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Acta Agronomica Sinica ›› 2024, Vol. 50 ›› Issue (5): 1136-1146.doi: 10.3724/SP.J.1006.2024.34152

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

A combination of genome-wide association and transcriptome analysis reveal candidate genes affecting seed oil accumulation in Brassica napus

CAO Song(), YAO Min, REN Rui, JIA Yuan, XIANG Xing-Ru, LI Wen, HE Xin, LIU Zhong-Song, GUAN Chun-Yun, QIAN Lun-Wen*(), XIONG Xing-Hua*()   

  1. College of Agronomy, Hunan Agricultural University, Changsha 410128, Hunan, China
  • Received:2023-09-08 Accepted:2024-01-12 Online:2024-05-12 Published:2024-01-25
  • Contact: E-mail: xiongene@hunau.edu.cn; E-mail: qianlunwen@163.com
  • Supported by:
    Science Foundation for Distinguished Youth Scholars of Hunan Province, China(2022JJ10027);Research Foundation of Education Bureau of Hunan Province, China(21A0135);National Key Science and Technology Project(2022ZD04009)

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Abstract:

Rapeseed (Brassica napus L.) is the main source of edible vegetable oil in China, and increasing seed oil content is the most effective way to increase the supply of rapeseed oil. In this study, 43 genes related to lipid synthesis were selected by analyzing the seed transcriptome data of 4 rapeseed inbred lines 25, 35, and 45 days after pollination. Among them, 33 genes were continuously up-expressed and 10 genes were continuously down-expressed from 25 to 45 days of seed development. The main genes included BnLEC1, BnABI5, BnOLEO4, and BnOBAP1a. At the same time, combined with the resequencing data of 50 semi-winter Brassica napus, 3 SNPs and 9 SNPs significantly related to oil content were detected to BnOBAP1a-A10 and BnABI5-A05, respectively, and the oil content of BnOBAP1A-A10_Hap1 was significantly higher than Hap2. The oil content of BnABI5-A05_Hap1 was significantly higher than Hap3. In addition, WGCNA was used to construct gene networks, and we found that BnOBAP1a and BnABI5 were indirectly connected through three transcription factors LEC1, HMGB3, and HTA11, which together formed a molecular network involved in the potential regulation of seed oil accumulation. The results of this study provide valuable insights for the development of haplotype functional markers, aiming to further enhance oil content in B. napus.

Key words: Brassica napus, oil content, transcriptome analysis, coexpression analysis, regional association analysis

Table 1

Statistics of oil content in mature seeds of four rapeseed varieties in Changsha"

品种
Variety		 最小值
Min.		 最大值
Max.		 平均值±标准差
Mean±SD		 变异系数
CV (%)
XY777 31.60 36.06 33.32±1.67 5.02
XY015 38.83 42.56 40.39±1.28 3.16
CS136 47.51 51.52 49.50±1.30 2.62
CS115 46.24 50.18 48.84±1.21 2.32

Fig. 1

Screening statistics of continuously up-regulated or down-regulated expression genes (a) the number of continuously up-regulated or down-regulated genes of four rapeseed varieties in Changsha area during 25-35 days and 35-45 days periods. (b) Venn diagrams of four varieties consistently up-regulated genes. (c) Venn diagrams of consistently down-regulated genes in four varieties."

Fig. 2

Enrichment analysis of 383 differential gene pathways The size of the circle represents the number of genes, and the heat map represents the value of -log10 (P-value)."

Fig. 3

Differently expressed genes (DEGs) related to oil content The expression values for RNA-seq data were log10 (fpkm+1) transformed and displayed as filled blocks, from blue to yellow to red."

Fig. 4

Correlation analysis of oil content in haplotype (1,944,128-1,994,025 bp) regions of 50 resequencing materials (a) Haplotype (1,944,128-1,994,025 bp; R2=0.99) oil content correlation analysis. The solid blue line indicates a threshold P-value of 1.0×10-4 for genome-wide significance. (b)-(c) three SNPs (Chr. A10: 1,969,139; Chr. A10: 1,969,444; Chr. A10: 1,969,452, P = 1.35×10-5) was significantly correlated with oil content and was localized in the promoter region of BnOBAP1a-A10 gene. Heat maps show a strong linkage imbalance in these SNPs. Two haplotype alleles were detected in the BnOBAP1a-A10 haplotype region. (d) Comparative analysis of the oil content of the materials corresponding to the two haplotype alleles. Haplotype alleles with frequencies greater than 0.01 in the population will be used for this analysis. The box pattern shows that the material corresponding to the BnOBAP1a-A10_Hap1 allele has a higher oil content than that of BnOBAP1a-A10_Hap2. *, **, and *** mean significant difference at the 0.05, 0.01, and 0.001 probability levels, respectively."

Fig. 5

Correlation analysis of oil content in haplotype (4,389,567-4,439,432 bp) regions of 50 resequenced materials (a) Haplotype (4,389,567-4,439,432 bp; R2=0.99) oil content correlation analysis. The solid blue line indicates a threshold P-value of 1.0×10-4 for genome-wide significance. (b)-(c) nine SNPs (A05: 4,414,567; P = 1.42×10-4) was significantly correlated with oil content and was localized in the BnABI5-A05 gene region. Heat maps show a strong linkage imbalance in these SNPs. Three haplotype alleles were detected in the haplotype region of BnABI5-A05. (d) Comparative analysis of the oil content of the materials corresponding to the three haplotype alleles. Haplotype alleles with frequencies greater than 0.01 in the population will be used for this analysis. The box pattern shows that the material corresponding to the BnABI5-A05_Hap1 allele has a higher oil content. *, **, and *** mean significant difference at the 0.05, 0.01, and 0.001 probability levels, respectively."

Fig. 6

Coexpression network analysis (a): dendrogram of module system. (b): correlation between modules and oil content. (c): comparison of gene numbers in modules. (d): gene network diagram. Octagonal red nodes represent candidate genes, and according to functional labeling, co-expression networks are divided into: lipid/fatty acid biosynthesis (red nodes), lipid transport (purple nodes), lipid/fatty acid oxidation (orange nodes), photosynthesis (green nodes), and carbohydrate metabolism (gray nodes)."

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