Detailed Genetic Analysis for Identifying QTLs Associated with Drought Tolerance at Seed Germination and Seedling Stages in Barley

GWAS identifies novel loci linked to seedling growth traits in highly diverse barley population under drought stress

Climate changes refer to long-term shifts in temperature and weather patterns that may cause drought, one of the major stresses hindering seed germination, plant growth, and crop productivity. Barley (Hordeum vulgare L) is considered one of the most drought-stress-tolerant cereals and may be used for elucidating genes for drought tolerance at seed germination and seedling stages that would pave the way toward improving the performance of all cereals. The current study was performed at IPK-Gatersleben (Germany) in 2023. Our aim was to explore the genetic basis of germination and seedling traits under drought stress (20% PEG6000 treatment) in a 198 global spring barley collection genotyped with 38,632 SNPs via Genotyping by Sequencing (GBS). The drought treatment significantly reduced the seed germination parameters and seedling traits in the genotypes of a global barley collection. Drought tolerance indices (DTI) for the measured germination and seedling traits indicate delayed and lower germination speed under drought stress than the control. The shoot fresh weight was the most affected trait, with a DTI of 37.4, followed by the seedling fresh weight SDLFW (DTI = 46.3) and root fresh weight (DTI = 47). In contrast, the root length DTI was the least affected trait by drought (78.2), followed by RDW DTI (72.8). GWAS was conducted using single-locus (CMLM) and multi-locus models (MLMM, Farm-CPU, BLINK), with significant marker-trait associations determined at -log10 (1.29E-06) ≥ 5.88. In our present study, we identified 79 highly significant SNPs distributed across the seven barley chromosomes related to the germination and seedling growth parameters under both control and drought conditions. Gene annotation of these highly significant SNPs revealed that 35 SNPs were in the exonic regions of genes that play roles in important plant biological and physiological processes. Further analysis exhibited 35 high-confidence candidate genes influencing barley germination and seedling growth under control and drought conditions. These genes represent promising targets for breeding and genetic enhancement efforts to improve drought tolerance in barley, potentially extending these benefits to other cereal crops.

Integrating Physiology, Transcriptome, and Metabolome Analyses Reveals the Drought Response in Two Quinoa Cultivars with Contrasting Drought Tolerance

Quinoa (Chenopodium quinoa Willd.) is an annual broadleaf plant belonging to the Amaranthaceae family. It is a nutritious food crop and is considered to be drought-tolerant, but drought is still one of the most important abiotic stress factors limiting its yield. Quinoa responses to drought are related to drought intensity and genotype. This study used two different drought-responsive quinoa cultivars, LL1 (drought-tolerant) and ZK1 (drought-sensitive), to reveal the important mechanisms of drought response in quinoa by combining physiological, transcriptomic, and metabolomic analyses. The physiological analysis indicated that Chla/Chlb might be important for drought tolerance in quinoa. A total of 1756 and 764 differentially expressed genes (DEGs) were identified in LL1 and ZK1, respectively. GO (Gene Ontology) enrichment analysis identified 52 common GO terms, but response to abscisic acid (GO:0009737) and response to osmotic stress (GO:0006970) were only enriched in LL1. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis revealed that glycerophospholipid metabolism (ko00564) and cysteine and methionine metabolism (ko00270) ranked at the top of the list in both cultivars. A total of 1844 metabolites were identified by metabolomic analysis. "Lipids and lipid-like" molecules had the highest proportions. The DEMs in LL1 and ZK1 were mainly categorized 6 and 4 Human Metabolome Database (HMDB) superclasses, respectively. KEGG analysis revealed that the 'α-linolenic acid metabolism' was enriched in both LL1 and ZK1. Joint KEGG analysis also revealed that the 'α-linolenic acid metabolism' pathway was enriched by both the DEGs and DEMs of LL1. There were 17 DEGs and 8 DEMs enriched in this pathway, and methyl jasmonate (MeJA) may play an important role in the drought response of quinoa. This study will provide information for the identification of drought resistance in quinoa, research on the molecular mechanism of drought resistance, and genetic breeding for drought resistance in quinoa.

