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Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (3): 354-364.doi: 10.3724/SP.J.1006.2019.84095

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

Identification and expression analysis of PEBP gene family in oilseed rape

Hong-Ju JIAN,Bo YANG,Yang-Yang LI,Hong YANG,Lie-Zhao LIU,Xin-Fu XU,Jia-Na LI()   

  1. College of Agronomy and Biotechnology / Chongqing Engineering Research Center for Rapeseed / Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
  • Received:2018-07-09 Accepted:2018-10-08 Online:2019-03-12 Published:2019-01-07
  • Contact: Jia-Na LI E-mail:ljn1950@swu.edu.cn
  • Supported by:
    This study was supported by the Project of Intellectual Base for Discipline Innovation in Colleges and Universities(B12006);the Special Project of Chongqing People’s Livelihood(cstc2016shms-ztzx80020);Chongqing Graduate Student Research Innovation Project(CYS17078)

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Abstract:

The plant phosphatidylethanolamine-binding protein (PEBP) genes play an important role in controlling flowering time. Rapeseed, as one of the most important oil crops in the world, has similar flowering habits with Arabidopsis thaliana. In this study, the PEBP family protein sequences of A. thaliana were used to perform BlastP analysis in the rapeseed genome. The members of the rape PEBP family were obtained, and the gene structure analysis, motif prediction, duplication analysis, phylogenetic tree construction, selective pressure analysis and tissue expression analysis were carried out on the family members. A total of 26 rapeseed PEBP gene members were identified, and most of them contained four exons and three introns, and motif-1 and motif-2 were the characteristics of PEBP members. Over 76.9% members were segmental duplicated. Phylogenetic tree analysis showed that PEBP was divided into three subfamilies. The tissue-specifics analysis based on RNA-Seq data showed that 26 PEBP members of rapeseed had very obvious tissue expression characteristics. All these results greatly enrich our understandings of flowering genes and regulation patterns in Brassica napus, and provide a theoretical basis for further molecular breeding in B. napus.

Key words: Brassica napus, flowering genes, PEBP, evolution analysis, expression analysis

Supplementarey table 1

Supplementarey table 1 Information of 111 materiels from ‘Zhongshuang 11’"

