Genome-Wide Identification of the VQ Gene Family and Their Responses to Heat Stress in Pea

doi:10.16420/j.issn.0513-353x.2025-0629

Acta Horticulturae Sinica ›› 2026, Vol. 53 ›› Issue (9): 2639-2656.doi: 10.16420/j.issn.0513-353x.2025-0629

• Genetic & Breeding · Germplasm Resources · Molecular Biology • Previous Articles Next Articles

Genome-Wide Identification of the VQ Gene Family and Their Responses to Heat Stress in Pea

LI Chengxun¹^,², XU Xiaoyu¹^,², LI Aiping¹^,²^,^*()

¹ Crop Research Institute， Fujian Academy of Agricultural Sciences
² Fujian Engineering Research Center for Characteristic Dry Crop Varieties Breeding， Fuzhou 350013， China

Received:2026-05-11 Revised:2026-07-28 Online:2026-09-25 Published:2026-09-20
Contact: LI Aiping

Abstract

Abstract:

The VQ gene family plays significant roles in plant growth，development，and stress response. In this study，members of the VQ gene family in pea（Pisum sativum）were identified through bioinformatics approaches，and their physicochemical properties，evolutionary relationships，gene structures，promoter elements，and synteny were analyzed. The expression patterns were analyzed by combining RNA-seq and qRT-PCR，and gene functions were verified through Arabidopsis genetic transformation. A total of 28 pea VQ genes were identified in this study，with subcellular localization mainly in the nucleus，and phylogenetically classified into three subfamilies. The VQ gene structure was predominantly single-exon，and the promoters were enriched with various cis-acting elements involved in light response，hormone response，stress response，and growth and development regulation. Four intraspecific syntenic gene pairs were identified in the pea VQ gene family，with 18，15，19，36，and 76 syntenic gene pairs detected between pea and the other five species，respectively，indicating a relatively conserved evolutionary pattern. Expression analysis revealed that pea VQ genes exhibited tissue-specific expression patterns，and certain members responded to high temperature stress. Functional verification demonstrated that，overexpression of PsVQ15 in Arabidopsis resulted in significantly longer roots，while both PsVQ15- and PsVQ26-overexpressing lines significantly elevated survival rates and total chlorophyll content under heat stress；the PsVQ26-overexpressing line exhibited the highest survival，superior phenotype，and thus stronger thermotolerance. In conclusion，the VQ gene family in pea plays a crucial role in plant growth，development，and heat response.

Key words: pea, VQ gene family, genome-wide identification, bioinformatics analysis, expression pattern, functional verification, heat stress response

CLC Number:

S643.3

LI Chengxun, XU Xiaoyu, LI Aiping. Genome-Wide Identification of the VQ Gene Family and Their Responses to Heat Stress in Pea[J]. Acta Horticulturae Sinica, 2026, 53(9): 2639-2656.

Figures/Tables 14

Table 1 Primers sequences used in this study

用途Purpose	引物名称Primer name	正向引物序列（5′-3′）Forward sequence	反向引物序列（5′-3′）Reverse sequence
基因的qPCR验证 Gene validation by qPCR	Actin-qPCR	CACAATTGGCGCTGAAAGAT	TAATTGAGTTAAATGTCGTCTCATGGAT
	PsVQ1-qPCR	GTGTCATCCACACTACGCCT	TCTCCCACCATCTCACTCGT
	PsVQ15-qPCR	GCTTTCCCGGGTTTGGTAGA	CAAAGGGGAAAACCCGGAGA
	PsVQ26-qPCR	TCCTGCGGAACCTTAACACC	TGATGAGAGGTTGTCGGTGC
	PsVQ28-qPCR	TCGTCTAACCCAAGCCCAAC	AACATCGTGGGTGTTTCCGA
基因克隆 Gene cloning	PsVQ15	GGGGTACCATGGATAAAGGCTCTGCA	TTCCGCGGCCGCTATGGCCGACGTCGACTCAAATTTCTCTCCACCG
基因克隆 Gene cloning	PsVQ26	GGGGTACCATGAACCTACCGGAATTT	TTCCGCGGCCGCTATGGCCGACGTCGACTTAGTCGAATATACTAAACAGATC
过表达载体验证 Validation of overexpression constructs	PsVQ15-1305a.1	GGGGGACATGGGTACCATGGATAA	TGCCTGCAGGTCGACTCAAAT
过表达载体验证 Validation of overexpression constructs	PsVQ26-1305a.1	CGGGGGACATGGGTACCATG	GCCTGCAGGTCGACTTAGTCGA