Genetic Control of Tolerance to Drought Stress in Wild Soybean (Glycine soja) at the Vegetative and the Germination Stages

Drought stress, which is becoming more prevalent due to climate change, is a significant abiotic factor that adversely impacts crop production and yield stability. Cultivated soybean (Glycine max), a versatile crop for humans and animals, exhibits sensitivity to drought, resulting in reduced growth and development under drought conditions. However, few genetic studies have assessed wild soybean's (Glycine soja) response to drought stress. In this work, we conducted a genome-wide association study (GWAS) and analysis of wild soybean accessions to identify loci responsible for drought tolerance at the vegetative (n = 187) and the germination stages (n = 135) using the available resequencing data. The GWAS analysis of the leaf wilting score (LWS) identified eight single-nucleotide polymorphisms (SNPs) on chromosomes 10, 11, and 19. Of these, wild soybeans with both SNPs on chromosomes 10 (adenine) and 11 (thymine) produced lower LWS, indicating that these SNPs have an important role in the genetic effect on LWS for drought tolerance at the vegetative stage. At the germination stage, nine SNPs associated with five phenotypic measurements were identified on chromosomes 6, 9, 10, 13, 16, and 17, and the genomic regions identified at the germination stage were different from those identified for the LWS, supporting our previous finding that there may not be a robust correlation between the genes influencing phenotypes at the germination and vegetative stages. This research will benefit marker-assisted breeding programs aimed at enhancing drought tolerance in soybeans.

Detection of closely linked QTLs and candidate genes controlling germination indices in response to drought and salinity stresses in barley

The aim of current study was to identify closely linked QTLs and candidate genes related to germination indices under control, salinity and drought conditions in barley. A total of nine (a major), 28 (eight major) and 34 (five major) closely linked QTLs were mapped on the seven chromosomes in response to control, drought and salinity conditions using genome-wide composite interval mapping, respectively. The major QTLs can be used in marker-assisted selection (MAS) projects to increase tolerance to drought and salinity stresses during the germination. Overall, 422 unique candidate genes were associated with most major QTLs. Moreover, gene ontology analysis showed that candidate genes mostly involved in biological process related to signal transduction and response to stimulus in the pathway of resistance to drought and salinity stresses. Also, the protein-protein interaction network was identified 10 genes. Furthermore, 10 genes were associated with receptor-like kinase family. In addition, 16 transcription factors were detected. Three transcription factors including B3, bHLH, and FAR1 had the most encoding genes. Totally, 60 microRNAs were traced to regulate the target genes. Finally, the key genes are a suitable and reliable source for future studies to improve resistance to abiotic stress during the germination of barley.

Genome-wide scanning to identify and validate single nucleotide polymorphism markers associated with drought tolerance in spring wheat seedlings

Unlike other growth stages of wheat, very few studies on drought tolerance have been done at the seedling stage, and this is due to the complexity and sensitivity of this stage to drought stress resulting from climate change. As a result, the drought tolerance of wheat seedlings is poorly understood and very few genes associated with drought tolerance at this stage were identified. To address this challenge, a set of 172 spring wheat genotypes representing 20 different countries was evaluated under drought stress at the seedling stage. Drought stress was applied on all tested genotypes by water withholding for 13 days. Two types of traits, namely morphological and physiological traits were scored on the leaves of all tested genotypes. Genome-wide association study (GWAS) is one of the effective genetic analysis methods that was used to identify target single nucleotide polymorphism (SNP) markers and candidate genes for later use in marker-assisted selection. The tested plant materials were genotyped using 25k Infinium iSelect array (25K) (herein after it will be identified as 25K) (for 172 genotypes) and genotyping-by-sequencing (GBS) (for 103 genotypes), respectively. The results of genotyping revealed 21,093 25K and 11,362 GBS-SNPs, which were used to perform GWAS analysis for all scored traits. The results of GWAS revealed that 131 and 55 significant SNPs were controlling morphological and physiological traits, respectively. Moreover, a total of eight and seven SNP markers were found to be associated with more than one morphological and physiological trait under drought stress, respectively. Remarkably, 10 significant SNPs found in this study were previously reported for their association with drought tolerance in wheat. Out of the 10 validated SNP markers, four SNPs were associated with drought at the seedling stage, while the remaining six SNPs were associated with drought stress at the reproductive stage. Moreover, the results of gene enrichment revealed 18 and six pathways as highly significant biological and molecular pathways, respectively. The selection based on drought-tolerant alleles revealed 15 genotypes with the highest number of different drought-tolerant alleles. These genotypes can be used as candidate parents in future breeding programs to produce highly drought-tolerant genotypes with high genetic diversity. Our findings in this study provide novel markers and useful information on the genetic basis of drought tolerance at early growth stages.

