Systematic Analysis of NB-ARC Gene Family in Rice and Functional Characterization of GNP12

The NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) gene family plays a critical role in plant development. However, our understanding of the mechanisms of how NB-ARC genes regulate plant development in the plant panicle is still limited. Here, we subjected 258 NB-ARC gen...

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Published inFrontiers in genetics Vol. 13; p. 887217
Main Authors Pan, Ying-Hua, Chen, Lei, Guo, Hai-Feng, Feng, Rui, Lou, Qi-Jin, Rashid, Muhammad Abdul Rehman, Zhu, Xiao-Yang, Qing, Dong-Jin, Liang, Hai-Fu, Gao, Li-Jun, Huang, Cheng-Cui, Zhao, Yan, Deng, Guo-Fu
Format Journal Article
LanguageEnglish
Published Switzerland Frontiers Media S.A 16.06.2022
Subjects
evolution
expression
Genetics
NB-ARC family
panicle development
rice
NB-ARC family
expression
evolution
rice
panicle development
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Abstract The NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) gene family plays a critical role in plant development. However, our understanding of the mechanisms of how NB-ARC genes regulate plant development in the plant panicle is still limited. Here, we subjected 258 NB-ARC genes in rice to genome-wide analysis to characterize their structure, function, and expression patterns. The NB-ARC genes were classified into three major groups, and group II included nine subgroups. Evolutionary analysis of NB-ARC genes in a dicotyledon plant ( ) and two monocotyledonous plants ( L. and ) indicated that homologous genome segments were conserved in monocotyledons and subjected to weak positive selective pressure during evolution. Dispersed and proximal replication events were detected. Expression analysis showed expression of most NB-ARC genes in roots, panicles, and leaves, and regulation at the panicle development stage in rice Ce253. The gene encodes RGH1A protein, which regulates rice yield according to panicle length, grain number of panicle, and grain length, with eight major haplotypes. Most members of NB-ARC protein family are predicted to contain P-loop conserved domains and localize on the membrane. The results of this study will provide insight into the characteristics and evolution of NB-ARC family and suggest that positively regulates panicle development.
AbstractList The NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) gene family plays a critical role in plant development. However, our understanding of the mechanisms of how NB-ARC genes regulate plant development in the plant panicle is still limited. Here, we subjected 258 NB-ARC genes in rice to genome-wide analysis to characterize their structure, function, and expression patterns. The NB-ARC genes were classified into three major groups, and group II included nine subgroups. Evolutionary analysis of NB-ARC genes in a dicotyledon plant ( ) and two monocotyledonous plants ( L. and ) indicated that homologous genome segments were conserved in monocotyledons and subjected to weak positive selective pressure during evolution. Dispersed and proximal replication events were detected. Expression analysis showed expression of most NB-ARC genes in roots, panicles, and leaves, and regulation at the panicle development stage in rice Ce253. The gene encodes RGH1A protein, which regulates rice yield according to panicle length, grain number of panicle, and grain length, with eight major haplotypes. Most members of NB-ARC protein family are predicted to contain P-loop conserved domains and localize on the membrane. The results of this study will provide insight into the characteristics and evolution of NB-ARC family and suggest that positively regulates panicle development.
The NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) gene family plays a critical role in plant development. However, our understanding of the mechanisms of how NB-ARC genes regulate plant development in the plant panicle is still limited. Here, we subjected 258 NB-ARC genes in rice to genome-wide analysis to characterize their structure, function, and expression patterns. The NB-ARC genes were classified into three major groups, and group II included nine subgroups. Evolutionary analysis of NB-ARC genes in a dicotyledon plant (Arabidopsis thaliana) and two monocotyledonous plants (Oryza sativa L. and Triticum aestivum) indicated that homologous genome segments were conserved in monocotyledons and subjected to weak positive selective pressure during evolution. Dispersed and proximal replication events were detected. Expression analysis showed expression of most NB-ARC genes in roots, panicles, and leaves, and regulation at the panicle development stage in rice Ce253. The GNP12 gene encodes RGH1A protein, which regulates rice yield according to panicle length, grain number of panicle, and grain length, with eight major haplotypes. Most members of NB-ARC protein family are predicted to contain P-loop conserved domains and localize on the membrane. The results of this study will provide insight into the characteristics and evolution of NB-ARC family and suggest that GNP12 positively regulates panicle development.The NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) gene family plays a critical role in plant development. However, our understanding of the mechanisms of how NB-ARC genes regulate plant development in the plant panicle is still limited. Here, we subjected 258 NB-ARC genes in rice to genome-wide analysis to characterize their structure, function, and expression patterns. The NB-ARC genes were classified into three major groups, and group II included nine subgroups. Evolutionary analysis of NB-ARC genes in a dicotyledon plant (Arabidopsis thaliana) and two monocotyledonous plants (Oryza sativa L. and Triticum aestivum) indicated that homologous genome segments were conserved in monocotyledons and subjected to weak positive selective pressure during evolution. Dispersed and proximal replication events were detected. Expression analysis showed expression of most NB-ARC genes in roots, panicles, and leaves, and regulation at the panicle development stage in rice Ce253. The GNP12 gene encodes RGH1A protein, which regulates rice yield according to panicle length, grain number of panicle, and grain length, with eight major haplotypes. Most members of NB-ARC protein family are predicted to contain P-loop conserved domains and localize on the membrane. The results of this study will provide insight into the characteristics and evolution of NB-ARC family and suggest that GNP12 positively regulates panicle development.
The NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) gene family plays a critical role in plant development. However, our understanding of the mechanisms of how NB-ARC genes regulate plant development in the plant panicle is still limited. Here, we subjected 258 NB-ARC genes in rice to genome-wide analysis to characterize their structure, function, and expression patterns. The NB-ARC genes were classified into three major groups, and group II included nine subgroups. Evolutionary analysis of NB-ARC genes in a dicotyledon plant ( Arabidopsis thaliana ) and two monocotyledonous plants ( Oryza sativa L. and Triticum aestivum ) indicated that homologous genome segments were conserved in monocotyledons and subjected to weak positive selective pressure during evolution. Dispersed and proximal replication events were detected. Expression analysis showed expression of most NB-ARC genes in roots, panicles, and leaves, and regulation at the panicle development stage in rice Ce253. The GNP12 gene encodes RGH1A protein, which regulates rice yield according to panicle length, grain number of panicle, and grain length, with eight major haplotypes. Most members of NB-ARC protein family are predicted to contain P-loop conserved domains and localize on the membrane. The results of this study will provide insight into the characteristics and evolution of NB-ARC family and suggest that GNP12 positively regulates panicle development.
The NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) gene family plays a critical role in plant development. However, our understanding of the mechanisms of how NB-ARC genes regulate plant development in the plant panicle is still limited. Here, we subjected 258 NB-ARC genes in rice to genome-wide analysis to characterize their structure, function, and expression patterns. The NB-ARC genes were classified into three major groups, and group II included nine subgroups. Evolutionary analysis of NB-ARC genes in a dicotyledon plant (Arabidopsis thaliana) and two monocotyledonous plants (Oryza sativa L. and Triticum aestivum) indicated that homologous genome segments were conserved in monocotyledons and subjected to weak positive selective pressure during evolution. Dispersed and proximal replication events were detected. Expression analysis showed expression of most NB-ARC genes in roots, panicles, and leaves, and regulation at the panicle development stage in rice Ce253. The GNP12 gene encodes RGH1A protein, which regulates rice yield according to panicle length, grain number of panicle, and grain length, with eight major haplotypes. Most members of NB-ARC protein family are predicted to contain P-loop conserved domains and localize on the membrane. The results of this study will provide insight into the characteristics and evolution of NB-ARC family and suggest that GNP12 positively regulates panicle development.
Author Pan, Ying-Hua
Qing, Dong-Jin
Deng, Guo-Fu
Feng, Rui
Chen, Lei
Gao, Li-Jun
Huang, Cheng-Cui
Rashid, Muhammad Abdul Rehman
Lou, Qi-Jin
Zhu, Xiao-Yang
Liang, Hai-Fu
Guo, Hai-Feng
Zhao, Yan
AuthorAffiliation 2 State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement , College of Agronomy and Biotechnology , China Agricultural University , Beijing , China
1 Rice Research Institute , Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding , Nanning , China
3 Department of Bioinformatics and Biotechnology , Government College University Faisalabad , Faisalabad , Pakistan
4 Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory , Nanning , China
5 State Key Laboratory of Crop Biology , Shandong Key Laboratory of Crop Biology , College of Agronomy , Shandong Agricultural University , Tai’an , China
AuthorAffiliation_xml – name: 2 State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement , College of Agronomy and Biotechnology , China Agricultural University , Beijing , China
– name: 3 Department of Bioinformatics and Biotechnology , Government College University Faisalabad , Faisalabad , Pakistan
– name: 4 Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory , Nanning , China
– name: 1 Rice Research Institute , Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding , Nanning , China
– name: 5 State Key Laboratory of Crop Biology , Shandong Key Laboratory of Crop Biology , College of Agronomy , Shandong Agricultural University , Tai’an , China
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  givenname: Guo-Fu
  surname: Deng
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  organization: Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
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Copyright Copyright © 2022 Pan, Chen, Guo, Feng, Lou, Rashid, Zhu, Qing, Liang, Gao, Huang, Zhao and Deng.
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Keywords NB-ARC family
expression
evolution
rice
panicle development
Language English
License Copyright © 2022 Pan, Chen, Guo, Feng, Lou, Rashid, Zhu, Qing, Liang, Gao, Huang, Zhao and Deng.
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Edited by: Genlou Sun, Saint Mary’s University, Canada
These authors have contributed equally to this work
Reviewed by: Yunpeng Cao, Chinese Academy of Sciences (CAS), China
This article was submitted to Evolutionary and Population Genetics, a section of the journal Frontiers in Genetics
Tao Xu, Jiangsu Normal University, China
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Snippet The NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) gene family plays a critical role in plant development. However, our...
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StartPage 887217
SubjectTerms evolution
expression
Genetics
NB-ARC family
panicle development
rice
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Title Systematic Analysis of NB-ARC Gene Family in Rice and Functional Characterization of GNP12
URI https://www.ncbi.nlm.nih.gov/pubmed/35783267
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https://pubmed.ncbi.nlm.nih.gov/PMC9244165
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Volume 13
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