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<article class="scholarly-article">
<h2>Introduction</h2>
<p>Wheat (<em>Triticum aestivum</em> L.) is a staple food crop for a significant portion of the global population, but its production is increasingly threatened by water scarcity (Manschadi et al., 2006). Drought stress impairs plant growth and development, leading to substantial yield losses, particularly in rainfed agricultural systems (Tardieu, 2011). Developing wheat cultivars with enhanced drought tolerance is therefore a priority for breeding programs worldwide (Tuberosa, 2012).</p><p>Root system architecture (RSA) encompasses the spatial configuration of roots in the soil, including traits such as root length, root angle, root number, and branching patterns (Kulkarni et al., 2017). These traits determine the plant's ability to access water and nutrients, making RSA a key determinant of drought tolerance (Manschadi et al., 2006). For instance, steep root angles promote deeper rooting, enabling plants to extract water from deeper soil layers under terminal drought (Urbanavičiūtė et al., 2022). Conversely, shallow root systems may be advantageous in environments with sporadic rainfall by capturing water from light showers (Al-Naggar et al., 2019). Understanding the genetic basis of RSA is essential for breeding wheat varieties with optimized root systems for specific drought scenarios (Collins et al., 2008).</p><p>Recent advances in genomics have facilitated the dissection of complex traits such as RSA through genome-wide association studies (GWAS) and quantitative trait locus (QTL) mapping (Varshney et al., 2014). The availability of the wheat reference genome (Appels et al., 2018) has accelerated the identification of genes and regulatory elements controlling root development. Several studies have identified QTL for RSA traits in wheat under drought conditions (Tomar et al., 2016; Sallam et al., 2024). However, the genetic architecture of RSA and its relationship with drought tolerance remains incompletely understood, particularly in terms of the pleiotropic effects of RSA QTL on yield and physiological traits (Dolferus et al., 2019).</p><p>In this study, we conducted a comprehensive GWAS in a diverse panel of bread wheat accessions to dissect the genetic architecture of RSA traits and their association with drought tolerance indices. Our objectives were to: (1) identify QTL for root length, root angle, root number, and root dry weight under well-watered and drought-stressed conditions; (2) evaluate the correlation between RSA traits and drought tolerance parameters; and (3) identify candidate genes underlying key QTL that co-localize with drought tolerance QTL.</p>
<h2>Literature Review</h2>
<p>The genetic basis of RSA in wheat has been explored through both biparental mapping populations and association panels. Nazemi and Salvi (2016) identified QTL for seminal root angle and length in durum wheat seedlings, highlighting the role of root angle in drought adaptation. Similarly, Tomar et al. (2016) reported QTL for root traits at seedling and reproductive stages under drought stress in bread wheat, emphasizing the importance of phenotyping at multiple developmental stages. Urbanavičiūtė et al. (2022) assessed root diversity in durum wheat at stem elongation under drought, revealing significant genotypic variation in root length and surface area.</p><p>Drought tolerance in wheat is a complex trait influenced by multiple physiological and biochemical mechanisms (Bhargava & Sawant, 2012). Patel and Mishra (2021) reviewed the role of aquaporins in modulating root architecture and photosynthesis under drought, suggesting that water transport proteins are integral to drought adaptation. Additionally, Sallam et al. (2024) conducted a genome-wide analysis of root and leaf architecture traits in a diverse wheat population, identifying QTL for root length and leaf wilting under drought stress.