Breeding for water-use efficiency in wheat: progress, challenges and prospects

Drought poses a significant challenge to wheat production globally, leading to substantial yield losses and affecting various agronomic and physiological traits. The genetic route offers potential solutions to improve water-use efficiency (WUE) in wheat and mitigate the negative impacts of drought stress. Breeding for drought tolerance involves selecting desirable plants such as efficient water usage, deep root systems, delayed senescence, and late wilting point. Biomarkers, automated and high-throughput techniques, and QTL genes are crucial in enhancing breeding strategies and developing wheat varieties with improved resilience to water scarcity. Moreover, the role of root system architecture (RSA) in water-use efficiency is vital, as roots play a key role in nutrient and water uptake. Genetic engineering techniques offer promising avenues to introduce desirable RSA traits in wheat to enhance drought tolerance. These technologies enable targeted modifications in DNA sequences, facilitating the development of drought-tolerant wheat germplasm. The article highlighted the techniques that could play a role in mitigating drought stress in wheat.

Environmental parameters factors exploration on lettuce seed germination with hydrogel

Lettuce (Lactuca sativa) germination is sensitive to environmental conditions. Recently, hydrogel has received increased attention as an alternative media to soil for seed germination. Compared to soil seeding, hydrogel-aided germination provides more controlled seeding environments. However, there are still challenges preventing hydrogel-aided seed germination from being widely used in industry production or academic studies, such as hydrogel formulation variations, seeding operation standardization, and germination evaluation. In this study, we tested how the combination of multiple environmental conditions affect lettuce seed germination time, which is measured as the time needed for the first pair of leaves to appear (leaf emergence) or, alternatively, the third leaf to appear (leaf development). We found that germination time and success rate of two lettuce varieties (Iceberg A and Butter Crunch) showed different sensitivities to pH, Hoagland formulations and concentrations, light intensity, and hydrogel content. We have conducted statistical analysis on the correlation between germination time and these environmental conditions.

A High-Resolution Linkage Map Construction and QTL Analysis for Morphological Traits in Anthurium (Anthurium andraeanum Linden)

Anthurium andraeanum Linden is a prominent ornamental plant belonging to the family Araceae and is cultivated worldwide. The morphology characteristics are crucial because they significantly impact ornamental values, commercial properties, and the efficiency of space utilization in production. However, only a few related investigations have been conducted in anthurium to date. In this study, an F1 genetic segregation population containing 160 progenies was generated through hybridization between potted and cut anthurium varieties. Fifteen morphological traits were assessed and revealed substantial levels of genetic variation and widespread positive correlation. Based on specific length amplified fragment (SLAF) sequencing technology, 8171 single nucleotide polymorphism (SNP) markers were developed, and the high-density linkage map of 2202.27 cM in length distributed on 15 linkage groups was constructed successfully, with an average distance of 0.30 cM. Using the inclusive composite interval mapping (ICIM) method, 59 QTLs related to 15 key morphological traits were successfully identified, which explained phenotypic variance (PVE) ranging from 6.21% to 17.74%. Thirty-three of those associated with 13 traits were designated as major QTLs with PVE > 10%. These findings offer valuable insights into the genetic basis of quantitative traits and are beneficial for molecular marker-assisted selection (MAS) in anthurium breeding.

