甘蓝型油菜BnKNOX基因家族的鉴定与分析

doi:10.3724/SP.J.1006.2023.34027

Abstract

Abstract:

The plant specific KNOTTED-LIKE HOMEOBOX (KNOX) protein is a transcription factor family that plays an important role in plant growth and development, as well as responses to various stresses. KNOX proteins contain four conserved domains [a three amino acid loop extension (TALE) type homeodomain (HD), ELK domain, and two subdomains (KNOX1 and KNOX2)]. At present, the comprehensive study of BnKNOX genes in Brassica napus has not been reported yet. In this study, 36 BnKNOX family members were identified in B. napus genome via bioinformatic analyses, which were classified into three sub-families (I, II, and M-type) based on sequence alignment and phylogenetic analyses. Evolutionary analysis showed that the whole genome duplication (WGD) and segmental duplication were the main driving forces for the expansion of BnKNOX gene family. Based on the RNA-seq data of developing tissues and organs of B. napus, BnKNAT25/26/29/30 were specifically expressed in endosperm and developing seeds, while BnKNAT31/32/34 were highly expressed in mature seeds. We analyzed the cis-acting elements and expression pattern of BnKNOXs under various abiotic stresses, and identified 17 BnKNOX members that might be involved in drought and osmotic stress responses.

Key words: Brassica napus, KNOX, gene family, expression pattern, abiotic stress

CHEN Wu-Jun, LIU Jiang-Dong, JIANG Kai-Xuan, WANG You-Ping, JIANG Jin-Jin. Identification and analysis of BnKNOX gene family in Brassica napus[J].Acta Agronomica Sinica, 2023, 49(11): 2991-3006.

Figures/Tables 13

Table 1

Fig. 1

Table 2

Information of BnKNOX protein members in Brassica napus"

基因号 Gene ID	基因名 Gene name	拟南芥号 Arabidopsis thaliana locus	蛋白长度 Protein length (AA)	分子量 Molecular weight (kD)	等电点Isoelectric point (pI)	亚细胞定位 Localization
BnaA03g23610D	BnKNAT1	AT4G08150.1	402	46.36	5.82	细胞核Nucleus
BnaC03g28030D	BnKNAT2	AT4G08150.1	193	23.07	7.55	细胞核Nucleus
BnaCnng59830D	BnKNAT3	AT4G08150.1	349	40.19	5.89	细胞核Nucleus
BnaA02g14950D	BnKNAT4	AT1G70510.1	327	36.94	4.81	细胞核Nucleus
BnaC02g19900D	BnKNAT5	AT1G70510.1	327	36.90	4.80	细胞核Nucleus
BnaA02g32110D	BnKNAT6	AT5G25220.1	420	46.29	5.40	细胞核Nucleus
BnaA06g27560D	BnKNAT7	AT5G25220.1	299	33.43	5.82	细胞核Nucleus
BnaC02g40790D	BnKNAT8	AT5G25220.1	404	44.84	5.44	细胞核Nucleus
BnaC07g29530D	BnKNAT9	AT5G25220.1	444	48.91	5.11	细胞核Nucleus
BnaA02g00810D	BnKNAT10	AT5G11060.1	393	44.28	5.65	细胞核Nucleus
BnaA03g03190D	BnKNAT11	AT5G11060.1	386	43.15	5.67	细胞核Nucleus
BnaC03g04580D	BnKNAT12	AT5G11060.1	302	33.77	5.99	细胞核Nucleus
BnaCnng20070D	BnKNAT13	AT5G11060.1	393	44.23	5.62	细胞核Nucleus
BnaA01g04870D	BnKNAT14	AT4G32040.1	374	41.91	5.56	细胞核Nucleus
BnaA03g51900D	BnKNAT15	AT4G32040.1	382	43.18	5.48	细胞核Nucleus
BnaC01g06410D	BnKNAT16	AT4G32040.1	374	41.86	5.71	细胞核Nucleus
BnaC07g43650D	BnKNAT17	AT4G32040.1	400	45.35	5.37	细胞核Nucleus
BnaA08g20500D	BnKNAT18	AT1G23380.1	208	22.92	4.49	细胞核Nucleus
BnaA08g20510D	BnKNAT19	AT1G23380.1	121	14.03	8.25	细胞核Nucleus
BnaA09g31100D	BnKNAT20	AT1G23380.1	235	26.11	4.41	细胞核Nucleus
BnaAnng30720D	BnKNAT21	AT1G23380.1	204	23.26	5.96	细胞核Nucleus
BnaC05g18670D	BnKNAT22	AT1G23380.1	221	24.45	4.35	细胞核Nucleus
BnaC08g06320D	BnKNAT23	AT1G23380.1	314	35.23	5.10	细胞核Nucleus
BnaCnng70390D	BnKNAT24	AT1G23380.2	205	23.48	6.22	细胞核Nucleus
BnaA09g12980D	BnKNAT25	AT1G62990.1	293	33.02	5.62	细胞核Nucleus
BnaA09g52990D	BnKNAT26	AT1G62990.1	294	33.10	5.85	细胞核Nucleus
BnaC04g20090D	BnKNAT27	AT1G62990.1	104	11.46	4.90	细胞核Nucleus
BnaC04g20110D	BnKNAT28	AT1G62990.1	222	25.73	7.84	细胞核Nucleus
BnaC09g12900D	BnKNAT29	AT1G62990.1	102	11.09	5.15	细胞核Nucleus
BnaCnng51440D	BnKNAT30	AT1G62990.1	294	33.09	5.78	细胞核Nucleus
BnaA06g09570D	BnKNAT31	AT1G14760.2	141	16.25	4.57	细胞核Nucleus
BnaA09g45470D	BnKNAT32	AT1G14760.2	135	15.31	4.36	细胞核Nucleus
BnaC05g10940D	BnKNAT33	AT1G14760.2	137	15.70	4.95	细胞核Nucleus
BnaC08g39310D	BnKNAT34	AT1G14760.2	135	15.25	4.37	细胞核Nucleus
BnaA09g13310D	BnSTM1	AT1G62360.1	383	43.11	5.82	细胞核Nucleus
BnaC09g13580D	BnSTM2	AT1G62360.1	383	43.20	5.92	细胞核Nucleus