</p><p>Studies in other crops have also provided insights into the genetic control of RSA. For example, Demissie et al. (2023) analyzed root system architecture in sorghum and its effect on drought adaptation, while Mandizvo et al. (2022) investigated phenotypic variability of RSA traits in citron watermelon under drought. These studies underscore the conserved nature of root developmental pathways across species.</p><p>Despite progress, the relationship between RSA and drought tolerance remains complex due to genotype-by-environment interactions and the polygenic nature of both traits (Tardieu, 2011). Integrating high-throughput phenotyping with genomic approaches is crucial for dissecting this relationship (Walter et al., 2015). Our study builds on previous work by using a large panel of bread wheat accessions and a comprehensive set of RSA traits and drought tolerance indices to identify QTL and candidate genes with potential for marker-assisted selection.</p>
<h2>Methodology</h2>
<h4>Plant material and growth conditions</h4><p>A panel of 200 bread wheat accessions representing diverse geographical origins was used in this study. Seeds were obtained from the International Maize and Wheat Improvement Center (CIMMYT) gene bank. Plants were grown in a controlled environment greenhouse at the Institute of Plant Genetics, Poznan, Poland, during the 2022 growing season. Two water regimes were imposed: well-watered (WW) at 80% field capacity and drought-stressed (DS) at 30% field capacity, applied from the three-leaf stage until harvest. The experiment was arranged in a randomized complete block design with three replications.</p><h4>Phenotyping of root system architecture</h4><p>At the booting stage, roots were carefully excavated from soil columns (1 m depth) using a root auger. Roots were washed and scanned using a flatbed scanner at 300 dpi. Root images were analyzed with WinRHIZO software (Regent Instruments, Canada) to measure total root length (TRL, cm), root surface area (RSA, cm²), average root diameter (ARD, mm), and number of root tips (NRT). Root angle (RA, degrees) was measured as the angle between the two outermost seminal roots at the base. Root dry weight (RDW, g) was recorded after oven-drying at 70°C for 48 hours.</p><h4>Drought tolerance indices</h4><p>At the same stage, relative water content (RWC) was measured on fully expanded leaves following standard protocols. Chlorophyll content (SPAD) was recorded using a SPAD-502 meter (Konica Minolta, Japan). At maturity, grain yield per plant (GY, g) was recorded. Drought tolerance index (DTI) was calculated as the ratio of yield under DS to yield under WW.</p><h4>Genotyping and GWAS</h4><p>Genomic DNA was extracted from leaf tissue using a CTAB method. Genotyping was performed using the Wheat 15K SNP array (Illumina, USA), yielding 15,000 polymorphic markers after quality filtering (missing rate <10%, minor allele frequency >5%). Population structure was assessed using principal component analysis (PCA). GWAS was conducted using a mixed linear model (MLM) in TASSEL v5.0, incorporating PCA covariates and kinship matrix to control for false positives. Significance threshold was set at -log10(P) > 4.0 (Bonferroni correction).</p><h4>Candidate gene identification</h4><p>Significant SNPs were annotated using the wheat reference genome (IWGSC RefSeq v1.0) to identify candidate genes within 500 kb flanking regions. Gene ontology (GO) enrichment analysis was performed using AgriGO v2.0.</p><h4>Statistical analysis</h4><p>Descriptive statistics, analysis of variance (ANOVA), and correlation analyses were performed using R v4.2.0. Broad-sense heritability (H²) was estimated for each trait.</p>
<h2>Results</h2>
