Vol.
32 No.
September 2025 1135-1146 DOI:10.
4308/hjb.
ISSN: 1978-3019
EISSN: 2086-4094
H A Y AT I
Journal of Biosciences Research Article Genome-wide Analysis of CONSTANS-like (CqCOL) Transcription Factors in Quinoa (Chenopodium quino.
: Structural Diversity.
Phylogeny, and Stress-Responsive Expression Huyen Thi Thanh Tran1.
Gioi Huy Dong2.
Ha Duc Chu3.
Phi Bang Cao4* Faculty of Biology.
Hanoi National University of Education.
Hanoi City 122300.
Vietnam Faculty of Biotechnology.
Vietnam National University of Agriculture.
Hanoi City 122300.
Vietnam Faculty of Agricultural Technology.
University of Engineering and Technology.
Vietnam National University Hanoi.
Xuan Thuy Road.
Cau Giay District.
Hanoi City 122300.
Vietnam Faculty of Natural Sciences.
Hung Vuong University.
Phu Tho Province 35000.
Vietnam
ARTICLE INFO
Article history:
Received October 29, 2024 Received in revised form December 20, 2024 Accepted January 20, 2025 KEYWORDS:
CONSTANS,
transcription factor, expression pattern, cis-regulatory element Copyright .
2025@ author.
ABSTRACT
Quinoa (Chenopodium quino.
is an ancient grain renowned for its remarkable nutritional value and remarkable adaptability to diverse environmental conditions, making it a valuable crop for enhancing food security.
Understanding the molecular mechanisms triggering its development and stress responses is crucial for crop improvement.
This study conducted a comprehensive analysis of the CONSTANS-like (CqCOL) transcription factors in quinoa, which play a pivotal role in photoperiodic flowering regulation.
We identified and characterized 20 CqCOL genes, analyzing their physicochemical properties, phylogenetic relationships, gene structures, and promoter regions.
Our findings revealed significant diversity among the CqCOL proteins and suggested potential functional specialization within the family.
Promoter analysis uncovered various stress-responsive and phytohormone-responsive cis-regulatory elements, revealing that CqCOL genes may be associated with stress adaptation and hormonal signaling pathways.
Transcriptomic analyses under different conditions supported these insights, highlighting the importance of CqCOL genes in quinoa's developmental processes and stress responses.
Specifically, most CqCOL genes exhibited stable expression under heat stress, except CqCOL02 and CqCOL12, which were induced in roots by 1.
85- and 91-fold, respectively.
Under normal conditions.
CqCOL01.
CqCOL11, and CqCOL18 showed organ-specific expression, particularly in flowers and leaves, with no expression detected in roots.
This study enhances our understanding of the CqCOL transcription factor family.
It provides a foundation for future functional studies and breeding strategies aimed at improving stress tolerance and optimizing flowering time in quinoa.
Introduction Quinoa (Chenopodium quino.
is an important pseudocereal that originates from the Andean region * Corresponding Author E-mail Address: phibang.
cao@hvu.
of South America, where it has been cultivated for over 5,000 years (Angeli & Silva 2.
Indigenous populations in South America have long relied on quinoa as a staple food due to its remarkable adaptability to harsh environmental conditions (Bazile et al.
Hinojosa et al.
In recent decades, quinoa Tran HTT et al.
has garnered global attention due to its exceptional nutritional profile, which includes a complete amino acid composition, high protein content, essential vitamins, minerals, and dietary fiber (Turcios et al.
Pereira et al.
Pathan & Siddiqui 2.
Its gluten-free nature further enhances its appeal, making it a suitable option for those with gluten intolerance or celiac disease.
The crop's resilience and nutritional richness position it as a valuable asset in addressing food security challenges, especially in the context of a growing global population and climate change (Guo et al.
Nguyen et al.
Recent studies demonstrated that regulating flowering time in quinoa plants is essential for optimizing reproductive success and maximizing crop yields (Patiranage et Oustani et al.
This regulation relies on the plant's physiological response to the duration of light and darkness, synchronizing flowering with favorable environmental conditions.
