Analysis on Expression and DNA Variation of TGA Genes in Sorghum （Sorghum bicolor） in Response to Sporisorium reilianum Infection

doi:10.13560/j.cnki.biotech.bull.1985.2024-0979

Abstract

Abstract:

Objective The TGA family is a very important group of bZIP transcription factors. This study is aimed to identify the TGA gene family members of the sorghum genome, analyse gene expression and natural allele variation analysis, and screen the genes and cis-acting elements that respond to the infection of Sporisorium reilianum. Method We identified the members of SbTGAs gene family in the whole genome through bioinformatic and molecular biological methods, and analysed their chromosome location, gene structure, protein physicochemical properties, evolutionary relationship, cis-regulatory elements of their putative promoters, collinearity analysis, and transcriptional expression characteristics after the infection of head smut fungus. Result In sorghum genome there were 17 SbTGA family members, all of them contained the DOG1 domain and most carried bZIP domain. All SbTGAs were located in the nucleus, and most of the SbTGA gene had 3‒12 introns. Phylogenetic analysis showed that the TGA gene family could be divided into five subfamilies. There were 15 genes in Zea mays having collinearity withsorghum, and their genetic relationships were closer. Gene expression analysis showed that the expressions of SbTGA2.1b were significant in the roots and leaves, and significantly induced after infection by S. reilianum in both lines with resistance and susceptability to head smut. It can be seen that the expressions of SbTGA2.2, SbTGA5 and SbTGA6.6g in healthy lines were up-regulated compared with that in susceptible lines. The synthetic analysis of whole genome resequencing data revealed five genes, including SbTGA2.1a and SbTGA6.6g, carrying multiple non-synonymous SNP and INDEL variations. Conclusion SbTGAs including SbTGA2.1b are hypothesized to associate with sorghum head smut resistance. These findings provide an evidences for breeding sorghum for resistance to head smut.

Key words: sorghum, TGA, head smut fungus Sporisorium reilianum, gene expression, DNA variation

LIU Zhuo-jun, CHAI Wen-ting, REN Yi-le, WANG Xin-yu, ZHU Li-xun, ZHAO Shan-shan, YANG Bo-hui, FAN Jia-li, LI Xin-feng, ZHAO Wei-jun, LYU Jin-hui, ZHANG Chun-lai. Analysis on Expression and DNA Variation of TGA Genes in Sorghum （Sorghum bicolor） in Response to Sporisorium reilianum Infection[J]. Biotechnology Bulletin, 2025, 41(5): 90-103.

Figures/Tables 17

References 27

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基因编号 Gene ID	基因名称 Gene name	染色体 Chromosome	基因位置 Genome location （bp）	基因长度 Length （bp）
Sobic.003G329500	SbTGA1.3g	03	65 465 408‒65 471 285	5 877
Sobic.009G180700 Sobic.002G247300 Sobic.002G424000	SbTGA1.9g SbTGA2.1a SbTGA2.1b	09 02 02	53 491 550‒53 494 415 63 528 681‒63 539 526 77 105 916‒77 111 030	3 266 10 846 5 114
Sobic.001G390800	SbTGA2.2	01	67 724 716‒67 732 814	8 098
Sobic.003G081000	SbTGA2.3	03	6 962 855‒6 973 141	10 286
Sobic.010G110100	SbTGA3	10	11 004 657‒11 007 712	3 055
Sobic.005G038700	SbTGA4.5g	05	3 538 193‒3 544 684	6 491
Sobic.008G037900 Sobic.003G363600 Sobic.009G155050	SbTGA4.8g SbLG2 SbTGA5	08 03 09	3 557 720‒3 568 195 68 107 428‒68 115 976 51 158 262‒51 167 491	10 476 8 549 9 128
Sobic.006G233500	SbTGA6.6g	06	57 541 249‒57 549 389	8 140
Sobic.007G061100 Sobic.002G153100	SbTGA6.7g SbTGA7	07 02	6 413 340‒ 6 427 344 45 762 133‒45 770 211	14 005 8 078
Sobic.010G192366	SbTGA8	10	53 452 812‒53 453 964	1 152
Sobic.004G078800	SbTGA9	04	6 496 341‒6 505 629	9 288
Sobic.001G243800	SbTGA10	01	25 331 187‒25 332 625	1 438

基因编号 Gene ID	基因名称 Gene name	染色体 Chromosome	基因位置 Genome location （bp）	基因长度 Length （bp）
Sobic.003G329500	SbTGA1.3g	03	65 465 408‒65 471 285	5 877
Sobic.009G180700 Sobic.002G247300 Sobic.002G424000	SbTGA1.9g SbTGA2.1a SbTGA2.1b	09 02 02	53 491 550‒53 494 415 63 528 681‒63 539 526 77 105 916‒77 111 030	3 266 10 846 5 114
Sobic.001G390800	SbTGA2.2	01	67 724 716‒67 732 814	8 098
Sobic.003G081000	SbTGA2.3	03	6 962 855‒6 973 141	10 286
Sobic.010G110100	SbTGA3	10	11 004 657‒11 007 712	3 055
Sobic.005G038700	SbTGA4.5g	05	3 538 193‒3 544 684	6 491
Sobic.008G037900 Sobic.003G363600 Sobic.009G155050	SbTGA4.8g SbLG2 SbTGA5	08 03 09	3 557 720‒3 568 195 68 107 428‒68 115 976 51 158 262‒51 167 491	10 476 8 549 9 128
Sobic.006G233500	SbTGA6.6g	06	57 541 249‒57 549 389	8 140
Sobic.007G061100 Sobic.002G153100	SbTGA6.7g SbTGA7	07 02	6 413 340‒ 6 427 344 45 762 133‒45 770 211	14 005 8 078
Sobic.010G192366	SbTGA8	10	53 452 812‒53 453 964	1 152
Sobic.004G078800	SbTGA9	04	6 496 341‒6 505 629	9 288
Sobic.001G243800	SbTGA10	01	25 331 187‒25 332 625	1 438