Table 2

Fig. 2

Fig. 3

Fig. 4

Table S1

Duplication type of BnKNOX genes in Brassica napus"

基因号 Gene ID	基因名称 Gene name	复制方式 Duplication type
BnaA03g23610D	BnKNAT1	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC03g28030D	BnKNAT2	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaCnng59830D	BnKNAT3	分散复制Dispersed duplication
BnaA02g14950D	BnKNAT4	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC02g19900D	BnKNAT5	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA02g32110D	BnKNAT6	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA06g27560D	BnKNAT7	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC02g40790D	BnKNAT8	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC07g29530D	BnKNAT9	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA02g00810D	BnKNAT10	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA03g03190D	BnKNAT11	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC03g04580D	BnKNAT12	分散复制Dispersed duplication
BnaCnng20070D	BnKNAT13	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA01g04870D	BnKNAT14	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA03g51900D	BnKNAT15	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC01g06410D	BnKNAT16	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC07g43650D	BnKNAT17	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA08g20500D	BnKNAT18	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA08g20510D	BnKNAT19	分散复制Dispersed duplication
BnaA09g31100D	BnKNAT20	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaAnng30720D	BnKNAT21	分散复制Dispersed duplication
BnaC05g18670D	BnKNAT22	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC08g06320D	BnKNAT23	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaCnng70390D	BnKNAT24	分散复制Dispersed duplication
BnaA09g12980D	BnKNAT25	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA09g52990D	BnKNAT26	分散复制Dispersed duplication
BnaC04g20090D	BnKNAT27	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC04g20110D	BnKNAT28	分散复制Dispersed duplication
BnaC09g12900D	BnKNAT29	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaCnng51440D	BnKNAT30	分散复制Dispersed duplication
BnaA06g09570D	BnKNAT31	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA09g45470D	BnKNAT32	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC05g10940D	BnKNAT33	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC08g39310D	BnKNAT34	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA09g13310D	BnSTM1	全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC09g13580D	BnSTM2	全基因组复制或片段复制Whole genome duplication or segmental duplication

Table S1

Fig. 5

Fig. 6

Table S2

RNA-seq data (FPKM) of BnKNOX genes in different tissues and developmental stages in Brassica napus"