CONSTANS
(CO) transcription factors (TF.
play a central role in photoperiodic flowering regulation across various plant species, including quinoa.
While no studies have specifically explored the CO TF family in quinoa, its interaction with genes such as FLOWERING LOCUS T (FT) and other flowering-related regulators in other species suggests a broader network of genetic control affecting reproductive development.
Understanding how these genes interact to modulate reproductive success under diverse environmental conditions remains a critical area for further research.
Of interest to us is the CO TF, which is a critical regulator of photoperiodic flowering in numerous plant species (Suarez-Lopez et al.
Kim et al.
Structurally, it features two specific B-box zinc finger domains at the N-terminal, which mediate protein interactions and DNA binding, and a CCT domain at the C-terminal, essential for nuclear localization and interactions with regulatory proteins (Robson et al.
Wenkel et al.
Functionally.
CO functions as a transcriptional activator, linking environmental light cues and the circadian clock to regulate key flowering genes, particularly FT (Suarez-Lopez et al.
Cai et al.
Under favorable photoperiodic conditions.
CO accumulates in the nucleus, binds target gene promoters, and activates FT, initiating the transition from vegetative growth to flowering.
CO activity is finely regulated through transcriptional control, post-translational modifications, and interactions with light signaling Understanding CO's structure and function is essential for elucidating photoperiodic flowering mechanisms and holds potential for optimizing flowering time to improve crop yields.
Recently, the CO TF families have been investigated in a large number of higher plant species, including barley (Griffiths et al.
, rice (Griffiths et al.
Arabidopsis (Griffiths et al.
, mango (Liu et 2.
Chinese white pear (Wang et al.
grapevine (Wang et al.
, sugar beet (Chia et al.
, chrysanth (Fu et al.
, and gingko (Yan et al.
A previous study provided insights into the genetic diversity of flowering time regulators in quinoa, specifically FT and CO genes, highlighting the association of sequence variations and haplotypes with flowering responses under different photoperiods and their correlation with geographical distribution (Patiranage et al.
However, no comprehensive study has concerned the CO TF family in quinoa.
This current study aimed to perform a comprehensive identification, characterization, and expression analysis of the CO TF family in quinoa based on computational approaches.
By examining their gene structures, evolutionary relationships, physicochemical properties, cis-regulatory elements, and expression patterns across diverse tissues and environmental conditions, the current research seeks to explain the functional roles of CO genes in photoperiodic flowering and stress responses.
The anticipated findings are expected to deepen our understanding of the CO TF family within the quinoa and contribute to future strategies for crop Materials and Methods Search of CO Transcription Factors in Quinoa To seek the CO TFs within the quinoa genome (Jarvis et al.
, we utilized a homology-based approach anchored on well-characterized CO genes from Arabidopsis (Griffiths et al.
as recently reported (Chu et al.
Niu et al.
First.
CO protein sequences were obtained from a recent study (Griffiths et 2.
to serve as reference queries.
These sequences were employed in BLAST searches against the quinoa assembly (Jarvis et al.
to detect homologous The resulting candidate proteins were then analyzed using HMMER software (Potter et al.
employing conserved CO domain profiles (Robson et 2.
sourced from the Pfam database (Mistry et HAYATI J Biosci Vol.
32 No.
September 2025 2.
to verify the presence of characteristic CO An E-value threshold of < 1E-10 was applied to ensure domain detection's reliability.
Proteins that exhibited the conserved CO domains were designated as putative CO TFs in quinoa and were selected for subsequent characterization and analysis.
GSDS platform (Hu et al.
, which allows for the visualization and analysis of gene structures.
The tool aligns the genomic DNA with the coding DNA sequence to generate a schematic representation of exons, introns, and untranslated regions.
Analysis of Properties of CO Transcription Factors in Quinoa To analyze the cis-regulatory elements (CRE.
in the promoter sequences of the CO genes in quinoa, we first collected the 2 kb upstream of the transcription start site of the CO gene.
These sequences, representing the promoter regions, were extracted from the quinoa genome database (Jarvis et al.
and are accessible in the Phytozome portal (Goodstein et al.
