Genome-wide Identification and Expression Analysis of SBP Genes in Panicum miliaceum

doi:10.11983/CBB23065

Abstract

Abstract: Squamosa promoter binding protein (SBP) gene family is widely involved in plant growth and development, signal transduction, and many physiological and biochemical processes. Here, we identified a total of 25 SBP genes in the proso millet (Panicum miliaceum) genome, which were divided into 6 subfamilies through phylogenetic analysis. The members of the same subfamily had similar gene structure and conserved motifs. The collinearity analysis revealed 7 pairs of orthologous genes with Arabidopsis thaliana AtSBP and 31 pairs with Oryza sativa OsSBP. The analysis of cis-acting elements showed that the promoter region of SBP genes in P. miliaceum was rich in elements related to stress, plant light response and plant hormone signal response. The analysis of gene expression patterns showed that the SBP genes in P. miliaceum had obvious tissue specificity, variety specificity, and developmental stage specificity, suggesting important roles of SBP genes in the growth and development of P. miliaceum. The results provide a basis for further studying the biological function of SBP gene family in the growth and development of P. miliaceum and a reference for studying the SBP genes in other crops.

Key words: Panicum miliaceum, SBP gene, whole genome identification, analysis of gene expression

Zhengyong Duan, Min Ding, Yuzhuo Wang, Yibing Ding, Ling Chen, Ruiyun Wang, Zhijun Qiao. Genome-wide Identification and Expression Analysis of SBP Genes in Panicum miliaceum[J]. Chinese Bulletin of Botany, 2024, 59(2): 231-244.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB23065

https://www.chinbullbotany.com/EN/Y2024/V59/I2/231

Figures/Tables 11

References 39

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Gene name	Forward primer (5′-3′)	Reverse primer (5′-3′)
PM13G22100	CTCATATGGCAGCCAGGGTA	CAGGCATTGACGCAGCAC
PM10G18000	AGTTCGACGAGGCCAAGAG	TGGTGTAGGAGCCCGTCAT
PM07G33040	GCTTCCCTTTCCTGACCAAT	ACAGTTGCCGTTGCTATGCT
PM03G01570	GGTCACAATGAGCGTCGG	CCAGGCTCTTGAAATGATGC
Actin	CGAAGCCCCTCTTAACCC	GTATGGCTGACACCATCACC

Gene name	Forward primer (5′-3′)	Reverse primer (5′-3′)
PM13G22100	CTCATATGGCAGCCAGGGTA	CAGGCATTGACGCAGCAC
PM10G18000	AGTTCGACGAGGCCAAGAG	TGGTGTAGGAGCCCGTCAT
PM07G33040	GCTTCCCTTTCCTGACCAAT	ACAGTTGCCGTTGCTATGCT
PM03G01570	GGTCACAATGAGCGTCGG	CCAGGCTCTTGAAATGATGC
Actin	CGAAGCCCCTCTTAACCC	GTATGGCTGACACCATCACC

Gene name	Gene ID	Number of amino acids	Molecular weight (Da)	Theoretical pI	Instability index	Aliphatic index	Grand average of hydropathicity	Subcellular localization
PmSBP1	PM13G22100	389	40425.64	9.02	59.42	53.57	-0.554	Nucleus
PmSBP2	PM15G18460	391	40589.82	9.03	59.36	51.79	-0.586	Nucleus
PmSBP3	PM04G19860	351	36740.87	9.15	50.66	54.27	-0.508	Nucleus
PmSBP4	PM03G01570	373	38851.28	9.11	51.60	55.01	-0.454	Nucleus
PmSBP5	PM07G33040	378	39705.20	9.41	50.71	58.47	-0.470	Nucleus
PmSBP6	PM16G15940	405	40953.59	9.61	58.23	55.11	-0.442	Nucleus
PmSBP7	PM15G16820	398	40086.69	9.43	59.47	53.39	-0.441	Nucleus
PmSBP8	PM10G18000	416	43996.51	9.18	63.21	57.09	-0.528	Nucleus
PmSBP9	PM09G20570	423	45069.55	9.14	65.80	57.07	-0.590	Nucleus
PmSBP10	PM03G07850	181	18864.75	9.80	70.12	49.34	-0.796	Nucleus
PmSBP11	PM11G14200	475	51028.91	9.10	45.90	60.06	-0.577	Nucleus
PmSBP12	PM12G02720	474	51043.79	9.10	47.15	61.22	-0.573	Nucleus
PmSBP13	PM03G07830	195	20090.95	9.71	65.22	40.77	-0.962	Nucleus
PmSBP14	PM12G04460	439	46205.92	6.84	59.02	61.07	-0.423	Nucleus
PmSBP15	PM11G16250	249	27804.58	9.66	58.67	57.27	-0.726	Nucleus
PmSBP16	PM01G25080	953	104207.41	5.74	46.12	78.91	-0.310	Nucleus
PmSBP17	PM12G04270	331	36135.41	8.90	58.10	58.76	-0.670	Nucleus
PmSBP18	PM13G22370	1107	121234.39	6.64	55.79	75.46	-0.482	Nucleus
PmSBP19	PM15G18240	1109	121513.62	6.55	55.94	74.96	-0.491	Nucleus
PmSBP20	PM06G21970	855	94067.89	5.78	53.45	82.02	-0.327	Nucleus
PmSBP21	PM05G24780	857	94363.22	5.74	54.80	82.07	-0.336	Nucleus
PmSBP22	PM07G07420	540	60348.18	5.60	56.90	82.19	-0.396	Nucleus
PmSBP23	PM04G25580	105	11903.20	11.92	86.68	33.52	-1.624	Nucleus
PmSBP24	PM11G02690	403	42276.93	6.22	57.12	61.64	-0.481	Nucleus
PmSBP25	PM13G17660	255	27293.16	7.92	46.21	58.31	-0.555	Nucleus

