Identification of the NF-YC Genes in Hordeum vulgare and Expression Analysis Under Salt Stress

doi:10.11983/CBB22177

Abstract

Abstract: Nuclear factor-Y (NF-Y) is a ubiquitous transcription factor in eukaryotes, which consists of three subunits, NF-YA, NF-YB and NF-YC. NF-Y is widely involved in the regulation of plant growth and development and responses to abiotic stress. In this study, we comprehensively analyzed the NF-YC gene family in barley using bioinformatics methods. First, 11 HvNF-YC members were identified based on the barley genome database, and they are distributed on 6 chromosomes of barley except the second chromosome with 0-5 introns. Phylogenetic analysis showed that the NF-YC family members of barley, Arabidopsis and rice could be divided into five groups. Gene replication analysis showed that six HvNF-YC genes had fragment duplication, and three HvNF-YC genes had tandem duplication. Analysis of cis-acting elements in promoter revealed that most HvNF-YC contained cis-acting elements related to abiotic stress and hormone responses. Analysis of the expression patterns of HvNF-YC members in different tissues at different stages showed that there were significant differences in the spatial and temporal expression of different members, among which HvNF-YC9 and 11 may play important roles in the early stage of grain development. By analyzing the changes of HvNF-YC expression in roots and leaves in salt-tolerant and salt-sensitive barley varieties, and HvNF-YC3, HvNF-YC6 and HvNF-YC10 genes were pivotal in the early stage of salt stress response; while HvNF-YC9 gene played essential roles in the late stage of long-term salt treatment. Therefore, we speculated that HvNF-YC9, 10, and 11 genes could be used as candidates to further explore the mechanism of NF-YC functions in salt tolerance, which will lay the foundation for further analysis of the function of HvNF-YC in barley salt tolerance.

Key words: NF-YC, gene family analysis, barley, salt stress, gene expression

Feifei Wang, Zhenxiang Zhou, Yi Hong, Yangyang Gu, Chao Lü, Baojian Guo, Juan Zhu, Rugen Xu. Identification of the NF-YC Genes in Hordeum vulgare and Expression Analysis Under Salt Stress[J]. Chinese Bulletin of Botany, 2023, 58(1): 140-149.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB22177

https://www.chinbullbotany.com/EN/Y2023/V58/I1/140

Figures/Tables 9

Table 1 Sequence information of HvNF-YCs gene family

Gene name	Gene ID	Chromo- some	Location	Amino acid length (aa)	Protein molecular weight (kDa)	pI	Instability index	Aliphatic index	Subcellular location
HvNF-YC1	HORVU.MOREX.- r3.1HG0069390.1	1	447067437- 447072149	282	31.44	5.4	48.23	75.07	Nucleus
HvNF-YC2	HORVU.MOREX.- r3.1HG0081770.1	1	489164568- 489164978	136	14.07	9.5	38.39	79.78	Nucleus
HvNF-YC3	HORVU.MOREX.- r3.3HG0237950.1	3	54989815- 54991052	371	39.09	4.74	52.22	66.66	Nucleus
HvNF-YC4	HORVU.MOREX.- r3.4HG0364520.1	4	231786893- 231791804	255	28.09	5.93	59.67	65.76	Nucleus
HvNF-YC5	HORVU.MOREX.- r3.4HG0391570.1	4	499791697- 499793529	241	25.63	5.32	60.13	66.18	Nucleus
HvNF-YC6	HORVU.MOREX.- r3.5HG0489580.1	5	474074907- 474075856	203	21.78	5.39	59.79	72.91	Nucleus
HvNF-YC7	HORVU.MOREX.- r3.6HG0571700.1	6	135835186- 135838701	260	28.59	4.87	81.41	71.81	Nucleus
HvNF-YC8	HORVU.MOREX.- r3.7HG0677850.1	7	160202157- 160203122	199	21.57	5.52	65.36	71.86	Nucleus
HvNF-YC9	HORVU.MOREX.- r3.7HG0737530.1	7	597862664- 597863461	265	29.76	4.79	69.77	63.06	Nucleus
HvNF-YC10	HORVU.MOREX.- r3.7HG0737680.1	7	598086832- 598087587	251	27.85	6.22	68.44	73.19	Nucleus
HvNF-YC11	HORVU.MOREX.- r3.7HG0737720.1	7	598116971- 598117753	260	28.62	4.66	80.61	68.81	Nucleus

Figure 1 Cluster analysis (A), conserved motif (B) and gene structure (C) of HvNF-YC family members CDS: Coding sequence; UTR: Untranslated region

Figure 2 Sequence alignment of NF-YC family members in Hordeum vulgare

Figure 3 Phylogenetic analysis of NF-YC family in Arabidopsis thaliana, Oryza sativa, and Hordeum vulgare

Figure 4 Distribution of NF-YC gene family members on chromosomes in Hordeum vulgare

Figure 5 Analysis of duplicated NF-YC gene pairs in Hordeum vulgare

Figure 6 Statistics analysis of cis-acting elements of NF-YC gene family in Hordeum vulgare

Figure 7 Cis-acting elements analysis of NF-YC gene family in Hordeum vulgare

Figure 8 Tissue expression profile of NF-YC gene family members in Hordeum vulgare (A) and HvNF-YC expressions in the leaf and root of NN and TX varieties under salt stress (B) ROO1: Roots from seedlings (10 cm shoot stage); LEA: Shoots from seedlings (10 cm shoot stage); INF1: Young developing inflorescences (5 mm); INF2: Developing inflorescences (1-1.5 cm); NOD: Developing tillers (3rd internode); CAR5: Developing grain (5 days after pollination (DAP)); CAR15: Developing grain (15 DAP); ET1: Etiolated seedling (dark condition,10 days); LEM: Inflorescences (lemma, 42 DAP); LOD: Inflorescences (lodicule, 42 DAP); EPI: Epidermal strips (28 DAP); RAC: Inflorescences (rachis, 35 DAP); ROO2: Roots (28 DAP); SEN: Senescing leaves (56 DAP)

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