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Article

Exploring Genetic Variation in Root Traits and Root–Fungal Associations in Aegilops tauschii

by
Ahmed Khaled Hassan Mohammedali
1,2,*,
Yasir Serag Alnor Gorafi
2,3,
Nasrein Mohamed Kamal
2,4,
Izzat Sidahmed Ali Tahir
2,4,
Hisashi Tsujimoto
4 and
Takeshi Taniguchi
4
1
United Graduate School of Agricultural Sciences (UGSAS), Tottori University, 4-101, Koyamacho-Minami, Tottori 680-8553, Japan
2
Agricultural Research Corporation (ARC), Wad Medani P.O. Box 126, Sudan
3
Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
4
International Platform for Dryland Research and Education (IPDRE), Tottori University, Tottori 680-0001, Japan
*
Author to whom correspondence should be addressed.
Agriculture 2025, 15(17), 1889; https://doi.org/10.3390/agriculture15171889
Submission received: 24 July 2025 / Revised: 2 September 2025 / Accepted: 3 September 2025 / Published: 5 September 2025
(This article belongs to the Special Issue Arbuscular Mycorrhiza in Cropping Systems)
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Abstract

Wheat domestication and selection for aboveground traits may have influenced belowground traits, reducing genetic diversity critical for adaptation to stress such as drought. However, the impacts on root system architecture and root–endophytic fungal interactions remain unclear. This study evaluated variation in root traits and associations with arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE) among nine diploid Aegilops tauschii accessions (wild progenitor), one tetraploid Triticum turgidum cv. ‘Langdon’ (LNG), and one hexaploid Triticum aestivum cv. ‘Norin 61’ (N61). Root traits and fungal colonization varied significantly among genotypes. All Ae. tauschii accessions showed superior root development and lower DSE colonization compared to LNG and N61. AMF colonization was highest in accessions AT76 and KU-2126 (54% and 53%, respectively), while N61 exhibited the highest specific root length (SRL) and DSE colonization. AMF positively correlated with most root traits (except SRL), while DSE showed the opposite trend. Although Ae. tauschii accessions shared broadly favorable root traits, variation in their fungal interactions were more pronounced. A clustering heatmap incorporating both root and biotic traits clustered the genotypes into four groups, clearly separating the Ae. tauschii accessions into two clusters based on their root characteristics and root-fungal associations. These results highlight the hidden interspecific and intraspecific variations in Ae. tauschii and its potential as a genetic resource for optimizing root–endophytic fungal interactions, and improving wheat resilience to biotic and abiotic stress in a changing climate.

1. Introduction

Biotic and abiotic stress tolerance and good crop growth are key traits for sustainable crop production in low-input systems under global warming. As the root system is integral to these traits, to meet the food demands of the 21st century, plant scientists must turn their attention to this so-called “hidden half” of the crop [1,2]. Plant root systems, typically occupied and bounded by a diverse microbial community called the root microbiome, capture the water and nutrients needed for plant growth [3,4]. Increasing our knowledge of the “hidden half” of crop plants and directly selecting for root system architecture are essential for further crop improvement [3]. In addition, the root system can contribute to carbon sequestration, and root secretions could be engineered to tailor the root microbiome [3,5].
Tetraploid and hexaploid wheat (Triticum spp.), aligned with the diploid wild ancestor grass Aegilops tauschii, played an enormous role in global food security, with distinct genetic compositions and traits acquired through both natural evolution and human selection [6]. The natural hybridization of tetraploid wheat (Triticum turgidum subsp. durum, AABB genome) and a diploid wild grass (Aegilops tauschii, DD genome), native to the south region of the Caspian Sea, the Fertile Crescent of the Middle East, and Western Asia [7,8], gave us hexaploid wheat (Triticum aestivum, L., AABBDD genome), with wide genetic diversity. The AB genome of tetraploid wheat is associated mainly with aboveground traits [9], and the D genome from Ae. tauschii potentially contributes to belowground traits such as root morphology, nutrient uptake, and interactions with beneficial microbes [8,10]. Understanding the influence of ploidy on root traits in wheat is crucial for optimizing root function and developing beneficial interactions with soil microbes [11,12,13]. Ae. tauschii harbors several genes and alleles for tolerance to heat and drought stress and resistance to fungal diseases [14]. As Ae. tauschii has more lateral roots and larger root biomass than Triticum spp. [7,15], variation within the D genome might enhance the association with arbuscular mycorrhizal fungi (AMF) in hexaploid wheat [7,11], offering potential for root-related benefits.
The wheat domestication and selection during the breeding process might have unintentionally altered belowground traits, narrowed genetic diversity, and favored the AB genome over the D genome [7,15,16]. This polyploidy diversity bottleneck could have weakened beneficial associations with root endophytes, particularly AMF, which form mutually beneficial relationships with wheat, promoting its growth and health by providing essential nutrients and alleviating stresses [17,18,19,20,21]; however, DSE can act as beneficial partners, saprophytes, or pathogens depending on the host plant and environmental conditions [22,23,24]. Yet, the relationship between root traits of wheat relatives, including Ae. tauschii, and fungal colonization by AMF and DSE remains poorly understood and advancing such knowledge may lead to the effective utilization of Ae. tauschii accessions in breeding new stress-tolerant wheat cultivars.
The study investigated the variation in root traits and AMF–DSE interactions using a unique set of diploids (Ae. tauschii accessions), a tetraploid, and a hexaploid wheat and studied root architectural, morphological, physiological, and biotic traits critical to the plant–microbe interface. We identified Ae. tauschii accessions with superior root traits, enhanced AMF colonization, and lower DSE colonization. The findings can guide breeding programs to develop wheat cultivars with optimized root traits and enhanced beneficial root–endophytic fungal interactions to improve stress resilience and increase productivity.

