Transcriptome Analysis Reveal Candidate Genes Affecting Seed Oil Accumulation in Brassica napus

doi:10.7668/hbnxb.20195591

Abstract

Abstract:

In order to clarify the regulatory network of oil accumulation in Brassica napus and breed oilseed rapeseed varieties with high oil content.The seed transcriptome data of four rapeseed inbred lines at 25,35,and 45 days after flowering were used to identify candidate genes affecting oil content by transcriptome analysis and correlation analysis.Consequently,a total of 1 530 genes were identified exhibiting differential expression across all three period,comprising 986 up-regulated genes and 544 down-regulated genes.GO enrichment analysis of these differentially expressed genes detected 83 lipid biosynthesis genes,79 lipid degradation genes,21 lipid transporter genes and 80 transcription factors.To further analysis of these differentially expressed transcription factors,genes including BnTT8,BnGL2,and BnNAC082 were identified.Combined with the oil content data of 50 semi-winter rapeseed in three different regions over two years,four SNPs were identified in the exons region of the BnNAC082-A03 significantly associated with oil content using genome-wide association studies.Two haplotypes were detected in the region of this gene and BnNAC082-A03_Hap1 corresponding accessions showed significantly higher oil content than that of Hap2.Additionally,it utilized these transcriptomic data to construct co-expression analysis network,and in the sub-network revealed that BnNAC082-A03 was directly connected with BnTT8-A09 and BnGL2-C06,forming a potential molecular regulatory network affecting seed lipid accumulation.

Key words: Brassica napus, Oil content, Transcriptome analysis, Co-expression networks, GWAS

CLC Number:

S565.4

LI Wen, YAO Min, HE Dan, QIU Ping, HE Xin, XIONG Xinghua, LIU Zhongsong, QIAN Lunwen. Transcriptome Analysis Reveal Candidate Genes Affecting Seed Oil Accumulation in Brassica napus[J]. Acta Agriculturae Boreali-Sinica, 2025, 40(5): 47-54. doi: 10.7668/hbnxb.20195591.

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Figures/Tables 8

Tab.1 The oil content in seeds of four rapeseed varieties in Changsha %

品种 Varieties	含油量Oil content
品种 Varieties	15 d	20 d	25 d	30 d	35 d	40 d	45 d
XY777	2.83±0.69a	2.92±1.02a	3.36±0.48a	6.74±2.01a	31.70±1.81b	35.79±2.32b	37.36±1.67b
XY015	2.04±0.77a	2.38±0.88a	2.93±0.91a	7.74±1.33a	34.71±1.67b	39.63±1.88b	40.39±1.28b
CS136	1.48±1.32a	1.66±1.21a	2.78±1.25a	9.12±0.54a	42.54±2.12a	46.54±1.45a	49.50±1.30a
CS115	1.14±1.03a	1.32±1.03a	2.79±1.11a	8.97±0.75a	38.26±2.01a	45.01±1.01a	48.84±1.21a

Fig.1 PCA of oil content between four rapeseed varieties

Fig.2 The number of differentially expressed genes

Fig.3 Statistics of differentially expressed genes and GO enrichment analysis A. Graph of differentially expressed genes Venn in different oil content varieties; B. Venn diagram of differentially expressed in three time.

Fig.4 GO enrichment analysis of differentially expressed gene 1.Organic acid biosynthetic process;2.Phenylpropanoid catabolic process;3.Regulation of flavonoid biosynthetic process;4.Seed coat development;5.Fatty acid transport;6.Seedling development;7.Response to lipid;8.Phenylpropanoid biosynthetic process;9.Phenylpropanoid metabolic process;10.Fatty acid homeostasis;11.Lipid catabolic process;12.Lipid oxidation;13.Fatty acid beta-oxidation;14.Fatty acid metabolic process;15.Proanthocyanidin biosynthetic process;16.Flavonoid metabolic process;17.Flavonoid biosynthetic process;18.Protein metabolic process;19.Protein transport;20.Protein folding;21.Metabolic process;22.Organonitrogen compound biosynthetic process;23.Organophosphate metabolic process;24.Cellular component biogenesis;25.Embryo development ending in seed dormancy;26.Lipid modification;27.Fatty acid catabolic process;28.Embryo development;29.Fatty acid oxidation;30.Regulation of primary metabolic process;31.Regulation of nucleic acid-templated transcription;32.Biosynthetic process;33.Regulation of transcription,DNA-templated;34.Regulation of RNA biosynthetic process;35.Transcription,DNA-templated;36.RNA biosynthetic process;37.Gene expression;38.Photosynthesis;39.Organic substance biosynthetic process.

Fig.5 The heatmap displaying the expression levels of transcription factors Gene expression values are transformed into log₂(FPKM+1) replaced with blue to white to red instead from small to large.

Fig.6 Candidate genes were identified by association analysis A.Regional Manhattan plot surrounding the peak signals on QTL-A03,green dots indicate SNPs located in the BnNAC082-A03 gene regions which significantly associated with oil content; B.Genetic structure variations of BnNAC082-A03; C.Comparative analysis of the oil content of the materials corresponding to the two haplotype alleles.Different small letters indicate significant (P<0.05) between different haplotypes under the same trait.

Fig.7 Gene co-expression networks A.Network module partitioning,using different colors to delineate different modules; B.Gene network diagram.According to functional labeling,networks are divided into:transcription factor (blue nodes),fatty acid biosynthesis (red nodes),lipid biosynthesis (orange nodes),photosynthesis (purple nodes),carbohydrate metabolism (green nodes) and flavonoid biosynthetic (yellow nodes); C.Correlation between the expression (FPKM) of BnNAC082-A03 with oil content; D.Correlation between the expression (FPKM) of BnTT8-A09 with oil content; E.Correlation between the expression (FPKM) of BnGL2-C06 with oil content.

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