Genome-wide Characterization of bZIP Transcription Factors in Foxtail Millet and Their Expression Profiles in Response to Drought and Salt Stresses

doi:10.11983/CBB15148

Abstract

Abstract: The bZIP protein family is one of the largest and most conserved transcription factor families regulating multiple physiology processes in plants. Foxtail millet (Setaria italica) is an important C4 cereal crop with increased resistance to drought stress. However, little is known about bZIP family members and their functions in this crop. In the present study, we identified and characterized 73 SibZIP transcription factors in foxtail millet genome by using bioinformatics. These SibZIPs are classified into 9 groups, including A, B, C, D, E, G, H, I and X subfamilies. Compared to the sequenced cereal crops, the foxtail millet bZIP family underwent contraction in evolution. In all, 25 conserved motifs were detected among SibZIPs. RNA-seq and qPCR analysis revealed that a number of SibZIPs are induced to change expression levels in response to drought and salt stresses, which suggests that they have important functions in the foxtail millet response to stress. Moreover, correlation analysis of co-expression of the protein coding genes under various stress conditions demonstrates that a set of 19 SibZIPs may mediate the regulation network controlling stress responses by cooperating with some protein kinases or NPR1-related regulatory protein in foxtail millet. Our results could provide new valuable information for comprehensively understanding SibZIP protein structure and their biological functions, the molecular mechanism of drought response, and stress resistance breeding in foxtail millet and related crops.

Baoling Liu, Li Zhang, Yan Sun,Jinai Xue, Changyong Gao, Lixia Yuan, Jiping Wang, Xiaoyun Jia, Runzhi Li. Genome-wide Characterization of bZIP Transcription Factors in Foxtail Millet and Their Expression Profiles in Response to Drought and Salt Stresses[J]. Chinese Bulletin of Botany, 2016, 51(4): 473-487.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB15148

https://www.chinbullbotany.com/EN/Y2016/V51/I4/473

Figures/Tables 6

References 36

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Gene name	Forward primer (5'-3')	Reverse primer (5'-3')
18S rRNA	CCACAGATTGAAAACCGCATTA	ACCTCCCACCAGCAGAACC
SibZIP2	ATGGGACAGATGGCGATGG	AAGAGCACGCAGCCGAGA
SibZIP3	ATGAGCTGCATTGGCAACG	CTCCTTGAGATGGTTCAGTTCG
SibZIP7	GCCGTCCGACCACAACAG	CCTCTTGACACGCTTGGGA
SibZIP8	CCCCAACAATCTCAGGGAAGG	GAGCGTGTTGTTCTCGTTCTGG
SibZIP21	CCAGTCCTCCTCCTGCTCC	CTCCATCACCAGGTCCTTCTCC
SibZIP24	ACGAGAAGGCCGAGCTGG	TGGTGCTGGTGGTGTTGTTG
SibZIP37	TACGCCCGATGGTTAGAAGA	ATCGATCAGCCGTCGTTG
SibZIP45	GTAGCCCGAGCCCTGACA	AGCTCGCGGTCGAAGGTC
SibZIP51	AATCCCTCGGCTAAAA	ACCCACAAAGCATCACAAGG
SibZIP57	GGCATCAGCACAGCCAGT	CCTGTCCTGTCGCTACCTTCA
SibZIP60	CTCCAAACCCAGCATTCCA	GCTCATCCTCTGCCATCACC
SibZIP73	AGCGTGGGCAGGGTAAATG	CAGGAGCACCCCAGTAATCTAC

Gene name	Forward primer (5'-3')	Reverse primer (5'-3')
18S rRNA	CCACAGATTGAAAACCGCATTA	ACCTCCCACCAGCAGAACC
SibZIP2	ATGGGACAGATGGCGATGG	AAGAGCACGCAGCCGAGA
SibZIP3	ATGAGCTGCATTGGCAACG	CTCCTTGAGATGGTTCAGTTCG
SibZIP7	GCCGTCCGACCACAACAG	CCTCTTGACACGCTTGGGA
SibZIP8	CCCCAACAATCTCAGGGAAGG	GAGCGTGTTGTTCTCGTTCTGG
SibZIP21	CCAGTCCTCCTCCTGCTCC	CTCCATCACCAGGTCCTTCTCC
SibZIP24	ACGAGAAGGCCGAGCTGG	TGGTGCTGGTGGTGTTGTTG
SibZIP37	TACGCCCGATGGTTAGAAGA	ATCGATCAGCCGTCGTTG
SibZIP45	GTAGCCCGAGCCCTGACA	AGCTCGCGGTCGAAGGTC
SibZIP51	AATCCCTCGGCTAAAA	ACCCACAAAGCATCACAAGG
SibZIP57	GGCATCAGCACAGCCAGT	CCTGTCCTGTCGCTACCTTCA
SibZIP60	CTCCAAACCCAGCATTCCA	GCTCATCCTCTGCCATCACC
SibZIP73	AGCGTGGGCAGGGTAAATG	CAGGAGCACCCCAGTAATCTAC