Fig. 1 Chromosomal localization and phylogenetic analysis of the VQ gene family in pea A：Distribution of the VQ gene family on pea chromosomes；B：Phylogenetic tree of VQ genes from pea（Ps）and Arabidopsis（At）

Fig. 2 Gene structures of the VQ family and conserved motif composition of VQ proteins in pea

Table 2 Conserved motif information of VQ proteins in pea

基序 Motif	序列 Sequence	氨基酸数目 Number of amino acids	Pfam注释 Pfam annotation
Motif1	PTVVHTDASNFRAVVQKLTGS	21	VQ
Motif2	EEEEKAIKEKGFYLHPSPR	19	-
Motif3	MGCDENDFMVVAVPPLVDSDEQVVEPGGECSYEGFDEDVLLIPQMVENIW	50	-
Motif4	KPHPFRYDKQKHNINGPPPTPLMIRKPNSSHKQQRQPIIIY	41	-
Motif5	QHEGDETTSTTSSVEKEGVNSNINDDEQSPNNMMKFAEMPLFTPTSCDFF	50	-
Motif6	TNVTKSIKKRSRASKRAP	18	-
Motif7	GFKLYERRNSLK	12	-
Motif8	EILSPSILDFPSLVLSPVTPLIPDPFDR	28	-
Motif9	NLSGFDEAACENGDDGRNSFFISDLLLKECDLLHRELQPNNHFFF	45	-
Motif10	HQHHHQQQQQH	11	-

Fig. 3 cis-Acting element analysis of the promoters of the pea VQ gene family

Fig. 4 Intraspecific syntenic relationships of the VQ gene family in pea

Table 3 Ka/Ks values and divergence time of intraspecific syntenic PsVQ gene pairs in pea

重复类型 Duplication type	重复基因1 Duplicated gene 1	重复基因2 Duplicated gene 2	Ka	Ks	Ka/Ks	分化时间/MYA Divergence time
片段重复 Segmental	PsVQ7	PsVQ21	0.30	2.87	0.10	95.52
	PsVQ1	PsVQ23	0.67	-	-	-
	PsVQ7	PsVQ27	0.25	0.90	0.28	29.92
	PsVQ16	PsVQ26	0.54	1.52	0.36	50.75

Fig. 5 Syntenic analysis of VQ genes between pea and five other plant species

Fig. 6 Evolutionary analysis of VQ genes between pea and five other plant species A：Distribution of Ks values across the syntenic VQ gene pairs；B：Ks values of the syntenic VQ gene pairs；C：Ka values of the syntenic VQ gene pairs；D：Ka/Ks values of the syntenic VQ gene pairs Ps：Pisum sativum；At：Arabidopsis thaliana；Ca：Cicer arietinum；Cc：Cajanus cajan：Pv：Phaseolus vulgaris；Gm：Glycine max

Fig. 7 Expression heatmap of the VQ gene family in different tissues/organs of pea

Fig. 8 Expression heatmap of the VQ gene family in pea under heat stress CK1：PR11-90 control；HS1：PR11-90 under heat stress；CK2：PR11-2 control；HS2：PR11-2 under heat stress

Fig. 9 Validation of 4 differentially expressed genes by qRT-PCR and RNA-Seq Different lowercase letters indicate the significant difference at P < 0.05 level（n = 3）. The same below

Fig. 10 Electrophoresis detection of overexpression vector construction and Arabidopsis genetic transformation for PsVQ15 and PsVQ26 A：PCR products of PsVQ15 and PsVQ26 gene；B：Bacterial PCR identification of recombinant plasmids transformed into E.coli DH5α；C：Bacterial PCR identification of recombinant plasmids transformed into Agrobacterium tumefaciens GV3101；D：PCR identification of T2 generation transgenic Arabidopsis plants. M：DL2000 marker；WT：Wild type

Fig. 11 Phenotypic analysis of Arabidopsis overexpressing PsVQ15 and PsVQ26 under heat stress A：Growth performance of Arabidopsis seedlings under different treatments；B：Expression levels of PsVQ15 and PsVQ26 in the overexpressing plants；C：Survival rate，total chlorophyll content and root lengths of Arabidopsis seedlings under different treatments. WT：Wild type

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Genome-Wide Identification of the VQ Gene Family and Their Responses to Heat Stress in Pea

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