Plant Tolerance to Drought Stress with Emphasis on Wheat

Environmental stresses, such as drought, have negative effects on crop yield. Drought is a stress whose impact tends to increase in some critical regions. However, the worldwide population is continuously increasing and climate change may affect its food supply in the upcoming years. Therefore, there is an ongoing effort to understand the molecular processes that may contribute to improving drought tolerance of strategic crops. These investigations should contribute to delivering drought-tolerant cultivars by selective breeding. For this reason, it is worthwhile to review regularly the literature concerning the molecular mechanisms and technologies that could facilitate gene pyramiding for drought tolerance. This review summarizes achievements obtained using QTL mapping, genomics, synteny, epigenetics, and transgenics for the selective breeding of drought-tolerant wheat cultivars. Synthetic apomixis combined with the msh1 mutation opens the way to induce and stabilize epigenomes in crops, which offers the potential of accelerating selective breeding for drought tolerance in arid and semi-arid regions.

Impact of climate perturbations on seeds and seed quality for global agriculture

In agriculture, seeds are the most basic and vital input on which croplands productivity depends. These implies a good starting material, good production lines and good storage options. High-quality seed lots must be free of pests and pathogens and contain a required degree of genetic purity. Seeds need also to be stored in good condition between harvest and later sowing, to insure later on the field a good plant density and higher crop yield. In general, these parameters are already widely accepted and considered in many countries where advanced technologies evaluate them. However, the more and more frequently devastating climate changes observed around the world has put seed quality under threat, and current seeds may not be adapted to hazardous and unpredictable conditions. Climate-related factors such as temperature and water availability directly affect seed development and later germination. For these reasons, investigating seed quality in response to climate changes is a step to propose new crop varieties and practices that will bring solutions for our future.

Screening Spring Wheat Genotypes for TaDreb-B1 and Fehw3 Genes under Severe Drought Stress at the Germination Stage Using KASP Technology

Drought stress is a major yield-limiting factor throughout the world in wheat (Triticum aestivum L.), causing losses of up to 80% of the total yield. The identification of factors affecting drought stress tolerance in the seedling stage is especially important to increase adaptation and accelerate the grain yield potential. In the current study, 41 spring wheat genotypes were tested for their tolerance to drought at the germination stage under two different polyethylene glycol concentrations (PEG) of 25% and 30%. For this purpose, twenty seedlings from each genotype were evaluated in triplicate with a randomized complete block design (RCBD) in a controlled growth chamber. The following nine parameters were recorded: germination pace (GP), germination percentage (G%), number of roots (NR), shoot length (SL), root length (RL), shoot-root length ratio (SRR), fresh biomass weight (FBW), dry biomass weight (DBW), and water content (WC). An analysis of variance (ANOVA) revealed highly significant differences (p < 0.01) among the genotypes, treatments (PEG25%, PEG30%) and genotypes × treatment interaction, for all traits. The broad-sense heritability (H2) estimates were very high in both concentrations. They ranged from 89.4 to 98.9% under PEG25% and from 70.8 to 98.7% under PEG30%. Citr15314 (Afghanistan) was among the best performing genotypes under both concentrations for most of the germination traits. Two KASP markers for TaDreb-B1 and Fehw3 genes were used to screen all genotypes and to study the effect of these on drought tolerance at the germination stage. All genotypes with Fehw3 (only) showed a better performance for most traits under both concentrations compared to other genotypes having TaDreb-B1 or having both genes. To our knowledge, this work is the first report showing the effect of the two genes on germination traits under severe drought stress conditions.

Validation of a QTL on Chromosome 1DS Showing a Major Effect on Salt Tolerance in Winter Wheat

