Genome-Wide Identification and Expression Analysis of 1-Aminocyclopropane-1-Carboxylate Synthase (ACS) Gene Family in Chenopodium quinoa

Abstract

Ethylene plays an important role in plant development and stress resistance. The rate-limiting enzyme in ethylene biosynthesis is 1-aminocyclopropane-1-carboxylic acid synthase (ACS). C. quinoa (Chenopodium quinoa) is an important food crop known for its strong tolerance to abiotic stresses. However, knowledge regarding the ACS gene family in C. quinoa remains restricted. In this study, we successfully identified 12 ACS genes (CqACSs) from the C. quinoa genome. Through thorough analysis of their sequences and phylogenetic relationships, it was verified that 8 out of these 12 CqACS isozymes exhibited substantial resemblance to ACS isozymes possessing ACS activity. Furthermore, these eight isozymes could be categorized into three distinct groups. The four remaining CqACS genes grouped under category IV displayed notable similarities with AtACS10 and AtACS12, known as amido transferases lacking ACS activity. The CqACS proteins bore resemblance to the AtACS proteins and had the characteristic structural features typically observed in plant ACS enzymes. Twelve CqACS genes were distributed across 8 out of the 18 chromosomes of C. quinoa. The CqACS genes were expanded from segment duplication. Many cis-regulatory elements related with various abiotic stresses, phytohormones, and light were found. The expression patterns of ACS genes varied across different tissues of C. quinoa. Furthermore, the analysis of gene expression patterns under abiotic stress showed that CqACS genes can be responsive to various stresses, implying their potential functions in adapting to various abiotic stresses. The findings from this research serve as a foundation for delving deeper into the functional roles of CqACS genes.

Keywords: ACS genes; C. quinoa; abiotic stress; ethylene; expression patterns.

Figure 1

Phylogeny relationship of the ACS proteins in C. quinoa and other species. The neighbor-joining phylogenetic tree was constructed based on a multiple sequences alignment of 38 ACS protein sequences from five species including Zea mays (ZmACS), Pyrus communis (PcACS), Chenopodium quinoa (CqACS), Oryza sativa (OsACS), and A. thaliana (AtACS), with 1000 bootstraps and model of a Poisson model.

Figure 2

Phylogenetic relationships, exon–intron structure, and conserved protein motifs of CqACSs. (A) A dendrogram illustrating the evolutionary relationships among CqACSs based on their sequences. According to phylogenetic relationships, 12 CqACSs were clustered into four groups (I–IV). (B) The arrangement of exons and introns in CqACSs is depicted, with UTR regions represented by green boxes, exons by violet boxes, and introns by black lines. (C) CqACSs showcase a diverse motif composition, with each unique motif represented by differently colored boxes.

Figure 3

Chromosomal distribution of CqACS genes. Moving from the outermost to the innermost circles, the first circle represents chromosome coordinates, while the second, third, and fourth circles illustrate the distribution of gene density; purple lines connect gene pairs.

Figure 4

Synteny analysis of ACS genes between C. quinoa and A. thaliana. The collinear blocks generated by the C. quinoa and A. thaliana genomes are represented by gray lines in the background, while syntenic ACS gene pairs are indicated with cyan blue lines.

Figure 5

Cis-elements in the promoters of CqACSs. Cis-elements possessing comparable functions are represented within identical blocks and color codes.

Figure 6

Expression patterns of CqACS genes in different tissues. The heatmap shows the expression levels of CqACS genes in nine tissues, including apical meristems, flowers and immature seeds, leaves petioles, stems, internode stems, seedling, inflorescences, leaves, and dry seeds.

Figure 7

Heatmap of CqACS genes expression in shoot and root tissues of quinoa under abiotic stress.

Figure 8

Expression analyses of CqACS genes under different abiotic stress conditions by qRT-PCR. Leaves and roots were collected from C. quinoa treated with 300 mM NaCl and 20% PEG 6000 stresses, respectively. R-N (root under the treatment of 300 mM NaCl); R-P (root under the treatment of 20% PEG 6000); L-N (leaves under the treatment of 300 mM NaCl); and L-P (leaves under the treatment of 20% PEG 6000). The CqTub gene was used as an internal control. The y-axis represents relative expression, calculated using the 2^−ΔΔCt formula. Student’s t-test: * p < 0.05; ** p < 0.01; and *** p < 0.001.