Once the upstream sequences were obtained, the PlantCARE web-based tool (Lescot et al.
was employed to predict and identify potential CREs within these To analyze the physicochemical properties of the CO TFs in quinoa, the ProtParam tool available on the ExPASy website (Gasteiger et al.
was applied as previously described (Niu et al.
Initially, we obtained the full-length amino acid .
sequences of all CO proteins in quinoa (Jarvis et al.
Each sequence was individually input into ProtParam, which computes various physicochemical parameters based solely on the protein's amino acid composition.
The parameters assessed included molecular weight .
W), aliphatic index (AI), theoretical isoelectric point .
I), and grand average of hydropathicity (GRAVY).
Generation of The Phylogenetic Tree of CO Transcription Factors in Quinoa To elucidate the relationships among the CO TFs in quinoa, we generated a phylogenetic tree by using the MEGA tool (Kumar et al.
as recently guided (La et al.
Chu et al.
Initially, the fulength aa sequences of all identified CO proteins were retrieved from the quinoa proteome database.
Wellcharacterized CO TF proteins from Arabidopsis and sugar beet were also obtained from previous studies (Griffiths et al.
Chia et al.
to serve as reference sequences for analysis.
Multiple sequence alignments were carried out by using the ClustalW algorithm integrated into MEGA software.
Following alignment, an unrooted phylogenetic tree was generated by employing the Maximum Likelihood To assess the statistical robustness of the inferred phylogenetic relationships, a bootstrap analysis with 1,000 replicates was applied.
Analysis of Gene Structure of CO in Quinoa We utilized the GSDS tool (Hu et al.
to conduct the structural analysis of CO genes in quinoa, as previously reported (Niu et al.
Initially, the genomic and corresponding coding sequences of each CO gene were retrieved from the quinoa These sequences were then uploaded to the Promoter Analysis of CO Genes in Quinoa Transcriptome Analysis Transcription Factors in Quinoa To access the expression profiles of the CO genes in quinoa, we utilized three publicly available microarray datasets from the NCBI GEO (Barrett et al.
including GSE128155 (Tovar & Quillatupa 2.
GSE139174 (Liu et al.
, and GSE156523.
The raw sequencing data were downloaded and subjected to quality control using FastQC to assess sequencing quality and identify technical issues.
Gene expression levels were quantified by using the fold-change and FPKM values.
Visualization tools such as heatmaps and expression profile plots were generated using packages like ggplot2 in R.
Results Comprehensive Identification of The CO TF Family in Quinoa To identify CO TFs within the quinoa genome, we employed a homology-based approach anchored on wellcharacterized CO genes from Arabidopsis.
After screening by using the Pfam database, a total of 20 members of the CO TF family in quinoa have been reported.
The locus name of each member of the CO TF family in quinoa has been provided in Table 1.
At the same time, their coding DNA sequences, genomic DNA sequences, and full-length protein sequences were obtained for further To systematically represent the CO TF family in quinoa, we have designated these genes as "CqCOL.
The prefix "Cq" denotes Chenopodium quinoa, directly Tran HTT et al.
Table 1.
Information on the CO TF family in quinoa
Gene name
CqCOL01
CqCOL02
CqCOL03
CqCOL04
CqCOL05
CqCOL06
CqCOL07
CqCOL08
CqCOL09
CqCOL10
CqCOL11
CqCOL12
CqCOL13
CqCOL14
CqCOL15
CqCOL16
CqCOL17
CqCOL18
CqCOL19
CqCOL20
Locus name
AUR62035217
AUR62035221
AUR62041089
AUR62030805
AUR62040293
AUR62037849
AUR62009440
AUR62023118
AUR62037140
AUR62034638
AUR62020307
AUR62002867
AUR62028867
AUR62025058
AUR62039984
AUR62001856
AUR62008578
AUR62030486
AUR62005692
AUR62009650
Length .
mW (KD.
Gravy linking the gene nomenclature to the studied species.
The suffix "COL" stands for "CONSTANS-LIKE", a standard convention used to identify genes homologous to the original CONSTANS gene characterized in Arabidopsis.
(CqCOL.
42 (CqCOL.
