An Integration of Genome-Wide Association Study and Gene Co-expression Network Analysis Identifies Candidate Genes of Stem Lodging-Related Traits in Brassica napus
Lodging is a persistent problem which severely reduce yield and impair seed quality in rapeseed (Brassica napus L.). Enhancing stem strength (SS) has proven to be an effective approach to decrease lodging risk. In the present study, four interrelated stem lodging-related traits, including stem break...
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ftdoajarticles:oai:doaj.org/article:b74aed268c2a42fb9fc97eb82c3270a5 2023-05-15T16:07:20+02:00 An Integration of Genome-Wide Association Study and Gene Co-expression Network Analysis Identifies Candidate Genes of Stem Lodging-Related Traits in Brassica napus Hongge Li Xi Cheng Liping Zhang Jihong Hu Fugui Zhang Biyun Chen Kun Xu Guizhen Gao Hao Li Lixia Li Qian Huang Zaiyun Li Guixin Yan Xiaoming Wu 2018-06-01T00:00:00Z https://doi.org/10.3389/fpls.2018.00796 https://doaj.org/article/b74aed268c2a42fb9fc97eb82c3270a5 EN eng Frontiers Media S.A. https://www.frontiersin.org/article/10.3389/fpls.2018.00796/full https://doaj.org/toc/1664-462X 1664-462X doi:10.3389/fpls.2018.00796 https://doaj.org/article/b74aed268c2a42fb9fc97eb82c3270a5 Frontiers in Plant Science, Vol 9 (2018) Brassica napus L stem lodging-related traits genome-wide association study gene co-expression network candidate genes Plant culture SB1-1110 article 2018 ftdoajarticles https://doi.org/10.3389/fpls.2018.00796 2022-12-31T13:34:36Z Lodging is a persistent problem which severely reduce yield and impair seed quality in rapeseed (Brassica napus L.). Enhancing stem strength (SS) has proven to be an effective approach to decrease lodging risk. In the present study, four interrelated stem lodging-related traits, including stem breaking resistance (SBR), stem diameter (SD), SS, and lodging coefficient (LC), were investigated among 472 rapeseed accessions. A genome-wide association study (GWAS) using Brassica 60K SNP array for stem lodging-related traits identified 67 significantly associated quantitative trait loci (QTLs) and 71 candidate genes. In parallel, a gene co-expression network based on transcriptome sequencing was constructed. The module associated with cellulose biosynthesis was highlighted. By integrating GWAS and gene co-expression network analysis, some promising candidate genes, such as ESKIMO1 (ESK1, BnaC08g26920D), CELLULOSE SYNTHASE 6 (CESA6, BnaA09g06990D), and FRAGILE FIBER 8 (FRA8, BnaC04g39510D), were prioritized for further research. These findings revealed the genetic basis underlying stem lodging and provided worthwhile QTLs and genes information for genetic improvement of stem lodging resistance in B. napus. Article in Journal/Newspaper eskimo* Directory of Open Access Journals: DOAJ Articles Frontiers in Plant Science 9 |
institution |
Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Brassica napus L stem lodging-related traits genome-wide association study gene co-expression network candidate genes Plant culture SB1-1110 |
spellingShingle |
Brassica napus L stem lodging-related traits genome-wide association study gene co-expression network candidate genes Plant culture SB1-1110 Hongge Li Xi Cheng Liping Zhang Jihong Hu Fugui Zhang Biyun Chen Kun Xu Guizhen Gao Hao Li Lixia Li Qian Huang Zaiyun Li Guixin Yan Xiaoming Wu An Integration of Genome-Wide Association Study and Gene Co-expression Network Analysis Identifies Candidate Genes of Stem Lodging-Related Traits in Brassica napus |
topic_facet |
Brassica napus L stem lodging-related traits genome-wide association study gene co-expression network candidate genes Plant culture SB1-1110 |
description |
Lodging is a persistent problem which severely reduce yield and impair seed quality in rapeseed (Brassica napus L.). Enhancing stem strength (SS) has proven to be an effective approach to decrease lodging risk. In the present study, four interrelated stem lodging-related traits, including stem breaking resistance (SBR), stem diameter (SD), SS, and lodging coefficient (LC), were investigated among 472 rapeseed accessions. A genome-wide association study (GWAS) using Brassica 60K SNP array for stem lodging-related traits identified 67 significantly associated quantitative trait loci (QTLs) and 71 candidate genes. In parallel, a gene co-expression network based on transcriptome sequencing was constructed. The module associated with cellulose biosynthesis was highlighted. By integrating GWAS and gene co-expression network analysis, some promising candidate genes, such as ESKIMO1 (ESK1, BnaC08g26920D), CELLULOSE SYNTHASE 6 (CESA6, BnaA09g06990D), and FRAGILE FIBER 8 (FRA8, BnaC04g39510D), were prioritized for further research. These findings revealed the genetic basis underlying stem lodging and provided worthwhile QTLs and genes information for genetic improvement of stem lodging resistance in B. napus. |
format |
Article in Journal/Newspaper |
author |
Hongge Li Xi Cheng Liping Zhang Jihong Hu Fugui Zhang Biyun Chen Kun Xu Guizhen Gao Hao Li Lixia Li Qian Huang Zaiyun Li Guixin Yan Xiaoming Wu |
author_facet |
Hongge Li Xi Cheng Liping Zhang Jihong Hu Fugui Zhang Biyun Chen Kun Xu Guizhen Gao Hao Li Lixia Li Qian Huang Zaiyun Li Guixin Yan Xiaoming Wu |
author_sort |
Hongge Li |
title |
An Integration of Genome-Wide Association Study and Gene Co-expression Network Analysis Identifies Candidate Genes of Stem Lodging-Related Traits in Brassica napus |
title_short |
An Integration of Genome-Wide Association Study and Gene Co-expression Network Analysis Identifies Candidate Genes of Stem Lodging-Related Traits in Brassica napus |
title_full |
An Integration of Genome-Wide Association Study and Gene Co-expression Network Analysis Identifies Candidate Genes of Stem Lodging-Related Traits in Brassica napus |
title_fullStr |
An Integration of Genome-Wide Association Study and Gene Co-expression Network Analysis Identifies Candidate Genes of Stem Lodging-Related Traits in Brassica napus |
title_full_unstemmed |
An Integration of Genome-Wide Association Study and Gene Co-expression Network Analysis Identifies Candidate Genes of Stem Lodging-Related Traits in Brassica napus |
title_sort |
integration of genome-wide association study and gene co-expression network analysis identifies candidate genes of stem lodging-related traits in brassica napus |
publisher |
Frontiers Media S.A. |
publishDate |
2018 |
url |
https://doi.org/10.3389/fpls.2018.00796 https://doaj.org/article/b74aed268c2a42fb9fc97eb82c3270a5 |
genre |
eskimo* |
genre_facet |
eskimo* |
op_source |
Frontiers in Plant Science, Vol 9 (2018) |
op_relation |
https://www.frontiersin.org/article/10.3389/fpls.2018.00796/full https://doaj.org/toc/1664-462X 1664-462X doi:10.3389/fpls.2018.00796 https://doaj.org/article/b74aed268c2a42fb9fc97eb82c3270a5 |
op_doi |
https://doi.org/10.3389/fpls.2018.00796 |
container_title |
Frontiers in Plant Science |
container_volume |
9 |
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1766403392923500544 |