Genome-Wide Identification and Characterization of the HAK Gene Family in Quinoa (Chenopodium quinoa Willd.) and Their Expression Profiles under Saline and Alkaline Conditions

Abstract

The high-affinity K⁺ transporter (HAK) family, the most prominent potassium transporter family in plants, which involves K⁺ transport, plays crucial roles in plant responses to abiotic stresses. However, the HAK gene family remains to be characterized in quinoa (Chenopodium quinoa Willd.). We explored HAKs in quinoa, identifying 30 members (CqHAK1-CqHAK30) in four clusters phylogenetically. Uneven distribution was observed across 18 chromosomes. Furthermore, we investigated the proteins' evolutionary relationships, physicochemical properties, conserved domains and motifs, gene structure, and cis-regulatory elements of the CqHAKs family members. Transcription data analysis showed that CqHAKs have diverse expression patterns among different tissues and in response to abiotic stresses, including drought, heat, low phosphorus, and salt. The expressional changes of CqHAKs in roots were more sensitive in response to abiotic stress than that in shoot apices. Quantitative RT-PCR analysis revealed that under high saline condition, CqHAK1, CqHAK13, CqHAK19, and CqHAK20 were dramatically induced in leaves; under alkaline condition, CqHAK1, CqHAK13, CqHAK19, and CqHAK20 were dramatically induced in leaves, and CqHAK6, CqHAK9, CqHAK13, CqHAK23, and CqHAK29 were significantly induced in roots. Our results establish a foundation for further investigation of the functions of HAKs in quinoa. It is the first study to identify the HAK gene family in quinoa, which provides potential targets for further functional study and contributes to improving the salt and alkali tolerance in quinoa.

Keywords: HAK gene family; alkali stress; expression profile; quinoa; salt stress.

Figure 1

Phylogenetic analysis of the HAK families in quinoa, Arabidopsis thaliana, Beta vulgaris and Oryza sativa. The phylogenetic tree was constructed using the IQ tree. Four clusters (I, II, III, IV) were labeled as red, blue, green and yellow respectively.

Figure 2

Phylogenetic relationships, gene structure, and motifs of the HAK genes in C. quinoa using TBtools. (A) The ML method constructed the phylogenetic tree based on the full-length sequences of the CqHAK proteins. (B) The motif and domain composition of the CqHAK proteins. The conserved domains and motifs were indicated on the protein sequences’ upper and lower sides, respectively. (C) Exon–intron structures of the CqHAK genes. Blue–green boxes indicate untranslated 5′- and 3′- regions, yellow boxes indicate exons, and black lines indicate introns.

Figure 3

Chromosome distributions of the HAK genes in C. quinoa using TBtools. (A) The chromosomal location and interchromosomal relationship of the HAK genes in C. quinoa. (B) Synteny analysis of the HAK genes between C. quinoa and A. thaliana, and C. quinoa and B. vulgaris. Gray lines in the background indicate the collinear blocks, and the red lines highlight the syntenic HAK gene pairs.

Figure 4

Putative cis-acting elements and transcription factor binding sites in the promoter regions of the HAK genes in C. quinoa (A), and four functional types of cis-acting elements and their proportion in all the CqHAKs genes (B).

Figure 5

Heatmap of HAK gene expression in different tissues (A) and treatments in the quinoa roots and shoots (B). CK represented as blank control group, where quinoa was grown in soil without any treatment.

Figure 6

Expression profiling of the CqHAK genes under salt (300 mM NaCl) and alkali (40 mM Na₂CO₃ and NaHCO₃ mixture, with mole ratio = 1:2, pH = 9.38) stresses, respectively, in the quinoa roots (A) and leaves (B) at the seedling stage. The expression levels of CqTUB-9 was used to normalize the expression levels of the CqHAK genes. CK represent the treatment of quinoa seedlings with 1/2 Hogland nutrient solution. The data are the mean ± SEM of three independent biological samples, and the vertical bar represents the standard error of the mean. Lowercase letters indicated the significant difference at p  <  0.05.