Gene name	Phytozome identifier	Chromosome location (bp)	Protein length (aa)	Theore- tical pI	Molecular weight (Da)	Phylogeny group	NCBI accession No.
SibZIP1	Si000955m	Chr.5: 42034648-42041849	538	6	58030.2	D	XP_004970651
SibZIP2	Si001292m	Chr.5: 39537137-39542647	473	6	51362.5	D	XP_004970302
SibZIP3	Si001731m	Chr.5: 42027056-42028626	399	6	42138.5	A	XP_004970655
SibZIP4	Si001929m	Chr.5: 31392517-31397217	368	9	39273.7	G	XP_004969366
SibZIP5	Si002173m	Chr.5: 39683613-39687077	333	9	36026.4	A	XP_004970325
SibZIP6	Si002192m	Chr.5: 3576665-3581966	330	7	36678.2	D	XP_004967673
SibZIP7	Si002311m	Chr.5: 13207621-13209504	314	6	34130.9	E	XP_004968609
SibZIP8	Si002989m	Chr.5: 10278963-10280748	196	10	20861.9	H	XP_004968380
SibZIP9	Si003247m	Chr.5: 42311957-42314982	147	10	16539.8	A	XP_002458823
SibZIP10	Si003289m	Chr.5: 246101970-24611764	140	9	15506.5	C	XP_004968894
SibZIP11	Si006417m	Chr.4: 33420130-33425120	449	9	48149.5	D	XP_004965885
SibZIP12	Si006667m	Chr.4: 11743965-11745864	379	8	41521.2	D	XP_004966886
SibZIP13	Si006889m	Chr.4: 6541497-4646365	325	9	35254.3	A	XP_004964902
SibZIP14	Si006978m	Chr.4: 33015635-33017728	303	5	32514.6	B	XP_004965858
SibZIP15	Si007043m	Chr.4: 30527846-30530681	285	6	30388.8	C	XP_004965642
SibZIP16	Si007412m	Chr.4: 39706531-39709069	157	9	17268.5	A	XP_004966480
SibZIP17	Si007892m	Chr.4: 12607851-12608351	167	9	18839.9	C	XP_004965226
SibZIP18	Si010177m	Chr.7: 31096934-31105294	427	7	47577	D	XP_004976974
SibZIP19	Si010440m	Chr.7: 32666098-32669917	359	9	39895	E	XP_004977157
SibZIP20	Si010549m	Chr.7: 33666577-33670528	335	6	36005.8	I	XP_004977320
SibZIP21	Si012481m	Chr.7: 34001430-34002276	185	9	19986.3	X	XP_004978331
SibZIP22	Si013904m	Chr.6: 30497939-30500723	390	6	41467.1	A	XP_004973666
SibZIP23	Si013962m	Chr.6: 3422261-3424756	367	7	40266.7	D	XP_004972733
SibZIP24	Si014433m	Chr.6: 31421965-31422818	219	9	23535.9	C	XP_004973757
SibZIP25	Si014523m	Chr.6: 21075712-21078072	175	9	19443.7	C	XP_004973271
SibZIP26	Si014546m	Chr.6: 35057931-35059283	169	9	18500.6	A	XP_004974151
SibZIP27	Si014861m	Chr.6: 34473052-34479032	553	8	60827.5	D	XP_004978700
SibZIP28	Si017618m	Chr.1: 39059405-39061854	357	6	38234.6	A	XP_004954028
SibZIP29	Si017637m	Chr.1: 8783667-8786862	354	5	37572.7	G	XP_004952026
SibZIP30	Si017778m	Chr.1: 6341933-6345399	325	6	34446.2	C	XP_004951739
SibZIP31	Si018161m	Chr.1: 1679857-1681771	252	6	26940.2	E	XP_004951321
SibZIP32	Si018524m	Chr.1: 4311195-4313806	167	10	18441.4	H	XP_004951525
SibZIP33	Si019099m	Chr.1: 5311182-5311658	158	6	18128.3	C	XP_008645357
SibZIP34	Si019656m	Chr.1: 8856565-8857280	101	12	11586.4	C	XP_006362088
SibZIP35	Si019897m	Chr.1: 36896832-36897341	169	8	19639.9	C	XP_004953778
SibZIP36	Si021442m	Chr.3: 20717700-20721220	645	9	68096.2	B	XP_004962093