基因号 Gene ID	基因名称Gene name	叶片Leaf	子叶Cotyledon	下胚轴Hypocotyl	根 Root	茎尖分生组织SAM	茎Stem	花苞Bud	花Flower	胚乳Endosperm	授粉后14 d角果Silique-14 DAP	授粉后21 d种子Seed-21 DAP	授粉后28 d种子Seed-28 DAP	授粉后35 d种子Seed-35 DAP	授粉后42 d种子Seed-42 DAP	授粉后50 d种子Seed-50 DAP
BnaA03g23610D	BnKNAT1	0.016	0.010	38.382	1.843	3.479	29.144	1.896	2.620	0.005	0.915	0.118	0.771	0.135	0.038	0.000
BnaC03g28030D	BnKNAT2	0.016	0.200	45.299	2.049	5.101	51.947	2.567	3.286	0	1.399	0.370	1.185	0.139	0.023	0.018
BnaCnng59830D	BnKNAT3	0	0.027	14.658	0.836	1.934	13.746	0.691	0.851	0	0.425	0.207	0.656	0.041	0	0
BnaA02g14950D	BnKNAT4	0.018	0.364	6.640	2.548	1.230	3.904	0.957	0.890	0	0.746	0.133	1.078	0.471	0.998	1.078
BnaC02g19900D	BnKNAT5	0.191	0.507	8.285	2.451	4.376	9.119	1.963	1.544	0	1.744	0.438	0.989	0.543	1.121	0.927
BnaA02g32110D	BnKNAT6	2.760	10.350	5.929	1.369	4.090	2.329	5.397	8.268	0.830	9.239	2.211	1.630	0.838	1.501	1.715
BnaA06g27560D	BnKNAT7	15.294	66.703	14.521	5.061	45.785	7.394	21.312	27.772	8.066	26.798	13.314	8.149	3.248	5.073	2.501
BnaC02g40790D	BnKNAT8	3.086	21.930	18.387	3.817	7.507	2.332	3.834	2.333	0.439	8.187	1.745	0.699	0.251	0.962	2.632
BnaC07g29530D	BnKNAT9	21.780	35.189	8.946	10.544	48.375	8.729	24.791	30.841	4.942	31.374	18.312	7.426	3.727	4.128	4.535
BnaA02g00810D	BnKNAT10	6.884	8.202	1.289	0.033	16.883	1.866	7.954	5.470	1.157	11.089	1.673	3.216	0.577	0.097	0.089
BnaA03g03190D	BnKNAT11	10.194	2.581	0.646	0.135	10.561	2.062	1.017	2.510	0.125	4.394	0.372	1.823	0.454	0.072	0.116
BnaC03g04580D	BnKNAT12	5.192	8.137	1.622	0.472	8.129	1.447	1.784	3.371	0.372	4.989	0.574	2.097	0.444	0.066	0.033
BnaCnng20070D	BnKNAT13	2.811	0	0	0	7.802	0.882	6.550	7.581	1.448	6.022	0.836	1.446	0.447	0.018	0.012
BnaA01g04870D	BnKNAT14	1.749	8.448	14.776	12.178	2.868	2.952	1.899	0.651	0	5.498	3.699	1.433	4.451	2.595	2.046
BnaA03g51900D	BnKNAT15	7.624	34.107	35.739	56.554	10.255	4.506	3.373	3.358	6.662	8.299	7.237	6.074	3.798	4.120	3.453
BnaC01g06410D	BnKNAT16	0.679	3.106	4.643	2.947	1.017	0.940	0.692	0.080	0	1.220	0.530	0.904	2.461	0.995	0.785
BnaC07g43650D	BnKNAT17	6.761	15.548	31.413	34.109	9.369	6.851	4.481	4.621	8.137	10.765	14.927	9.026	6.043	3.595	1.987
BnaA08g20500D	BnKNAT18	0.006	0	9.688	1.984	1.673	6.009	2.118	2.704	0.010	0.095	0.146	0.285	0.210	0.177	0.385
BnaA08g20510D	BnKNAT19	0.006	0	9.688	1.984	1.673	6.009	2.118	2.704	0.010	0.095	0.146	0.285	0.210	0.177	0.385
BnaA09g31100D	BnKNAT20	0.019	0	2.196	0.385	1.311	1.625	0.478	0.229	0.128	0.197	0.315	0.377	0.110	0.062	0.106
BnaAnng30720D	BnKNAT21	0.011	0.043	2.302	0.614	0.684	1.250	0.441	0.244	0.181	0.336	0.693	0.312	0.022	0.264	0.088
BnaC05g18670D	BnKNAT22	0.023	0.022	1.390	0.582	0.768	1.340	0.687	0.474	0.002	0.078	0.044	0.126	0.039	0.060	0.031
BnaC08g06320D	BnKNAT23	0.023	0.357	23.487	2.001	5.116	12.296	2.922	4.588	0	0.213	0.162	1.089	1.002	0.716	2.628
BnaCnng70390D	BnKNAT24	0.045	0.032	1.723	1.409	1.276	2.123	1.039	0.811	0.019	0.079	0.118	0.275	0.113	0.074	0.044
BnaA09g12980D	BnKNAT25	1.334	0.865	5.515	5.768	1.228	3.900	7.155	4.796	11.808	11.919	24.940	13.193	8.877	5.448	0.014
BnaA09g52990D	BnKNAT26	1.294	0.096	0.444	0.534	0.549	17.354	12.259	5.379	22.756	21.863	50.558	28.156	24.423	7.101	0.053
BnaC04g20090D	BnKNAT27	0.070	0.037	0.121	0.116	0.296	1.135	0.391	0.107	0.512	0.472	2.355	0.660	0.797	0.168	0.016
BnaC04g20110D	BnKNAT28	0	0	0	0	0	0.079	0.023	0	0	0	0	0	0	0	0
BnaC09g12900D	BnKNAT29	2.546	0.378	1.021	0.379	1.235	3.922	4.268	7.819	7.158	14.842	16.892	9.738	6.075	3.079	0.032
BnaCnng51440D	BnKNAT30	1.390	0.146	0.978	0.900	1.741	13.686	10.700	5.352	21.985	16.103	37.943	19.860	17.638	5.264	0.017
BnaA06g09570D	BnKNAT31	0	0	0	0.060	1.292	0	4.234	2.614	0	0.083	0.862	0	0	0.188	1.526
BnaA09g45470D	BnKNAT32	0	0	0	0.688	1.327	0	0	0	0	0.034	0.398	0.348	0.080	1.149	3.517
BnaC05g10940D	BnKNAT33	0	0	0	0	0.966	0.024	7.893	4.128	0	0	0.172	0.370	0.055	0.080	0.089
BnaC08g39310D	BnKNAT34	0	0	0	0.245	1.902	0	0.021	0	0.067	0.114	3.166	0.137	0.063	0.239	1.408
BnaA09g13310D	BnSTM1	0.020	0	0.735	1.191	5.619	66.414	8.814	11.525	0	2.708	0.166	0.286	0.160	0.022	0.027
BnaC09g13580D	BnSTM2	0.010	0	6.015	0.037	8.231	85.818	12.789	16.183	0	2.980	0.284	0.485	0.133	0.051	0.074