These physicochemical parameters establish a foundational profile of the CqCOL protein family in quinoa, facilitating further biochemical and structural investigations.
Estimation of The General Parameters of The CO TF Family in Quinoa Phylogenetic Categorization of The CO TF Family in Quinoa In this study, we assessed the parameters of the CO TFs in quinoa, including mW, pI.
AI, and GRAVY.
evaluating these properties, a comprehensive profile of the structural and stability characteristics of the CqCOL proteins was established, providing essential information for further biochemical and structural studies.
As a result, the general characteristics of the CqCOL proteins in quinoa are provided in Table 1.
The physicochemical features of the CqCOL TFs in quinoa were comprehensively analyzed using ProtParam, revealing significant diversity among the family members.
The mW of the CqCOL proteins ranged from approximately 29 (CqCOL.
00 kilodaltons (CqCOL.
, indicating variability in their amino acid lengths and The theoretical pI varied widely, spanning from pH 4.
61 (CqCOL.
to pH 6.
59 (CqCOL.
, which suggests differences in their net electrical charges under physiological conditions.
The AI values differed among the CqCOL proteins, between 54.
01 (CqCOL.
and 18 (CqCOL.
, providing insights into their relative thermostability, with higher values suggesting greater stability at elevated temperatures.
The GRAVY values of all CqCOL proteins were negative, ranging from -0.
To investigate the evolutionary relationships among CO TFs in quinoa, we constructed an unrooted phylogenetic This analysis included 20 CO protein sequences from quinoa, along with well-characterized CO proteins from Arabidopsis and sugar beet serving as reference sequences.
Utilizing the Maximum Likelihood method, we generated a phylogenetic tree presented in Figure 1.
This figure illustrated the relationships among all members of the CO TF families in the quinoa and related species, providing valuable insights into their evolutionary connections.
Based on the phylogenetic analysis of the CqCOL TFs in quinoa, these members can be classified into three distinct groups.
The first group, group I, consists of 6 .
ut of .
CqCOL proteins.
Group II includes 6 .
ut of .
CqCOL proteins, while group i contains 8 remaining CqCOL proteins.
Investigation of The Gene Organization of The CO TF Family in Quinoa This study analyzed the gene structure of CqCOL genes in quinoa to investigate exon-intron arrangements and structural diversity within the gene family.
Using the GSDS tool, full-length genomic sequences were HAYATI J Biosci Vol.
32 No.
September 2025 Figure 1.
Phylogenetic categorization of the CO TF families in quinoa, arabidopsis, and sugar beet aligned with their corresponding coding sequences to identify exon/intron structure.
The analysis revealed notable variation in the exon-intron structures among the 20 CqCOL genes (Figure .
The results indicated that the number of exons varied from 2 to 4, reflecting structural diversity in the gene family.
Specifically, 8 out of the 20 CqCOL genes exhibited a simple structure with only 2 exons separated by a single intron.
Another 8 genes displayed more complex architectures, containing 4 exons, while the remaining 4 genes had 3 exons.
These variations in exonintron organization suggest evolutionary diversification within the CqCOL gene family, potentially influencing the functional roles of individual genes in photoperiodic flowering regulation and other developmental processes.
Analysis of Stress-Responsive and Phytohormone-Responsive CREs in The Promoter Sequences of The CO TF Family in Quinoa To analyze CREs in the promoter sequences of CqCOL genes in quinoa, we extracted the 2 kb upstream of the transcription start site for each CO gene.
Using the PlantCARE tool, several putative CREs related to phytohormone and stress responsiveness were explored.
As a result.
Tables 2 and 3 described the foundation of the stress-responsive and phytohormone-inducible CREs of all members of the CqCOL genes in quinoa, respectively.
The analysis of the promoter regions of CqCOL genes in quinoa revealed the presence of 4 key stress-responsive CREs.
These include the LTRE (CRE associated with low-temperature responsivenes.
MYBRS (MYB recognize site involved in drought responsivenes.
MBS (MYB binding site involved in drought-inducibilit.
, and TC-rich repeats .
lement linked to defense and stress responsivenes.
