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Genome-wide association analysis of panicle exsertion and uppermost internode in rice (Oryza sativa L.)

BACKGROUND: Rice (Oryza sativa L.) yield is seriously influenced by panicle exsertion (PE) and the uppermost internode (UI) through panicle enclosure or energy transport during grain-filling stages. We evaluated the traits of PE and UI of 205 rice accessions in two independent environments and perfo...

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Autores principales: Zhan, Chengfang, Hu, Jiaxiao, Pang, Qiao, Yang, Bin, Cheng, Yanhao, Xu, Enshun, Zhu, Peiwen, Li, Yingyi, Zhang, Hongsheng, Cheng, Jinping
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer US 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6751241/
https://www.ncbi.nlm.nih.gov/pubmed/31535313
http://dx.doi.org/10.1186/s12284-019-0330-x
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author Zhan, Chengfang
Hu, Jiaxiao
Pang, Qiao
Yang, Bin
Cheng, Yanhao
Xu, Enshun
Zhu, Peiwen
Li, Yingyi
Zhang, Hongsheng
Cheng, Jinping
author_facet Zhan, Chengfang
Hu, Jiaxiao
Pang, Qiao
Yang, Bin
Cheng, Yanhao
Xu, Enshun
Zhu, Peiwen
Li, Yingyi
Zhang, Hongsheng
Cheng, Jinping
author_sort Zhan, Chengfang
collection PubMed
description BACKGROUND: Rice (Oryza sativa L.) yield is seriously influenced by panicle exsertion (PE) and the uppermost internode (UI) through panicle enclosure or energy transport during grain-filling stages. We evaluated the traits of PE and UI of 205 rice accessions in two independent environments and performed genome-wide association (GWAS) to explore the key genes controlling PE and UI, which could be used to improve panicle enclosure in rice breeding. RESULTS: In this study, extensive genetic variation was found in both PE and UI among the 205 rice accessions, and 10.7% of accessions had panicle enclosure (PE/UI ≤ 0). Correlation analysis revealed that PE was significantly positively correlated with 1000-grain weight (1000-GW) but negatively correlated with heading date (HD), and UI was significantly positively correlated with HD but no significantly correlated with 1000-GW. A total of 22 and 24 quantitative trait loci (QTLs) were identified for PE and UI using GWAS, respectively. Eight loci for PE and nine loci for UI were simultaneously detected both in 2015 and in 2016, seven loci had adjacent physical positions between PE and UI, and ten loci for PE and seven loci for UI were located in previously reported QTLs. Further, we identified the CYP734A4 gene, encoding a cytochrome P450 monooxygenase, and the OsLIS-L1 gene, encoding a lissencephaly type-1-like protein, as causal genes for qPE14 and qUI14, and for qPE19, respectively. PE and UI were both significantly shorter in these two genes’ mutants than in WT. Allelic Hap.1/2/4 of CYP734A4 and Hap.1/2/4 of OsLIS-L1 increased PE, UI, PE/UI, and 1000-GW, but Hap.3 of CYP734A4 and Hap.3 of OsLIS-L1 reduced them. In addition, six candidate genes were also detected for four key novel loci, qPE16, qPE21, qUI1, and qUI18, that seemed to be related to PE and UI. CONCLUSIONS: Our results provide new information on the genetic architecture of PE and UI in rice, confirming that the CYP734A4 and OsLIS-L1 genes participate in PE and UI regulation, which could improve our understanding of the regulatory mechanism of PE and UI for rice breeding in the future.
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spelling pubmed-67512412019-10-04 Genome-wide association analysis of panicle exsertion and uppermost internode in rice (Oryza sativa L.) Zhan, Chengfang Hu, Jiaxiao Pang, Qiao Yang, Bin Cheng, Yanhao Xu, Enshun Zhu, Peiwen Li, Yingyi Zhang, Hongsheng Cheng, Jinping Rice (N Y) Original Article BACKGROUND: Rice (Oryza sativa L.) yield is seriously influenced by panicle exsertion (PE) and the uppermost internode (UI) through panicle enclosure or energy transport during grain-filling stages. We evaluated the traits of PE and UI of 205 rice accessions in two independent environments and performed genome-wide association (GWAS) to explore the key genes controlling PE and UI, which could be used to improve panicle enclosure in rice breeding. RESULTS: In this study, extensive genetic variation was found in both PE and UI among the 205 rice accessions, and 10.7% of accessions had panicle enclosure (PE/UI ≤ 0). Correlation analysis revealed that PE was significantly positively correlated with 1000-grain weight (1000-GW) but negatively correlated with heading date (HD), and UI was significantly positively correlated with HD but no significantly correlated with 1000-GW. A total of 22 and 24 quantitative trait loci (QTLs) were identified for PE and UI using GWAS, respectively. Eight loci for PE and nine loci for UI were simultaneously detected both in 2015 and in 2016, seven loci had adjacent physical positions between PE and UI, and ten loci for PE and seven loci for UI were located in previously reported QTLs. Further, we identified the CYP734A4 gene, encoding a cytochrome P450 monooxygenase, and the OsLIS-L1 gene, encoding a lissencephaly type-1-like protein, as causal genes for qPE14 and qUI14, and for qPE19, respectively. PE and UI were both significantly shorter in these two genes’ mutants than in WT. Allelic Hap.1/2/4 of CYP734A4 and Hap.1/2/4 of OsLIS-L1 increased PE, UI, PE/UI, and 1000-GW, but Hap.3 of CYP734A4 and Hap.3 of OsLIS-L1 reduced them. In addition, six candidate genes were also detected for four key novel loci, qPE16, qPE21, qUI1, and qUI18, that seemed to be related to PE and UI. CONCLUSIONS: Our results provide new information on the genetic architecture of PE and UI in rice, confirming that the CYP734A4 and OsLIS-L1 genes participate in PE and UI regulation, which could improve our understanding of the regulatory mechanism of PE and UI for rice breeding in the future. Springer US 2019-09-18 /pmc/articles/PMC6751241/ /pubmed/31535313 http://dx.doi.org/10.1186/s12284-019-0330-x Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
spellingShingle Original Article
Zhan, Chengfang
Hu, Jiaxiao
Pang, Qiao
Yang, Bin
Cheng, Yanhao
Xu, Enshun
Zhu, Peiwen
Li, Yingyi
Zhang, Hongsheng
Cheng, Jinping
Genome-wide association analysis of panicle exsertion and uppermost internode in rice (Oryza sativa L.)
title Genome-wide association analysis of panicle exsertion and uppermost internode in rice (Oryza sativa L.)
title_full Genome-wide association analysis of panicle exsertion and uppermost internode in rice (Oryza sativa L.)
title_fullStr Genome-wide association analysis of panicle exsertion and uppermost internode in rice (Oryza sativa L.)
title_full_unstemmed Genome-wide association analysis of panicle exsertion and uppermost internode in rice (Oryza sativa L.)
title_short Genome-wide association analysis of panicle exsertion and uppermost internode in rice (Oryza sativa L.)
title_sort genome-wide association analysis of panicle exsertion and uppermost internode in rice (oryza sativa l.)
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6751241/
https://www.ncbi.nlm.nih.gov/pubmed/31535313
http://dx.doi.org/10.1186/s12284-019-0330-x
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