Identification and Characterization of IPT Gene Family in Brassica rapa L.

doi:10.13304/j.nykjdb.2022.0373

Abstract

Abstract:

Isopentenyltransferase （IPT） is the first limiting enzyme for cytokinin biosynthesis， so to analyze the function of the IPT gene family in Brassica rapa L.， a total of 13 BrIPT genes were identified from the genome of Brassica rapa L. by bioinformatics， which were heterogeneously distributed on 7 chromosomes. These BrIPT geneswere divided into 4 substrates and each BrIPT gene included 8~10 conserved motifs and 1~2 UTR regions. The promoter regions of BrIPT genes contained numerous responsive elements. The BrIPT genes were regulated by environmental factors， biohormones， defense and stress. The qRT-PCR results showed that the tRNA-IPT genes BrIPT4， BrIPT6 and BrIPT9 were expressed in various parts of Brassica rapa L.. The expressions of IPT genes in Brassica rapa L. were higher at the mature stage than those at the seedling stage. The above results provided some basis for subsequent in-depth studies on the physiological and biochemical functions of IPT gene family members.

Key words: Brassica rapa L., IPT gene family, cytokinin, bioinformatics analysis

摘要：

异戊烯基转移酶（isopentenyltransferase，IPT）是细胞分裂素生物合成的第一限速酶，为分析IPT基因家族在白菜型油菜生长中的功能，利用生物信息学方法从其基因组中鉴定出13个BrIPT基因，它们不均匀地分布在7条染色体上。BrIPTs可分为4个亚族，各家族成员均含有8~10个保守基序和1~2个UTR区。BrIPT基因的启动子区域包含众多响应元件。BrIPT基因家族成员受环境因子、生物激素及防御与应激调控。qRT-PCR结果显示，tRNA-IPT基因BrIPT4、BrIPT6、BrIPT9在白菜型油菜体内各个部位均有表达。相比于苗期，成熟期白菜型油菜IPT基因的表达量更高，为后续深入研究IPT基因家族成员的生理生化功能提供了理论依据。

关键词: 白菜型油菜, IPT基因家族, 细胞分裂素, 生物信息学分析

CLC Number:

S565.4

Bo LIU, Wangtian WANG, Li MA, Junyan WU, Yuanyuan PU, Lijun LIU, Yan FANG, Wancang SUN, Yan ZHANG, Ruimin LIU, Xiucun ZENG. Identification and Characterization of IPT Gene Family in Brassica rapa L.[J]. Journal of Agricultural Science and Technology, 2024, 26(2): 56-66.

刘博, 王旺田, 马骊, 武军艳, 蒲媛媛, 刘丽君, 方彦, 孙万仓, 张岩, 刘睿敏, 曾秀存. 白菜型油菜IPT基因家族鉴定及表达分析[J]. 中国农业科技导报, 2024, 26(2): 56-66.

Figures/Tables 10

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基因名称	上游引物序列	下游引物序列
Gene name	Forward primer sequence （5’-3’）	Reverse primer sequence （5’-3’）
BrIPT1	CAAGATTCTCCCAAGCCTCGTCTG	CGCCTGAGCAAGAAGTGGAAGTC
BrIPT2	TCCTTCATTCATGCCCTCCTTGTTG	CACCCAGAGGAAGCAGCAATCG
BrIPT3	GTGAACGGTTACACGGTGGATTAGG	CCTAACACATATCGGACGGCAACC
BrIPT4	AGGATTGTTCATCGGTGTTGGAGTG	GCAAGTGGTGTTACGTTGTTGTTCC
BrIPT5	CCTCACATTCCCTTCTTCCCTTCAC	GGTTGCTCCTAAGATGACGACGATC
BrIPT6	GCAACCGCCGTGCCTTATAC	GCCGGTGGGACCAGATATCA
BrIPT7	GCAGCTCGTTTCTCCGGAGA	TGCGGAGTAGATGGTGAGCG
BrIPT8	ATGGGTGCTACCGGAACAGG	GCAACTCTCCTCGGTCGTGA
BrIPT9	GCGGAATCGACGAAGCGAAG	CGCCAAGTCTACGGCTAGCT
BrIPT10	TCGCATGATGGAAGCAGGATTACTC	TGTACCACGGTCCACTAGAGATTCG
BrIPT11	GGAGAAGGAGGGAGAGTGGGATTC	CTTCACTACCTGTCTCTTCGCCAAC
BrIPT12	TCCGACAAGATCCAAGTTCACCAAG	GAGGCGGCAAAACACTGAGGAG
BrIPT13	ATCGTCACCAACAAAGTCACTCCAG	GTAATCCTCCGCCGTGAAATCCTC
Actin	TGTGCCAATCTACGAGGGTTT	TTTCCCGCTCGGCTGTTGT