SibZIP37	Si022106m	Chr.3: 18527822-18531435	431	6	48135.2	D	XP_004961926
SibZIP38	Si022325m	Chr.3: 5860297-5865473	384	7	40757.5	G	XP_004960729
SibZIP39	Si022331m	Chr.3: 48207088-48212169	383	6	41545.1	C	XP_004963102
SibZIP40	Si022388m	Chr.3: 9871788-9876447	373	9	39693.2	G	XP_004961173
SibZIP41	Si022626m	Chr.3: 14850120-14852158	331	8	36509.2	D	XP_004961656
SibZIP42	Si022639m	Chr.3: 15026867-15029429	328	5	35423.8	A	XP_004961686
SibZIP43	Si023448m	Chr.3: 19115835-19117133	170	9	18373.5	A	XP_004961973
SibZIP44	Si023541m	Chr.3: 42857978-42859308	149	7	16621.5	C	XP_004962768
SibZIP45	Si023562m	Chr.3: 3146171-3147458	145	9	15989	C	XP_004960384
SibZIP46	Si024325m	Chr.3: 50281135-50281679	175	11	19023.7	C	XP_004964234
Gene name	Phytozome identifier	Chromosome location (bp)	Protein length (aa)	Theore- tical pI	Molecular weight (Da)	Phylogeny group	NCBI accession No.
SibZIP47	Si026421m	Chr.8: 2241219-2245356	418	6	45444.7	D	XP_004978700
SibZIP48	Si026452m	Chr.8: 2350696-2353211	403	7	42267.1	X	XP_004978712
SibZIP49	Si026561m	Chr.8: 12073275-12076909	357	9	39171.5	E	XP_004979095
SibZIP50	Si026605m	Chr.8: 3317921-3321817	336	7	35850.7	I	XP_004978752
SibZIP51	Si029351m	Chr.2: 46950969-46953724	571	6	60447.1	B	XP_004958502
SibZIP52	Si029606m	Chr.2: 35632657-35640776	497	7	55157.1	D	XP_004957190
SibZIP53	Si029966m	Chr.2: 24028261-24036295	417	8	46056.5	D	XP_004956460
SibZIP54	Si029970m	Chr.2: 4745736-4748783	416	5	45187.2	C	XP_004955660
SibZIP55	Si030114m	Chr.2: 33169494-33171523	390	9	41890.8	A	XP_004957010
SibZIP56	Si030123m	Chr.2: 7037626-7041762	389	7	39918.8	G	XP_004955801
SibZIP57	Si030182m	Chr.2: 37345091-37349203	378	6	40638.3	I	XP_004957354
SibZIP58	Si030224m	Chr.2: 48343483-48348262	371	6	39761.6	I	XP_004958698
SibZIP59	Si031077m	Chr.2: 38684243-38685591	216	9	22457.3	A	XP_004957504
SibZIP60	Si031238m	Chr.2: 34573960-34574626	181	7	20285.7	C	XP_004957101
SibZIP61	Si031353m	Chr.2: 25296856-25298971	159	9	17806.8	C	XP_004956521
SibZIP62	Si032429m	Chr.2: 1879467-1880494	315	10	33579.7	C	XP_004958923
SibZIP63	Si032507m	Chr.2: 37624846-37627738	482	10	50744.7	I	XP_002460540
SibZIP64	Si035062m	Chr.9: 3209713-3215709	541	5	56605	C	XP_004981429
SibZIP65	Si035841m	Chr.9: 57321111-57323641	423	6	45305.5	I	XP_004985885
SibZIP66	Si036380m	Chr.9: 47061608-47065486	353	6	38129.3	I	XP_004984459
SibZIP67	Si036527m	Chr.9: 47985071-47991293	335	9	37389.2	D	XP_004984573
SibZIP68	Si038381m	Chr.9: 47741259-47744465	70	10	8263.2	A	XP_004987020
SibZIP69	Si039367m	Chr.9: 2420394-2422861	344	6	36158.7	G	XP_004981331
SibZIP70	Si039558m	Chr.9: 9034726-9035118	131	12	14050	C	XP_004986317
SibZIP71	Si039566m	Chr.9: 40545110-40547482	375	8	40649.5	I	XP_004983840
SibZIP72	Si039895m	Chr.9: 48442410-48442913	167	10	18179	C	XP_004987029
SibZIP73	Si040286m	Chr.9: 51600068-51604903	381	9	40899.1	G	XP_004985055