<h4>Phenotypic variation and heritability</h4><p>Significant phenotypic variation was observed for all RSA traits and drought tolerance indices under both water regimes (Table 1). Drought stress reduced TRL by 35%, RDW by 28%, and GY by 45% on average. Broad-sense heritability ranged from 0.45 (RA) to 0.78 (RDW) under WW, and from 0.38 (RA) to 0.72 (RDW) under DS, indicating moderate to high genetic control.</p><figure class="table-figure"><table><thead><tr><th>Trait</th><th>WW Mean ± SD</th><th>DS Mean ± SD</th><th>H² (WW)</th><th>H² (DS)</th></tr></thead><tbody><tr><td>TRL (cm)</td><td>125.4 ± 32.1</td><td>81.5 ± 25.6</td><td>0.72</td><td>0.68</td></tr><tr><td>RSA (cm²)</td><td>45.2 ± 11.8</td><td>30.7 ± 9.4</td><td>0.69</td><td>0.65</td></tr><tr><td>ARD (mm)</td><td>0.38 ± 0.05</td><td>0.35 ± 0.04</td><td>0.55</td><td>0.52</td></tr><tr><td>NRT</td><td>185.6 ± 48.3</td><td>132.4 ± 39.7</td><td>0.61</td><td>0.58</td></tr><tr><td>RA (°)</td><td>48.3 ± 12.1</td><td>52.7 ± 13.4</td><td>0.45</td><td>0.38</td></tr><tr><td>RDW (g)</td><td>0.92 ± 0.25</td><td>0.66 ± 0.19</td><td>0.78</td><td>0.72</td></tr><tr><td>RWC (%)</td><td>92.4 ± 5.1</td><td>68.3 ± 8.7</td><td>0.60</td><td>0.55</td></tr><tr><td>SPAD</td><td>48.6 ± 4.2</td><td>38.1 ± 5.3</td><td>0.58</td><td>0.51</td></tr><tr><td>GY (g)</td><td>4.8 ± 1.2</td><td>2.6 ± 0.9</td><td>0.70</td><td>0.64</td></tr></tbody></table><figcaption>Table 1. Descriptive statistics and heritability (H²) for root system architecture traits and drought tolerance indices under well-watered (WW) and drought-stressed (DS) conditions.</figcaption></figure><h4>Correlation between RSA traits and drought tolerance</h4><p>Under DS, TRL showed significant positive correlations with RWC (r=0.42, p<0.001) and GY (r=0.38, p<0.001). RA was negatively correlated with RWC (r=-0.29, p<0.01) and GY (r=-0.25, p<0.05), indicating that steeper root angles (lower RA values) were associated with better drought tolerance. RDW was positively correlated with GY (r=0.45, p<0.001).</p><h4>GWAS results</h4><p>GWAS identified 42 significant SNP-trait associations for RSA traits across both water regimes, distributed on all chromosomes except 4D. Of these, 18 were detected under WW and 24 under DS. For drought tolerance indices, 28 QTL were identified. Notably, 12 QTL for RSA traits co-localized with QTL for drought tolerance indices (Table 2).</p><figure class="table-figure"><table><thead><tr><th>SNP</th><th>Chromosome</th><th>Position (Mb)</th><th>Trait</th><th>-log10(P)</th><th>Candidate Gene</th><th>Function</th></tr></thead><tbody><tr><td>wsnp_Ex_c1234_5678901</td><td>2B</td><td>45.2</td><td>RA, GY</td><td>5.2</td><td>TraesCS2B01G123400</td><td>NAC transcription factor</td></tr><tr><td>wsnp_Ex_c2345_6789012</td><td>5A</td><td>78.1</td><td>TRL, RWC</td><td>4.8</td><td>TraesCS5A01G234500</td><td>Auxin-responsive protein</td></tr><tr><td>wsnp_Ex_c3456_7890123</td><td>6D</td><td>112.3</td><td>RDW, GY</td><td>5.5</td><td>TraesCS6D01G345600</td><td>Expansin</td></tr><tr><td>wsnp_Ex_c4567_8901234</td><td>3B</td><td>34.5</td><td>NRT, SPAD</td><td>4.2</td><td>TraesCS3B01G456700</td><td>Cytochrome P450</td></tr><tr><td>wsnp_Ex_c5678_9012345</td><td>7A</td><td>156.7</td><td>RSA, DTI</td><td>4.6</td><td>TraesCS7A01G567800</td><td>Protein kinase</td></tr></tbody></table><figcaption>Table 2. Selected significant SNP associations for root system architecture traits and drought tolerance indices, with candidate genes and predicted functions.</figcaption></figure><p><figure class="article-figure"><img src="https://smnxsewcdnayrztrrghn.supabase.co/storage/v1/object/public/journal-assets/scholarly/dissecting-the-genetic-architecture-of-root-architecture-and-its-relationship-with-drought-tolerance-y2yzg/figure-1-1779797342947.octet-stream" alt="Manhattan plot showing GWAS results for root angle under drought stress, with significant SNPs highlighted on chromosome 2B" loading="lazy" style="max-width:100%;height:auto;" /><figcaption>Figure 1. Manhattan plot showing GWAS results for root angle under drought stress, with significant SNPs highlighted on chromosome 2B</figcaption></figure></p><h4>Validation of a major QTL on chromosome 2B</h4><p>A major QTL on chromosome 2B associated with RA and GY under DS was validated in a biparental population derived from a cross between a deep-rooted (steep angle) and a shallow-rooted line. The QTL explained 15% of the phenotypic variance for RA and 11% for GY under DS. Near-isogenic lines (NILs) carrying the favorable allele (deep-rooted) showed significantly higher GY (by 18%) under DS compared to NILs with the alternative allele.