Table S2

Fig. 7

Fig. 8

Fig. 9

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基因名称 Gene name	正向引物序列 Forward primer sequence (5'-3')	反向引物序列 Reverse primer sequence (5'-3')
BnKNAT1	AGCCATCCACAATACTCAAGAA	CGCCGTAATTTTATCAACCACT
BnKNAT2	AGATTAGCATGTTGTGTCAGGA	ATCCACTGTACTTCTTCAGCAA
BnKNAT3	ACCTGAGGTGGTCGATAAAATT	AAGAAACGACCCACATGAATTG
BnKNAT4	CGAAAATCGCTTCTCATCCTTT	CGTTTCGATCTTGTTCAGGAAA
BnKNAT5	TTCTTCGGAGAGTCTTATGTCG	GAATCTCTTCCAACACATACGC
BnKNAT11	CTCTCATCCACTATACGAGCAG	AGTGGTCAAGCTCCTTATCATC
BnKNAT12	GTGACGCCATGGAAAACATTAC	CTGCTCGTATAGTGGATGAGAG
BnKNAT13	CACTATACGAACGGCTTTTGTC	GTCCATAGTAGAGTACTTGGCC
BnKNAT18	GATGGAATGTACGGCTTTCATC	AGTCGGAAGGAAACATCAGATT
BnKNAT19	GAAAGCTACCAAGAGAAGCAAG	CAAAAGGCATATTCTCGGACTG
BnKNAT20	CCTTCTGATTACCAAACCTTGC	TACAAAGGATGACAAGCGATCT
BnKNAT22	GTCTCTCTCGGTATCATCAAGG	CCTTGCGAGATCCGACTTATAT
BnKNAT23	ATGTGACTACTCAGATAAGCCG	GGATACGAAGGATGACAAGCTA
BnKNAT24	TGACACAATGACAATGGAGGTA	ATCTTCGCATATTTGTTTCCCG
BnKNAT25	TACCATGTGCGAGCAATTATTG	GCTGTTCTTTGAAGCTACACAA
BnKNAT33	TAAGGGAGTTGAAGGAAGCAAT	TAGCACCGAATATAGCTGTCAG
BnSTM2	GTAGTAATGGACGCAACACATC	GTGCAACGTTCCTAAGTATTCC

Identification and analysis of BnKNOX gene family in Brassica napus

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