Genome-wide identification of the GLK gene family in alfalfa and their transcript profiles under osmotic stress

doi:10.11686/cyxb2024133

Abstract

Abstract:

GLK （Golden2-like or G2-like） transcription factors belong to the GARP superfamily， whose members play crucial roles in plant growth and development. Members of the GLK gene family play important roles in regulating plant chloroplast development， chlorophyll biosynthesis， and the abiotic stress response. The GLK gene family has been systematically identified in many plant species， but not yet in tetraploid alfalfa （Medicago sativa）. In this study， we used bioinformatics methods to identify 100 GLK genes （MsGLKs） in the genome of the alfalfa cultivar “Xinjiang Daye”. Further analyses were conducted to explore the physicochemical properties of their putative encoded products， chromosome localization， phylogenetic relationships， cis-acting elements in their promoter regions， and transcript profiles under osmotic stress and exogenous abscisic acid （ABA） treatment. The results showed that the 100 MsGLK genes were unevenly distributed on the 32 chromosomes， and encoded polypeptides with sequence lengths ranging from 201 to 860 amino acids. In a phylogenetic analysis， the MsGLK family members were divided into 13 groups. A collinearity analysis detected 193 MsGLK gene duplicates in the alfalfa genome， and a analysis of the ratio of the number of nonsynonymous substitutions per nonsynonymous site to the number of synonymous substitutions per synonymous site （Ka/Ks） revealed that most of the duplicated gene pairs have undergone purification selection. A range of cis-acting elements were detected in MsGLK gene promoter regions， and were involved in plant growth and development， hormone responses， and stress responses. Analyses of gene transcript profiles revealed that 12 MsGLKs showed tissue-specific expression patterns， and 25 MsGLKs were expressed in all tissues. Further RT-qPCR analyses revealed that some MsGLK genes were activated to some degree in response to drought stress， salt stress， and exogenous ABA treatment. The results of this study provide reference information for further research on the function of MsGLK genes and for the genetic improvement of stress resistance in alfalfa.

Key words: alfalfa, GLK gene, bioinformatics, osmotic stress, expression patterns

Chao MA, Xi-jing SUN, Ya-lan FENG, Shuang ZHOU, Ji-hao JU, Yi WU, Tian-ning WANG, Bin-bin GUO, Jun ZHANG. Genome-wide identification of the GLK gene family in alfalfa and their transcript profiles under osmotic stress[J]. Acta Prataculturae Sinica, 2025, 34(1): 174-190.

Figures/Tables 10

References 56

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基因Gene	正向引物Forward primer （5′-3′）	反向引物Reverse primer （5′-3′）
MsGLK10	CAGATGAAGTCGGATGAGCCT	GGTGGTGCGGTAAGTTGGTC
MsGLK17	TACCACAGCAAGGGAAGCAG	GAATGGAACGGCGATGAACT
MsGLK29	GCAAGTGGAGGCAGAGAAGC	GGGTGGGATGGTTTGAGGA
MsGLK33	AAACCTGCCTCTTTACCGATTC	GTTGCTCTTTCTTGCCCTCC
MsGLK36	GCAAGTGGAGGCAGAGAAGC	GGGTGGGATGGTTTGAGGA
MsGLK62	CATCACTCATCCCTTTCACCTC	CCTGCCAATCATTTCGCTT
MsGLK65	AACACTTCCGCTGTCCCAT	TCTCATTGCCGTCGTCATTT
MsGLK75	CTTCATCACTCATCCCTTTCACC	GCAGGCACCGCTCTCTACTT
MsGLK83	ATATCCAGGGTCATAGTATTTTCCA	CGTTGTTTTCAGTTCTTCCTCTTG
MsActin	ACTGGAATGGTGAAGGCTGG	TGACAATACCGTGCTCAATGG

基因Gene	正向引物Forward primer （5′-3′）	反向引物Reverse primer （5′-3′）
MsGLK10	CAGATGAAGTCGGATGAGCCT	GGTGGTGCGGTAAGTTGGTC
MsGLK17	TACCACAGCAAGGGAAGCAG	GAATGGAACGGCGATGAACT
MsGLK29	GCAAGTGGAGGCAGAGAAGC	GGGTGGGATGGTTTGAGGA
MsGLK33	AAACCTGCCTCTTTACCGATTC	GTTGCTCTTTCTTGCCCTCC
MsGLK36	GCAAGTGGAGGCAGAGAAGC	GGGTGGGATGGTTTGAGGA
MsGLK62	CATCACTCATCCCTTTCACCTC	CCTGCCAATCATTTCGCTT
MsGLK65	AACACTTCCGCTGTCCCAT	TCTCATTGCCGTCGTCATTT
MsGLK75	CTTCATCACTCATCCCTTTCACC	GCAGGCACCGCTCTCTACTT
MsGLK83	ATATCCAGGGTCATAGTATTTTCCA	CGTTGTTTTCAGTTCTTCCTCTTG
MsActin	ACTGGAATGGTGAAGGCTGG	TGACAATACCGTGCTCAATGG