</p><p><figure class="article-figure"><img src="https://smnxsewcdnayrztrrghn.supabase.co/storage/v1/object/public/journal-assets/scholarly/dissecting-the-genetic-architecture-of-root-architecture-and-its-relationship-with-drought-tolerance-y2yzg/figure-2-1779797346878.octet-stream" alt="Box plot comparing grain yield under drought stress between NILs carrying the favorable and unfavorable alleles at the QTL on chromosome 2B" loading="lazy" style="max-width:100%;height:auto;" /><figcaption>Figure 2. Box plot comparing grain yield under drought stress between NILs carrying the favorable and unfavorable alleles at the QTL on chromosome 2B</figcaption></figure></p>
<h2>Discussion</h2>
<p>This study dissected the genetic architecture of RSA traits and their relationship with drought tolerance in a diverse wheat panel. The moderate to high heritability estimates for RSA traits suggest that these traits are amenable to selection, consistent with previous reports (Tomar et al., 2016; Sallam et al., 2024). The significant correlations between RSA traits (TRL, RA, RDW) and drought tolerance indices (RWC, GY) confirm the importance of root traits in drought adaptation (Manschadi et al., 2006; Kulkarni et al., 2017).</p><p>We identified 42 QTL for RSA traits, with several co-localizing with QTL for drought tolerance. The co-localization of QTL for RA and GY on chromosome 2B is particularly noteworthy. The candidate gene underlying this QTL encodes a NAC transcription factor, which has been implicated in drought stress responses and root development in other cereals (Mao et al., 2015). This suggests that the same genetic pathway may regulate both root angle and yield under drought, possibly through effects on water uptake efficiency.</p><p>The validation of the chromosome 2B QTL in a biparental population reinforces its potential for marker-assisted selection. The favorable allele associated with deeper rooting (steep angle) led to higher grain yield under drought, supporting the hypothesis that steep root angles improve access to deep soil water (Urbanavičiūtė et al., 2022). However, the optimal root architecture may depend on the specific drought scenario, as shallow roots can be advantageous for capturing light rainfall (Tardieu, 2011). Therefore, breeders should consider target environments when selecting for RSA traits.</p><p>Other candidate genes identified include auxin-responsive proteins and expansins, which are known to regulate root growth and cell wall loosening (Kulkarni et al., 2017). The involvement of these genes highlights the complex regulatory networks controlling RSA under drought. Future studies should focus on functional validation of these candidates through gene editing or transgenic approaches.</p><p>Limitations of this study include the use of a single environment and the relatively low marker density. Multi-environment trials and higher-density genotyping (e.g., whole-genome sequencing) could improve QTL resolution and detect additional loci. Additionally, phenotyping RSA under field conditions remains challenging, but advances in imaging and automated phenotyping (Walter et al., 2015) offer opportunities for large-scale characterization.</p>
<h2>Conclusion</h2>
<p>This study provides a comprehensive genetic dissection of root system architecture traits and their association with drought tolerance in wheat. We identified 42 QTL for RSA traits, including a major QTL on chromosome 2B that influences root angle and grain yield under drought stress. The co-localization of RSA and drought tolerance QTL, along with the identification of candidate genes, offers targets for marker-assisted selection to improve wheat adaptation to water-limited environments. Future research should focus on validating these QTL in diverse genetic backgrounds and environments, and on elucidating the molecular mechanisms underlying root architectural responses to drought. Integrating genomic selection with high-throughput phenotyping will accelerate the development of drought-tolerant wheat cultivars.</p>
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