蛋白 Protein	氨基酸数目 Number of amino acids	分子量 Molecular weigh （Da）	等电点 Theoretical pI	不稳定系数 Instability index	脂溶系数 Aliphatic index	亲水性均值 Average hydrophilicity	亚细胞定位 Subcellular localization
SbTGA1.3g	468	51 130.35	6.39	55.59	77.50	-0.498	细胞核Nucleus
SbTGA1.9g	332	36 982.68	6.43	58.95	84.22	-0.519	细胞核Nucleus
SbTGA2.1a	500	55 731.81	6.91	68.96	75.00	-0.561	细胞核Nucleus
SbTGA2.1b	333	37 184.12	8.90	55.31	85.11	-0.515	细胞核Nucleus
SbTGA2.2	335	37 433.39	8.92	54.43	81.67	-0.532	细胞核Nucleus
SbTGA2.3	330	36 580.06	7.88	57.45	79.64	-0.583	细胞核Nucleus
SbTGA3	462	50 093.64	6.34	53.46	81.60	-0.110	细胞核Nucleus
SbTGA4.5g	488	53 416.73	6.13	53.23	72.38	-0.458	细胞核Nucleus
SbTGA4.8g	483	52 724.80	6.15	46.42	71.28	-0.480	细胞核Nucleus
SbLG2	533	57 914.08	6.26	53.50	75.65	-0.379	细胞核Nucleus
SbTGA5	520	56 977.68	5.83	64.27	72.60	-0.456	细胞核Nucleus
SbTGA6.6g	408	45 366.65	6.29	49.07	78.09	-0.375	细胞核Nucleus
SbTGA6.7g	516	56 764.99	9.05	49.25	86.18	-0.150	细胞核Nucleus
SbTGA7	409	45 255.64	8.46	59.10	84.01	-0.361	细胞核Nucleus
SbTGA8	158	17 172.66	5.93	52.20	89.11	-0.055	细胞核Nucleus
SbTGA9	487	52 197.54	8.55	56.19	70.99	-0.456	细胞核Nucleus
SbTGA10	311	34 461.24	8.80	50.33	88.30	-0.341	细胞核Nucleus

蛋白 Protein	氨基酸数目 Number of amino acids	分子量 Molecular weigh （Da）	等电点 Theoretical pI	不稳定系数 Instability index	脂溶系数 Aliphatic index	亲水性均值 Average hydrophilicity	亚细胞定位 Subcellular localization
SbTGA1.3g	468	51 130.35	6.39	55.59	77.50	-0.498	细胞核Nucleus
SbTGA1.9g	332	36 982.68	6.43	58.95	84.22	-0.519	细胞核Nucleus
SbTGA2.1a	500	55 731.81	6.91	68.96	75.00	-0.561	细胞核Nucleus
SbTGA2.1b	333	37 184.12	8.90	55.31	85.11	-0.515	细胞核Nucleus
SbTGA2.2	335	37 433.39	8.92	54.43	81.67	-0.532	细胞核Nucleus
SbTGA2.3	330	36 580.06	7.88	57.45	79.64	-0.583	细胞核Nucleus
SbTGA3	462	50 093.64	6.34	53.46	81.60	-0.110	细胞核Nucleus
SbTGA4.5g	488	53 416.73	6.13	53.23	72.38	-0.458	细胞核Nucleus
SbTGA4.8g	483	52 724.80	6.15	46.42	71.28	-0.480	细胞核Nucleus
SbLG2	533	57 914.08	6.26	53.50	75.65	-0.379	细胞核Nucleus
SbTGA5	520	56 977.68	5.83	64.27	72.60	-0.456	细胞核Nucleus
SbTGA6.6g	408	45 366.65	6.29	49.07	78.09	-0.375	细胞核Nucleus
SbTGA6.7g	516	56 764.99	9.05	49.25	86.18	-0.150	细胞核Nucleus
SbTGA7	409	45 255.64	8.46	59.10	84.01	-0.361	细胞核Nucleus
SbTGA8	158	17 172.66	5.93	52.20	89.11	-0.055	细胞核Nucleus
SbTGA9	487	52 197.54	8.55	56.19	70.99	-0.456	细胞核Nucleus
SbTGA10	311	34 461.24	8.80	50.33	88.30	-0.341	细胞核Nucleus

基因 Gene	非同义突变率 Ka	同义突变率 Ks	Ka/Ks
SbTGA1.3g	0.026 806	0.110 230	0.143 179
SbTGA1.9g	0.031 715	0.119 848	0.164 627
SbTGA2.1a	0.013 625	0.122 884	0.110 880
SbTGA2.1b	0.022 205	0.125 714	0.098 377
SbTGA2.2	0.010 432	0.115 926	0.089 984
SbTGA2.3	0.005 987	0.165 411	0.036 197
SbTGA3	0.046 521	0.140 532	0.331 034
SbTGA4.5g	0.018 687	0.193 302	0.096 673
SbTGA4.8g	0.056 425	0.168 138	0.110 432
SbLG2	0.024 716	0.120 180	0.104 636
SbTGA5	0.026 103	0.303 343	0.086 050
SbTGA6.6g	0.042 216	0.169 735	0.148 720
SbTGA6.7g	0.055 926	0.198 823	0.181 286
SbTGA7	0.028 116	0.142 082	0.197 886
SbTGA8	0.051 141	0.111 611	0.458 203
SbTGA9	0.070 751	0.182 973	0.386 674
SbTGA10	0.081 083	0.104 734	0.396 043