We realized that two droughtresponsive CREs were localized in 8 CO genes, including CqCOL03.
CqCOL06.
CqCOL07.
CqCOL12.
CqCOL15.
CqCOL16.
CqCOL17, and CqCOL18.
The presence of LTRE was also recorded in the promoter sequences of 4 CO genes, including CqCOL02.
CqCOL06.
CqCOL07, and CqCOL08, while TC-rich repeats have been found in the promoter sequences of 8 CO genes, such as CqCOL04.
CqCOL07.
CqCOL08.
CqCOL10.
CqCOL15.
CqCOL16, and CqCOL19.
Our predictions suggested that these CO genes may be putative in stress responsiveness.
Next, we investigated the occurrences of phytohormoneresponsive CREs in the promoter sequences of the CqCOL genes.
Briefly, a total of 10 CREs related to Tran HTT et al.
Figure 2.
Structural analysis of genes encoding the CO TF family in quinoa Table 2.
A list of stress-responsive cis-regulatory elements in the promoter regions of genes encoding the CO TF family in Gene name
CqCOL01
CqCOL02
CqCOL03
CqCOL04
CqCOL05
CqCOL06
CqCOL07
CqCOL08
CqCOL09
CqCOL10
CqCOL11
CqCOL12
CqCOL13
CqCOL14
CqCOL15
CqCOL16
CqCOL17
CqCOL18
CqCOL19
CqCOL20
MYBRS
Stress-related CREs
LTRE
MBS
TC-rich repeats MYBRS: MYB recognize site involved in drought responsiveness.
LTRE: CRE associated with low-temperature responsiveness.
MBS: MYB binding site involved in drought-inducibility.
TCrich repeats: element linked to defense and stress responsiveness phytohormone responsiveness, including ABRE .
bscisic acid-responsive elemen.
TATC-box (CRE related to gibberellin-responsivenes.
TGACG-motif (CRE involved in the jasmonic acid-responsivenes.
ERE .
thylene-responsive elemen.
TCA-element (CRE involved in salicylic acid responsivenes.
GARE-motif (Gibberellin-responsive elemen.
P-box (Gibberellin responsive elemen.
TGA-element .
uxin-responsive elemen.
TGACG-motif (CRE related to the jasmonic acid-responsivenes.
CGTCA-motif (CRE related to the jasmonic acid-responsivenes.
, has been predicted.
As expected, a foundation of the hormone-responsive elements was enriched in the promoter sequences of the CO genes in quinoa.
Among them, a large number .
out of .
CO genes contained ABRE, while 12 .
ut of .
CO genes had 3 CREs related to gibberellin-responsiveness (GARE-motif.
TATC-box, and P-bo.
Next, 3 CREs involved in jasmonic acid-responsiveness, including TGACG-motif.
CGTCA-motif, and TGACG-motif, were identified in the promoter sequences of 11 CO genes.
Additionally, 1, 4, and 7 CO genes contained CREs related to ethylene, auxin, and salicylic acid-responsiveness.
This finding provided important insights into the potential regulatory pathways involved in the stress adaptation of quinoa.
HAYATI J Biosci Vol.
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September 2025 Table 3.
A list of phytohormone-induced cis-regulatory elements in the promoter regions of genes encoding the CO TF family in quinoa
Gene name
CqCOL01
CqCOL02
CqCOL03
CqCOL04
CqCOL05
CqCOL06
CqCOL07
CqCOL08
CqCOL09
CqCOL10
CqCOL11
CqCOL12
CqCOL13
CqCOL14
CqCOL15
CqCOL16
CqCOL17
CqCOL18
CqCOL19
CqCOL20
ABRE
TATC
TGACG
ERE
GARE
TGA
TCA
TGACG
CGTCA
ABRE: abscisic acid-responsive element.
TATC: TATC-box (CRE involved in gibberellin-responsivenes.
TGACG: TGACG-motif (CRE involved in the jasmonic acid-responsivenes.
ERE: ethylene-responsive element.
GARE: GARE-motif (Gibberellin-responsive elemen.
P: P-box (Gibberellin responsive elemen.
TGA: TGA-element .
uxin-responsive elemen.
