Comparative transcriptome analysis identifies candidate genes related to seed coat color in rapeseed
Yellow seed coat in rapeseed (Brassica napus) is a desirable trait that can be targeted to improve the quality of this oilseed crop. To better understand the inheritance mechanism of the yellow-seeded trait, we performed transcriptome profiling of developing seeds in yellow- and black-seeded rapesee...
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Frontiers Media S.A.
2023-03-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1154208/full |
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| author | Mingwei Guan Mingwei Guan Mingwei Guan Xiangtian Shi Xiangtian Shi Xiangtian Shi Si Chen Si Chen Si Chen Yuanyuan Wan Yuanyuan Wan Yuanyuan Wan Yunshan Tang Yunshan Tang Yunshan Tang Tian Zhao Tian Zhao Tian Zhao Lei Gao Lei Gao Lei Gao Fujun Sun Fujun Sun Fujun Sun Nengwen Yin Nengwen Yin Nengwen Yin Huiyan Zhao Huiyan Zhao Huiyan Zhao Kun Lu Kun Lu Kun Lu Jiana Li Jiana Li Jiana Li Cunmin Qu Cunmin Qu Cunmin Qu |
| author_facet | Mingwei Guan Mingwei Guan Mingwei Guan Xiangtian Shi Xiangtian Shi Xiangtian Shi Si Chen Si Chen Si Chen Yuanyuan Wan Yuanyuan Wan Yuanyuan Wan Yunshan Tang Yunshan Tang Yunshan Tang Tian Zhao Tian Zhao Tian Zhao Lei Gao Lei Gao Lei Gao Fujun Sun Fujun Sun Fujun Sun Nengwen Yin Nengwen Yin Nengwen Yin Huiyan Zhao Huiyan Zhao Huiyan Zhao Kun Lu Kun Lu Kun Lu Jiana Li Jiana Li Jiana Li Cunmin Qu Cunmin Qu Cunmin Qu |
| author_sort | Mingwei Guan |
| collection | DOAJ |
| description | Yellow seed coat in rapeseed (Brassica napus) is a desirable trait that can be targeted to improve the quality of this oilseed crop. To better understand the inheritance mechanism of the yellow-seeded trait, we performed transcriptome profiling of developing seeds in yellow- and black-seeded rapeseed with different backgrounds. The differentially expressed genes (DEGs) during seed development showed significant characteristics, these genes were mainly enriched for the Gene Ontology (GO) terms carbohydrate metabolic process, lipid metabolic process, photosynthesis, and embryo development. Moreover, 1206 and 276 DEGs, which represent candidates to be involved in seed coat color, were identified between yellow- and black-seeded rapeseed during the middle and late stages of seed development, respectively. Based on gene annotation, GO enrichment analysis, and protein–protein interaction network analysis, the downregulated DEGs were primarily enriched for the phenylpropanoid and flavonoid biosynthesis pathways. Notably, 25 transcription factors (TFs) involved in regulating flavonoid biosynthesis pathway, including known (e.g., KNAT7, NAC2, TTG2 and STK) and predicted TFs (e.g., C2H2-like, bZIP44, SHP1, and GBF6), were identified using integrated gene regulatory network (iGRN) and weight gene co-expression networks analysis (WGCNA). These candidate TF genes had differential expression profiles between yellow- and black-seeded rapeseed, suggesting they might function in seed color formation by regulating genes in the flavonoid biosynthesis pathway. Thus, our results provide in-depth insights that facilitate the exploration of candidate gene function in seed development. In addition, our data lay the foundation for revealing the roles of genes involved in the yellow-seeded trait in rapeseed. |
| first_indexed | 2024-04-10T00:49:33Z |
| format | Article |
| id | doaj.art-3a232c3b333346caa0a5e8e469d875ca |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-10T00:49:33Z |
| publishDate | 2023-03-01 |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-3a232c3b333346caa0a5e8e469d875ca2023-03-13T14:53:33ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-03-011410.3389/fpls.2023.11542081154208Comparative transcriptome analysis identifies candidate genes related to seed coat color in rapeseedMingwei Guan0Mingwei Guan1Mingwei Guan2Xiangtian Shi3Xiangtian Shi4Xiangtian Shi5Si Chen6Si Chen7Si Chen8Yuanyuan Wan9Yuanyuan Wan10Yuanyuan Wan11Yunshan Tang12Yunshan Tang13Yunshan Tang14Tian Zhao15Tian Zhao16Tian Zhao17Lei Gao18Lei Gao19Lei Gao20Fujun Sun21Fujun Sun22Fujun Sun23Nengwen Yin24Nengwen Yin25Nengwen Yin26Huiyan Zhao27Huiyan Zhao28Huiyan Zhao29Kun Lu30Kun Lu31Kun Lu32Jiana Li33Jiana Li34Jiana Li35Cunmin Qu36Cunmin Qu37Cunmin Qu38Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, ChinaAcademy of Agricultural Sciences, Southwest University, Chongqing, ChinaAffiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, ChinaAcademy of Agricultural Sciences, Southwest University, Chongqing, ChinaAffiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, ChinaAcademy of Agricultural Sciences, Southwest University, Chongqing, ChinaAffiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, ChinaAcademy of Agricultural Sciences, Southwest University, Chongqing, ChinaAffiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, ChinaAcademy