谷子HAK/KUP/KT钾转运蛋白家族全基因组鉴定及其对低钾和高盐胁迫的响应

doi:10.3724/SP.J.1006.2023.24194

Abstract

Abstract:

KT/HAK/KUP (HAK) family is the most abundant potassium (K⁺) transporter family in plants, which plays important roles in plant growth and environmental adaptation. Foxtail millet (Setaria italic L. Beauv) is a model plant for studies on stress resistance mechanisms. However, the HAK family has not yet been well characterized in foxtail millet. In this study, 29 Setaria italic HAK genes (SiHAKs) were identified based on genome-wide sequence information, and the basic characteristics, protein structure, chromosome location, gene replication, expression pattern, and responses to stress were comprehensively analyzed. The results showed as followes: (1) SiHAKs were divided into five phylogenetic clusters (Cluster I-Cluster V), containing 11, 9, 3, 3 and 3 members, respectively. Gene structure and conserved motif analyses indicated that SiHAKs was high conserved, and the conservatisms were as follows: Cluster III = Cluster V > Cluster II > Cluster I > Cluster IV. (2) Tandem replication was the main contribution to the amplification of SiHAKs. 15 SiHAKs were located in tandem replication. (3) 171 transcription factors, including a large number of members of ERF, NAC, MYB and WRKY families, may bind to the promoter sequences of SiHAKs, which may confer SiHAKs diverse response mechanisms to abiotic stress. (4) SiHAKs were divided into three groups (Group I, Group II, and Group III) by gene expression Cluster Ing. The relative expression patterns of most SiHAKs were consistent in the two varieties (Zhanggu and Yugu 1). The relative expression levels of SiHAKs from the five clusters were generally as follows: Cluster III > Cluster V > Cluster II > Cluster I> Cluster IV. (5) Eleven SiHAKs with high expression levels in root were selected to detect the responses to low K⁺ and high salt stress. Under K⁺ deficiency treatment, eight SiHAKs were markedly upregulated in the expression levels, one SiHAK was significantly decreased, and two SiHAKs had no obvious changes. Under high salt stress, Three SiHAKs were significantly increased in the expression levels, two SiHAKs were significantly decreased, and the remaining six SiHAKs had no obvious changes. Remarkably, SiHAK15 had the strongest response to K⁺ deficiency and high salt stress, its expression level was 151 times and 22 times of the control, respectively. (6) The differences of gene expression profiles reflected the function differences among SiHAKs from different clusters. SiHAKs from Cluster I were mainly expressed in root, implying their important roles in K⁺ absorption in root. SiHAKs from Cluster II generally had no tissue-specific expression characteristics, and might be involved in many biological processes, such as K⁺ absorption and transport, plant growth and development. SiHAKs from Cluster III were upregulated by K⁺ deficiency and high salt stress, inferring their potential roles in maintaining K⁺/Na⁺ balance and resisting salt stress. SiHAKs from Cluster IV were almost undetectable in gene expression in the tested tissues. SiHAKs from Cluster V had different responses to K⁺ deficiency and high salt stresses. Some of them were upregulated in gene expression, while others were inhibited, thus indicating that the members from Cluster V were functionally differentiated. This results not only provide the foundation for further functional studies of SiHAKs, but also provide the valuable guidance for the study of K⁺ efficient utilization and salt tolerance mechanism in plants.

Key words: foxtail millet, potassium transporter, KT/HAK/KUP family, salt stress, the relative expression analysis

DAI Shu-Tao, ZHU Can-Can, MA Xiao-Qian, QIN Na, SONG Ying-Hui, WEI Xin, WANG Chun-Yi, LI Jun-Xia. Genome-wide identification of the HAK/KUP/KT potassium transporter family in foxtail millet and its response to K⁺ deficiency and high salt stress[J].Acta Agronomica Sinica, 2023, 49(8): 2105-2121.

Figures/Tables 10

Table S1

Table 1

Basic information of SiHAK genes and proteins in foxtail millet"

