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Genome-wide association study reveals novel QTLs and candidate genes for seed vigor in rice
Highly seed vigor (SV) is essential for rice direct seeding (DS). Understanding the genetic mechanism of SV-related traits could contribute to increasing the efficiency of DS. However, only a few genes responsible for SV have been determined in rice, and the regulatory network of SV remains obscure....
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9645239/ https://www.ncbi.nlm.nih.gov/pubmed/36388599 http://dx.doi.org/10.3389/fpls.2022.1005203 |
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author | Dai, Liping Lu, Xueli Shen, Lan Guo, Longbiao Zhang, Guangheng Gao, Zhenyu Zhu, Li Hu, Jiang Dong, Guojun Ren, Deyong Zhang, Qiang Zeng, Dali Qian, Qian Li, Qing |
author_facet | Dai, Liping Lu, Xueli Shen, Lan Guo, Longbiao Zhang, Guangheng Gao, Zhenyu Zhu, Li Hu, Jiang Dong, Guojun Ren, Deyong Zhang, Qiang Zeng, Dali Qian, Qian Li, Qing |
author_sort | Dai, Liping |
collection | PubMed |
description | Highly seed vigor (SV) is essential for rice direct seeding (DS). Understanding the genetic mechanism of SV-related traits could contribute to increasing the efficiency of DS. However, only a few genes responsible for SV have been determined in rice, and the regulatory network of SV remains obscure. In this study, the seed germination rate (GR), seedling shoot length (SL), and shoot fresh weight (FW) related to SV traits were measured, and a genome-wide association study (GWAS) was conducted to detect high-quality loci responsible for SV using a panel of 346 diverse accessions. A total of 51 significant SNPs were identified and arranged into six quantitative trait locus (QTL) regions, including one (qGR1-1), two (qSL1-1, qSL1-2), and three (qFW1-1, qFW4-1, and qFW7-1) QTLs associated with GR, SL, and FW respectively, which were further validated using chromosome segment substitution lines (CSSLs). Integrating gene expression, gene annotation, and haplotype analysis, we found 21 strong candidate genes significantly associated with SV. In addition, the SV-related functions of LOC_Os01g11270 and LOC_Os01g55240 were further verified by corresponding CRISPR/Cas9 gene-edited mutants. Thus, these results provide clues for elucidating the genetic basis of SV control. The candidate genes or QTLs would be helpful for improving DS by molecular marker-assisted selection (MAS) breeding in rice. |
format | Online Article Text |
id | pubmed-9645239 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-96452392022-11-15 Genome-wide association study reveals novel QTLs and candidate genes for seed vigor in rice Dai, Liping Lu, Xueli Shen, Lan Guo, Longbiao Zhang, Guangheng Gao, Zhenyu Zhu, Li Hu, Jiang Dong, Guojun Ren, Deyong Zhang, Qiang Zeng, Dali Qian, Qian Li, Qing Front Plant Sci Plant Science Highly seed vigor (SV) is essential for rice direct seeding (DS). Understanding the genetic mechanism of SV-related traits could contribute to increasing the efficiency of DS. However, only a few genes responsible for SV have been determined in rice, and the regulatory network of SV remains obscure. In this study, the seed germination rate (GR), seedling shoot length (SL), and shoot fresh weight (FW) related to SV traits were measured, and a genome-wide association study (GWAS) was conducted to detect high-quality loci responsible for SV using a panel of 346 diverse accessions. A total of 51 significant SNPs were identified and arranged into six quantitative trait locus (QTL) regions, including one (qGR1-1), two (qSL1-1, qSL1-2), and three (qFW1-1, qFW4-1, and qFW7-1) QTLs associated with GR, SL, and FW respectively, which were further validated using chromosome segment substitution lines (CSSLs). Integrating gene expression, gene annotation, and haplotype analysis, we found 21 strong candidate genes significantly associated with SV. In addition, the SV-related functions of LOC_Os01g11270 and LOC_Os01g55240 were further verified by corresponding CRISPR/Cas9 gene-edited mutants. Thus, these results provide clues for elucidating the genetic basis of SV control. The candidate genes or QTLs would be helpful for improving DS by molecular marker-assisted selection (MAS) breeding in rice. Frontiers Media S.A. 2022-10-26 /pmc/articles/PMC9645239/ /pubmed/36388599 http://dx.doi.org/10.3389/fpls.2022.1005203 Text en Copyright © 2022 Dai, Lu, Shen, Guo, Zhang, Gao, Zhu, Hu, Dong, Ren, Zhang, Zeng, Qian and Li https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Dai, Liping Lu, Xueli Shen, Lan Guo, Longbiao Zhang, Guangheng Gao, Zhenyu Zhu, Li Hu, Jiang Dong, Guojun Ren, Deyong Zhang, Qiang Zeng, Dali Qian, Qian Li, Qing Genome-wide association study reveals novel QTLs and candidate genes for seed vigor in rice |
title | Genome-wide association study reveals novel QTLs and candidate genes for seed vigor in rice |
title_full | Genome-wide association study reveals novel QTLs and candidate genes for seed vigor in rice |
title_fullStr | Genome-wide association study reveals novel QTLs and candidate genes for seed vigor in rice |
title_full_unstemmed | Genome-wide association study reveals novel QTLs and candidate genes for seed vigor in rice |
title_short | Genome-wide association study reveals novel QTLs and candidate genes for seed vigor in rice |
title_sort | genome-wide association study reveals novel qtls and candidate genes for seed vigor in rice |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9645239/ https://www.ncbi.nlm.nih.gov/pubmed/36388599 http://dx.doi.org/10.3389/fpls.2022.1005203 |
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