编号
Code		 生育期
Growth stage		 器官
Organ		 取样时间
Treatment time		 编号
Code		 生育期
Growth stage		 器官
Organ		 取样时间
Treatment time
Ro_24h 种子萌发 胚根 萌发后24 h Se_7d 青荚期 种子 花后7 d
Ro_48h 种子萌发 胚根 萌发后48 h Se_10d 青荚期 种子 花后10 d
Ro_72h 种子萌发 胚根 萌发后72 h Se_13d 青荚期 种子 花后13 d
Hy_24h 种子萌发 下胚轴 萌发后24 h Se_19d 青荚期 种子 花后19 d
Hy_48h 种子萌发 下胚轴 萌发后48 h Se_21d 青荚期 种子 花后21 d
Hy_72h 种子萌发 下胚轴 萌发后72 h Se_24d 青荚期 种子 花后24 d
Co_24h 种子萌发 子叶 萌发后24 h Se_27d 青荚期 种子 花后27 d
Co_48h 种子萌发 子叶 萌发后48 h Se_30d 青荚期 种子 花后30 d
Co_72h 种子萌发 子叶 萌发后72 h Se_35d 青荚期 种子 花后35 d
GS_12h 种子萌发 整个种子 萌发后12 h Se_40d 青荚期 种子 花后40 d
GS_24h 种子萌发 整个种子 萌发后24 h Se_43d 青荚期 种子 花后43 d
Ro_s 苗期-温室 根 Se_46d 青荚期 种子 花后46 d
Ro_s_f 苗期-大田 根 Se_49d 青荚期 种子 花后49 d
Ro_b 蕾期 根 Em_19d 青荚期 种胚 花后19 d
Ro_i 初花期 根 Em_21d 青荚期 种胚 花后21 d
Ro_f 盛花期 根 Em_24d 青荚期 种胚 花后24 d
St_b 蕾期 茎秆 Em_27d 青荚期 种胚 花后27 d
St_i 初花期 茎秆 Em_30d 青荚期 种胚 花后30 d
St_f 盛花期 茎秆 Em_35d 青荚期 种胚 花后35 d
St_24d 青荚期 茎秆 花后24 d Em_40d 成熟期 种胚 花后40 d
St_50d 成熟期 茎秆 花后50 d Em_43d 成熟期 种胚 花后43 d
Le_s 苗期-温室 叶片 Em_46d 成熟期 种胚 花后46 d
Le_s_f 苗期-大田 叶片 Em_49d 成熟期 种胚 花后49 d
LeY_b 蕾期 幼叶 Ra_40d 成熟期 胚芽 花后40 d
LeY_i 初花期 幼叶 Ra_43d 成熟期 胚芽 花后43 d
LeY_f 盛花期 幼叶 Ra_46d 成熟期 胚芽 花后46 d
LeY_10d 青荚期 幼叶 花后10 d Ra_49d 成熟期 胚芽 花后49 d
LeY_24d 青荚期 幼叶 花后24 d SC_19d 青荚期 种皮 花后19 d
LeY_30d 青荚期 幼叶 花后30 d SC_21d 青荚期 种皮 花后21 d
LeO_b 蕾期 成熟叶片 SC_27d 青荚期 种皮 花后27 d
LeO_i 初花期 成熟叶片 SC_30d 青荚期 种皮 花后30 d
LeO_f 盛花期 成熟叶片 SC_35d 青荚期 种皮 花后35 d
LeO_10d 青荚期 成熟叶片 花后10 d SC_40d 青荚期 种皮 花后40 d
LeO_24d 青荚期 成熟叶片 花后24 d SC_43d 成熟期 种皮 花后43 d
LeO_30d 青荚期 成熟叶片 花后30 d En_21d 青荚期 内种皮 花后21 d
Bu_b 蕾期 蕾 En_24d 青荚期 内种皮 花后24 d
Ao_i 初花期 花柄 Ep_24d 青荚期 外种皮 花后24 d
Ao_f 盛花期 花柄 Ep_30d 青荚期 外种皮 花后30 d
Cal_i 初花期 萼片 Fu_27d 青荚期 珠柄 花后27 d
Cal_f 盛花期 萼片 Fu_35d 青荚期 珠柄 花后35 d
Pe_i 初花期 花瓣 SP_3d 青荚期 角果皮 花后3 d
Pe_f 盛花期 花瓣 SP_5d 青荚期 角果皮 花后3 d
Pi_f_un 盛花期 雌蕊-未授粉 SP_7d 青荚期 角果皮 花后7 d
Pi_i 初花期 雌蕊 SP_10d 青荚期 角果皮 花后10 d
Pi_f 盛花期 雌蕊 SP_13d 青荚期 角果皮 花后13 d
Sta_i 初花期 雄蕊 SP_16d 青荚期 角果皮
Sta_f 盛花期 雄蕊 SP_19d 青荚期 角果皮 花后19 d
At_i 初花期 花药 SP_21d 青荚期 角果皮 花后21 d
At_f 盛花期 花药 SP_24d 青荚期 角果皮 花后24 d
Cap_i 初花期 花丝 SP_27d 青荚期 角果皮 花后27 d
Cap_f 盛花期 花丝 SP_30d 青荚期 角果皮 花后30 d
IT_b 蕾期 主序顶端 SP_35d 青荚期 角果皮 花后35 d
IT_i 初花期 主序顶端 SP_40d 成熟期 角果皮 花后40 d
IT_f 盛花期 主序顶端 SP_43d 成熟期 角果皮 花后43 d
Se_3d 青荚期 种子 花后3 d SP_46d 成熟期 角果皮 花后46 d
Se_5d 青荚期 种子 花后3 d

Table 1

Information of PEBP homologs genes in B. napus, B. rapa, and B. oleracea based on A. thaliana sequences using BlastP approaches"

