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Genome-Wide Association Study (GWAS) for Mesocotyl Elongation in Rice (Oryza sativa L.) under Multiple Culture Conditions

Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in dry direct-seeded rice. However, the genetic mechanisms of mesocotyl elongation remains unclear. In our study, 208 rice accessions were used to identify the SNPs significant...

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Autores principales: Liu, Hongyan, Zhan, Junhui, Li, Jiaolong, Lu, Xiang, Liu, Jindong, Wang, Yamei, Zhao, Quanzhi, Ye, Guoyou
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7017202/
https://www.ncbi.nlm.nih.gov/pubmed/31906181
http://dx.doi.org/10.3390/genes11010049
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author Liu, Hongyan
Zhan, Junhui
Li, Jiaolong
Lu, Xiang
Liu, Jindong
Wang, Yamei
Zhao, Quanzhi
Ye, Guoyou
author_facet Liu, Hongyan
Zhan, Junhui
Li, Jiaolong
Lu, Xiang
Liu, Jindong
Wang, Yamei
Zhao, Quanzhi
Ye, Guoyou
author_sort Liu, Hongyan
collection PubMed
description Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in dry direct-seeded rice. However, the genetic mechanisms of mesocotyl elongation remains unclear. In our study, 208 rice accessions were used to identify the SNPs significantly associated with mesocotyl length under various culture conditions, including sand, water and soil. The mesocotyl length ranges from 0 to 4.88 cm, 0 to 3.99 cm and 0 to 4.51 cm in sand, water and soil covering, respectively. A total of 2,338,336 SNPs were discovered by re-sequencing of 208 rice accessions. Genome-wide association study (GWAS) based on mixed linear model (MLM) was conducted and 16 unique loci were identified on chromosomes 1, 2 (2), 3, 4, 5 (2), 6 (2), 7, 8, 9 (2) and 12 (3), respectively, explaining phenotypic variations ranging from 6.3 to 15.9%. Among these loci, 12 were stable across two or more environments. Ten out of the sixteen loci coincided with known genes or quantitative trait locus (QTL), whereas the other six were potentially novel loci. Furthermore, five high-confidence candidate genes related to mesocotyl elongation were identified on chromosomes 1, 3, 5, 9 and 12. Moreover, qRT-PCR analysis showed that all the five genes showed significant expression difference between short-mesocotyl accessions and long-mesocotyl accessions. This study provides new insights into the genetic architecture of rice mesocotyl, the associated SNPs and germplasms with long mesocotyl could be useful in the breeding of mechanized dry direct-seeded rice.
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spelling pubmed-70172022020-02-28 Genome-Wide Association Study (GWAS) for Mesocotyl Elongation in Rice (Oryza sativa L.) under Multiple Culture Conditions Liu, Hongyan Zhan, Junhui Li, Jiaolong Lu, Xiang Liu, Jindong Wang, Yamei Zhao, Quanzhi Ye, Guoyou Genes (Basel) Article Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in dry direct-seeded rice. However, the genetic mechanisms of mesocotyl elongation remains unclear. In our study, 208 rice accessions were used to identify the SNPs significantly associated with mesocotyl length under various culture conditions, including sand, water and soil. The mesocotyl length ranges from 0 to 4.88 cm, 0 to 3.99 cm and 0 to 4.51 cm in sand, water and soil covering, respectively. A total of 2,338,336 SNPs were discovered by re-sequencing of 208 rice accessions. Genome-wide association study (GWAS) based on mixed linear model (MLM) was conducted and 16 unique loci were identified on chromosomes 1, 2 (2), 3, 4, 5 (2), 6 (2), 7, 8, 9 (2) and 12 (3), respectively, explaining phenotypic variations ranging from 6.3 to 15.9%. Among these loci, 12 were stable across two or more environments. Ten out of the sixteen loci coincided with known genes or quantitative trait locus (QTL), whereas the other six were potentially novel loci. Furthermore, five high-confidence candidate genes related to mesocotyl elongation were identified on chromosomes 1, 3, 5, 9 and 12. Moreover, qRT-PCR analysis showed that all the five genes showed significant expression difference between short-mesocotyl accessions and long-mesocotyl accessions. This study provides new insights into the genetic architecture of rice mesocotyl, the associated SNPs and germplasms with long mesocotyl could be useful in the breeding of mechanized dry direct-seeded rice. MDPI 2019-12-31 /pmc/articles/PMC7017202/ /pubmed/31906181 http://dx.doi.org/10.3390/genes11010049 Text en © 2019 by the authors. 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 (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Liu, Hongyan
Zhan, Junhui
Li, Jiaolong
Lu, Xiang
Liu, Jindong
Wang, Yamei
Zhao, Quanzhi
Ye, Guoyou
Genome-Wide Association Study (GWAS) for Mesocotyl Elongation in Rice (Oryza sativa L.) under Multiple Culture Conditions
title Genome-Wide Association Study (GWAS) for Mesocotyl Elongation in Rice (Oryza sativa L.) under Multiple Culture Conditions
title_full Genome-Wide Association Study (GWAS) for Mesocotyl Elongation in Rice (Oryza sativa L.) under Multiple Culture Conditions
title_fullStr Genome-Wide Association Study (GWAS) for Mesocotyl Elongation in Rice (Oryza sativa L.) under Multiple Culture Conditions
title_full_unstemmed Genome-Wide Association Study (GWAS) for Mesocotyl Elongation in Rice (Oryza sativa L.) under Multiple Culture Conditions
title_short Genome-Wide Association Study (GWAS) for Mesocotyl Elongation in Rice (Oryza sativa L.) under Multiple Culture Conditions
title_sort genome-wide association study (gwas) for mesocotyl elongation in rice (oryza sativa l.) under multiple culture conditions
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7017202/
https://www.ncbi.nlm.nih.gov/pubmed/31906181
http://dx.doi.org/10.3390/genes11010049
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