Integrative omics analysis reveals the genetic basis of fatty acid composition in Brassica napus seeds
Abstract Background The fatty acid content represents a crucial quality trait in Brassica napus or rapeseed. Improvements in fatty acid composition markedly enhance the quality of rapeseed oil. Results Here, we perform a genome-wide association study (GWAS) to identify quantitative trait locus (QTLs...
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| Format: | Article |
| Language: | English |
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BMC
2025-04-01
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| Series: | Genome Biology |
| Online Access: | https://doi.org/10.1186/s13059-025-03558-x |
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| author | Yuting Zhang Yunhao Liu Zhanxiang Zong Liang Guo Wenhao Shen Hu Zhao |
| author_facet | Yuting Zhang Yunhao Liu Zhanxiang Zong Liang Guo Wenhao Shen Hu Zhao |
| author_sort | Yuting Zhang |
| collection | DOAJ |
| description | Abstract Background The fatty acid content represents a crucial quality trait in Brassica napus or rapeseed. Improvements in fatty acid composition markedly enhance the quality of rapeseed oil. Results Here, we perform a genome-wide association study (GWAS) to identify quantitative trait locus (QTLs) associated with fatty acid content. We identify a total of seven stable QTLs and find two loci, qFA.A08 and qFA.A09.1, subjected to strong selection pressure. By transcriptome-wide association analysis (TWAS), we characterize 3295 genes that are significantly correlated with the composition of at least one fatty acid. To elucidate the genetic underpinnings governing fatty acid composition, we then employ a combination of GWAS, TWAS, and dynamic transcriptomic analysis during seed development, along with the POCKET algorithm. We predict six candidate genes that are associated with fatty acid composition. Experimental validation reveals that four genes (BnaA09.PYRD, BnaA08.PSK1, BnaA08.SWI3, and BnaC02.LTP15) positively modulate oleic acid content while negatively impact erucic acid content. Comparative analysis of transcriptome profiles suggests that BnaA09.PYRD may influence fatty acid composition by regulating energy metabolism during seed development. Conclusions This study establishes a genetic framework for a better understanding of plant oil biosynthesis in addition to providing theoretical foundation and valuable genetic resources for enhancing fatty acid composition in rapeseed breeding. |
| format | Article |
| id | doaj-art-2a995d78fb92488f984c0dc52a90dcfc |
| institution | OA Journals |
| issn | 1474-760X |
| language | English |
| publishDate | 2025-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-2a995d78fb92488f984c0dc52a90dcfc2025-08-20T01:54:19ZengBMCGenome Biology1474-760X2025-04-0126112010.1186/s13059-025-03558-xIntegrative omics analysis reveals the genetic basis of fatty acid composition in Brassica napus seedsYuting Zhang0Yunhao Liu1Zhanxiang Zong2Liang Guo3Wenhao Shen4Hu Zhao5Yazhouwan National LaboratoryYazhouwan National LaboratoryNational Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural UniversityYazhouwan National LaboratoryNational Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural UniversityAbstract Background The fatty acid content represents a crucial quality trait in Brassica napus or rapeseed. Improvements in fatty acid composition markedly enhance the quality of rapeseed oil. Results Here, we perform a genome-wide association study (GWAS) to identify quantitative trait locus (QTLs) associated with fatty acid content. We identify a total of seven stable QTLs and find two loci, qFA.A08 and qFA.A09.1, subjected to strong selection pressure. By transcriptome-wide association analysis (TWAS), we characterize 3295 genes that are significantly correlated with the composition of at least one fatty acid. To elucidate the genetic underpinnings governing fatty acid composition, we then employ a combination of GWAS, TWAS, and dynamic transcriptomic analysis during seed development, along with the POCKET algorithm. We predict six candidate genes that are associated with fatty acid composition. Experimental validation reveals that four genes (BnaA09.PYRD, BnaA08.PSK1, BnaA08.SWI3, and BnaC02.LTP15) positively modulate oleic acid content while negatively impact erucic acid content. Comparative analysis of transcriptome profiles suggests that BnaA09.PYRD may influence fatty acid composition by regulating energy metabolism during seed development. Conclusions This study establishes a genetic framework for a better understanding of plant oil biosynthesis in addition to providing theoretical foundation and valuable genetic resources for enhancing fatty acid composition in rapeseed breeding.https://doi.org/10.1186/s13059-025-03558-x |
| spellingShingle | Yuting Zhang Yunhao Liu Zhanxiang Zong Liang Guo Wenhao Shen Hu Zhao Integrative omics analysis reveals the genetic basis of fatty acid composition in Brassica napus seeds Genome Biology |
| title | Integrative omics analysis reveals the genetic basis of fatty acid composition in Brassica napus seeds |
| title_full | Integrative omics analysis reveals the genetic basis of fatty acid composition in Brassica napus seeds |
| title_fullStr | Integrative omics analysis reveals the genetic basis of fatty acid composition in Brassica napus seeds |
| title_full_unstemmed | Integrative omics analysis reveals the genetic basis of fatty acid composition in Brassica napus seeds |
| title_short | Integrative omics analysis reveals the genetic basis of fatty acid composition in Brassica napus seeds |
| title_sort | integrative omics analysis reveals the genetic basis of fatty acid composition in brassica napus seeds |
| url | https://doi.org/10.1186/s13059-025-03558-x |
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