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Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (3): 416-426.doi: 10.3724/SP.J.1006.2021.04108


Bioinformatics analysis of SnRK gene family and its relation with seed oil content of Brassica napus L.

TANG Jing-Quan(), WANG Nan, GAO Jie, LIU Ting-Ting, WEN Jing, YI Bin, TU Jin-Xing, FU Ting-Dong, SHEN Jin-Xiong*   

  1. National Key Laboratory of Crop Genetic Improvement / National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, Hubei, China
  • Received:2020-05-15 Accepted:2020-08-19 Online:2021-03-12 Published:2020-09-08
  • Contact: SHEN Jin-Xiong E-mail:519736700@qq.com
  • Supported by:
    This study was supported by the National Natural Science Foundation of China(31871654)


Sucrose non-fermenting-1-related protein kinase (SnRK) is a widely existed serine/threonine protein kinase in plants, which is involved in the regulation of biological processes such as signal transduction, stress response and seed growth. In order to explore the mechamism of the SnRK gene families and its influence on the seed oil content of Brassica napus L., BnSnRK gene family system evolution, gene structure, physical and chemical properties of protein, conservative motif, protein secondary structure, cis-element and subcellular localization prediction were analyzed, and BnSnRK genes affecting oil content of seeds were screened by candidate genes association analysis, haplotype analysis and qRT-PCR. The results showed that 92 BnSnRK members were identified and divided into three subgroups, distributed on 19 chromosomes of Brassica napus L. The physical and chemical properties of proteins were significantly different among subgroups. Most genes had 7-14 exons; the motifs of the same subfamily were more similar in distribution. The BnSnRK family was mainly expressed in the cytoplasm. 12 family members related to the oil content were screened out by association analysis in rapeseed. Genes BnaC02g10730D might negatively regulate seed oil content, while genes BnaA07g12290D, BnaA10g22850D, BnaA08g18050D, and BnaC04g44390D might positively regulate seed oil content of Brassica napus L. There were significant differences in seed oil content under different environments, and 12 oil-related members all contained MYB, MYC and ABA response elements. Environment-specific oil-related genes might be related to plant abiotic stress response. This study provides a theoretical basis for BnSnRK gene functional verification and breeding.

Key words: Brassica napus, seed oil content, sucrose non-fermenting-1-related protein kinase, association analysis, bioinformation analysis

Fig. 1

Association analysis of seed oil content and fatty acid components based on BnSnRK in rapeseed The figure shows the summary of the association analysis results under the looser screening conditions. There were eight layers of dotted labeling, and the phenotypes from inner to outer circles in order were oil content, palmitic acid, stearic acid, oleic acid, linoleic acid, linoleic acid, linolenic acid, erucic acid, and arachidonic acid. The square label shows the composition of 18 carbon fatty acids."

Fig. s2

Comparison of physical and chemical properties of SnRK subfamilies"

Table s1

Secondary structure analysis of BnSnRK protein (%)"

Structure type
Standard deviation
Standard deviation
Standard deviation
Alpha helix
31.62 34.83 0.98 31.58 45.50 3.52 31.62 41.12 2.14
Beta angle
5.85 7.44 0.58 4.14 8.65 1.29 8.14 12.56 0.96
Irregular crimp
40.70 44.92 1.30 34.05 43.09 2.50 29.95 39.92 2.50
Extending chain
15.82 18.96 0.91 13.01 20.35 1.83 15.73 21.10 1.22

Fig. s3

Enrichment analysis of BnSnRK gene family members"

Fig. s1

Prediction of subcellular localization of SnRK gene family"

Fig. s4

Copert-acting element analysis of BnSnRK family promoter MYB: MYB tran-scription factor response element; MYC: MYC transcription factor response element; MBS: MYB binding site."

Fig. 2

Phylogenetic tree, CDD conservative structures, and gene structures of representative members of BnSnRK gene family The BnSnRK gene family are divided into three subfamilies: the red region represents SnRK1 subfamily, the blue region represents SnRK2 subfamily, and the yellow region represents SnRK3 subfamily."

Fig. s5

Conservative motif analysis of some members of BnSnRK"

Fig. 10

Fig. S6 Manhattan diagram of association analysis of seed oil content in E4 environment"

Table 1

Repeatedly detected sites associated with seed oil content of rapeseed"

Gene name
LOD value
-log10 (P)
R2 (%)
Haplotype frequency
BnaA07g12290D E2 s5667 A7 3.79 4.53 7.79 0.42
BnaA10g22850D E2 s7970 A10 4.50 5.33 12.95 0.30
BnaA07g12290D E4 s5664 A7 3.42 4.14 1.99 0.48
BnaA07g12290D E4 s5675 A7 4.46 5.23 3.07 0.28
BnaA10g22850D E4 s8059 A10 5.44 6.26 6.70 0.11
BnaA10g22850D E4 s8018 A10 8.16 9.06 6.34 0.09
BnaA07g12290D E5 s5674 A7 5.07 5.87 4.16 0.28

Fig. s7

Haplotype analysis boxplot Haplotype ACT and haplotype CTC were the haplotypes with the lowest and highest oil content of gene BnaA10g28850D, respectively, and were represented by green boxes in E2, E4, and E5 environments. Haplotype GGGT and TAAC were the haplotypes with the lowest and highest oil content of gene BnaA07g12290D, respectively. The borders of the boxes in each environment are colored differently."

Table s2

Multiple comparisons of haplotype analysis"

因变量: 含油量
Dependent variable: oil content
(I) 单倍型
Haploid type
(J) 单倍型
Haploid type
Average difference
Standard error
BnaA07g12290D GAGT GGAC -0.48587 0.59894 0.418
GGGT 0.31362 0.59408 0.598
TAAC -1.04697 0.56187 0.063
GGAC GAGT 0.48587 0.59894 0.418
GGGT 0.79949* 0.37903 0.035
TAAC -0.5611 0.32624 0.086
GGGT GAGT -0.31362 0.59408 0.598
GGAC -0.79949* 0.37903 0.035
TAAC -1.36059* 0.31722 0.000
TAAC GAGT 1.04697 0.56187 0.063
GGAC 0.5611 0.32624 0.086
GGGT 1.36059* 0.31722 0.000
BnaA10g22850D ACT CTC -2.57628* 0.44087 0.000
CTT -1.01843 0.85095 0.232
CTC ACT 2.57628* 0.44087 0.000
CTT 1.55785* 0.76008 0.041
CTT ACT 1.01843 0.85095 0.232
CTC -1.55785* 0.76008 0.041

Fig. 3

Expression levels of oil-related candidate genes in the seed of Brassica napus A: expression of oil-related candidate genes of BnSnRK gene family in young seeds of rapeseed detected by qRT-PCR; B: relative expression of all candidate genes."

Fig. s8

Chromosome location distribution of SnRK gene family In the figure, the member names of BnSnRK1, BnSnRK2, and BnSnRK3 subgroup are represented by green, red, and black respectively. Random chromosome without member distribution does not appear in the figure."

Fig. 4

Homologous comparison of SnRK gene family in Brassica napus (A) and collinear association of cabbage, Brassica napus, and Chinese cabbage (B) The light blue background line in figure A is a collinearity gene pair between SnRK gene family members of Brassica napus. The color line will highlight gene member that may be related to the seed oil content of Brassica napus. In figure B, the gray background line represents the collinear block in the whole genome, and the highlighted line represents the collinear relationship between the BnSnRK gene family members in three species."

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