TCA-element (CRE involved in salicylic acid responsivenes.
TGACG: TGACG-motif (CRE involved in the jasmonic acid-responsivenes.
CGTCA: CGTCA-motif (CRE involved in the jasmonic acid-responsivenes.
Transcriptomic Analysis of The CO Genes in Quinoa Under Adverse Environmental Conditions To access the expression profiles of the CO genes in quinoa, we performed a comprehensive transcriptomic analysis under various treatments by exploring recent RNA-Seq datasets.
As a result.
Figures 3 and 4 were constructed to describe the expression levels of the CqCOL genes under high-temperature stress and normal conditions, respectively.
Firstly, most .
out of .
CqCOL genes exhibited non-different expression (.
old-chang.
< 1.
in heated roots and/or shoots.
Meanwhile, only two CqCOL genes.
CqCOL02 and CqCOL12, were up-regulated in treated roots by approximately 1.
85 and 1.
91-fold, respectively.
Interestingly, the promoter regions of CqCOL02 and CqCOL12 contained CREs involved in the gibberellin, auxin, jasmonic acid, and abscisic acid responsiveness.
These findings suggested that these CO genes may act as positive regulators in heat stress response via the crosstalk between gibberellin, auxin, jasmonic acid, and abscisic Additionally, the CO genes exhibited variable expression profiles in major organs in quinoa plants under normal conditions.
Among them, the expression levels of 3 CO genes.
CqCOL01.
CqCOL11, and CqCOL18, were high in flower tissues of both white quinoa and/or yellow quinoa plants (Figure 4A).
Under normal conditions, it has been realized that 2 CO genes, particularly CqCOL01 and CqCOL11, were specific in stem and leaf tissues, while CqCOL18 was exclusively expressed in leaf tissues of yellow quinoa plants (Figure 4B).
We also found that no CqCOL genes were expressed in examined root samples.
Our findings strongly suggested a hypothesis of the potential function of expressed CqCOL genes in specific organs related to regulating photoperiodic flowering and other developmental processes in quinoa plants.
Discussion Phylogenetic and Structural Diversity of CO Transcription Factors Across Plant Species A comparative analysis of the CO TF families across various plant species reveals notable differences in the number of CO genes, highlighting the evolutionary complexity and functional multiplicity within this TF family.
We identified twenty CO family genes in quinoa, which is relatively higher than several other For example, in the model plant Arabidopsis, 16 CO TFs have been found and thoroughly annotated (Griffiths et al.
Rice also possesses 16 CO genes, as previously reported (Griffiths et al.
In the Chinese white pear, 15 CO genes were detected Tran HTT et al.
Figure 3.
Expression levels of genes encoding the CO TF family in quinoa under heat stress condition Figure 4.
Expression levels of genes encoding the CO TF family in (A) flower and fruit tissues in white quinoa and yellow quinoa plants and (B) root, stem, and leaf in yellow quinoa plants HAYATI J Biosci Vol.
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September 2025 in the latest assembly (Wang et al.
Conversely, chrysanth has at least 7 CO genes reported in its genome (Fu et al.
Additionally, 19 members of the CO family have been identified in ginkgo (Yan et al.
, and mango has been found to contain 21 such genes (Liu et al.
This variation in CO gene numbers among different species underscores the intricate evolutionary dynamics.
It suggested that gene expansion or contraction may be crucial in regulating flowering time and facilitating adaptation to diverse environmental conditions.
Previous studies have extensively investigated the characteristics of CO TF families in various higher plant species, revealing significant diversity in their genetic sequences and physicochemical properties.
For instance, in mango, the CO TF family has been reported to possess gene sequences ranging from 492 to 1,536 base pairs in length (Liu et al.
These sequences encode proteins consisting of 163 to 511 aa residues, resulting in mW values between 18.
11 and 63 kilodaltons and predicted pI spanning from 3.
85 (Liu et al.
This wide range indicates considerable protein size variation and net charges under physiological pH conditions (Liu et al.
Similarly, in grapevine, the predicted open reading frames of CO genes exhibit substantial variation, ranging from approximately 1,044 base pairs for VviCOL4 to about 1,425 base pairs for VviCOL14b (Wang et al.