Salt stress is one the most destructive abiotic stressors, causing yield losses in wheat worldwide. A prerequisite for improving salt tolerance is the identification of traits for screening genotypes and uncovering causative genes. Two populations of F3 lines developed from crosses between sensitive and tolerant parents were tested for salt tolerance at the seedling stage. Based on their response, the offspring were classified as salt sensitive and tolerant. Under saline conditions, tolerant genotypes showed lower Na+ and proline content but higher K+, higher chlorophyll content, higher K+/Na+ ratio, higher PSII activity levels, and higher photochemical efficiency, and were selected for further molecular analysis. Five stress responsive QTL identified in a previous study were validated in the populations. A QTL on the short arm of chromosome 1D showed large allelic effects in several salt tolerant related traits. An expression analysis of associated candidate genes showed that TraesCS1D02G052200 and TraesCS5B02G368800 had the highest expression in most tissues. Furthermore, qRT-PCR expression analysis revealed that ZIP-7 had higher differential expressions under saline conditions compared to KefC, AtABC8 and 6-SFT. This study provides information on the genetic and molecular basis of salt tolerance that could be useful in development of salt-tolerant wheat varieties.

Growth responses and genetic variation among highly ecologically diverse spring wheat genotypes grown under seawater stress

Most of the freshwaters worldwide are used for agriculture. Freshwater sources are expected to decline and will not suffice to support the food production needed for the growing population. Therefore, growing crops with seawater might constitute a solution. However, very little work has been done on the effect of seawater stress on wheat, an important cereal crop. The present study aimed to determine whether particular wheat genotypes provided better resistance to seawater stress. A set of 80 highly diverse spring wheat genotypes collected from different countries in Europe, Asia, Africa, North and South America was exposed to 50% seawater stress at the early growth stage. Four seeding shoot and root traits were scored for all genotypes. High genetic variations were found among all genotypes for the epicotyl length (EL), hypocotyl length (HL), number of radicles (NOR), and fresh weight (FW). Eight genotypes with high-performance scores of seedling traits were selected. The correlation analyses revealed highly significant correlations among all traits scored in this study. The strongest correlation was found between the NOR and the other seeding traits. Thus, the NOR might be an important adaptive trait for seawater tolerance. The genetic diversity among all genotypes was investigated based on genetic distance. A wide range of genetic distances among all genotypes was found. There was also a great genetic distance among the eight selected genotypes. In particular, the genetic distance between ATRI 5310 (France) and the other seven genotypes was the greatest. Such high genetic diversity might be utilized to select highly divergent genotypes for crossing in a future breeding program. The present study provides very useful information on the presence of different genetic resources in wheat for seawater tolerance.

Genetic and morpho-physiological analyses of the tolerance and recovery mechanisms in seedling stage spring wheat under drought stress

Drought is one of the complex abiotic stresses that affect the growth and production of wheat in arid and semiarid countries. In this study, a set of 172 diverse spring wheat genotypes from 20 different countries were assessed under drought stress at the seedling stage. Besides seedling length, two types of traits were recorded, namely: tolerance traits (days to wilting, leaf wilting, and the sum of leaf wilting), and recovery traits (days to regrowth, regrowth biomass, and drought survival rate). In addition, tolerance index, recovery index, and drought tolerance index (DTI) were estimated to select the most drought tolerant genotypes. Moreover, leaf protein content (P), amino acid (AM), proline content (PRO), glucose (G), fructose (F), and total soluble carbohydrates (TSC) were measured under control and drought conditions to study the changes in each physiological trait due to drought stress. All genotypes showed a high significant genetic variation in all the physio-morphological traits scored under drought stress. High phenotypic and genotypic correlations were found among all seedling morphological traits. Among the studied indices, the drought tolerance index (DTI) had the highest phenotypic and genotypic correlations with all tolerance and recovery traits. The broad-sense heritability (H²) estimates were high for morphological traits (83.85–92.27), while the physiological traits ranged from 96.41 to 98.68 under the control conditions and from 97.13 to 99.99 under drought stress. The averages of the physiological traits (proteins, amino acids, proline, glucose, fructose, and total soluble carbohydrates) denoted under drought stress were higher than those recorded under well-watered conditions except for proteins. In this regard, amino acids, glucose, and total soluble carbohydrates had a significant correlation with all morphological traits. The selection for drought tolerance revealed 10 tolerant genotypes from different countries (8 genotypes from Egypt, one from Morocco, and one from the United States). These selected genotypes were screened for the presence of nine specific TaDREB1 alleles. Six primers were polymorphic among the selected genotypes. Genetic diversity among the selected genotypes was investigated using 21,450 SNP markers. The results of the study shed light on the different mechanisms for drought tolerance that wheat plants use to tolerate and survive under drought stress. The genetic analysis performed in this study suggested the most suitable genotypes for selective breeding at the seedling stage under water deficit.