Gene name	Phytozome identifier	Chromosome location (bp)	Protein length (aa)	Theore- tical pI	Molecular weight (Da)	Phylogeny group	NCBI accession No.
SibZIP1	Si000955m	Chr.5: 42034648-42041849	538	6	58030.2	D	XP_004970651
SibZIP2	Si001292m	Chr.5: 39537137-39542647	473	6	51362.5	D	XP_004970302
SibZIP3	Si001731m	Chr.5: 42027056-42028626	399	6	42138.5	A	XP_004970655
SibZIP4	Si001929m	Chr.5: 31392517-31397217	368	9	39273.7	G	XP_004969366
SibZIP5	Si002173m	Chr.5: 39683613-39687077	333	9	36026.4	A	XP_004970325
SibZIP6	Si002192m	Chr.5: 3576665-3581966	330	7	36678.2	D	XP_004967673
SibZIP7	Si002311m	Chr.5: 13207621-13209504	314	6	34130.9	E	XP_004968609
SibZIP8	Si002989m	Chr.5: 10278963-10280748	196	10	20861.9	H	XP_004968380
SibZIP9	Si003247m	Chr.5: 42311957-42314982	147	10	16539.8	A	XP_002458823
SibZIP10	Si003289m	Chr.5: 246101970-24611764	140	9	15506.5	C	XP_004968894
SibZIP11	Si006417m	Chr.4: 33420130-33425120	449	9	48149.5	D	XP_004965885
SibZIP12	Si006667m	Chr.4: 11743965-11745864	379	8	41521.2	D	XP_004966886
SibZIP13	Si006889m	Chr.4: 6541497-4646365	325	9	35254.3	A	XP_004964902
SibZIP14	Si006978m	Chr.4: 33015635-33017728	303	5	32514.6	B	XP_004965858
SibZIP15	Si007043m	Chr.4: 30527846-30530681	285	6	30388.8	C	XP_004965642
SibZIP16	Si007412m	Chr.4: 39706531-39709069	157	9	17268.5	A	XP_004966480
SibZIP17	Si007892m	Chr.4: 12607851-12608351	167	9	18839.9	C	XP_004965226
SibZIP18	Si010177m	Chr.7: 31096934-31105294	427	7	47577	D	XP_004976974
SibZIP19	Si010440m	Chr.7: 32666098-32669917	359	9	39895	E	XP_004977157
SibZIP20	Si010549m	Chr.7: 33666577-33670528	335	6	36005.8	I	XP_004977320
SibZIP21	Si012481m	Chr.7: 34001430-34002276	185	9	19986.3	X	XP_004978331
SibZIP22	Si013904m	Chr.6: 30497939-30500723	390	6	41467.1	A	XP_004973666
SibZIP23	Si013962m	Chr.6: 3422261-3424756	367	7	40266.7	D	XP_004972733
SibZIP24	Si014433m	Chr.6: 31421965-31422818	219	9	23535.9	C	XP_004973757
SibZIP25	Si014523m	Chr.6: 21075712-21078072	175	9	19443.7	C	XP_004973271
SibZIP26	Si014546m	Chr.6: 35057931-35059283	169	9	18500.6	A	XP_004974151
SibZIP27	Si014861m	Chr.6: 34473052-34479032	553	8	60827.5	D	XP_004978700
SibZIP28	Si017618m	Chr.1: 39059405-39061854	357	6	38234.6	A	XP_004954028
SibZIP29	Si017637m	Chr.1: 8783667-8786862	354	5	37572.7	G	XP_004952026
SibZIP30	Si017778m	Chr.1: 6341933-6345399	325	6	34446.2	C	XP_004951739
SibZIP31	Si018161m	Chr.1: 1679857-1681771	252	6	26940.2	E	XP_004951321
SibZIP32	Si018524m	Chr.1: 4311195-4313806	167	10	18441.4	H	XP_004951525
SibZIP33	Si019099m	Chr.1: 5311182-5311658	158	6	18128.3	C	XP_008645357
SibZIP34	Si019656m	Chr.1: 8856565-8857280	101	12	11586.4	C	XP_006362088
SibZIP35	Si019897m	Chr.1: 36896832-36897341	169	8	19639.9	C	XP_004953778
SibZIP36	Si021442m	Chr.3: 20717700-20721220	645	9	68096.2	B	XP_004962093