基因名 Gene name	基因登录号 Gene ID	PL （aa）	Mw （kDa）	pI	Sl	基因名 Gene name	基因登录号 Gene ID	PL （aa）	Mw （kDa）	pI	Sl
MsGLK1	MS.gene005086.t1	388	43.19	4.73	Nuc	MsGLK51	MS.gene76602.t1	352	39.86	5.75	Nuc
MsGLK2	MS.gene005866.t1	378	42.16	7.72	Nuc	MsGLK52	MS.gene55246.t1	352	40.14	5.54	Nuc
MsGLK3	MS.gene041038.t1	281	32.18	8.66	Nuc	MsGLK53	MS.gene028039.t1	277	31.24	6.03	Nuc
MsGLK4	MS.gene37289.t1	231	26.06	8.63	Nuc	MsGLK54	MS.gene045645.t1	353	40.08	5.75	Nuc
MsGLK5	MS.gene60590.t1	379	42.20	7.18	Nuc	MsGLK55	MS.gene070117.t1	277	31.32	5.82	Nuc
MsGLK6	MS.gene43963.t1	388	43.13	4.76	Nuc	MsGLK56	MS.gene032930.t1	352	39.83	5.75	Nuc
MsGLK7	MS.gene001686.t1	378	42.16	7.73	Nuc	MsGLK57	MS.gene87987.t1	393	44.55	6.20	Nuc
MsGLK8	MS.gene070698.t1	437	48.03	6.98	Nuc	MsGLK58	MS.gene85671.t1	308	34.34	9.37	Nuc
MsGLK9	MS.gene026358.t1	201	23.51	8.81	Nuc	MsGLK59	MS.gene68923.t1	393	44.48	6.16	Nuc
MsGLK10	MS.gene036427.t1	388	43.13	4.76	Nuc	MsGLK60	MS.gene042587.t1	393	44.45	6.07	Nuc
MsGLK11	MS.gene21397.t1	297	33.01	6.43	Nuc	MsGLK61	MS.gene66964.t1	393	44.48	6.16	Nuc
MsGLK12	MS.gene60862.t1	378	42.15	7.72	Nuc	MsGLK62	MS.gene018653.t1	489	53.80	5.42	Nuc
MsGLK13	MS.gene055776.t1	423	46.76	5.86	Nuc	MsGLK63	MS.gene017974.t1	359	40.43	6.92	Nuc
MsGLK14	MS.gene35408.t1	373	41.81	7.74	Nuc	MsGLK64	MS.gene017688.t1	301	32.94	6.56	Nuc
MsGLK15	MS.gene35289.t1	257	28.82	8.91	Nuc	MsGLK65	MS.gene013905.t1	281	30.65	5.79	Nuc
MsGLK16	MS.gene62480.t1	365	40.90	8.66	Cyt	MsGLK66	MS.gene99484.t1	350	39.92	5.48	Nuc
MsGLK17	MS.gene003164.t1	860	94.37	8.47	Chl	MsGLK67	MS.gene84188.t1	238	26.82	9.64	Nuc
MsGLK18	MS.gene003165.t1	330	36.16	6.19	Nuc	MsGLK68	MS.gene035191.t1	489	53.78	5.42	Nuc
MsGLK19	MS.gene043457.t1	423	46.73	5.86	Nuc	MsGLK69	MS.gene52648.t1	351	39.53	6.70	Nuc
MsGLK20	MS.gene84326.t1	373	41.81	7.74	Nuc	MsGLK70	MS.gene013966.t1	301	32.84	6.56	Nuc
MsGLK21	MS.gene073152.t1	313	35.17	6.98	Nuc	MsGLK71	MS.gene068055.t1	283	30.79	5.94	Nuc
MsGLK22	MS.gene066206.t1	375	41.71	8.37	Nuc	MsGLK72	MS.gene069022.t1	350	39.82	5.48	Nuc
MsGLK23	MS.gene01976.t1	331	36.21	6.23	Nuc	MsGLK73	MS.gene77355.t1	256	28.91	9.60	Nuc
MsGLK24	MS.gene01975.t1	382	41.62	8.62	Chl	MsGLK74	MS.gene024551.t1	439	48.79	5.11	Nuc
