Genome-wide Identification and Transcript Response to Sclerotinia of F-BOX Genes in Chinese Cabbage
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摘要:
目的 筛选参与菌核病应答反应的F-BOX基因，为大白菜抗菌核病基因的功能研究及抗病品种的选育提供基础。 方法 基于核盘菌侵染大白菜转录组测序数据，对大白菜F-BOX基因家族进行鉴定，进行亚细胞定位、染色体定位、保守结构域等生物信息学分析。分析F-BOX基因在核盘菌侵染下的差异表达，并采用q-PCR技术检测F-BOX基因在0 h和36 h的表达情况。 结果 共鉴定32个BraF-BOX基因，分子量介于34751.13～105942.22 Da；亚细胞定位表明，26个F-BOX基因定位在细胞核和细胞质中，6个定位在叶绿体中；系统进化树分析将BraF-BOX分为4个亚族；基因结构分析结果表明，每个BraF-BOX家族成员均含有Motif 1，序列中均含有外显子；组织特异性表达分析结果表明在不同大白菜部位，表达量有差异；在核盘菌处理36 h时，q-PCR检测6个基因的相对表达量趋势与转录组数据一致，其中Bra037120、Bra011427、Bra009835等3个基因表达上调，核盘菌侵染时间越长，表达量越大。 结论 综合BraF-BOX基因生物信息学及转录组数据分析，Bra037120、Bra011427、Bra009835基因可能参与大白菜菌核病抗性功能，为后续基因功能研究提供研究基础。 Abstract:Objective F-BOX genes responsible for the resistance of Brassica rapa to sclerotinia were investigated. Method Suspected members of F-BOX family were identified at the transcriptome level to identify their subcellular localization, chromosomal localization, and conserved domains as well as expressions by q-PCR under artificial induction of sclerotinia. Result There were 32 BraF-BOX genes classified into 4 subgroups with the relative molecular masses varying from 34 751.13 Da to 105 942.22 Da. The predicted subcellular localizations of 26 F-BOX were in the nucleus and cytoplasm, and 6 in the chloroplast. The genetic structures of all 32 genes contained Motif 1 and exon in the DNA sequences with expressions differed in different parts of Chinese cabbage. The relative expressions by q-PCR of 6 genes agreed with the transcriptome data at 36 h. The expressions of Bra037120, Bra011427, and Bra009835 were upregulated and increased with prolonged induction. Conclusion The bioinformatics and transcriptome data analysis on the BraF-BOX genes suggested that Bra037120, Bra011427, and Bra009835 were potentially associated with the sclerotinia resistance of Chinese cabbage. -
Key words:
- Chinese cabbage /
- F-BOX gene family /
- sclerotinia stem rot /
- gene expression
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图 1 大白菜和拟南芥F-BOX家族进化树
Bra：大白菜；At：拟南芥。
Figure 1. Unrooted phylogenetic tree of F-BOX family between B. rapa and A. thaliana
Bra: B. rapa; At: Arabidopsis thaliana.