Association mapping and candidate genes for physiological non-destructive traits: Chlorophyll content, canopy temperature, and specific leaf area under normal and saline conditions in wheat

Wheat plants experience substantial physiological adaptation when exposed to salt stress. Identifying such physiological mechanisms and their genetic control is especially important to improve its salt tolerance. In this study, leaf chlorophyll content (CC), leaf canopy temperature (CT), and specific leaf area (SLA) were scored in a set of 153 (103 having the best genotypic data were used for GWAS analysis) highly diverse wheat genotypes under control and salt stress. On average, CC and SLA decreased under salt stress, while the CT average was higher under salt stress compared to the control. CT was negatively and significantly correlated with CC under both conditions, while no correlation was found between SLA and CC and CT together. High genetic variation and broad-sense-heritability estimates were found among genotypes for all traits. The genome wide association study revealed important QTLs for CC under both conditions (10) and SLA under salt stress (four). These QTLs were located on chromosomes 1B, 2B, 2D, 3A, 3B, 5A, 5B, and 7B. All QTLs detected in this study had major effects with R² extending from 20.20% to 30.90%. The analysis of gene annotation revealed three important candidate genes (TraesCS5A02G355900, TraesCS1B02G479100, and TraesCS2D02G509500). These genes are found to be involved in the response to salt stress in wheat with high expression levels under salt stress compared to control based on mining in data bases.

Role of Signaling Molecules Sodium Nitroprusside and Arginine in Alleviating Salt-Induced Oxidative Stress in Wheat

Nitric oxide (NO) is a well-accepted signaling molecule that has regulatory effects on plants under various stresses. Salinity is a major issue that adversely affects plant growth and productivity. The current study was carried out to investigate changes in the growth, biochemical parameters, and yield of wheat plants in response to NO donors, namely sodium nitroprusside (SNP) (2.5 and 5.0 mM) and arginine (10 and 20 mM), under two salinity levels (1.2 mM and 85.5 mM NaCl). Salinity stress significantly decreased the lengths and weights of plant parts (shoot, tiller, and root) and reduced the flag leaf area, photosynthetic pigments, indole acetic acid (IAA), and yield and its components. Moreover, salt stress induced a significant accumulation of some osmoprotectants (total soluble sugars (TSS) and amino acids, especially proline) and triggered the accumulation of hydrogen peroxide (H₂O₂) and lipid peroxidation in wheat leaves. In contrast, arginine and SNP treatments significantly mitigated the negative impacts of salinity on growth and productivity via enhancing photosynthetic pigments, nitrate reductase, phenolic compounds, IAA, TSS, free amino acids, and proline. In addition, SNP and arginine potentially reduced oxidative damage by decreasing H₂O₂ and lipid peroxidation through the induction of antioxidant enzymes. The individual amino acid composition of wheat grains under the interactive effect of salinity and NO sources has been scarcely documented until now. In this study, the NO sources restrained the reduction in essential amino acids (isoleucine and lysine) of wheat grains under salinity stress and further stimulated the contents of non-essential and total aromatic amino acids. Interestingly, the applied protectants recovered the decrease in arginine and serine induced by salinity stress. Thus, SNP or arginine at the levels of 5.0 and 20 mM, respectively, had a profound effect on modulating the salt stress of wheat throughout the life cycle.