2. Materials and Methods

2.1. Plant Materials and Experimental Conditions

In this study, nine Ae. tauschii accessions (diploid, DD), one Triticum turgidum var. durum cv. ‘Langdon’ (tetraploid, AABB), and one Triticum aestivum L. cv. ‘Norin 61’ (hexaploid, AABBDD) were used (Table 1). The experiment was conducted in a greenhouse at the Arid Land Research Center (ALRC), Tottori University, Japan (35°32′04.5″ N 134°12′42.0″ E), from 30 March to 30 June 2023. Temperature and relative humidity were monitored with a datalogger (SK-L754; Sato Keiryoki Mfg. Co. Ltd., Tokyo, Japan) (Figure S1). Daily temperatures ranged from 13 to 33 °C with an average of 23 °C, and relative humidity ranged from 33% to 92%, with an average of 58%.

2.2. Plant Growth and Experiment Setup

Seeds were sown in tall pots designed for Glycyrrhiza cultivation (60 cm high, 10 cm wide), filled with approximately 4000 cm3 of sandy soil obtained from the ALRC wheat field. The pH of the soil (H2O) was 5.98, and its cation exchange capacity (CEC) was 2.00 meq/100 g. The exchangeable cation contents of (NH4)+, K+, Ca2+, and Mg2+ were 0.0, 0.06, 0.35, and 0.68, respectively. Initial soil screening indicated low total culturable fungi (≈103 CFU g−1 soil) and low AMF spore abundance (≈5.1 spores g−1). To achieve ecologically relevant exposure while ensuring adequate AMF presence, we combined (i) a crude fungal suspension extracted from field soil (106 CFU mL−1; preparation below) with (ii) a commercial AMF product, Mycogel (Agrocode Bioscience, Roquetas de Mar, Almería, Spain), containing Rhizophagus irregularis at 5 × 103 spores mL−1 [26]. The mixing ratio was chosen to approximate the field AMF:total fungi proportion (≈5.1/103 = 00 < 0.0051 spores·CFU−1). Given the stock concentrations, the approximate V_AMF: V_crude ratio was 1.02:1. For each pot, a fresh aliquot of the mixture was prepared, and a total of 1.00 mL was applied 12 days after germination. This consisted of 0.505 mL of the AMF suspension and 0.495 mL of the crude suspension. Before and during dosing, the tubes were gently inverted and vortexed for ~3–5 s every 3–4 pots to minimize settling. Wide-bore tips were used to reduce clogging. The 1.00 mL dose was delivered in four equal drops around the seedling, approximately 1–2 cm from the stem, to target the rhizosphere and allow both AMF and the DSE to interact with and penetrate the root cortical cells. The experiment was arranged in a randomized complete block design with six replicates to minimize intra-treatment variation. Pots within each replication were positioned in a north–south direction to maximize light exposure and were regularly rotated to minimize positional effects. Irrigation was adjusted throughout the experiment: 100–150 mL every 3 days pre-germination, 200–300 mL after inoculation, and 300–400 mL after 60 days from germination. To ensure uniformity across pots, soil moisture was maintained gravimetrically by refilling trays when indicated ≈ 10% moisture loss, and visually monitored to prevent under-/overwatering. No fertilizers, insecticides, or fungicides were used.

2.2.1. Crude Field Inoculum

The crude fungal suspension (106 CFU mL−1) was prepared by shaking field sand/soil (collected from the same site as the baseline counts) with sterile distilled water (1:5 w/v, 15 min, 180 rpm), passing the slurry through 250-µm and then 45-µm sieves to remove debris, allowing 2 min settling, and collecting the supernatant. The supernatant was adjusted to 106 CFU mL−1 by serial dilution/concentration (centrifugation at low speed to pellet debris, resuspension in sterile water as needed), with CFU verified by plating on PDA and counting colonies after 48–72 h. This crude inoculum was used to maintain a community background resembling a field non-AMF fungus; it was not AMF-enriched

2.2.2. Quality and Uniformity Controls

To promote uniform exposure across replicates, the inoculum was prepared in a single batch per dosing session, mixed as above, and aliquoted immediately; the order of pot dosing was randomized within blocks. We relied on the manufacturer’s certificate of analysis for AMF spore titer and viability for the specific lot used and did not conduct an independent AMF germination assay. No fertilizers, insecticides, or fungicides were applied; pots were irrigated every 3 days. The experiment followed a randomized complete block design with six replicates to minimize intra-treatment variation.