图 3 大白菜F-BOX基因家族的进化树和保守基序
Figure 3. Phylogenetic relationships and motif of F-BOX family in B. rapa
图 5 大白菜F-BOX基因家族的进化树和基因结构
Figure 5. Phylogenetic relationships and gene structure of F-BOX family in B. rapa
图 6 F-BOX基因在大白菜不同组织中的表达模式
Figure 6. Expressions of F-BOX in different tissues of B. rapa
图 7 BraF-BOX在核盘菌诱导下的表达分析
Figure 7. Expressions of BraF-BOX in response to sclerotinia induction
图 8 BraF-BOX基因核盘菌诱导表达的qRT-PCR验证
Figure 8. Expressions of BraF-BOX in response to sclerotinia induction by qRT-PCR
表 1 荧光定量PCR引物
Table 1. Primers for RT q-PCR
基因名称
Gene name基因序列（5′-3′）
Primer sequence (5′-3′)Bra037120 GTGCGTTGAGGAAGTTCTGTAT TCTCTTAGCCATTCTCCAATCTCT Bra003518 ATGATGCGTTGGTAGCGATT CATCCAGTGGCTCTAGTGTTAG Bra009835 CTCCTCTGCCATCATCATCAAC CATCCGTCACTCCGTTCAATC Bra011427 CGTATCACAATCGCTTCCAACT GGCATCCACCATCATCACTG Bra011207 GACATCTTCTCACGCCTTAGC TCGGGAATCCACCAGTTGAT Bra010279 GGAAGTCAACGACGAAGGAG ACGGTTAGCCGTGAGAAGAT 
下载: 导出CSV
表 2 大白菜F-BOX家族基因理化性质
Table 2. Physiochemical properties of F-BOX family genes in B. rapa
基因名称
Gene name理论等电点
pI分子量
Molecular weight/Da氨基酸大小
Amino acids脂肪系数
Aliphatic index不稳定系数
Instability index亲水性
GRAVY亚细胞定位
Subcellular locationBra011427 5.16 72453.74 660 105.06 52.40 0.168 细胞核 Nuclear Bra011207 5.80 35574.12 310 91.81 50.55 −0.093 细胞质 Cytoplasmic Bra029994 8.81 55946.13 511 99.96 43.48 0.002 细胞质 Cytoplasmic Bra036542 8.34 65257.97 616 99.66 43.79 0.114 细胞核 Nuclear Bra016754 6.17 66444.72 590 97.85 48.47 −0.091 细胞质 Cytoplasmic Bra036607 8.36 70484.33 639 113.35 32.68 0.137 细胞核 Nuclear Bra010279 5.93 34751.13 301 84.85 54.23 −0.327 细胞质 Cytoplasmic Bra017245 5.53 105942.22 949 105.16 44.32 0.077 细胞核 Nuclear Bra005669 8.73 72644.85 668 109.31 36.41 0.158 细胞核 Nuclear Bra029656 8.02 43507.11 395 103.11 41.00 0.058 细胞质 Cytoplasmic Bra009931 8.58 70575.49 640 114.75 34.01 0.142 细胞质 Cytoplasmic Bra003692 6.83 39588.79 359 98.58 44.58 0.020 细胞质 Cytoplasmic Bra032213 8.78 56034.25 514 98.68 50.56 0.016 叶绿体 Chloroplst Bra029367 8.26 44895.2 411 102.92 31.44 0.037 叶绿体 Chloroplst Bra009671 6.26 43986.92 405 104.22 34.75 0.077 细胞质 Cytoplasmic Bra008461 7.41 52042.84 467 112.44 35.06 0.131 细胞核 Nuclear Bra034254 7.29 65953.34 622 104.08 42.07 0.187 细胞核 Nuclear Bra024055 5.87 34885.23 304 84.90 45.33 −0.276 细胞核 Nuclear Bra034551 6.18 97726.55 890 107.15 47.88 0.179 细胞质 Cytoplasmic Bra015699 7.45 39102.24 354 97.51 42.73 −0.012 细胞核 Nuclear Bra016422 7.42 38869.11 353 97.54 42.43 0.038 细胞质 Cytoplasmic Bra012785 8.75 67864.12 632 104.32 41.69 0.150 叶绿体 Chloroplst Bra032954 6.61 64664.61 575 96.31 46.97 −0.077 细胞核 Nuclear Bra014568 5.25 74292.77 666 93.27 34.90 −0.176 细胞核 Nuclear Bra000604 5.54 67952.33 607 87.23 54.69 −0.101 叶绿体 Chloroplst Bra037324 5.02 68165.97 619 102.23 38.77 −0.060 细胞核 Nuclear Bra037120 8.20 56893.49 526 92.30 38.63 −0.103 叶绿体 Chloroplst Bra003518 7.94 66765.54 594 95.81 51.87 −0.014 细胞核 Nuclear Bra009835 8.41 65245.08 622 99.97 44.73 0.166 细胞核 Nuclear Bra000842 5.57 65632.15 586 99.13 43.70 −0.032 细胞质 Cytoplasmic Bra026953 6.35 65169.16 578 95.83 45.94 −0.118 细胞核 Nuclear Bra034191 8.14 66378.14 585 96.46 47.23 −0.117 叶绿体 Chloroplst
下载: 导出CSV
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