Comparative transcriptome analysis identifies candidate genes related to seed coat color in rapeseed

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.

Omics-driven advances in the understanding of regulatory landscape of peanut seed development

“…Comparative studies between peanut varieties with different seed sizes and oil levels identified genes and networks involved in fatty acid synthesis, suggesting strategies for improving seed yield and quality (Yang et al, 2023). Similar to research conducted on peanuts, studies in other crops like safflower, soybean, and rapeseed have also explored key genes and networks involved in regulating traits such as like seed size, oil content, and fatty acid composition (Fan et al, 2023;Guan et al, 2023;Zhao et al, 2023). Research on oleic acid content between cultivars highlighted the role of FAB2 in unsaturated fatty acid biosynthesis and lipid oxidation (Liu et al, 2018), which agreed with the reports in other plants (Dar et al, 2017;He et al, 2020).…”

Genotyping-by-Sequencing Analysis Reveals Associations between Agronomic and Oil Traits in Gamma Ray-Derived Mutant Rapeseed (Brassica napus L.)

“…In terms of the MF category, major polymorphic SNPs were linked to GO terms such as binding (GO:0005488), organic cyclic compound binding (GO:0097159), heterocyclic compound binding (GO:1901363), ion binding (GO:0043167), and protein binding (GO:0005515). Guan et al (2023) previously reported that the GO enrichment analysis of highly expressed genes during seed development in B. napus highlighted the importance of gene expression, translational initiation, and cellular nitrogen compound metabolic processes in the BP category; intracellular anatomical structures, organelles, and intracellular organelles in the CC category; and translation regulator activity, translation factor activity, RNA binding, and nucleic acid binding in the MF category [ 27 ]. These findings align with our results, thus confirming the significance of these terms in seed development in rapeseed.…”

Association Study of Agronomic and Oil Traits in Rapeseed (Brassica napus L.) Mutant Lines Using Genotyping-by-Sequencing

“…In terms of the MF category, the major polymorphic SNPs were linked to GO terms such as binding (GO:0005488), organic cyclic compound binding (GO:0097159), heterocyclic compound binding (GO:1901363), ion binding (GO:0043167), and protein binding (GO:0005515). Guan et al (2023) reported that GO enrichment analysis of genes with high expression levels during seed development showed in B. napus that the top three terms were gene expression, translational initiation, and cellular nitrogen compound metabolic process in the BP category; intracellular anatomical structure, organelle, and intracellular organelle in the CC category; and translation regulator activity, translation factor activity, RNA binding, and translation regulator activity, nucleic acid binding in the MF category [35]. These results suggest that the top three GO terms may play an important role in seed development in B. napus, and our results confirmed all of these terms (Table S5).…”