2.3. Data Collection

After 3 months, all plants were removed carefully from the pots. The shoots and root systems were separated, and the root system was washed clean with tap water. We then assessed root architectural, morphological, physiological, and biotic traits [27].

2.3.1. Architectural Traits

Architectural traits that determine the spatial configuration of the plant root system include root length, surface area, volume, and weight. Harvested roots were carefully washed and digitally scanned using a flatbed scanner (Perfection V500 Photo; Epson, Japan) at 400 dpi resolution. Images were analyzed with WinRhizo Pro 2008a software (Regent Instruments Inc., Quebec City, QC, Canada) to quantify total root length (L, cm), surface area (SA, cm2), and volume (V, cm3) (Table S1). Thresholding was performed using the software’s automatic grayscale mode with manual adjustment when needed to optimize root-background contrast. Background correction was enabled. Image smoothing was kept at a low level to preserve fine root structures. Roots were classified into two diameter categories: thin (0.0 > 0.5 mm) and thick (0.5–1.0 mm) for subsequent analyses (Figure S2). A representative fraction of fresh roots was sampled for mycorrhizal and DSE colonization assessment. The remaining roots were weighed to determine fresh biomass, then oven-dried at 68 °C for 48 h to obtain dry biomass. Water content was calculated as the difference between fresh and dry weights

2.3.2. Morphological Traits

Morphological traits comprise individual root diameter, specific length, and tissue density. Root diameter (mm) was measured using WinRhizo. Specific root length (SRL) and root tissue density (RTD) were calculated as follows:
SRL (cm/g) = root length (cm)/root dry weight (g)
RTD (g/cm3) = root dry weight (g)/root volume (cm3)

2.3.3. Physiological Traits

Physiological root traits comprise total carbon, total nitrogen, and C/N ratio. Dried roots were ground in a multi-bead shocker (Yasui Kikai Co., Osaka, Japan), and 38 mg of root powder was analyzed in a CN Corder (JM 1000 CN Macro Corder, J-Science Lab, Kyoto, Japan) (Table S2).

2.3.4. Root Biotic Traits

Biotic traits are involved in direct interactions between roots and soil biota that affect nutrient capture. Root colonization by AMF and DSE was assessed following staining by the method of [28]. Root fragments were disinfected in 70% ethanol, soaked in 10% KOH overnight, rinsed with distilled water, acidified in 5% HCl for 3 min, and stained with trypan blue (500 mL glycerol, 475 mL distilled water, 25 mL acetic acid, 0.1 g trypan blue) overnight. After rinsing with acidified water, random root fragments of (1–2 cm) were mounted in a 9 cm plastic Petri dish with a gridline of 1 cm, and 60–68 intersections per sample were observed under a digital microscope (VHX-7000; Keyence, Osaka, Japan) (Table S3). Colonization levels were quantified by the gridline intersect method [29].
To ensure consistency, scoring was conducted by a single trained observer, and repeat counts on a subset of samples confirmed the repeatability of the measurements. Representative images with scale bars are provided in the Supplementary Materials to illustrate the diagnostic structures used for identification. AMF colonization was confirmed based on the morphology of Rhizophagus irregularis structures (arbuscules, vesicles, hyphae), which were uniform across inoculated samples. DSE was identified based on its morphological traits: septate, darkly pigmented, branching hyphae; conidiophores with muriform; and verrucose, dark brown walls.

2.3.5. Shoot System Traits

The shoots system were weighed to record fresh biomass, then oven-dried at 68 °C for 48 h to determine dry biomass. Water content was calculated as the difference between fresh and dry weights.

2.4. Statistical Analysis

Due to significant heteroscedasticity indicated by Levene’s test, Welch’s ANOVA and Games–Howell post hoc tests (* p < 0 < 0.5) were used to assess significant differences among group means. Relationships among root traits were evaluated using Spearman’s rank correlation; significance (** p < 0.01; * p < 0 < 0.5, two-tailed) was determined using Fisher’s r-to-z transformation with standard error calculated via the Fieller, Hartley, and Pearson formula. No data transformation was applied. These analyses were performed in SPSS v.29 software (IBM Corp., New York, NY, USA).
For multivariate analysis, data were standardized using a z-score. A hierarchical clustering heatmap and PCA were then performed in R Statistical Software [30], and the quality of representation (Cos2) for the 16 root traits was assessed using the corrplot package.

