Volume 17, Issue 3 (9-2025)
J Crop Breed 2025, 17(3): 45-59 |
Back to browse issues page
Download citation:
BibTeX | RIS | EndNote | Medlars | ProCite | Reference Manager | RefWorks
Send citation to:
BibTeX | RIS | EndNote | Medlars | ProCite | Reference Manager | RefWorks
Send citation to:
Dogmechi Karimi G, Bernousi I, Amini A, Alipour H. (2025). Association Analysis for Main Seedling Characteristics in Wheat Advanced Varieties and Lines under Non-Stressed and Salt-Stressed Conditions. J Crop Breed. 17(3), 45-59. doi:10.61882/jcb.2024.1503
URL: http://jcb.sanru.ac.ir/article-1-1503-en.html
URL: http://jcb.sanru.ac.ir/article-1-1503-en.html
1- Department of Plant Production and Genetics, Urmia University, Urmia, Iran
2- Seed and Plant Breeding Research Institute, Agricultural Education and Extension Research Organization, Karaj, Iran
2- Seed and Plant Breeding Research Institute, Agricultural Education and Extension Research Organization, Karaj, Iran
Abstract: (431 Views)
Extended Abstract
Background: Wheat (Triticum aestivum L.) is a strategic cereal crop that plays a vital role in global food security, serving as a primary source of nutrition for over 35% of the world's population. However, the sustainable production of this crucial crop faces numerous challenges, including abiotic stresses. Among these, salinity stress stands out as one of the most significant factors limiting wheat production in many regions worldwide. Salinity stress negatively impacts not only seed germination and seedling establishment but also severely affects various growth stages, final yield, and even grain quality parameters. The mechanisms of salt-induced damage include osmotic stress, ionic toxicity, nutritional imbalance, and oxidative stress. Given the increasing expansion of saline soils and the reduction of quality water resources, identifying and developing salt-tolerant cultivars has become essential in wheat breeding programs. Salt tolerance is a complex quantitative trait controlled by numerous genes and intricate physiological and biochemical networks. Since these mechanisms involve multiple physiological and morphological characteristics, assessing genetic diversity and identifying molecular markers associated with key physiological and morphological traits represents a crucial step for the genetic improvement of this crop. The utilization of molecular markers, particularly Simple Sequence Repeats (SSRs), which are linked to genomic regions controlling salt tolerance, enables more precise and efficient selection of tolerant genotypes through Marker-Assisted Selection (MAS).
Therefore, this study was conducted to identify genetic diversity and important molecular markers associated with key seedling traits in wheat genotypes under both non-stress and salt-stress conditions.
Methods: In the phenotypic evaluation phase, 37 wheat genotypes, including commercial varieties and promising lines, were studied in a Randomized Complete Block Design (RCBD) with three replications under two non-stress and salt stress conditions. The experiment was conducted in 2020 in the Salinity Research Greenhouse of the Cereal Research Department at the Seed and Plant Improvement Institute (SPII), Karaj, using the Hoagland nutrient solution as the growth medium.
A standard Hoagland nutrient solution was used for the control treatment (non-stress). The salt stress treatment consisted of the Hoagland solution supplemented with NaCl to achieve a salinity level of 12 dS/m.
Important physiological and morphological traits were measured after a six-week growth period, including leaf chlorophyll content (using a SPAD meter), flag leaf length, width and area (measured using ImageJ software), total biomass, and concentrations of sodium (Na⁺) and potassium (K⁺) ions (measured by flame photometry), subsequently calculating the K⁺/Na⁺ ratio.
In the molecular phase, genomic DNA was extracted from young, disease-free leaves using the CTAB method. The quality and quantity of the extracted DNA, including concentration and purity, were assessed using spectrophotometry and 1% agarose gel electrophoresis. All genotypes were evaluated using 27 SSR markers previously reported to be associated with Quantitative Trait Loci (QTLs) for salt tolerance in wheat. For morphological data analysis, the analysis of variance (ANOVA) was performed using SPSS software (version 21). In the molecular analyses, population structure was determined using the Bayesian method implemented in the Structure software (version 2.3.4). Diversity indices and molecular variance (AMOVA) were calculated using GenAlEx software (version 6.501). Principal Coordinate Analysis (PCoA) and cluster analysis based on the UPGMA algorithm were performed using DARwin software (version 6). Association analysis was conducted using the Mixed Linear Model (MLM) in TASSEL software (version 4).
Results: The ANOVA for the measured traits under both conditions revealed statistically significant differences (p < 0.01) among the genotypes for all traits: leaf chlorophyll content, flag leaf length, width and area, total biomass, sodium ion concentration, potassium ion concentration, and the K⁺/Na⁺ ratio. These results indicate the presence of high genetic diversity among the investigated genotypes, providing a basis for selecting superior genotypes. Population structure analysis based on the maximum value of ∆K classified the genotypes into two potential subpopulations (K=2). Subpopulation 1 comprised 18 genotypes (four commercial varieties and 14 promising lines), while subpopulation 2 contained 19 genotypes (10 commercial varieties and nine promising lines). Based on various diversity indices (e.g., Shannon's Information Index, Nei's gene diversity), subpopulation 2 exhibited considerably higher genetic diversity than subpopulation 1. AMOVA also confirmed significant genetic differentiation between the two subpopulations. Based on the results of the association analysis using the Mixed Linear Model (MLM), 29 significant (p < 0.01) marker-trait associations (MTAs) were identified under non-stress conditions, and 30 significant (p < 0.01) MTAs were found under salt stress conditions. Under salt stress, the markers gwm108 and gwm47 showed strong associations with sodium ion concentration and the K⁺/Na⁺ ratio, indicating their potential utility for identifying salt-tolerant genotypes.
