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Yao M, He D, Li W, Xiong X, He X, Liu Z, Guan C, Qian L. Identification of environment-insensitive genes for oil content by combination of transcriptome and genome-wide association analysis in rapeseed. Biotechnol Biofuels Bioprod 2024; 17:29. [PMID: 38383469 PMCID: PMC10882896 DOI: 10.1186/s13068-024-02480-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/15/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND The primary objective of rapeseed breeding is to enhance oil content, which is predominantly influenced by environmental factors. However, the molecular mechanisms underlying the impact of these environmental factors on oil accumulation remain inadequately elucidated. In this study, we used transcriptome data from two higher (HOC) and two lower oil content (LOC) inbred lines at 35 days after pollination (DAP) to investigate genes exhibiting stable expression across three different environments. Meanwhile, a genome-wide association study (GWAS) was utilized to detect candidate genes exhibiting significant associations with seed oil content across three distinct environments. RESULTS The study found a total of 405 stable differentially expressed genes (DEGs), including 25 involved in lipid/fatty acid metabolism and 14 classified as transcription factors. Among these genes, BnBZIP10-A09, BnMYB61-A06, BnAPA1-A08, BnPAS2-A10, BnLCAT3-C05 and BnKASIII-C09 were also found to exhibit significant associations with oil content across multiple different environments based on GWAS of 50 re-sequenced semi-winter rapeseed inbred lines and previously reported intervals. Otherwise, we revealed the presence of additive effects among BnBZIP10-A09, BnKASIII-C09, BnPAS2-A10 and BnAPA1-A08, resulting in a significant increase in seed oil content. Meanwhile, the majority of these stable DEGs are interconnected either directly or indirectly through co-expression network analysis, thereby giving rise to an elaborate molecular network implicated in the potential regulation of seed oil accumulation and stability. CONCLUSIONS The combination of transcription and GWAS revealed that natural variation in six environment-insensitive gene regions exhibited significant correlations with seed oil content phenotypes. These results provide important molecular marker information for us to further improve oil content accumulation and stability in rapeseed.
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Affiliation(s)
- Min Yao
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Dan He
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Wen Li
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Xinghua Xiong
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Xin He
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Zhongsong Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Chunyun Guan
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Yuelushan Laboratory, Changsha, 410128, China
| | - Lunwen Qian
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
- Yuelushan Laboratory, Changsha, 410128, China.
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Li X, Yell V, Li X. Two Arabidopsis promoters drive seed-coat specific gene expression in pennycress and camelina. Plant Methods 2023; 19:140. [PMID: 38053155 DOI: 10.1186/s13007-023-01114-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/20/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Pennycress and camelina are two important novel biofuel oilseed crop species. Their seeds contain high content of oil that can be easily converted into biodiesel or jet fuel, while the left-over materials are usually made into press cake meals for feeding livestock. Therefore, the ability to manipulate the seed coat encapsulating the oil- and protein-rich embryos is critical for improving seed oil production and press cake quality. RESULTS Here, we tested the promoter activity of two Arabidopsis seed coat genes, AtTT10 and AtDP1, in pennycress and camelina by using eGFP and GUS reporters. Overall, both promoters show high levels of activities in the seed coat in these two biofuel crops, with very low or no expression in other tissues. Importantly, AtTT10 promoter activity in camelina shows differences from that in Arabidopsis, which highlights that the behavior of an exogenous promoter in closely related species cannot be assumed the same and still requires experimental determination. CONCLUSION Our work demonstrates that AtTT10 and AtDP1 promoters are suitable for driving gene expression in the outer integument of the seed coat in pennycress and camelina.
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Affiliation(s)
- Xin Li
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, 28081, USA
| | - Victoria Yell
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, 28081, USA
| | - Xu Li
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, 28081, USA.
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