3. Results

3.1. Root Trait Variations Among Wheat Genotypes

One-way Welch’s ANOVA revealed significant differences among the genotypes in all traits except carbon and nitrogen percentages and C/N ratio (Table 2).

3.1.1. Root Architectural Traits

All architectural traits differed significantly among the three genotypes (Ae. tauschii, LNG, and N61) (Table 2, Figure 1 and Figure S3). Within Ae. tauschii, the omnibus test did not detect significant differences among accessions. However, when compared across genotypes, all Ae. tauschii accessions had significantly longer total, thin (0 < 0.5 mm diameter), and thick (0.5–1.0 mm diameter) roots than LNG and N61 (Figure 1A). Likewise, all Ae. tauschii accessions had significantly greater total and thin root surface areas than N61, and four and seven accessions had significantly greater total and thin root surface areas, respectively, than LNG (Figure 1B). For thick root surface area, only KU20-8 was significantly greater than LNG, while KU20-8, KU-2126, AT76, and IG126387 were significantly greater than N61 (Figure 1B). 0 < 0.5 Ae. tauschii accessions had significantly greater total, thin, and thick root volumes (except for the total root volume of IG47259) than N61 (Figure 1C). Four Ae. tauschii accessions had greater thin and thick root volumes, whereas only one accession showed greater total root volume than LNG (Figure 1C). These three root architectural traits of Ae. tauschii accessions were always superior, in the order of Ae. tauschii > LNG > N61. Thin roots contributed more to total root length and surface area, while thick roots contributed more to total root volume. Root dry weights tended to be higher in Ae. tauschii accessions than in LNG and N61; those of KU-2126, AT76, KU20-8, and IG126387 were significantly higher (Figure 1D). The root fresh weights of four and seven Ae tauschii accessions were significantly higher than those of LNG and N61, respectively (Figure 1D).

3.1.2. Morphological and Physiological Root Traits

Root morphological traits varied significantly among genotypes. All Ae. tauschii accessions, except IG126387, had significantly higher RTD than LNG and N61 (Figure 2A). The higher SRL (Figure 2B) and lower average root diameter (Figure 2C) of N61 than of LNG and Ae. tauschii accessions suggest that N61 had thinner roots.
No significant differences were found among genotypes in root carbon, nitrogen, or C/N ratio (Table 2).

3.1.3. Biotic Traits

Colonization by root endophytic fungi differed significantly among genotypes (Table 2, Figure S4). The Ae. tauschii accessions had higher percentages of AMF in their roots than LNG and N61 (Figure 3). Conversely, N61 had significantly higher DSE colonization than LNG and Ae. tauschii accessions. Even within the Ae. tauschii accessions, AMF and DSE colonization varied significantly: KU-2126 and AT76 had higher AMF and lower DSE colonization than other accessions; and KU-2076 and KU-2136 had significantly lower AMF and slightly higher DSE colonization. LNG had significantly lower colonization of both AMF and DSE (Figure 3).

3.1.4. Shoot System Traits

No significant differences were found among genotypes in shoot fresh weight, dry weight, or water content (Tables S4–S6).

3.2. Association Among Root Traits

AMF colonization rate was significantly and positively correlated (p < 0 < 0.5) with all root architectural traits (root length, surface area, volume, and dry weight) and RTD (Figure 4). Notably, AMF was more strongly correlated with thin root traits than with thick root traits. However, it was negatively correlated with SRL and the DSE colonization rate. In contrast, the DSE colonization rate tended to be correlated negatively with all architectural and morphological root traits except SRL. All architectural traits were strongly correlated with each other, especially within the same category (total, thin, and thick root diameters), as well as with the morphological traits, except SRL and root diameter. SRL was correlated negatively with all architectural and morphological root traits.

3.3. Wheat Accession Grouping and Association by Root Traits

The hierarchical clustering heatmap identified two main groups by root traits (Figure 5): a larger one consisted of AMF colonization rate and all other root traits except SRL, and the other consisted of DSE colonization rate and SRL. The larger group was further divided into four subgroups, in which AMF colonization rate was sub-grouped with thin roots, total root length, and surface area. Thick roots, total volume, and root fresh and dry weight were in the second subgroup, RTD in the third subgroup, and average root diameter in the fourth subgroup. Hierarchical clustering divided the accessions into two main groups: all Ae. tauschii accessions versus LNG and N61. The Ae. tauschii group was further subdivided into two subgroups: KU-2126, KU20-8, AT76, and IG126387 versus the remaining accessions. Likewise, LNG and N61 were subdivided into their own subgroups.
PCA revealed key patterns among genotypes associated with their root traits (Figure 6 and Tables S7–S9). The first two principal components (PC1 and PC2) explained 82.7% and 10.9% of the total variation (Figure 6). The Ae. tauschii accessions KU-2126, KU20-8, and AT76 were strongly associated with almost all architectural and morphological traits and AMF colonization except SRL, DSE colonization, and root diameter (Figure 6). The other Ae. tauschii accessions were similarly associated to a lesser extent. In contrast, the hexaploid N61 had positive relationships with DSE colonization and SRL, while the tetraploid LNG was not significantly related to any of the traits. These results suggest that, Ae. tauschii accessions generally have superior root traits toLNG and N61 used in this study.