Conclusion: This study provides valuable information regarding the genetic diversity of the investigated wheat genotypes and the genetic basis of the studied traits under salt stress. The identification of molecular markers significantly associated with key physiological and morphological traits under salinity stress enables the application of Marker-Assisted Selection for improving salt tolerance in wheat. These findings can be utilized to advance wheat breeding programs for the selection and development of high-yielding, salt-tolerant genotypes. The identified markers, particularly gwm108 and gwm47, can serve as valuable molecular tools in wheat breeding programs targeting salinity-affected regions.
Background: Wheat (Triticum aestivum L.) is a strategic cereal crop that plays a vital role in global food security, serving as a primary source of nutrition for over 35% of the world's population. However, the sustainable production of this crucial crop faces numerous challenges, including abiotic stresses. Among these, salinity stress stands out as one of the most significant factors limiting wheat production in many regions worldwide. Salinity stress negatively impacts not only seed germination and seedling establishment but also severely affects various growth stages, final yield, and even grain quality parameters. The mechanisms of salt-induced damage include osmotic stress, ionic toxicity, nutritional imbalance, and oxidative stress. Given the increasing expansion of saline soils and the reduction of quality water resources, identifying and developing salt-tolerant cultivars has become essential in wheat breeding programs. Salt tolerance is a complex quantitative trait controlled by numerous genes and intricate physiological and biochemical networks. Since these mechanisms involve multiple physiological and morphological characteristics, assessing genetic diversity and identifying molecular markers associated with key physiological and morphological traits represents a crucial step for the genetic improvement of this crop. The utilization of molecular markers, particularly Simple Sequence Repeats (SSRs), which are linked to genomic regions controlling salt tolerance, enables more precise and efficient selection of tolerant genotypes through Marker-Assisted Selection (MAS).
Therefore, this study was conducted to identify genetic diversity and important molecular markers associated with key seedling traits in wheat genotypes under both non-stress and salt-stress conditions.
Methods: In the phenotypic evaluation phase, 37 wheat genotypes, including commercial varieties and promising lines, were studied in a Randomized Complete Block Design (RCBD) with three replications under two non-stress and salt stress conditions. The experiment was conducted in 2020 in the Salinity Research Greenhouse of the Cereal Research Department at the Seed and Plant Improvement Institute (SPII), Karaj, using the Hoagland nutrient solution as the growth medium.
A standard Hoagland nutrient solution was used for the control treatment (non-stress). The salt stress treatment consisted of the Hoagland solution supplemented with NaCl to achieve a salinity level of 12 dS/m.
Important physiological and morphological traits were measured after a six-week growth period, including leaf chlorophyll content (using a SPAD meter), flag leaf length, width and area (measured using ImageJ software), total biomass, and concentrations of sodium (Na⁺) and potassium (K⁺) ions (measured by flame photometry), subsequently calculating the K⁺/Na⁺ ratio.
In the molecular phase, genomic DNA was extracted from young, disease-free leaves using the CTAB method. The quality and quantity of the extracted DNA, including concentration and purity, were assessed using spectrophotometry and 1% agarose gel electrophoresis. All genotypes were evaluated using 27 SSR markers previously reported to be associated with Quantitative Trait Loci (QTLs) for salt tolerance in wheat. For morphological data analysis, the analysis of variance (ANOVA) was performed using SPSS software (version 21). In the molecular analyses, population structure was determined using the Bayesian method implemented in the Structure software (version 2.3.4). Diversity indices and molecular variance (AMOVA) were calculated using GenAlEx software (version 6.501). Principal Coordinate Analysis (PCoA) and cluster analysis based on the UPGMA algorithm were performed using DARwin software (version 6). Association analysis was conducted using the Mixed Linear Model (MLM) in TASSEL software (version 4).
Results: The ANOVA for the measured traits under both conditions revealed statistically significant differences (p < 0.01) among the genotypes for all traits: leaf chlorophyll content, flag leaf length, width and area, total biomass, sodium ion concentration, potassium ion concentration, and the K⁺/Na⁺ ratio. These results indicate the presence of high genetic diversity among the investigated genotypes, providing a basis for selecting superior genotypes. Population structure analysis based on the maximum value of ∆K classified the genotypes into two potential subpopulations (K=2). Subpopulation 1 comprised 18 genotypes (four commercial varieties and 14 promising lines), while subpopulation 2 contained 19 genotypes (10 commercial varieties and nine promising lines). Based on various diversity indices (e.g., Shannon's Information Index, Nei's gene diversity), subpopulation 2 exhibited considerably higher genetic diversity than subpopulation 1. AMOVA also confirmed significant genetic differentiation between the two subpopulations. Based on the results of the association analysis using the Mixed Linear Model (MLM), 29 significant (p < 0.01) marker-trait associations (MTAs) were identified under non-stress conditions, and 30 significant (p < 0.01) MTAs were found under salt stress conditions. Under salt stress, the markers gwm108 and gwm47 showed strong associations with sodium ion concentration and the K⁺/Na⁺ ratio, indicating their potential utility for identifying salt-tolerant genotypes.
Conclusion: This study provides valuable information regarding the genetic diversity of the investigated wheat genotypes and the genetic basis of the studied traits under salt stress. The identification of molecular markers significantly associated with key physiological and morphological traits under salinity stress enables the application of Marker-Assisted Selection for improving salt tolerance in wheat. These findings can be utilized to advance wheat breeding programs for the selection and development of high-yielding, salt-tolerant genotypes. The identified markers, particularly gwm108 and gwm47, can serve as valuable molecular tools in wheat breeding programs targeting salinity-affected regions.
Send email to the article author
| Rights and permissions | |
 |
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. |