Gene name	Gene ID	Number of amino acids	Molecular weight (Da)	Theoretical pI	Instability index	Aliphatic index	Grand average of hydropathicity	Subcellular localization
PmSBP1	PM13G22100	389	40425.64	9.02	59.42	53.57	-0.554	Nucleus
PmSBP2	PM15G18460	391	40589.82	9.03	59.36	51.79	-0.586	Nucleus
PmSBP3	PM04G19860	351	36740.87	9.15	50.66	54.27	-0.508	Nucleus
PmSBP4	PM03G01570	373	38851.28	9.11	51.60	55.01	-0.454	Nucleus
PmSBP5	PM07G33040	378	39705.20	9.41	50.71	58.47	-0.470	Nucleus
PmSBP6	PM16G15940	405	40953.59	9.61	58.23	55.11	-0.442	Nucleus
PmSBP7	PM15G16820	398	40086.69	9.43	59.47	53.39	-0.441	Nucleus
PmSBP8	PM10G18000	416	43996.51	9.18	63.21	57.09	-0.528	Nucleus
PmSBP9	PM09G20570	423	45069.55	9.14	65.80	57.07	-0.590	Nucleus
PmSBP10	PM03G07850	181	18864.75	9.80	70.12	49.34	-0.796	Nucleus
PmSBP11	PM11G14200	475	51028.91	9.10	45.90	60.06	-0.577	Nucleus
PmSBP12	PM12G02720	474	51043.79	9.10	47.15	61.22	-0.573	Nucleus
PmSBP13	PM03G07830	195	20090.95	9.71	65.22	40.77	-0.962	Nucleus
PmSBP14	PM12G04460	439	46205.92	6.84	59.02	61.07	-0.423	Nucleus
PmSBP15	PM11G16250	249	27804.58	9.66	58.67	57.27	-0.726	Nucleus
PmSBP16	PM01G25080	953	104207.41	5.74	46.12	78.91	-0.310	Nucleus
PmSBP17	PM12G04270	331	36135.41	8.90	58.10	58.76	-0.670	Nucleus
PmSBP18	PM13G22370	1107	121234.39	6.64	55.79	75.46	-0.482	Nucleus
PmSBP19	PM15G18240	1109	121513.62	6.55	55.94	74.96	-0.491	Nucleus
PmSBP20	PM06G21970	855	94067.89	5.78	53.45	82.02	-0.327	Nucleus
PmSBP21	PM05G24780	857	94363.22	5.74	54.80	82.07	-0.336	Nucleus
PmSBP22	PM07G07420	540	60348.18	5.60	56.90	82.19	-0.396	Nucleus
PmSBP23	PM04G25580	105	11903.20	11.92	86.68	33.52	-1.624	Nucleus
PmSBP24	PM11G02690	403	42276.93	6.22	57.12	61.64	-0.481	Nucleus
PmSBP25	PM13G17660	255	27293.16	7.92	46.21	58.31	-0.555	Nucleus