基因名称	上游引物序列	下游引物序列
Gene name	Forward primer sequence （5’-3’）	Reverse primer sequence （5’-3’）
BrIPT1	CAAGATTCTCCCAAGCCTCGTCTG	CGCCTGAGCAAGAAGTGGAAGTC
BrIPT2	TCCTTCATTCATGCCCTCCTTGTTG	CACCCAGAGGAAGCAGCAATCG
BrIPT3	GTGAACGGTTACACGGTGGATTAGG	CCTAACACATATCGGACGGCAACC
BrIPT4	AGGATTGTTCATCGGTGTTGGAGTG	GCAAGTGGTGTTACGTTGTTGTTCC
BrIPT5	CCTCACATTCCCTTCTTCCCTTCAC	GGTTGCTCCTAAGATGACGACGATC
BrIPT6	GCAACCGCCGTGCCTTATAC	GCCGGTGGGACCAGATATCA
BrIPT7	GCAGCTCGTTTCTCCGGAGA	TGCGGAGTAGATGGTGAGCG
BrIPT8	ATGGGTGCTACCGGAACAGG	GCAACTCTCCTCGGTCGTGA
BrIPT9	GCGGAATCGACGAAGCGAAG	CGCCAAGTCTACGGCTAGCT
BrIPT10	TCGCATGATGGAAGCAGGATTACTC	TGTACCACGGTCCACTAGAGATTCG
BrIPT11	GGAGAAGGAGGGAGAGTGGGATTC	CTTCACTACCTGTCTCTTCGCCAAC
BrIPT12	TCCGACAAGATCCAAGTTCACCAAG	GAGGCGGCAAAACACTGAGGAG
BrIPT13	ATCGTCACCAACAAAGTCACTCCAG	GTAATCCTCCGCCGTGAAATCCTC
Actin	TGTGCCAATCTACGAGGGTTT	TTTCCCGCTCGGCTGTTGT

基因ID Gene ID	基因名 Gene name	氨基酸 Amino acids/aa	分子量 Molecular weight/Da	等电点PI	带负电荷残基数 Total number of negatively charged residues	带正电荷残基数 Total number of positively charged residue	不稳定指数Instability index	脂肪指数Aliphatic index
Brapa01T003069.1	BrIPT1	332	37 126.59	8.77	37	42	39.85	91.87
Brapa01T003426.1	BrIPT2	324	36 886.28	8.50	41	44	44.02	81.45
Brapa02T000813.1	BrIPT3	334	37 920.51	5.75	50	44	34.85	94.55
Brapa02T000886.1	BrIPT4	542	61 015.95	7.09	66	66	46.35	80.76
Brapa02T001911.1	BrIPT5	348	39 700.26	8.72	49	52	54.61	81.24
Brapa03T000921.1	BrIPT6	463	52 426.39	7.50	59	60	50.28	78.98
Brapa03T003913.1	BrIPT7	326	37 116.50	9.34	37	45	48.52	82.48
Brapa04T000031.1	BrIPT8	334	37 337.14	8.11	42	44	44.57	90.42
Brapa04T002174.1	BrIPT9	496	56 182.83	6.15	75	68	41.78	89.78
Brapa07T001138.1	BrIPT10	335	37 477.17	8.48	40	44	35.54	91.34
Brapa07T003284.1	BrIPT11	333	37 800.18	8.40	46	48	44.07	88.68
Brapa09T001382.1	BrIPT12	332	37 568.44	8.40	44	47	37.94	91.27
Brapa10T001241.1	BrIPT13	334	37 876.59	5.96	48	44	35.22	92.22

基因ID Gene ID	基因名 Gene name	氨基酸 Amino acids/aa	分子量 Molecular weight/Da	等电点PI	带负电荷残基数 Total number of negatively charged residues	带正电荷残基数 Total number of positively charged residue	不稳定指数Instability index	脂肪指数Aliphatic index
Brapa01T003069.1	BrIPT1	332	37 126.59	8.77	37	42	39.85	91.87
Brapa01T003426.1	BrIPT2	324	36 886.28	8.50	41	44	44.02	81.45
Brapa02T000813.1	BrIPT3	334	37 920.51	5.75	50	44	34.85	94.55
Brapa02T000886.1	BrIPT4	542	61 015.95	7.09	66	66	46.35	80.76
Brapa02T001911.1	BrIPT5	348	39 700.26	8.72	49	52	54.61	81.24
Brapa03T000921.1	BrIPT6	463	52 426.39	7.50	59	60	50.28	78.98
Brapa03T003913.1	BrIPT7	326	37 116.50	9.34	37	45	48.52	82.48
Brapa04T000031.1	BrIPT8	334	37 337.14	8.11	42	44	44.57	90.42
Brapa04T002174.1	BrIPT9	496	56 182.83	6.15	75	68	41.78	89.78
Brapa07T001138.1	BrIPT10	335	37 477.17	8.48	40	44	35.54	91.34
Brapa07T003284.1	BrIPT11	333	37 800.18	8.40	46	48	44.07	88.68
Brapa09T001382.1	BrIPT12	332	37 568.44	8.40	44	47	37.94	91.27
Brapa10T001241.1	BrIPT13	334	37 876.59	5.96	48	44	35.22	92.22

基因ID Gene ID	基因名Gene name	最大亲水值Maximum hydrophilic value	位置Position/aa	最大疏水值Maximum hydrophobic value	位置Position/aa	亲水性平均系数 Grand average of hydropathicity
Brapa01T003069.1	BrIPT1	1.956	40	-2.922	276	-0.262
Brapa01T003426.1	BrIPT2	1.856	47	-2.311	214	-0.338
Brapa02T000813.1	BrIPT3	2.122	318	-2.489	263	-0.224
Brapa02T000886.1	BrIPT4	3.300	63，64	-3.100	124	-0.390
Brapa02T001911.1	BrIPT5	2.389	66	-3.411	57	-0.412
Brapa03T000921.1	BrIPT6	1.700	274	-3.489	50	-0.433
Brapa03T003913.1	BrIPT7	2.144	48	-2.356	214	-0.331
Brapa04T000031.1	BrIPT8	2.144	47	-2.522	153	-0.137
Brapa04T002174.1	BrIPT9	2.822	17	-3.744	482	-0.458
Brapa07T001138.1	BrIPT10	1.956	40	-2.756	276	-0.210
Brapa07T003284.1	BrIPT11	2.389	52	-3.078	308	-0.343
Brapa09T001382.1	BrIPT12	2.144	47	-2.456	153	-0.187
Brapa10T001241.1	BrIPT13	1.956	43	-2.489	263	-0.225