The corresponding proteins vary in length from 347 to 474 aa residues, leading to calculated molecular masses between roughly 38.
43 kilodaltons (Wang et al.
In the case of Chrysanthemum, the sizes of CO TF proteins have been reported to range from 337 to 434 aa residues (Fu et al.
Additionally, in Chinese white pear, the CO TF family includes proteins varying between 340 and 488 aa residues in length (Wang et al.
These observations underscore the complexity and evolutionary dynamics of the CO TF family across different plant species.
The physicochemical properties, such as mW, pI.
AI, and GRAVY values, provide valuable insights into these proteins' structural stability and functional potential.
By comprehensively analyzing these physicochemical parameters, we establish a crucial groundwork for the CO TF family's future structural and functional studies.
This detailed characterization is instrumental in enhancing our understanding of the molecular mechanisms by which CO proteins regulate flowering time in response to photoperiodic signals.
We gain deeper insights into the complex regulatory networks governing plant growth and reproduction by elucidating how these proteins interact with environmental cues to influence developmental processes.
This advanced knowledge is vital for progress in plant developmental biology.
Moreover, it has significant practical implications, as it can guide breeding programs to enhance crop adaptation to various environmental conditions.
integrating this molecular-level understanding into agricultural practices, we can construct crop lines with improved resilience and productivity, contributing to food security and sustainable agriculture.
Previous research has documented the classification of CO TF families in various higher plant species.
grapevine, 20 CO genes were found and categorized into three groups via phylogenetic analysis (Wang et al.
Specifically, three genes.
VviCOL2.
VviCOL4, and VviCOL5, were assigned to group I.
VviCOL16a and VviCOL16b were placed in group II.
and the remaining CO genes, including VviCOL9a.
VviCOL9b.
VviCOL11a.
VviCOL11b.
VviCOL13.
VviCOL14a, and VviCOL14b, were grouped into group i (Wang et al.
Furthermore, to explore the relationships among CO members, a phylogenetic tree was constructed using 60 CO members from A.
thaliana, grapevine, and mango (Liu et al.
This analysis revealed that these CO proteins clustered into three separate clades, corresponding closely with their structural differences (Liu et al.
Similar classification models were reported in CO TF families of other crop species (Griffiths et al.
Fu et al.
Wang et al.
Yan et al.
Taken together, the classification of CqCOL TFs in quinoa, based on phylogenetic analysis, reveals evolutionary divergence and functional diversity similar to that observed in other plant species (Griffiths et al.
Fu et al.
Wang et al.
Yan et al.
Wang et al.
Liu et al.
Grouping the CqCOL proteins into three distinct clades emphasizes the conservation and diversification within this gene family.
This categorization highlights the critical function of CO TFs across various plant species.
Comparative analyses highlight similar structural variability in CO TF families across several crop species, including mango (Liu et al.
and grapevine (Wang et al.
For instance, in mango, the analysis of 30 CO genes revealed a range of intron numbers, from intronless genes (MiCOL.
to genes with up to 4 introns.
Notably, 10 genes had only 1 intron, while 8 and 9 genes possessed 3 and 2 introns, respectively (Liu et al.
This diversity in exon- intron organization suggests functional differentiation within the gene family, even within a single species.
In grapevine, a similar phenomenon of structural variability was recorded.
For example.
CO genes like VviCOL9a.
VviCOL11a, and VviCOL14a each contained 3 introns, whereas others, such as VviCOL2.
VviCOL4, and VviCOL16a, had only 1 intron (Wang et al.
These observations underscore the evolutionary dynamics of CO genes across plant species and suggest that differences in gene structure may have functional implications for their roles in developmental processes, including flowering This comparative insight enhances our investigation of the CqCOL gene family's diversity and its potential adaptive significance.
Regulatory Mechanisms of CO Genes in Quinoa: Insights from cis-regulatory Elements and Expression Profiles The transcriptional regulation of genes is largely influenced by CREs located in their promoter regions, which serve as binding sites for TFs and modulate gene expression in response to environmental and hormonal cues.