Identification of Putative SNP Markers Associated with Resistance to Egyptian Loose Smut Race(s) in Spring Barley

Loose smut (LS) disease is a serious problem that affects barley yield. Breeding of resistant cultivars and identifying new genes controlling LS has received very little attention. Therefore, it is important to understand the genetic basis of LS control in order to genetically improve LS resistance. To address this challenge, a set of 57 highly diverse barley genotypes were inoculated with Egyptian loose smut race(s) and the infected seeds/plants were evaluated in two growing seasons. Loose smut resistance (%) was scored on each genotype. High genetic variation was found among all tested genotypes indicating considerable differences in LS resistance that can be used for breeding. The broad-sense heritability (H²) of LS (0.95) was found. Moreover, genotyping-by-sequencing (GBS) was performed on all genotypes and generated in 16,966 SNP markers which were used for genetic association analysis using single-marker analysis. The analysis identified 27 significant SNPs distributed across all seven chromosomes that were associated with LS resistance. One SNP (S6_17854595) was located within the HORVU6Hr1G010050 gene model that encodes a protein kinase domain-containing protein (similar to the Un8 LS resistance gene, which contains two kinase domains). A TaqMan marker (0751D06 F6/R6) for the Un8 gene was tested in the diverse collection. The results indicated that none of the Egyptian genotypes had the Un8 gene. The result of this study provided new information on the genetic control of LS resistance. Moreover, good resistance genotypes were identified and can be used for breeding cultivars with improved resistance to Egyptian LS.

Overview of Identified Genomic Regions Associated with Various Agronomic and Physiological Traits in Barley under Abiotic Stresses

Climate change has caused breeders to focus on varieties that are able to grow under unfavorable conditions, such as drought, high and low temperatures, salinity, and other stressors. In recent decades, progress in biotechnology and its related tools has provided opportunities to dissect and decipher the genetic basis of tolerance to various stress conditions. One such approach is the identification of genomic regions that are linked with specific or multiple characteristics. Cereal crops have a key role in supplying the energy required for human and animal populations. However, crop products are dramatically affected by various environmental stresses. Barley (Hordeum vulgare L.) is one of the oldest domesticated crops that is cultivated globally. Research has shown that, compared with other cereals, barley is well adapted to various harsh environmental conditions. There is ample literature regarding these responses to abiotic stressors, as well as the genomic regions associated with the various morpho-physiological and biochemical traits of stress tolerance. This review focuses on (i) identifying the tolerance mechanisms that are important for stable growth and development, and (ii) the applicability of QTL mapping and association analysis in identifying genomic regions linked with stress-tolerance traits, in order to help breeders in marker-assisted selection (MAS) to quickly screen tolerant germplasms in their breeding cycles. Overall, the information presented here will inform and assist future barley breeding programs.

Combined GWAS and QTL mapping revealed candidate genes and SNP network controlling recovery and tolerance traits associated with drought tolerance in seedling winter wheat

To date, very little research on drought tolerance has been conducted at the seedling stage in winter wheat. In this study, two types of traits, namely tolerance and recovery traits, associated with drought tolerance were scored in biparental mapping population (BPP) and association mapping population (A-set). The results of this study revealed no or weak significant correlation between the two types of traits. Based on GWAS and QTL mapping analyses, all QTLs associated with recovery traits were completely different from those associated with tolerance traits except one QTL in each population that was found to be associated with one tolerance trait and one recovery trait. The analysis of SNP and gene networks confirmed the results of combined GWAS and QTL mapping. One SNP marker located on the 2B chromosome (S2B_26494801) was found to be associated with recovery traits in both populations. The results of this study provided new information on understanding and improving drought tolerance in winter wheat.

High-LD SNP markers exhibiting pleiotropic effects on salt tolerance at germination and seedlings stages in spring wheat