4. Discussion

Root architecture, morphology, and fungal colonization differed significantly among the studied materials, with Aegilops tauschii accessions always exhibiting superior root traits compared to LNG and N61. However, inter-and intraspecific variation within the studied Ae. tauschii accessions were found.
The better root architectural traits in diploid Ae. tauschii than the polyploidy LNG and N61 could be due to the role of the D genome in lateral root development. Wang et al. [7] reported that hexaploid wheats (AABBDD) had much fewer lateral roots on the primary root than their diploid (DD) progenitors but significantly more than their tetraploid (AABB) and diploid (AA and SS) progenitors. They stated that the D genome played a crucial role in the increased number of lateral roots of hexaploid wheat than of their tetraploid progenitors and that TaLBD16-D was one of the key genes involved in the determination of lateral root number. Also, Mohammedali et al. [31] reported that primary synthetic (PS) hexaploid wheat accessions with direct D genome from diverse Ae. tauschii accessions always exceeded their tetraploid parent LNG. However, since only a tetraploid and a hexaploid genotype were used in this study, further investigation using diverse sets of tetraploid and hexaploid wheat genotypes is warranted.
Another factor with a role in the well-developed root architectural traits of the Ae. tauschii accessions could be the effect of resource-limited environments: in soil with limited nutrients, Ae. tauschii may prioritize efficient root exploration for nutrient uptake, leading to enhanced root traits [10]. On the other hand, polyploid wheat, often grown under favorable conditions with adequate fertilizer, might favor aboveground biomass with a high harvest index, leading to a trade-off with root development [15].
Among morphological traits, RTD better discriminated genotypes than average root diameter or specific root length (SRL). This was evident in N61, which had a high SRL despite its low root dry weight and length. The RTD appears to be more adaptive to stressful environments, favoring denser roots for deeper resource acquisition [32]. In contrast, N61 exhibited high SRL despite low root biomass, aligning with reports that SRL reflects resource uptake efficiency under favorable conditions [33]. The stressful conditions of the unfertilized sandy soil in our experiment highlighted the advantage of RTD for such scenarios. The negative correlation between SRL and AMF colonization observed agrees with prior findings [32].
The genetic variation, and the habitat soil environment might have contributed to differential fungal interactions with the root systems. Within the biotic traits, Ae. tauschii generally had favorable root traits and promoted AMF symbiosis, nevertheless decreased DSE colonization, as AMF preferentially colonized longer, thinner roots, supporting their functional association with fine root traits [13]. While LNG decreased the colonization of both fungi, the weak architectural and morphological root traits of N61 were colonized by DSE more than AMF [14,34,35]. These results align with previous research [8,11,14], indicating the potential of Ae. tauschii genes to enhance wheat root traits. Another factor that influenced fungal interactions could be the soil environment of the habitat, as differences in fungal colonization might also reflect nutrient acquisition strategies, similar to those mentioned above regarding root architectural traits. Ae. tauschii, adapted to nutrient-poor environments, may rely heavily on AMF symbiosis, providing carbohydrates to fungi in exchange for nutrients [19,20]. In contrast, domesticated cultivars grown under fertilized conditions might experience less pressure to secrete strigolactones, the “cry for help” hormones, to establish strong AMF relationships [36,37]. Finally, soil types from native habitats likely modulate all root trait expression, highlighting complex accession-by-environment interactions governing belowground traits [31].
The Ae. tauschii accessions used in this study represent two lineages (TauL1 and TauL2) and diverse geographic origins (China, Iran, Syria, Turkey, Turkmenistan), and showed substantial inter- and intraspecific variations in root traits [25,31]. These variations within Ae. tauschii, were more pronounced in biotic traits, particularly AMF and DSE colonization, than in architectural and morphological root traits. A clustering heatmap, incorporating both root and biotic traits, distinguished four major groups, clearly separating the Ae. tauschii accessions into two clusters. Notably, each of the two clusters contained accessions from both lineages, demonstrating the intraspecific variation within lineages, as has been reported for other traits [38,39]. A similar clustering pattern was reported for primary synthetic accessions derived directly from diverse Ae. tauschii accessions, which revealed inter- and intraspecific variation within the primary synthetics and related them to the origin of soil class of the Ae. tauschii accessions rather than to their lineage [31].
Recently, a standardized protocol was developed to rapidly introgress the entire genome of Ae. tauschii into elite wheat backgrounds [40]. This will facilitate the introduction of genetic variation from wild relatives to improve the quality of hexaploid wheat breeding pools and may directly lead to the development of more climate-resilient cultivars.