AGI ID 油菜同源基因
B. napus homologs		 白菜或甘蓝同源基因
B. rapa or B. oleracea homologs		 基因模型
Gene models
AT5G62040 BnaA06g21490D Bra010052 BROTHER OF FT AND TFL1 (BFT)
AT5G62040 BnaC03g52010D Bol012573 BROTHER OF FT AND TFL1 (BFT)
AT5G62040 -— Bol015337 BROTHER OF FT AND TFL1 (BFT)
AT2G27550 BnaA03g22340D Bra000506 centroradialis (ATC)
AT2G27550 BnaA04g15930D Bra034357 centroradialis (ATC)
AT2G27550 BnaA07g13290D Bra012010 centroradialis (ATC)
AT2G27550 BnaC01g41050D -— centroradialis (ATC)
AT2G27550 BnaC03g47080D Bol026421 centroradialis (ATC)
AT2G27550 BnaC03g64560D -— centroradialis (ATC)
AT2G27550 BnaC04g39220D Bol032920 centroradialis (ATC)
AT2G27550 BnaC04g16750D -— centroradialis (ATC)
AT1G65480 BnaA02g12130D Bra022475 FLOWERING LOCUS T (FT)
AT1G65480 -— Bra004117 FLOWERING LOCUS T (FT)
AT1G65480 BnaC02g45250D Bol017639 FLOWERING LOCUS T (FT)
AT1G65480 BnaC04g14850D Bol039209 FLOWERING LOCUS T (FT)
AT1G18100 BnaA09g44700D Bra031016 MOTHER OF FT AND TFL1 (MFT)
AT1G18100 BnaA06g12320D Bra025930 MOTHER OF FT AND TFL1 (MFT)
AT1G18100 BnaC05g50120D Bol009744 MOTHER OF FT AND TFL1 (MFT)
AT1G18100 BnaC08g37400D Bol030802 MOTHER OF FT AND TFL1 (MFT)
AT5G03840 BnaA10g26300D Bra009508 TERMINAL FLOWER 1 (TFL1)
AT5G03840 BnaAnng00810D Bra028815 TERMINAL FLOWER 1 (TFL1)
AT5G03840 -— Bra005783 TERMINAL FLOWER 1 (TFL1)
AT5G03840 BnaC02g02900D Bol005471 TERMINAL FLOWER 1 (TFL1)
AT5G03840 BnaC03g01440D Bol010027 TERMINAL FLOWER 1 (TFL1)
AT5G03840 BnaCnng10680D Bol015337 TERMINAL FLOWER 1 (TFL1)
AT4G20370 BnaA07g25310D Bra022475 TWIN SISTER OF FT (TSF)
AT4G20370 BnaA07g33120D Bra015710 TWIN SISTER OF FT (TSF)
AT4G20370 BnaC02g23820D -— TWIN SISTER OF FT (TSF)
AT4G20370 BnaC06g27090D -— TWIN SISTER OF FT (TSF)

Fig. 1

Phylogenetic tree and gene structures of PEBP in B. napus"

Fig. 2

Motif prediction of PEBP genes in B. napus"

Fig. 3

Multiple alignment of PEBP protein sequences between B. napus and A. thaliana"

Fig. 4

Phylogenetic analysis of PEBP gene family in B. napus, B. rapa, B. oleracea, and A. thaliana"

Table 2

Ka/Ks valus of BEBP genes between B. napus and A. thaliana species"

油菜基因编号
Gene ID in B. napus		 拟南芥基因编号
Gene ID in A. thaliana		 基因模型
Gene model		 非同义突变频率
Ka		 同义突变频率
Ks		 Ka/Ks
BnaA02g12130D AT1G65480 FT 0.09 0.32 0.27
BnaC02g45250D AT1G65480 FT 0.08 0.35 0.24
BnaC04g14850D AT1G65480 FT 0.11 0.80 0.14
BnaA10g26300D AT5G03840 TFL1 0.08 0.37 0.23
BnaAnng00810D AT5G03840 TFL1 0.05 0.39 0.14
BnaC02g02900D AT5G03840 TFL1 0.05 0.39 0.14
BnaC03g01440D AT5G03840 TFL1 0.03 0.41 0.07
BnaCnng10680D AT5G03840 TFL1 0.08 0.35 0.22
BnaA07g25310D AT4G20370 TSF 0.10 0.80 0.12
BnaA07g33120D AT4G20370 TSF 0.09 0.45 0.21
BnaC02g23820D AT4G20370 TSF 0.13 0.45 0.30
BnaC06g27090D AT4G20370 TSF 0.23 0.88 0.26
BnaA03g22340D AT2G27550 ATC 0.02 0.31 0.07
BnaA04g15930D AT2G27550 ATC 0.03 0.33 0.08
BnaA07g13290D AT2G27550 ATC 0.03 0.49 0.06
BnaC01g41050D AT2G27550 ATC 0.03 0.33 0.08
BnaC03g47080D AT2G27550 ATC 0.03 0.31 0.10
BnaC03g64560D AT2G27550 ATC 0.03 0.33 0.08
BnaC04g16750D AT2G27550 ATC 0.03 0.52 0.07
BnaC04g39220D AT2G27550 ATC 0.06 0.39 0.15
BnaA06g21490D AT5G62040 BFT 0.05 0.31 0.17
BnaC03g52010D AT5G62040 BFT 0.05 0.31 0.18
BnaA09g44700D AT1G18100 MFT 0.02 0.40 0.05
BnaC08g37400D AT1G18100 MFT 0.02 0.45 0.05
BnaC05g50120D AT1G18100 MFT 0.03 0.37 0.08
BnaA06g12320D AT1G18100 MFT 0.03 0.37 0.09

Fig. 5

Tissues-specific analysis of PEBP gene members in B. napus Samples were listed in Supplementary table 1. Blue shows low expression levels and yellow shows high expression levels."

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