MsGLK25	MS.gene028866.t1	423	46.73	5.86	Nuc	MsGLK75	MS.gene23439.t1	489	53.78	5.42	Nuc
MsGLK26	MS.gene034456.t1	373	41.83	7.25	Nuc	MsGLK76	MS.gene04612.t1	359	40.43	6.92	Nuc
MsGLK27	MS.gene040544.t1	581	63.91	5.80	Nuc	MsGLK77	MS.gene58831.t1	298	32.76	6.56	Nuc
MsGLK28	MS.gene045711.t1	375	41.72	8.37	Nuc	MsGLK78	MS.gene77413.t1	350	39.94	5.56	Nuc
MsGLK29	MS.gene048293.t1	314	34.41	6.60	Nuc	MsGLK79	MS.gene94669.t1	256	28.93	9.78	Nuc
MsGLK30	MS.gene048294.t1	330	36.16	6.19	Nuc	MsGLK80	MS.gene050550.t1	439	48.79	5.11	Nuc
MsGLK31	MS.gene31432.t1	423	46.69	5.86	Nuc	MsGLK81	MS.gene96951.t1	489	53.73	5.37	Nuc
MsGLK32	MS.gene43040.t1	373	41.79	7.25	Nuc	MsGLK82	MS.gene41865.t1	283	30.79	5.94	Nuc
MsGLK33	MS.gene94587.t1	315	35.25	7.30	Nuc	MsGLK83	MS.gene95656.t1	350	39.85	5.48	Nuc
MsGLK34	MS.gene038958.t1	375	41.74	8.37	Nuc	MsGLK84	MS.gene95601.t1	238	26.83	9.64	Nuc
MsGLK35	MS.gene02861.t1	330	36.17	6.24	Nuc	MsGLK85	MS.gene036866.t1	434	47.87	6.66	Nuc
MsGLK36	MS.gene02867.t1	314	34.42	6.60	Nuc	MsGLK86	MS.gene61025.t1	352	39.45	6.50	Nuc
MsGLK37	MS.gene002965.t1	238	26.64	8.87	Nuc	MsGLK87	MS.gene068940.t1	345	38.77	6.64	Nuc
MsGLK38	MS.gene008318.t1	461	50.91	7.22	Nuc	MsGLK88	MS.gene060554.t1	434	47.88	6.66	Nuc
MsGLK39	MS.gene019228.t1	383	42.69	7.20	Chl	MsGLK89	MS.gene42755.t1	345	38.77	6.64	Nuc
MsGLK40	MS.gene061558.t1	426	47.13	7.99	Nuc	MsGLK90	MS.gene36713.t1	221	25.38	9.67	Chl
MsGLK41	MS.gene057902.t1	394	43.82	9.10	Nuc	MsGLK91	MS.gene87427.t1	650	71.83	5.55	Nuc
MsGLK42	MS.gene049714.t1	424	46.87	7.99	Nuc	MsGLK92	MS.gene36099.t1	346	38.76	6.64	Nuc
MsGLK43	MS.gene05012.t1	425	47.00	7.99	Nuc	MsGLK93	MS.gene88392.t1	302	33.85	8.12	Cyt
MsGLK44	MS.gene26549.t1	420	47.03	8.17	Nuc	MsGLK94	MS.gene056957.t1	363	40.53	9.07	Nuc
MsGLK45	MS.gene006790.t1	340	37.99	5.97	Nuc	MsGLK95	MS.gene056956.t1	434	47.87	6.66	Nuc
MsGLK46	MS.gene031499.t1	340	38.06	5.97	Nuc	MsGLK96	MS.gene038713.t1	434	47.87	6.66	Nuc
MsGLK47	MS.gene96791.t1	340	37.99	5.97	Nuc	MsGLK97	MS.gene066880.t1	346	38.90	6.68	Nuc
MsGLK48	MS.gene56537.t1	339	37.89	5.97	Nuc	MsGLK98	MS.gene00817.t1	238	26.61	8.87	Nuc
MsGLK49	MS.gene54226.t1	387	43.44	7.27	Nuc	MsGLK99	MS.gene02381.t1	238	26.66	8.87	Nuc
MsGLK50	MS.gene72865.t1	277	31.26	5.95	Nuc	MsGLK100	MS.gene072393.t1	351	39.62	6.73	Nuc

基因名 Gene name	基因登录号 Gene ID	PL （aa）	Mw （kDa）	pI	Sl	基因名 Gene name	基因登录号 Gene ID	PL （aa）	Mw （kDa）	pI	Sl
MsGLK1	MS.gene005086.t1	388	43.19	4.73	Nuc	MsGLK51	MS.gene76602.t1	352	39.86	5.75	Nuc
MsGLK2	MS.gene005866.t1	378	42.16	7.72	Nuc	MsGLK52	MS.gene55246.t1	352	40.14	5.54	Nuc
MsGLK3	MS.gene041038.t1	281	32.18	8.66	Nuc	MsGLK53	MS.gene028039.t1	277	31.24	6.03	Nuc
MsGLK4	MS.gene37289.t1	231	26.06	8.63	Nuc	MsGLK54	MS.gene045645.t1	353	40.08	5.75	Nuc
MsGLK5	MS.gene60590.t1	379	42.20	7.18	Nuc	MsGLK55	MS.gene070117.t1	277	31.32	5.82	Nuc
MsGLK6	MS.gene43963.t1	388	43.13	4.76	Nuc	MsGLK56	MS.gene032930.t1	352	39.83	5.75	Nuc
MsGLK7	MS.gene001686.t1	378	42.16	7.73	Nuc	MsGLK57	MS.gene87987.t1	393	44.55	6.20	Nuc
MsGLK8	MS.gene070698.t1	437	48.03	6.98	Nuc	MsGLK58	MS.gene85671.t1	308	34.34	9.37	Nuc
MsGLK9	MS.gene026358.t1	201	23.51	8.81	Nuc	MsGLK59	MS.gene68923.t1	393	44.48	6.16	Nuc
MsGLK10	MS.gene036427.t1	388	43.13	4.76	Nuc	MsGLK60	MS.gene042587.t1	393	44.45	6.07	Nuc
MsGLK11	MS.gene21397.t1	297	33.01	6.43	Nuc	MsGLK61	MS.gene66964.t1	393	44.48	6.16	Nuc
MsGLK12	MS.gene60862.t1	378	42.15	7.72	Nuc	MsGLK62	MS.gene018653.t1	489	53.80	5.42	Nuc
MsGLK13	MS.gene055776.t1	423	46.76	5.86	Nuc	MsGLK63	MS.gene017974.t1	359	40.43	6.92	Nuc
MsGLK14	MS.gene35408.t1	373	41.81	7.74	Nuc	MsGLK64	MS.gene017688.t1	301	32.94	6.56	Nuc
MsGLK15	MS.gene35289.t1	257	28.82	8.91	Nuc	MsGLK65	MS.gene013905.t1	281	30.65	5.79	Nuc
MsGLK16	MS.gene62480.t1	365	40.90	8.66	Cyt	MsGLK66	MS.gene99484.t1	350	39.92	5.48	Nuc
MsGLK17	MS.gene003164.t1	860	94.37	8.47	Chl	MsGLK67	MS.gene84188.t1	238	26.82	9.64	Nuc
MsGLK18	MS.gene003165.t1	330	36.16	6.19	Nuc	MsGLK68	MS.gene035191.t1	489	53.78	5.42	Nuc
MsGLK19	MS.gene043457.t1	423	46.73	5.86	Nuc	MsGLK69	MS.gene52648.t1	351	39.53	6.70	Nuc
MsGLK20	MS.gene84326.t1	373	41.81	7.74	Nuc	MsGLK70	MS.gene013966.t1	301	32.84	6.56	Nuc
MsGLK21	MS.gene073152.t1	313	35.17	6.98	Nuc	MsGLK71	MS.gene068055.t1	283	30.79	5.94	Nuc
MsGLK22	MS.gene066206.t1	375	41.71	8.37	Nuc	MsGLK72	MS.gene069022.t1	350	39.82	5.48	Nuc
MsGLK23	MS.gene01976.t1	331	36.21	6.23	Nuc	MsGLK73	MS.gene77355.t1	256	28.91	9.60	Nuc
MsGLK24	MS.gene01975.t1	382	41.62	8.62	Chl	MsGLK74	MS.gene024551.t1	439	48.79	5.11	Nuc
MsGLK25	MS.gene028866.t1	423	46.73	5.86	Nuc	MsGLK75	MS.gene23439.t1	489	53.78	5.42	Nuc
MsGLK26	MS.gene034456.t1	373	41.83	7.25	Nuc	MsGLK76	MS.gene04612.t1	359	40.43	6.92	Nuc
MsGLK27	MS.gene040544.t1	581	63.91	5.80	Nuc	MsGLK77	MS.gene58831.t1	298	32.76	6.56	Nuc
MsGLK28	MS.gene045711.t1	375	41.72	8.37	Nuc	MsGLK78	MS.gene77413.t1	350	39.94	5.56	Nuc
MsGLK29	MS.gene048293.t1	314	34.41	6.60	Nuc	MsGLK79	MS.gene94669.t1	256	28.93	9.78	Nuc
MsGLK30	MS.gene048294.t1	330	36.16	6.19	Nuc	MsGLK80	MS.gene050550.t1	439	48.79	5.11	Nuc
MsGLK31	MS.gene31432.t1	423	46.69	5.86	Nuc	MsGLK81	MS.gene96951.t1	489	53.73	5.37	Nuc
MsGLK32	MS.gene43040.t1	373	41.79	7.25	Nuc	MsGLK82	MS.gene41865.t1	283	30.79	5.94	Nuc
MsGLK33	MS.gene94587.t1	315	35.25	7.30	Nuc	MsGLK83	MS.gene95656.t1	350	39.85	5.48	Nuc
MsGLK34	MS.gene038958.t1	375	41.74	8.37	Nuc	MsGLK84	MS.gene95601.t1	238	26.83	9.64	Nuc
MsGLK35	MS.gene02861.t1	330	36.17	6.24	Nuc	MsGLK85	MS.gene036866.t1	434	47.87	6.66	Nuc
MsGLK36	MS.gene02867.t1	314	34.42	6.60	Nuc	MsGLK86	MS.gene61025.t1	352	39.45	6.50	Nuc
MsGLK37	MS.gene002965.t1	238	26.64	8.87	Nuc	MsGLK87	MS.gene068940.t1	345	38.77	6.64	Nuc
MsGLK38	MS.gene008318.t1	461	50.91	7.22	Nuc	MsGLK88	MS.gene060554.t1	434	47.88	6.66	Nuc
MsGLK39	MS.gene019228.t1	383	42.69	7.20	Chl	MsGLK89	MS.gene42755.t1	345	38.77	6.64	Nuc
MsGLK40	MS.gene061558.t1	426	47.13	7.99	Nuc	MsGLK90	MS.gene36713.t1	221	25.38	9.67	Chl
MsGLK41	MS.gene057902.t1	394	43.82	9.10	Nuc	MsGLK91	MS.gene87427.t1	650	71.83	5.55	Nuc
MsGLK42	MS.gene049714.t1	424	46.87	7.99	Nuc	MsGLK92	MS.gene36099.t1	346	38.76	6.64	Nuc
MsGLK43	MS.gene05012.t1	425	47.00	7.99	Nuc	MsGLK93	MS.gene88392.t1	302	33.85	8.12	Cyt
MsGLK44	MS.gene26549.t1	420	47.03	8.17	Nuc	MsGLK94	MS.gene056957.t1	363	40.53	9.07	Nuc
MsGLK45	MS.gene006790.t1	340	37.99	5.97	Nuc	MsGLK95	MS.gene056956.t1	434	47.87	6.66	Nuc
MsGLK46	MS.gene031499.t1	340	38.06	5.97	Nuc	MsGLK96	MS.gene038713.t1	434	47.87	6.66	Nuc
MsGLK47	MS.gene96791.t1	340	37.99	5.97	Nuc	MsGLK97	MS.gene066880.t1	346	38.90	6.68	Nuc
MsGLK48	MS.gene56537.t1	339	37.89	5.97	Nuc	MsGLK98	MS.gene00817.t1	238	26.61	8.87	Nuc
MsGLK49	MS.gene54226.t1	387	43.44	7.27	Nuc	MsGLK99	MS.gene02381.t1	238	26.66	8.87	Nuc
MsGLK50	MS.gene72865.t1	277	31.26	5.95	Nuc	MsGLK100	MS.gene072393.t1	351	39.62	6.73	Nuc

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[2]	Zheng-yan LI, Zhi-ming XU, Yan LI, Yang LI. Effects of short-term continuous cropping of alfalfa on the growth and soil microenvironment of subsequent sorghum-sudan grass hybrid crops in the Jianghuai area [J]. Acta Prataculturae Sinica, 2024, 33(9): 155-168.
[3]	Xiao-tong WANG, Xiao-hong LI, Xu-xia MA, Wen-qi CAI, Xue-li FENG, Shu-xia LI. Identification and analysis of members of the FBA gene family in alfalfa [J]. Acta Prataculturae Sinica, 2024, 33(9): 81-93.
[4]	Ying-ying ZHANG, Dan-dan HU, Chun-hui MA, Qian-bing ZHANG. Leaf structure and photosynthetic properties of alfalfa in response to bacteria and phosphorus addition [J]. Acta Prataculturae Sinica, 2024, 33(8): 133-144.
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