Association mapping unravels the genetics controlling seedling drought stress tolerance in winter wheat.

Drought is a major constraint in wheat (Triticum aestivum L.) grain yield. The present work aimed to identify quantitative trait nucleotides (QTNs)/ candidate genes influencing drought tolerance-related traits at the seedling stage in 261 accessions of a diverse winter wheat panel. Seeds from three consecutive years were exposed to polyethylene glycol 12% (PEG-6000) and a control treatment (distilled water). The Farm-CPU method was used for the association analysis with 17,093 polymorphic SNPs. PEG treatment reduced shoot length (SL) (-36.3%) and root length (RL) (-11.3%) compared with control treatments, while the coleoptile length (CL) was increased by 11% under drought conditions, suggesting that it might be considered as an indicator of stress-tolerance. Interestingly, we revealed 70 stable QTN across 17 chromosomes. Eight QTNs related to more than one trait were detected on chromosomes 1B, 2A (2), 2B, 2D, 4B, 7A, and 7B and located nearby or inside candidate genes within the linkage disequilibrium (LD) interval. For instance, the QTN on chromosome 2D is located inside the gene TraesCS2D02G133900 that controls the variation of CL_S and SL_C. The allelic variation at the candidate genes showed significant influence on the associated traits, demonstrating their role in controlling the natural variation of multi-traits of drought stress tolerance. The gene expression of these candidate genes under different stress conditions validates their biological role in stress tolerance. Our findings offer insight into understanding the genetic factors and diverse mechanisms in response to water shortage conditions that are important for wheat improvement and adaptation at early developmental stages.

Elucidating the genetic architecture controlling antioxidant status and ionic balance in barley under salt stress.

KEY MESSAGE: Association genetic analysis empowered us to identify candidate genes underlying natural variation of morpho-physiological, antioxidants, and grain yield-related traits in barley. Novel intriguing genomic regions were identified and dissected. Salinity stress is one of the abiotic stresses that influence the morpho-physiological, antioxidants, and yield-related traits in crop plants. The plants of a core set of 138 diverse barley accessions were analyzed after exposure to salt stress under field conditions during the reproductive phase. A genome-wide association scan (GWAS) was then conducted using 19,276 single nucleotide polymorphisms (SNPs) to uncover the genetic basis of morpho-physiological and grain-related traits. A wide range of responses to salt stress by the accessions was explored in the current study. GWAS detected 263 significantly associated SNPs with the antioxidants, K+/Na+ content ratio, and agronomic traits. Five genomic regions harbored interesting putative candidate genes within LD ± 1.2 Mbp. Choromosome 2H harbored many candidate genes associated with the antioxidants ascorbic acid (AsA) and glutathione (GSH), such as superoxide dismutase (SOD), ascorbate peroxidase (APX), and glutathione reductase (GR), under salt stress. Markedly, an A:C SNP at 153,773,211 bp on chromosome 7H is located inside the gene HORVU.MOREX.r3.7HG0676830 (153,772,300-153,774,057 bp) that was annotated as L-gulonolactone oxidase, regulating the natural variation of SOD_S and APX_S. The allelic variation at this SNP reveals a negative selection of accessions carrying the C allele, predominantly found in six-rowed spring landraces originating from Far-, Near-East, and central Asia carrying photoperiod sensitive alleles having lower activity of enzymatic antioxidants. The SNP-trait associations detected in the current study constitute a benchmark for developing molecular selection tools for antioxidant compound selection in barley.

Genetic analysis toward more nutritious barley grains for a food secure world.

