Frontiers in Plant Science (Mar 2023)
Comparative transcriptome analysis identifies candidate genes related to seed coat color in rapeseed
- 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
Affiliations
- Mingwei Guan
- Integrative 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, China
- Mingwei Guan
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Mingwei Guan
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
- Xiangtian Shi
- Integrative 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, China
- Xiangtian Shi
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Xiangtian Shi
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
- Si Chen
- Integrative 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, China
- Si Chen
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Si Chen
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
- Yuanyuan Wan
- Integrative 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, China
- Yuanyuan Wan
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Yuanyuan Wan
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
- Yunshan Tang
- Integrative 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, China
- Yunshan Tang
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Yunshan Tang
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
- Tian Zhao
- Integrative 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, China
- Tian Zhao
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Tian Zhao
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
- Lei Gao
- Integrative 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, China
- Lei Gao
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Lei Gao
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
- Fujun Sun
- Integrative 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, China
- Fujun Sun
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Fujun Sun
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
- Nengwen Yin
- Integrative 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, China
- Nengwen Yin
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Nengwen Yin
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
- Huiyan Zhao
- Integrative 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, China
- Huiyan Zhao
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Huiyan Zhao
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
- Kun Lu
- Integrative 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, China
- Kun Lu
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Kun Lu
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
- Jiana Li
- Integrative 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, China
- Jiana Li
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Jiana Li
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
- Cunmin Qu
- Integrative 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, China
- Cunmin Qu
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Cunmin Qu
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
- DOI
- https://doi.org/10.3389/fpls.2023.1154208
- Journal volume & issue
-
Vol. 14
Abstract
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.
Keywords
