TY - JOUR
T1 - eQTLS regulating transcript variations associated with rapid internode elongation in deepwater rice
AU - Kuroha, Takeshi
AU - Nagai, Keisuke
AU - Kurokawa, Usuke
AU - Nagamura, Yoshiaki
AU - Kusano, Miyako
AU - Yasui, Hideshi
AU - Ashikari, Motoyuki
AU - Fukushima, Atsushi
N1 - Funding Information:
This work was supported by MEXT/JSPS KAKENHI (Grant Numbers 22119007, 24114001, 24114005, 26850024, 16K18565, 17K07663, 17H06473), SATREPS by JICA and JST, and Core Research for Evolutional Science and Technology by JST. We thank Ms. Midori Ito for technical assistance with RNA extraction, Ms. Yoko Niimi for RIL genotyping, Ms. Ritsuko Motoyama for technical support in our microarray analysis, Mr. Tomonori Noda for assistance with genotyping, Dr. Yasunori Ichihashi for guidance in promoter enrichment analysis, Ms. Ursula Petralia for editorial assistance, and Professor Julin Moloof for permitting us to re-use and modify QTLVizR (https://github.com/tiaho/QTL-Visualization). The preservation of the seed stocks of RILs were supported by the National Bio-Resource Project (NBRP) executed under the MEXT, Japan (http://www.shigen.nig.ac.jp/rice/oryzabase/ top/top.jsp).
Publisher Copyright:
© 2017 Kuroha, Nagai, Kurokawa, Nagamura, Kusano, Yasui, Ashikari and Fukushima.
PY - 2017/10/13
Y1 - 2017/10/13
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85034073378&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85034073378&partnerID=8YFLogxK
U2 - 10.3389/fpls.2017.01753
DO - 10.3389/fpls.2017.01753
M3 - Article
AN - SCOPUS:85034073378
VL - 8
JO - Frontiers in Plant Science
JF - Frontiers in Plant Science
SN - 1664-462X
M1 - 1753
ER -