eQTLS regulating transcript variations associated with rapid internode elongation in deepwater rice

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

Research output: Contribution to journalArticle

4 Citations (Scopus)

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.

Original languageEnglish
Article number1753
JournalFrontiers in Plant Science
Volume8
DOIs
Publication statusPublished - Oct 13 2017

Fingerprint

internodes
quantitative trait loci
rice
submergence
chromosomes
genes
oxygen
molecular models
bioinformatics
inbred lines
hypoxia
ethylene
promoter regions
photosynthesis
genomics
gene expression
genetic markers
genotype
crops
sampling

All Science Journal Classification (ASJC) codes

  • Plant Science

Cite this

eQTLS regulating transcript variations associated with rapid internode elongation in deepwater rice. / Kuroha, Takeshi; Nagai, Keisuke; Kurokawa, Usuke; Nagamura, Yoshiaki; Kusano, Miyako; Yasui, Hideshi; Ashikari, Motoyuki; Fukushima, Atsushi.

In: Frontiers in Plant Science, Vol. 8, 1753, 13.10.2017.

Research output: Contribution to journalArticle

Kuroha, Takeshi ; Nagai, Keisuke ; Kurokawa, Usuke ; Nagamura, Yoshiaki ; Kusano, Miyako ; Yasui, Hideshi ; Ashikari, Motoyuki ; Fukushima, Atsushi. / eQTLS regulating transcript variations associated with rapid internode elongation in deepwater rice. In: Frontiers in Plant Science. 2017 ; Vol. 8.
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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.",
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AU - Kusano, Miyako

AU - Yasui, Hideshi

AU - Ashikari, Motoyuki

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