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RNA-Seq and Genome-Wide Association Studies Reveal Potential Genes for Rice Seed Shattering

The loss of the shattering ability is one of the key events in rice domestication. The strength of the seed shattering ability is closely related to the harvest yield and the adaptability of modern mechanical harvesting methods. In this study, using a population of 587 natural rice cultivars, quanti...

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Autores principales: Wu, Linxuan, Yue, Jicheng, Wang, Jiafeng, Lu, Wenyu, Huang, Ming, Guo, Tao, Wang, Hui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9736558/
https://www.ncbi.nlm.nih.gov/pubmed/36498964
http://dx.doi.org/10.3390/ijms232314633
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author Wu, Linxuan
Yue, Jicheng
Wang, Jiafeng
Lu, Wenyu
Huang, Ming
Guo, Tao
Wang, Hui
author_facet Wu, Linxuan
Yue, Jicheng
Wang, Jiafeng
Lu, Wenyu
Huang, Ming
Guo, Tao
Wang, Hui
author_sort Wu, Linxuan
collection PubMed
description The loss of the shattering ability is one of the key events in rice domestication. The strength of the seed shattering ability is closely related to the harvest yield and the adaptability of modern mechanical harvesting methods. In this study, using a population of 587 natural rice cultivars, quantitative trait loci associated with seed shattering were detected by genome-wide association studies (GWASs). We consider the quantitative trait loci (QTLs) qBTS1 and qBTS3 to be the key loci for seed shattering in rice. Additionally, the abscission zone (AZ) and nonabscission zone (NAZ) of materials with a loss of shattering (DZ129) and easy shattering (W517) were subjected to RNA-Seq, and high-quality differential expression profiles were obtained. The AZ-specific differentially expressed genes (DEGs) of W517 were significantly enriched in plant hormone signal transduction, while the AZ-specific DEGs of DZ129 were enriched in phenylpropanoid biosynthesis. We identified candidate genes for the lignin-associated laccase precursor protein (LOC_Os01g63180) and the glycoside hydrolase family (LOC_Os03g14210) in the QTLs qBTS1 (chromosome 1) and qBTS3 (chromosome 3), respectively. In summary, our findings lay the foundation for the further cloning of qBTS1 and qBTS3, which would provide new insights into seed shattering in rice.
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spelling pubmed-97365582022-12-11 RNA-Seq and Genome-Wide Association Studies Reveal Potential Genes for Rice Seed Shattering Wu, Linxuan Yue, Jicheng Wang, Jiafeng Lu, Wenyu Huang, Ming Guo, Tao Wang, Hui Int J Mol Sci Article The loss of the shattering ability is one of the key events in rice domestication. The strength of the seed shattering ability is closely related to the harvest yield and the adaptability of modern mechanical harvesting methods. In this study, using a population of 587 natural rice cultivars, quantitative trait loci associated with seed shattering were detected by genome-wide association studies (GWASs). We consider the quantitative trait loci (QTLs) qBTS1 and qBTS3 to be the key loci for seed shattering in rice. Additionally, the abscission zone (AZ) and nonabscission zone (NAZ) of materials with a loss of shattering (DZ129) and easy shattering (W517) were subjected to RNA-Seq, and high-quality differential expression profiles were obtained. The AZ-specific differentially expressed genes (DEGs) of W517 were significantly enriched in plant hormone signal transduction, while the AZ-specific DEGs of DZ129 were enriched in phenylpropanoid biosynthesis. We identified candidate genes for the lignin-associated laccase precursor protein (LOC_Os01g63180) and the glycoside hydrolase family (LOC_Os03g14210) in the QTLs qBTS1 (chromosome 1) and qBTS3 (chromosome 3), respectively. In summary, our findings lay the foundation for the further cloning of qBTS1 and qBTS3, which would provide new insights into seed shattering in rice. MDPI 2022-11-23 /pmc/articles/PMC9736558/ /pubmed/36498964 http://dx.doi.org/10.3390/ijms232314633 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Wu, Linxuan
Yue, Jicheng
Wang, Jiafeng
Lu, Wenyu
Huang, Ming
Guo, Tao
Wang, Hui
RNA-Seq and Genome-Wide Association Studies Reveal Potential Genes for Rice Seed Shattering
title RNA-Seq and Genome-Wide Association Studies Reveal Potential Genes for Rice Seed Shattering
title_full RNA-Seq and Genome-Wide Association Studies Reveal Potential Genes for Rice Seed Shattering
title_fullStr RNA-Seq and Genome-Wide Association Studies Reveal Potential Genes for Rice Seed Shattering
title_full_unstemmed RNA-Seq and Genome-Wide Association Studies Reveal Potential Genes for Rice Seed Shattering
title_short RNA-Seq and Genome-Wide Association Studies Reveal Potential Genes for Rice Seed Shattering
title_sort rna-seq and genome-wide association studies reveal potential genes for rice seed shattering
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9736558/
https://www.ncbi.nlm.nih.gov/pubmed/36498964
http://dx.doi.org/10.3390/ijms232314633
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