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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....

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
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.
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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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