5. Conclusions

This study reveals significant variation in root architectural, morphological, and biotic traits among Ae. tauschii accessions and the cultivated wheats LNG and N61. Generally, Ae. tauschii promoted favorable root traits alongside beneficial AMF colonization and reduced DSE colonization. In contrast, the LNG exhibited a lower colonization to both fungi, while the weak root system of N61 was associated with higher DSE than AMF colonization. Clustering identified a group of Ae. tauschii accessions (KU_2126, AT76, KU20_8, and IG126387) with better root traits and stronger associations with AMF. These findings provide an initial framework for understanding the contribution of Ae. tauschii to root-fungi associations and demonstrate its potential for developing more resilient wheat genotypes.

6. Limitations

A key limitation was the reliance on morphological identification for DSE. Furthermore, the experimental design focused on assessing root traits and their association with each fungus individually, rather than on testing for direct fungal interactions.

7. Future Directions

Future work should employ molecular fungal identification and a full factorial inoculation design to study the interaction between the fungi. Expanding research to the next generation of primary synthetic hexaploids and assessing the aboveground traits and reaching the experiment to the yield will be crucial for assessing the agronomic potential of this diversity.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/agriculture15171889/s1, Table S1: Root architectural and morphological traits of nine Ae. tauschii accessions, LNG, and N61. Quantified by WinRhizo.; Table S2: Carbon and nitrogen content of root powder samples from nine Ae. tauschii accessions, LNG, and N61 analyzed by C/N corder.; Table S3: Fungal colonization in roots of nine Ae. tauschii, LNG, and N61, observed by (VHX-7000; Keyence) microscope; Table S4: Descriptive statistics of Shoot System variables for 9 Ae. tauschii Accessions, LNG, and N61; Table S5: Welch’s ANOVA for Shoot System Variables of 9 Ae. tauschii Accessions, LNG, and N61; Table S6: Games–Howell Post Hoc Comparisons of Shoot System variables for 9 Ae. tauschii accessions, LNG and N61; Table S7: Eigenvalues and variance explained by principal components in the PCA biplot of 16 root traits for nine Ae. tauschii accessions, LNG, and N61; Table S8: PCA scores out of nine Ae. tauschii accessions, LNG, and N61 for root trait variation; Table S9: Variable loading of 16 root traits and the proportion of variation in each PCA Figure S1: 0 < 0.5Daily average temperature and relative humidity in greenhouse during the experiment (March 30th to June 30th, 2023); Figure S2: Image of 11 wheat accessions root system scanned with Epson scanner for WinRhizo analysis; Figure S3: Images of scanned root fragment illustrating the subcategory classes of the root according to the diameter: Thin root was 0 < 0.5 mm, and thick root was 0.5–1.0 mm; Figure S4: Images of root endophytic fungi structure inside wheat root cells: (A) AMF Vesicles. (B) AMF Arbuscules. (C) AMF spores. (D) DSE hyphae and dark septate structure. (E,F) AMF spores in dark blue color and DSE Structure in brown color. Visualized by Keyence VHX digital microscope.

Author Contributions

Conceptualization, A.K.H.M., N.M.K., Y.S.A.G., I.S.A.T., H.T. and T.T.; data curation, A.K.H.M., N.M.K. and T.T.; formal analysis, A.K.H.M. and N.M.K.; funding acquisition, T.T.; investigation, A.K.H.M., Y.S.A.G., I.S.A.T. and T.T.; methodology, A.K.H.M., Y.S.A.G., I.S.A.T. and T.T.; project administration, T.T.; resources, H.T. and T.T.; software, A.K.H.M. and N.M.K.; supervision, T.T.; validation, A.K.H.M., Y.S.A.G., I.S.A.T. and T.T.; visualization, A.K.H.M., N.M.K. and T.T.; writing—original draft, A.K.H.M.; writing—review and editing, N.M.K., Y.S.A.G., I.S.A.T., H.T. and T.T. All authors have read and agreed to the published version of the manuscript.

Funding

This research received no external funding.

Institutional Review Board Statement

The authors confirm that all applicable ethical standards were followed. No human or animal subjects were involved in this study.

Data Availability Statement

The data presented in this study are available in the article and Supplementary Materials.

Acknowledgments

The authors express their gratitude to Researcher Maha F. A. Hassan for her valuable contributions to formal Analysis. They also extend their appreciation to the members of the Laboratory of Microbial Ecology and Molecular Breeding and the technical staff of the Arid Land Research Center, Tottori University, for their invaluable laboratory assistance.

