Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) under abiotic stress conditions

Abstract

Background The trihelix family of transcription factors plays essential roles in the growth, development, and abiotic stress response of plants. Although several studies have been performed on the trihelix gene family in several dicots and monocots, this gene family is yet to be studied in Chenopodium quinoa (quinoa). Results In this study, 47 C. quinoa trihelix (CqTH) genes were in the quinoa genome. Phylogenetic analysis of the CqTH and trihelix genes from Arabidopsis thaliana and Beta vulgaris revealed that the genes were clustered into five subfamilies: SIP1, GTγ, GT1, GT2, and SH4. Additionally, synteny analysis revealed that the CqTH genes were located on 17 chromosomes, with the exception of chromosomes 8 and 11, and 23 pairs of segmental duplication genes were detected. Furthermore, expression patterns of 10 CqTH genes in different plant tissues and at different developmental stages under abiotic stress and phytohormone treatment were examined. Among the 10 genes, CqTH02, CqTH25, CqTH18, CqTH19, CqTH25, CqTH31, and CqTH36, were highly expressed in unripe achenes 21 d after flowering and in mature achenes compared with other plant tissues. Notably, the 10 CqTH genes were upregulated in UV-treated leaves, whereas CqTH36 was consistently upregulated in the leaves under all abiotic stress conditions. Conclusions The findings of this study suggest that gene duplication could be a major driver of trihelix gene evolution in quinoa. These findings could serve as a basis for future studies on the roles of CqTH transcription factors and present potential genetic markers for breeding stress-resistant and high-yielding quinoa varieties.

Current trends and prospects in quinoa research: An approach for strategic knowledge areas

“…Research focused on gene expression and regulation includes hybridization (Hodková & Mandák, 2018 ), phylogenetic (Li et al., 2022 ), and proteomic studies in relation to edaphoclimatic factors where cultivars are grown (Zhao et al., 2022 ). The main objective of genic expression studies has been to find the relationship between the agri‐environmental offer and the genetic variability associated with the greater production of seeds with high contents of vegetable proteins (El‐Hakim et al., 2022 ) and high‐value biocomposites (Campos‐Rodriguez et al., 2022 ).…”

Phylogenetic Determination of Chenopodium quinoaBased on the Chloroplast Genes rbcL and matK

“…Likewise, studies on genetic diversity among cultivated plant species are essential for conservation and improvement programs [24]. Tis study, where 32 Chenopodium accessions were analyzed by evaluating matK and rbcL genes, showed that these regions contain higher amounts of adenine + thymine (A + T) than guanine + cytosine (G + C) and that nucleotide substitution rates were high, as were genetic distances, demonstrating that the use of chloroplast molecular markers plays an important role in elucidating evolutionary relationships and identifying species, such as quinoa [25].…”

“…Studies on the Chenopodium genus have shown the ability of a single barcoding gene (rbcL) or a combination of these genes to distinguish individuals of the Chenopodium genus [15,35]. In addition, phylogeny factors and the identifcation of associated gene families are essential tools for understanding the evolution, mutation, and genetic factors associated with the main characteristics of the Chenopodium genus [25].…”

GT Transcription Factors of Rosa rugosa Thunb. Involved in Salt Stress Response

“…Further, the photosynthesis decreasing and poor growth under salt stress contributed to the losses of quality and yield of economic crops [17]. The expression profile studies predicted some GTs which responded to salt stress in many crops, like cotton [18], wheat [19], Brassica napus L. [20], quinoa [21], Sorghum bicolor L. [22], soybean [23] and rice [24]. Function studies have proved salt tolerance regulation roles of several crop GTs.…”