SibZIP37	Si022106m	Chr.3: 18527822-18531435	431	6	48135.2	D	XP_004961926
SibZIP38	Si022325m	Chr.3: 5860297-5865473	384	7	40757.5	G	XP_004960729
SibZIP39	Si022331m	Chr.3: 48207088-48212169	383	6	41545.1	C	XP_004963102
SibZIP40	Si022388m	Chr.3: 9871788-9876447	373	9	39693.2	G	XP_004961173
SibZIP41	Si022626m	Chr.3: 14850120-14852158	331	8	36509.2	D	XP_004961656
SibZIP42	Si022639m	Chr.3: 15026867-15029429	328	5	35423.8	A	XP_004961686
SibZIP43	Si023448m	Chr.3: 19115835-19117133	170	9	18373.5	A	XP_004961973
SibZIP44	Si023541m	Chr.3: 42857978-42859308	149	7	16621.5	C	XP_004962768
SibZIP45	Si023562m	Chr.3: 3146171-3147458	145	9	15989	C	XP_004960384
SibZIP46	Si024325m	Chr.3: 50281135-50281679	175	11	19023.7	C	XP_004964234
Gene name	Phytozome identifier	Chromosome location (bp)	Protein length (aa)	Theore- tical pI	Molecular weight (Da)	Phylogeny group	NCBI accession No.
SibZIP47	Si026421m	Chr.8: 2241219-2245356	418	6	45444.7	D	XP_004978700
SibZIP48	Si026452m	Chr.8: 2350696-2353211	403	7	42267.1	X	XP_004978712
SibZIP49	Si026561m	Chr.8: 12073275-12076909	357	9	39171.5	E	XP_004979095
SibZIP50	Si026605m	Chr.8: 3317921-3321817	336	7	35850.7	I	XP_004978752
SibZIP51	Si029351m	Chr.2: 46950969-46953724	571	6	60447.1	B	XP_004958502
SibZIP52	Si029606m	Chr.2: 35632657-35640776	497	7	55157.1	D	XP_004957190
SibZIP53	Si029966m	Chr.2: 24028261-24036295	417	8	46056.5	D	XP_004956460
SibZIP54	Si029970m	Chr.2: 4745736-4748783	416	5	45187.2	C	XP_004955660
SibZIP55	Si030114m	Chr.2: 33169494-33171523	390	9	41890.8	A	XP_004957010
SibZIP56	Si030123m	Chr.2: 7037626-7041762	389	7	39918.8	G	XP_004955801
SibZIP57	Si030182m	Chr.2: 37345091-37349203	378	6	40638.3	I	XP_004957354
SibZIP58	Si030224m	Chr.2: 48343483-48348262	371	6	39761.6	I	XP_004958698
SibZIP59	Si031077m	Chr.2: 38684243-38685591	216	9	22457.3	A	XP_004957504
SibZIP60	Si031238m	Chr.2: 34573960-34574626	181	7	20285.7	C	XP_004957101
SibZIP61	Si031353m	Chr.2: 25296856-25298971	159	9	17806.8	C	XP_004956521
SibZIP62	Si032429m	Chr.2: 1879467-1880494	315	10	33579.7	C	XP_004958923
SibZIP63	Si032507m	Chr.2: 37624846-37627738	482	10	50744.7	I	XP_002460540
SibZIP64	Si035062m	Chr.9: 3209713-3215709	541	5	56605	C	XP_004981429
SibZIP65	Si035841m	Chr.9: 57321111-57323641	423	6	45305.5	I	XP_004985885
SibZIP66	Si036380m	Chr.9: 47061608-47065486	353	6	38129.3	I	XP_004984459
SibZIP67	Si036527m	Chr.9: 47985071-47991293	335	9	37389.2	D	XP_004984573
SibZIP68	Si038381m	Chr.9: 47741259-47744465	70	10	8263.2	A	XP_004987020
SibZIP69	Si039367m	Chr.9: 2420394-2422861	344	6	36158.7	G	XP_004981331
SibZIP70	Si039558m	Chr.9: 9034726-9035118	131	12	14050	C	XP_004986317
SibZIP71	Si039566m	Chr.9: 40545110-40547482	375	8	40649.5	I	XP_004983840
SibZIP72	Si039895m	Chr.9: 48442410-48442913	167	10	18179	C	XP_004987029
SibZIP73	Si040286m	Chr.9: 51600068-51604903	381	9	40899.1	G	XP_004985055