Conflicts of Interest

All authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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Agriculture 15 01889 g001
Figure 1. Root architectural traits of Ae. tauschii accessions, LNG and N61. (A) Root length (cm), (B) surface area (cm2), and (C) volume (cm3); Across diameter classes (0 < 0.5 and 0.5–1 mm). (D) Root fresh, dry, and water content. Bars sharing the same letter within a class are not significantly different (Games–Howell test, p < 0 < 0.5). L, length; SA, surface area; V, volume.
Figure 1. Root architectural traits of Ae. tauschii accessions, LNG and N61. (A) Root length (cm), (B) surface area (cm2), and (C) volume (cm3); Across diameter classes (0 < 0.5 and 0.5–1 mm). (D) Root fresh, dry, and water content. Bars sharing the same letter within a class are not significantly different (Games–Howell test, p < 0 < 0.5). L, length; SA, surface area; V, volume.
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Figure 2. Root morphological traits of Ae. tauschii accessions, LNG, and N61. (A) Root tissue density (RTD, g/cm3), (B) specific root length (SRL, cm/g), and (C) average root diameter (cm). Bars sharing the same letter are not significantly different (Games–Howell test, p < 0 < 0.5).
Figure 2. Root morphological traits of Ae. tauschii accessions, LNG, and N61. (A) Root tissue density (RTD, g/cm3), (B) specific root length (SRL, cm/g), and (C) average root diameter (cm). Bars sharing the same letter are not significantly different (Games–Howell test, p < 0 < 0.5).
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Figure 3. Root colonization rates (%) by arbuscular mycorrhizal fungi (AMF) and Dark septate endophytes (DSE) in Ae. tauschii accessions, LNG, and N61. Bars sharing the same letter are not significantly different (Games–Howell test, p < 0 < 0.5).
Figure 3. Root colonization rates (%) by arbuscular mycorrhizal fungi (AMF) and Dark septate endophytes (DSE) in Ae. tauschii accessions, LNG, and N61. Bars sharing the same letter are not significantly different (Games–Howell test, p < 0 < 0.5).
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Figure 4. Spearman’s rank correlation coefficients between root traits and fungal colonization rates. Significance levels: * p < 0 < 0.5, ** p < 0.01. AMF, arbuscular mycorrhizal fungi colonization rate; DSE, Dark septate endophytes colonization rate; L, length; SA, surface area; V, volume; 0 < 0.5, thin roots (mm); 0.5–1, thick roots (mm); Root dry, root dry weight; RTD, root tissue density; SRL, specific root length.
Figure 4. Spearman’s rank correlation coefficients between root traits and fungal colonization rates. Significance levels: * p < 0 < 0.5, ** p < 0.01. AMF, arbuscular mycorrhizal fungi colonization rate; DSE, Dark septate endophytes colonization rate; L, length; SA, surface area; V, volume; 0 < 0.5, thin roots (mm); 0.5–1, thick roots (mm); Root dry, root dry weight; RTD, root tissue density; SRL, specific root length.
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Figure 5. Hierarchical clustering heatmap of 16 standardized root traits across accessions. The black line separates diploid Ae. tauschii accessions from LNG and N61. Red dashed lines indicate four clustering groups: (1) Ae. tauschii with superior root traits, (2) Ae. tauschii with lower root traits, (3) Langdon (LNG), and (4) Norin 61 (N61). The black dashed line differentiates trait clusters: one containing DSE colonization and specific root length (SRL), and another containing AMF colonization and all other root traits.
Figure 5. Hierarchical clustering heatmap of 16 standardized root traits across accessions. The black line separates diploid Ae. tauschii accessions from LNG and N61. Red dashed lines indicate four clustering groups: (1) Ae. tauschii with superior root traits, (2) Ae. tauschii with lower root traits, (3) Langdon (LNG), and (4) Norin 61 (N61). The black dashed line differentiates trait clusters: one containing DSE colonization and specific root length (SRL), and another containing AMF colonization and all other root traits.
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Figure 6. Principal component analysis (PCA) biplot of 16 standardized root traits across accessions. Dots represent individual accessions; vectors indicate trait contributions to the principal components (Dim1: 82.7%, Dim2: 10.9%; total variance explained: 93.6%). The analysis shows a clear separation between Ae. tauschii accessions, LNG and N61. AMF, arbuscular mycorrhizal fungi colonization; DSE, dark septate endophytes colonization; L, length; SA, surface area; V, volume; 0 < 0.5, thin roots; 0.5–1, thick roots; Root fresh/dry, root fresh/dry weight; RTD, root tissue density; SRL, specific root length.