基因名称 Gene name	基因序列号 Gene ID	染色体位置 Chromosome position	基因组大小 Genome size (bp)	编码序列长度 Coding sequence length (bp)	氨基酸 Amino acid (aa)	分子量 Molecular weight (kD)	等电点 Isoelectric point (pI)	亚细胞定位 Subcellular location
SiHAK1	Seita.1G175000	Chr.1:25211256..25214882 forward	3627	2193	731	80.02	8.26	质膜 Plasma membrane
SiHAK2	Seita.1G307200	Chr.1:37040523..37045883 forward	5361	2322	774	86.24	7.85	质膜 Plasma membrane
SiHAK3	Seita.2G129100	Chr.2:14902256..14908174 reverse	5919	2364	788	88.61	8.49	质膜 Plasma membrane
SiHAK4	Seita.2G192700	Chr.2:28886553..28891290 reverse	4738	2568	856	94.46	7.47	质膜 Plasma membrane
SiHAK5	Seita.2G224400	Chr.2:32661560..32666230 forward	4671	2133	711	78.65	9.21	质膜 Plasma membrane
SiHAK6	Seita.2G327100	Chr.2:41466190..41473814 reverse	7625	2559	853	94.42	5.94	质膜 Plasma membrane
SiHAK7	Seita.2G427100	Chr.2:47923110..47928818 forward	5709	2352	784	87.76	8.86	质膜 Plasma membrane
SiHAK8	Seita.2G432200	Chr.2:48265283..48269697 reverse	4415	2364	788	87.21	7.61	质膜 Plasma membrane
SiHAK9	Seita.4G119700	Chr.4:12129620..12135065 reverse	5446	2331	777	85.78	8.25	质膜 Plasma membrane
SiHAK10	Seita.4G209800	Chr.4:32743375..32748151 forward	4777	2448	816	90.27	8.47	质膜 Plasma membrane
SiHAK11	Seita.4G266200	Chr.4:38390011..38398958 reverse	8948	2322	774	85.41	8.22	质膜 Plasma membrane
SiHAK12	Seita.5G168000	Chr.5:16861878..16864997 reverse	3120	2442	814	89.65	8.60	质膜 Plasma membrane
SiHAK13	Seita.5G439500	Chr.5:45554118..45559684 forward	5567	2325	775	86.47	8.52	质膜 Plasma membrane
SiHAK14	Seita.5G441200	Chr.5:45651197..45655632 reverse	4436	2205	735	80.50	8.50	质膜 Plasma membrane
SiHAK15	Seita.5G444100	Chr.5:45784733..45789729 forward	4997	2361	787	88.43	9.07	质膜 Plasma membrane
SiHAK16	Seita.6G027600	Chr.6:1995986..2001010 reverse	5025	2367	789	88.43	8.34	质膜 Plasma membrane
SiHAK17	Seita.6G205800	Chr.6:32522339..32526598 forward	4260	2220	740	82.47	8.84	质膜 Plasma membrane
SiHAK18	Seita.7G082300	Chr.7:18653291..18658866 forward	5576	2322	774	86.58	8.64	质膜 Plasma membrane
SiHAK19	Seita.7G082600	Chr.7:18675471..18680567 forward	5097	2373	791	88.54	8.82	质膜 Plasma membrane
SiHAK20	Seita.7G082700	Chr.7:18682739..18686823 forward	4085	2331	777	87.11	8.92	质膜 Plasma membrane
SiHAK21	Seita.7G082800	Chr.7:18693088..18697351 forward	4264	2286	762	85.03	6.99	质膜 Plasma membrane
SiHAK22	Seita.7G232600	Chr.7:29611687..29616556 reverse	4870	2550	850	94.73	6.15	质膜 Plasma membrane
SiHAK23	Seita.7G235500	Chr.7:29787315..29792347 reverse	5033	2412	804	89.58	8.34	质膜 Plasma membrane
SiHAK24	Seita.9G182300	Chr.9:12585631..12590025 forward	4395	2415	805	91.00	8.64	质膜 Plasma membrane
SiHAK25	Seita.9G182400	Chr.9:12603097..12608101 forward	5005	2433	811	91.93	9.02	质膜 Plasma membrane
SiHAK26	Seita.9G182500	Chr.9:12637593..12642369 forward	4777	2403	801	90.86	8.84	质膜 Plasma membrane
SiHAK27	Seita.9G182600	Chr.9:12646706..12651914 forward	5209	2415	805	90.42	8.82	质膜 Plasma membrane
SiHAK28	Seita.9G412000	Chr.9:46973981..46979758 reverse	5778	2415	805	89.58	6.82	质膜 Plasma membrane
SiHAK29	Seita.J004400	scaffold_11:162273..168095 reverse	5823	2682	894	98.77	8.68	质膜 Plasma membrane

Table 1

Fig. 1

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基因 Gene	引物名称 Primer name	序列 Sequence (5°-3°)
SiHAK2	SiHAK2-F	CGGCGTCCTCTCCTTCGTCT
SiHAK2	SiHAK2-R	CCCGTGGCCTTCTCTTCCTC
SiHAK3	SiHAK3-F	TCTTTATTCACTGCTTTGCCG
SiHAK3	SiHAK3-R	TTCTGAGTTGGTGCCCCTCTA
SiHAK4	SiHAK4-F	AAAAGTTAGCCTGCTTCCGAA
SiHAK4	SiHAK4-R	GCCGTCACCAATCACCATAGA
SiHAK6	SiHAK6-F	AGGTTTCTCTTTCGTCGGGTC
SiHAK6	SiHAK6-R	TTCAAATGCTTGGGGGTTCTC
SiHAK7	SiHAK7-F	ACGTGACCCTGACATAAGCAAA
SiHAK7	SiHAK7-R	TCAAGAGCCAGAGCACAACAAT
SiHAK10	SiHAK10-F	CACGGAGAGCAACGAGGAGA
SiHAK10	SiHAK10-R	GCAGAGGAGGGAGTAGAGCG
SiHAK15	SiHAK15-F	GAATCCCCAAATGTAAGCCG
SiHAK15	SiHAK15-R	CATGATGTATGCCACCCCAG
SiHAK16	SiHAK16-F	CTCTTGCACTGGGTTGTTTTCC
SiHAK16	SiHAK16-R	GCATTTCCTATCTGGCTTTGGT
SiHAK18	SiHAK18-F	ACCTTCGCTCCTGTCATCTCG
SiHAK18	SiHAK18-R	CCATCCTTCCCATTCCTTTTG
SiHAK23	SiHAK23-F	CCCCCACATCTTCTCCCACT
SiHAK23	SiHAK23-R	CTTGTACCCGTACCTCGCCA
SiHAK24	SiHAK24-F	GCATCCCACCCATATTCCCT
SiHAK24	SiHAK24-R	TACCCATACCGTGCCACACA
Si-actin-2	Si-actin-2-F	ATCCAGCCCCTTGTATGTGA
Si-actin-2	Si-actin-2-R	ACGCCCAACAATACTTGGAA

Genome-wide identification of the HAK/KUP/KT potassium transporter family in foxtail millet and its response to K⁺ deficiency and high salt stress

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Genome-wide identification of the HAK/KUP/KT potassium transporter family in foxtail millet and its response to K+ deficiency and high salt stress

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Genome-wide identification of the HAK/KUP/KT potassium transporter family in foxtail millet and its response to K⁺ deficiency and high salt stress