensity; this reduces yield around the world. Some plants such as Oryza, Rumex, Rorippa, and Echinochloa genera can survive under this stressful condition by implementing specific strategies (Bailey-Serres and Voesenek, 2008). By the ‘escape strategy,’ the internodes of rice plants tolerant to deepwater flooding rapidly elongate as the water level rises (Nagai et al, 2010; Hattori et al, 2011). Deepwater rice can be grown in many flood-prone areas in South and Southeast Asia such as Bangladesh, Cambodia, and Thailand (Kende et al, 1998)

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