Salt tolerance at germination and seedling growth stages was investigated. GWAS revealed nine genomic regions with pleiotropic effects on salt tolerance. Salt tolerant genotypes were identified for future breeding program. With 20% of the irrigated land worldwide affected by it, salinity is a serious threat to plant development and crop production. While wheat is the most stable food source worldwide, it has been classified as moderately tolerant to salinity. In several crop plants; such as barley, maize and rice, it has been shown that salinity tolerance at seed germination and seedling establishment is under polygenic control. As yield was the ultimate goal of breeders and geneticists, less attention has been paid to understanding the genetic architecture of salt tolerance at early stages. Thus, the genetic control of salt tolerance at these stages is poorly understood relative to the late stages. In the current study, 176 genotypes of spring wheat were tested for salinity tolerance at seed germination and seedling establishment. Genome-Wide Association Study (GWAS) has been used to identify the genomic regions/genes conferring salt tolerance at seed germination and seedling establishment. Salinity stress negatively impacted all germination and seedling development parameters. A set of 137 SNPs showed significant association with the traits of interest. Across the whole genome, 33 regions showed high linkage disequilibrium (LD). These high LD regions harbored 15 SNPs with pleiotropic effect (i.e. SNPs that control more than one trait). Nine genes belonging to different functional groups were found to be associated with the pleiotropic SNPs. Noteworthy, chromosome 2B harbored the gene TraesCS2B02G135900 that acts as a potassium transporter. Remarkably, one SNP marker, reported in an early study, associated with salt tolerance was validated in this study. Our findings represent potential targets of genetic manipulation to understand and improve salinity tolerance in wheat.

A Genome Wide Association Study Revealed Key Single Nucleotide Polymorphisms/Genes Associated With Seed Germination in Gossypium hirsutum L

Fast and uniform seed germination is essential to stabilize crop yields in agricultural production. It is important to understand the genetic basis of seed germination for improving the vigor of crop seeds. However, little is known about the genetic basis of seed vigor in cotton. In this study, we evaluated four seed germination-related traits of a core collection consisting of 419 cotton accessions, and performed a genome-wide association study (GWAS) to explore important loci associated with seed vigor using 3.66 million high-quality single nucleotide polymorphisms (SNPs). The results showed that four traits, including germination potential, germination rate, germination index, and vigor index, exhibited broad variations and high correlations. A total of 92 significantly associated SNPs located within or near 723 genes were identified for these traits, of which 13 SNPs could be detected in multiple traits. Among these candidate genes, 294 genes were expressed at seed germination stage. Further function validation of the two genes of higher expression showed that Gh_A11G0176 encoding Hsp70-Hsp90 organizing protein negatively regulated Arabidopsis seed germination, while Gh_A09G1509 encoding glutathione transferase played a positive role in regulating tobacco seed germination and seedling growth. Furthermore, Gh_A09G1509 might promote seed germination and seedling establishment through regulating glutathione metabolism in the imbibitional seeds. Our findings provide unprecedented information for deciphering the genetic basis of seed germination and performing molecular breeding to improve field emergence through genomic selection in cotton.

Identification and Validation of High LD Hotspot Genomic Regions Harboring Stem Rust Resistant Genes on 1B, 2A (Sr38), and 7B Chromosomes in Wheat

Stem rust caused by Puccinia graminis f. sp. tritici Eriks. is an important disease of common wheat globally. The production and cultivation of genetically resistant cultivars are one of the most successful and environmentally friendly ways to protect wheat against fungal pathogens. Seedling screening and genome-wide association study (GWAS) were used to determine the genetic diversity of wheat genotypes obtained on stem rust resistance loci. At the seedling stage, the reaction of the common stem rust race QFCSC in Nebraska was measured in a set of 212 genotypes from F_3:6 lines. The results indicated that 184 genotypes (86.8%) had different degrees of resistance to this common race. While 28 genotypes (13.2%) were susceptible to stem rust. A set of 11,911 single-nucleotide polymorphism (SNP) markers was used to perform GWAS which detected 84 significant marker-trait associations (MTAs) with SNPs located on chromosomes 1B, 2A, 2B, 7B and an unknown chromosome. Promising high linkage disequilibrium (LD) genomic regions were found in all chromosomes except 2B which suggested they include candidate genes controlling stem rust resistance. Highly significant LD was found among these 59 significant SNPs on chromosome 2A and 12 significant SNPs with an unknown chromosomal position. The LD analysis between SNPs located on 2A and Sr38 gene reveal high significant LD genomic regions which was previously reported. To select the most promising stem rust resistant genotypes, a new approach was suggested based on four criteria including, phenotypic selection, number of resistant allele(s), the genetic distance among the selected parents, and number of the different resistant allele(s) in the candidate crosses. As a result, 23 genotypes were considered as the most suitable parents for crossing to produce highly resistant stem rust genotypes against the QFCSC.