Figure 6. Principal component analysis (PCA) biplot of 16 standardized root traits across accessions. Dots represent individual accessions; vectors indicate trait contributions to the principal components (Dim1: 82.7%, Dim2: 10.9%; total variance explained: 93.6%). The analysis shows a clear separation between Ae. tauschii accessions, LNG and N61. AMF, arbuscular mycorrhizal fungi colonization; DSE, dark septate endophytes colonization; L, length; SA, surface area; V, volume; 0 < 0.5, thin roots; 0.5–1, thick roots; Root fresh/dry, root fresh/dry weight; RTD, root tissue density; SRL, specific root length.
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Table 1. The genetic materials used in the study, with origin, and the lineage of Aegilops tauschii.
Table 1. The genetic materials used in the study, with origin, and the lineage of Aegilops tauschii.
Genebank AccessionOriginTaxonGenomeLineage
KU-2126IranAegilops tauschiiDTauL1 a
KU20-8IranAegilops tauschiiDTauL2 a
AT76ChinaAegilops tauschiiDTauL1
IG126387TurkmenistanAegilops tauschiiDTauL1
KU-2109IranAegilops tauschiiDTauL1
IG47259SyriaAegilops tauschiiDTauL1
KU-2074IranAegilops tauschiiDTauL2
KU-2076IranAegilops tauschiiDTauL2
KU-2136TurkeyAegilops tauschiiDTauL1
LPGKU2196 (LNG)American cultivarTriticum durumAB–
KT020-032 (N61)Japanese cultivarTriticum aestivumABD–
a TauL1: Aegilops tauschii Lineage 1, TauL2: Aegilops tauschii Lineage 2 [25].
Table 2. Root architectural, morphological, physiological, and biological traits and significance of differences among Aegilops tauschii and wheat accessions.
Table 2. Root architectural, morphological, physiological, and biological traits and significance of differences among Aegilops tauschii and wheat accessions.
VariableMean ± SEF-Statistic adf1df2p-Value
Root architectural trait
Total L (cm)4825 ± 35816.1061020.543≤0.0001 ***
L 0 < 0.5 (cm)4363 ± 31915.6911020.623≤0.0001 ***
L 0.5–1.0 (cm)462 ± 4525.9571020.073≤0.0001 ***
Total SA (cm2)380 ± 3017.4871020.174≤0.0001 ***
SA 0 < 0.5 (cm2)276 ± 2016.9971020.300≤0.0001 ***
SA 0.5–1.0 (cm2)104 ± 1024.1661020.049≤0.0001 ***
Total V (cm3)3.82 ± 0.3516.8681020 < 0.51≤0.0001 ***
V 0 < 0.5 (cm3)1.72 ± 0.1317.2041020.210≤0.0001 ***
V 0.5–1.0 (cm3)2.10 ± 0.2216.9761020.029≤0.0001 ***
Root fresh weight (g)2.54 ± 0.2512.8081020.635≤0.0001 ***
Root dry weight (g)0.38 ± 0.0412.9021020.190≤0.0001 ***
Root morphological trait
RTD (g/cm3)0.093 ± 0.0036.1061021.814≤0.0001 ***
SRL (cm/g)173 ± 116.2961020.890≤0.0001 ***
Average diameter (cm)0.28 ± 0.016.2511021.826≤0.0001 ***
Root physiological trait
Carbon (%)45.6 ± 0.21.8671021.7180.108
Nitrogen (%)1.43 ± 0.041.2821021.8650.299
C/N ratio33 ± 0.81.5401021.9090.191
Root biotic traits
AMF colonization rate (%)41 ± 2.051.7251021.867≤0.0001 ***
DSE colonization rate (%)20 ± 1.017.1781021.735≤0.0001 ***
Differences among accessions were analyzed by one-way Welch’s ANOVA. The F-statistic a; asymptotically F distributed the ratio of the variances between and within groups. Significance at, *** p < 0.001. L, length (cm); SA, surface area (cm2); V, volume (cm3); 0 < 0.5, thin root (mm); 0.5–1.0, thick root (mm); AMF, rate of colonization by arbuscular mycorrhizal fungi.
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Mohammedali, A.K.H.; Gorafi, Y.S.A.; Kamal, N.M.; Tahir, I.S.A.; Tsujimoto, H.; Taniguchi, T. Exploring Genetic Variation in Root Traits and Root–Fungal Associations in Aegilops tauschii. Agriculture 2025, 15, 1889. https://doi.org/10.3390/agriculture15171889

AMA Style

Mohammedali AKH, Gorafi YSA, Kamal NM, Tahir ISA, Tsujimoto H, Taniguchi T. Exploring Genetic Variation in Root Traits and Root–Fungal Associations in Aegilops tauschii. Agriculture. 2025; 15(17):1889. https://doi.org/10.3390/agriculture15171889

Chicago/Turabian Style

Mohammedali, Ahmed Khaled Hassan, Yasir Serag Alnor Gorafi, Nasrein Mohamed Kamal, Izzat Sidahmed Ali Tahir, Hisashi Tsujimoto, and Takeshi Taniguchi. 2025. "Exploring Genetic Variation in Root Traits and Root–Fungal Associations in Aegilops tauschii" Agriculture 15, no. 17: 1889. https://doi.org/10.3390/agriculture15171889

APA Style

Mohammedali, A. K. H., Gorafi, Y. S. A., Kamal, N. M., Tahir, I. S. A., Tsujimoto, H., & Taniguchi, T. (2025). Exploring Genetic Variation in Root Traits and Root–Fungal Associations in Aegilops tauschii. Agriculture, 15(17), 1889. https://doi.org/10.3390/agriculture15171889

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