In this study, a comprehensive analysis of the promoter sequences of CqCOL genes in quinoa revealed the presence of multiple CREs associated with stress responses and phytohormone signaling Among these, stress-responsive elements such as LTRE and MBS are involved in droughtinducibilit.
and TC-rich repeats .
ssociated with defense and stress response.
were identified in several CqCOL genes.
Notably, the presence of MBS elements in promoter regions of the CqCOL genes suggests their potential role in drought stress adaptation.
MYB TFs are known to regulate drought-responsive pathways in Similarly, the presence of LTRE indicated that these CqCOL genes may contribute to cold tolerance, aligning with previous studies that have linked LTREcontaining genes to low-temperature resilience.
Additionally, the analysis of hormone-responsive elements revealed an abundance of CREs associated with abscisic acid (ABRE), gibberellins (GARE-motif.
TATC-box, and P-bo.
, jasmonic acid (TGACG-motif and CGTCA-moti.
, and salicylic acid (TCA-elemen.
The enrichment of ABRE motifs in several CqCOL genes suggested a regulatory role in abscisic acidmediated stress responses, particularly in drought and osmotic stress conditions.
Furthermore, the presence of gibberellin-responsive elements supported the hypothesis that these CqCOL genes may be involved Tran HTT et al.
in growth and developmental processes, particularly in the regulation of flowering time.
Gibberellins are known to interact with CO genes to influence the transition from vegetative to reproductive phases in plants.
The identification of multiple hormoneresponsive elements in the promoter regions of CqCOL genes provides insights into their potential regulatory It suggests that these transcription factors play an integral role in coordinating stress adaptation and developmental processes in quinoa.
To elucidate the functional significance of CqCOL genes, we conducted a transcriptomic analysis under both normal and stress conditions.
The results indicated that while the majority of CqCOL genes exhibited stable expression patterns under heat stress, two genes.
CqCOL02 and CqCOL12, were significantly upregulated in root tissues.
This suggests that these genes may serve as key regulators in the heat stress response, potentially mediating signaling pathways that enhance root resilience under high-temperature The presence of gibberellin-, auxin-, and jasmonic acid-responsive elements in the promoter regions of these genes further supports their role in hormonal crosstalk during stress adaptation.
These findings align with previous studies demonstrating that CO genes can function in stress adaptation by integrating environmental signals with hormonal Overall, the integration of CRE analysis and expression profiling provides valuable insights into the regulatory mechanisms governing the CqCOL gene family in quinoa.
The presence of stress- and hormoneresponsive elements in their promoter regions, coupled with their dynamic expression under environmental and developmental conditions, underscores the complexity of their functional roles.
These findings highlight the importance of CqCOL genes in stress adaptation and flowering regulation and provide a molecular framework for future functional studies aimed at improving quinoaAos resilience and reproductive success.
In conclusion.
To sum up, this study presents a comprehensive analysis of the CO TFs in quinoa, identifying 20 members designated as CqCOL.
Physicochemical characterization revealed significant diversity among these proteins regarding mW, pI.
AI, and GRAVY values.
Phylogenetic analysis classified the CqCOL proteins into three distinct groups, indicating evolutionary divergence and potential functional differentiation.
Structural analysis showed diversity in exon-intron organization, with exon HAYATI J Biosci Vol.
32 No.
September 2025 numbers ranging from two to four, suggesting possible influences on gene expression and function.
Promoter analysis uncovered several stress-responsive and phytohormone-responsive CREs, implying that certain CqCOL genes may participate in stress responses and hormonal signaling pathways.
Transcriptomic analyses revealed that while most CqCOL genes did not significantly change expression under heat stress.
CqCOL02 and CqCOL12 were upregulated, suggesting roles in heat stress adaptation.
Additionally, tissuespecific expression patterns under normal conditions indicate potential involvement in photoperiodic flowering regulation and developmental processes.
These findings enhance our understanding of the CO TFs in quinoa and supply an establishment for future functional studies and breeding strategies to improve stress tolerance and optimize flowering time.
Acknowledgements This work was funded by Hung Vuong University.
References