of Agricultural Sciences, Southwest University, Chongqing, ChinaAffiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, ChinaAcademy of Agricultural Sciences, Southwest University, Chongqing, ChinaAffiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, ChinaAcademy of Agricultural Sciences, Southwest University, Chongqing, ChinaAffiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, ChinaAcademy of Agricultural Sciences, Southwest University, Chongqing, ChinaAffiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, ChinaAcademy of Agricultural Sciences, Southwest University, Chongqing, ChinaAffiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, ChinaAcademy of Agricultural Sciences, Southwest University, Chongqing, ChinaAffiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, ChinaAcademy of Agricultural Sciences, Southwest University, Chongqing, ChinaAffiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, ChinaAcademy of Agricultural Sciences, Southwest University, Chongqing, ChinaAffiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology and Academy of Agricultural Sciences, Southwest University, Chongqing, ChinaAcademy of Agricultural Sciences, Southwest University, Chongqing, ChinaAffiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, ChinaYellow seed coat in rapeseed (Brassica napus) is a desirable trait that can be targeted to improve the quality of this oilseed crop. To better understand the inheritance mechanism of the yellow-seeded trait, we performed transcriptome profiling of developing seeds in yellow- and black-seeded rapeseed with different backgrounds. The differentially expressed genes (DEGs) during seed development showed significant characteristics, these genes were mainly enriched for the Gene Ontology (GO) terms carbohydrate metabolic process, lipid metabolic process, photosynthesis, and embryo development. Moreover, 1206 and 276 DEGs, which represent candidates to be involved in seed coat color, were identified between yellow- and black-seeded rapeseed during the middle and late stages of seed development, respectively. Based on gene annotation, GO enrichment analysis, and protein–protein interaction network analysis, the downregulated DEGs were primarily enriched for the phenylpropanoid and flavonoid biosynthesis pathways. Notably, 25 transcription factors (TFs) involved in regulating flavonoid biosynthesis pathway, including known (e.g., KNAT7, NAC2, TTG2 and STK) and predicted TFs (e.g., C2H2-like, bZIP44, SHP1, and GBF6), were identified using integrated gene regulatory network (iGRN) and weight gene co-expression networks analysis (WGCNA). These candidate TF genes had differential expression profiles between yellow- and black-seeded rapeseed, suggesting they might function in seed color formation by regulating genes in the flavonoid biosynthesis pathway. Thus, our results provide in-depth insights that facilitate the exploration of candidate gene function in seed development. In addition, our data lay the foundation for revealing the roles of genes involved in the yellow-seeded trait in rapeseed.https://www.frontiersin.org/articles/10.3389/fpls.2023.1154208/fullBrassica napus L.yellow traittranscriptomeflavonoid pathwayprotein-protein interaction |
| spellingShingle | Mingwei Guan Mingwei Guan Mingwei Guan Xiangtian Shi Xiangtian Shi Xiangtian Shi Si Chen Si Chen Si Chen Yuanyuan Wan Yuanyuan Wan Yuanyuan Wan Yunshan Tang Yunshan Tang Yunshan Tang Tian Zhao Tian Zhao Tian Zhao Lei Gao Lei Gao Lei Gao Fujun Sun Fujun Sun Fujun Sun Nengwen Yin Nengwen Yin Nengwen Yin Huiyan Zhao Huiyan Zhao Huiyan Zhao Kun Lu Kun Lu Kun Lu Jiana Li Jiana Li Jiana Li Cunmin Qu Cunmin Qu Cunmin Qu Comparative transcriptome analysis identifies candidate genes related to seed coat color in rapeseed Frontiers in Plant Science Brassica napus L. yellow trait transcriptome flavonoid pathway protein-protein interaction |
| title | Comparative transcriptome analysis identifies candidate genes related to seed coat color in rapeseed |
| title_full | Comparative transcriptome analysis identifies candidate genes related to seed coat color in rapeseed |
| title_fullStr | Comparative transcriptome analysis identifies candidate genes related to seed coat color in rapeseed |
| title_full_unstemmed | Comparative transcriptome analysis identifies candidate genes related to seed coat color in rapeseed |
| title_short | Comparative transcriptome analysis identifies candidate genes related to seed coat color in rapeseed |
| title_sort | comparative transcriptome analysis identifies candidate genes related to seed coat color in rapeseed |
| topic | Brassica napus L. yellow trait transcriptome flavonoid pathway protein-protein interaction |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1154208/full |
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