BACKGROUND: Understanding the relationships between nutrition, human health and plant food source is among the highest priorities for public health. Therefore, enhancing the minerals content such as iron (Fe), zinc (Zn) and selenium (Se) in barley (Hordeum vulgare L.) grains is an urgent need to improve the nutritive value of barley grains in overcoming malnutrition and its potential consequencing. This study aimed to expedite biofortification of barley grains by elucidating the genetic basis of Zn, Fe, and Se accumulation in the grains, which will contribute to improved barley nutritional quality. RESULTS: A genome-wide association study (GWAS) was conducted to detect the genetic architecture for grain Zn, Fe, and Se accumulations in 216 spring barley accessions across two years. All the accessions were genotyped by single nucleotide polymorphisms (SNPs) molecular markers. Mineral heritability values ranging from moderate to high were revealed in both environments. Remarkably, there was a high natural phenotypic variation for all micronutrient accumulation in the used population. High-LD SNP markers (222 SNPs) were detected to be associated with all micronutrients in barley grains across the two environments plus BLUEs. Three genomic regions were detected based on LD, which were identified for the most effective markers that had associations with more than one trait. The strongest SNP-trait associations were found to be physically located within genes that may be involved in grain Zn and Fe homeostasis. Two putative candidate genes were annotated as Basic helix loop helix (BHLH) family transcription factor and Squamosa promoter binding-like protein, respectively, and have been suggested as candidates for increased grain Zn, Fe, and Se accumulation. CONCLUSIONS: These findings shed a light on the genetic basis of Zn, Fe, and Se accumulation in barley grains and have the potential to assist plant breeders in selecting accessions with high micronutrient concentrations to enhance grain quality and, ultimately human health.

Exploring genetic variation among Jordanian Solanum lycopersicon L. landraces and their performance under salt stress using SSR markers.

BACKGROUND: Tomatoes (Solanum lycopersicon L.) are one of the main daily consumed vegetables in the human diet. Tomato has been classified as moderately sensitive to salinity at most stages of plant development, including seed germination, seedling (vegetative), and reproduction phases. In this study, we evaluated the performance and response of 39 tomato landraces from Jordan under salt stress conditions. Furthermore, the landraces were also genetically characterized using simple sequence repeat (SSR) markers. RESULTS: The studied morphological-related traits at the seedling stage were highly varied among landraces of which the landrace number 24 (Jo970) showed the best performance with the highest salt tolerance. The total number of amplification products produced by five primers (LEaat002, LEaat006, LEaat008, LEga003, LEta019) was 346 alleles. Primer LEta 019 produced the highest number of alleles (134) and generated the highest degree of polymorphism (100%) among landraces in addition to primers (LEaat002, LEaat006, LEaat008). The lowest dissimilarity among landraces ranged from 0.04 between accessions 25 (Jo969) and 26 (Jo981) and the highest dissimilarity (1.45) was found between accessions 39 (Jo980) and both 3 (Jo960) and 23 (Jo978). The dendrogram showed two main clusters and separated 30 landraces from the rest 9 landraces. High genetic diversity was detected (0.998) based on the average polymorphism information. Therefore, the used SSRs in the current study provide new insights to reveal the genetic variation among thirty-nine Jordanian tomato landraces. According to functional annotations of the gene-associated SSRs in tomatoes, a few of SSR markers gene-associated markers, for example, LEaat002 and LEaat008 markers are related to MEIS1 Transcription factors genes (Solyc07g007120 and Solyc07g007120.2). The LEaat006 is related to trypsin and protease inhibitor (Kunitz_legume) gene (Solyc03g020010). Also, the SSR LEga003 marker was related to the Carbonic anhydrase gene (Solyc09g010970). CONCLUSIONS: The genetic variation of tomato landraces could be used for considering salt tolerance improvement in tomato breeding programs.

Genetic factors controlling nTiO2 nanoparticles stress tolerance in barley (Hordeum vulgare) during seed germination and seedling development.

Titanium dioxide nanoparticle (nTiO2) is one of the most produced nanoparticles worldwide. Its mechanism on crop development and performance is unclear as it is hard to predict their toxicity or benefit. Therefore, understanding the genetics of crop development under nTiO2 is a prerequisite for their applications in agriculture and crop improvement. Here, we aimed to examine the influnce of 300ppm nTiO2 on seed germination, seedling morphology, root-related traits in 121 worldwide spring barley (Hordeum vulgare L.) accessions. Results show that nTiO2 significantley affected all traits scored in this study. Response to nTiO2 treatment, clear wide natural variation among accesions was detected. Remarkably, 10 genotypes showed increased root length under nTiO2 at the seedling stage indicating that nTiO2 enhanced the root elongation. Genome-wide association scan (GWAS) was applied using 9K single nucleotide polymorphism (SNPs) in a mixed-linear model that revealed 86 significant marker-trait associations with all traits scored in this study. Many significant SNPs were physically located near candidate genes, of which 191 genes were detected within the linkage disequilibrium and distributed over all barley chromosomes. Mostly, the genes harboured by chromosome 2H, specially calcium-binding genes family, regulate the variation of seedling length-related traits. Candidate genes on 7H encode zinc finger protein that controls the rate of germination. