Differentially expressed genes and related pathways in root systems of Astragalus cicer under NaCl stress

doi:10.11686/cyxb2024185

Abstract

Abstract:

Soil salinization seriously affects the growth and yield of plants， and limits the development of agricultural and ecological economies. Astragalus cicer is a versatile ecological grass species， an efficient green manure crop， and a superior protein forage. Exploring the molecular mechanism of its adaptability to NaCl stress is of great significance for enhancing its salt tolerance and advancing its cultivation in saline soil. To investigate its responses to NaCl stress， transcriptomic analyses were performed on the roots of A. cicer at different time points （0， 12， 48， and 72 hours） during an NaCl treatment. The results showed that， compared with 0 hour， after 12， 48， and 72 hours of NaCl stress， there were， respectively， 46051， 45653， and 42869 differentially expressed genes （DEGs） in the roots of A. cicer， including 8027， 10053， and 11042 up-regulated DEGs and 38024， 35600， and 31827 down-regulated DEGs， respectively， at the three time points. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses showed that the pathways responding to NaCl stress in the roots of A. cicer were oxidoreductase activity， flavonoid biosynthesis， and phenylpropanoid biosynthesis. A trend analysis showed that the DEGs in phenylpropanoid biosynthesis and flavonoid biosynthesis pathway were still up-regulated or had returned to their baseline levels at 48 hours of NaCl treatment. Genes encoding C2H2， C3H， NAC， MYB， WRKY， and bZIP transcription factors were expressed at different time points during the NaCl treatment， suggesting that these transcription factors are closely related to salt tolerance in A. cicer. The results of this study provide basic data for further exploration of the mechanism of salt tolerance of A. cicer， and also provide theoretical support for breeding to improve salt tolerance.

Key words: Astragalus cicer, roots, transcriptome, NaCl stress, differentially expressed genes, metabolic pathway

Ting MA, Fen-qi CHEN, Yong WANG, Xue HA, Ya-jun LI, Hui-ling MA. Differentially expressed genes and related pathways in root systems of Astragalus cicer under NaCl stress[J]. Acta Prataculturae Sinica, 2025, 34(4): 104-123.

Figures/Tables 15

References 47

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名称Name	描述Description	上游引物Forward primer	下游引物Reverse primer
CHI	查尔酮异构酶Chalcone isomerase	TGCACCACCGAGGAAATAGG	GGGTATGGCAGCAACAATGG
CHR1	查尔酮还原酶1 Chalcone reductase 1	AGCTCTTGGGAACAAACGTG	AGCTAGCAGGGGACCAAATG
F3'H	类黄酮3'-羟化酶Flavonoid 3'-hydroxylase	CGTCCAGCACCAAAGGGTAT	GCCATAGCTCGTGACCCAAA
CHS	查尔酮合成酶Chalcone synthase	CCAGGTGGTCCTGCAATTCT	GAGGACACAAGCACTCGACA
CHS1A-like	查尔酮合成酶1A-like Chalcone synthase 1A-like	TGTCACACATGCGTCTGAACT	CCTGCCACTGTCTTGGCAAT
CYP450	细胞色素P450 Cytochrome P450	ACGCATTTTGCGCCAATGAT	TGGCCACCCAAGTTCTACAC
C4H	反肉桂酸4单加氧酶Trans-cinnamate 4-monooxygenase	TGCGCACACACACAAAAGAG	CTCCACATGAGGGACCAACC
PYL	脱落酸感受器Abscisic acid receptor	TGATGATGAACGCCACGTCA	TCCATGCGGAACATCAACCA
bZIP	bZIP转录因子bZIP transcription factor	TATGGTCCTAGTTTGGCGGC	ACAACACCAGCTCTCACCAA
Actin	肌动蛋白Actin	TGTTCCCTGGCATTGCTGAT	CTTTCTCTCGGGTGGTGCAA

名称Name	描述Description	上游引物Forward primer	下游引物Reverse primer
CHI	查尔酮异构酶Chalcone isomerase	TGCACCACCGAGGAAATAGG	GGGTATGGCAGCAACAATGG
CHR1	查尔酮还原酶1 Chalcone reductase 1	AGCTCTTGGGAACAAACGTG	AGCTAGCAGGGGACCAAATG
F3'H	类黄酮3'-羟化酶Flavonoid 3'-hydroxylase	CGTCCAGCACCAAAGGGTAT	GCCATAGCTCGTGACCCAAA
CHS	查尔酮合成酶Chalcone synthase	CCAGGTGGTCCTGCAATTCT	GAGGACACAAGCACTCGACA
CHS1A-like	查尔酮合成酶1A-like Chalcone synthase 1A-like	TGTCACACATGCGTCTGAACT	CCTGCCACTGTCTTGGCAAT
CYP450	细胞色素P450 Cytochrome P450	ACGCATTTTGCGCCAATGAT	TGGCCACCCAAGTTCTACAC
C4H	反肉桂酸4单加氧酶Trans-cinnamate 4-monooxygenase	TGCGCACACACACAAAAGAG	CTCCACATGAGGGACCAACC
PYL	脱落酸感受器Abscisic acid receptor	TGATGATGAACGCCACGTCA	TCCATGCGGAACATCAACCA
bZIP	bZIP转录因子bZIP transcription factor	TATGGTCCTAGTTTGGCGGC	ACAACACCAGCTCTCACCAA
Actin	肌动蛋白Actin	TGTTCCCTGGCATTGCTGAT	CTTTCTCTCGGGTGGTGCAA

样本 Sample	原始读数 Raw reads	原始数据量 Raw bases （Gb）	干净读数 Clean reads	干净数据量 Clean bases （Gb）	Q30 （%）	GC （%）	总对比率 Total mapped （%）
r_0_1	25608576	7.68	24842810	7.45	95.58	42.49	70.68
r_0_2	22654911	6.80	22160067	6.65	95.77	42.37	71.75
r_0_3	23401444	7.02	22736208	6.82	95.45	42.27	70.54
r_12_1	24325553	7.30	23233562	6.97	95.25	42.27	69.73
r_12_2	23471096	7.04	22839301	6.85	95.95	40.19	65.84
r_12_3	21972596	6.59	21124167	6.34	95.28	42.35	70.40
r_48_1	22903659	6.87	21974443	6.59	95.51	41.66	69.90
r_48_2	23716748	7.12	22832712	6.85	95.50	41.74	70.40
r_48_3	23380813	7.01	22673020	6.80	95.88	41.64	70.86
r_72_1	23445027	7.03	22237254	6.67	95.73	41.95	70.89
r_72_2	23476556	7.04	22400966	6.72	95.93	41.81	71.57
r_72_3	27057092	8.12	26181124	7.85	94.97	41.80	67.48

样本 Sample	原始读数 Raw reads	原始数据量 Raw bases （Gb）	干净读数 Clean reads	干净数据量 Clean bases （Gb）	Q30 （%）	GC （%）	总对比率 Total mapped （%）
r_0_1	25608576	7.68	24842810	7.45	95.58	42.49	70.68
r_0_2	22654911	6.80	22160067	6.65	95.77	42.37	71.75
r_0_3	23401444	7.02	22736208	6.82	95.45	42.27	70.54
r_12_1	24325553	7.30	23233562	6.97	95.25	42.27	69.73
r_12_2	23471096	7.04	22839301	6.85	95.95	40.19	65.84
r_12_3	21972596	6.59	21124167	6.34	95.28	42.35	70.40
r_48_1	22903659	6.87	21974443	6.59	95.51	41.66	69.90
r_48_2	23716748	7.12	22832712	6.85	95.50	41.74	70.40
r_48_3	23380813	7.01	22673020	6.80	95.88	41.64	70.86
r_72_1	23445027	7.03	22237254	6.67	95.73	41.95	70.89
r_72_2	23476556	7.04	22400966	6.72	95.93	41.81	71.57
r_72_3	27057092	8.12	26181124	7.85	94.97	41.80	67.48

项目Item	r_12 vs r_0	r_48 vs r_0	r_72 vs r_0	r_48 vs r_12	r_72 vs r_12	r_72 vs r_48
上调 Up-regulated	8027	10053	11042	11821	7633	4653
下调 Down-regulated	38024	35600	31827	5515	3768	4345
总数 Total	46051	45653	42869	17336	11401	8998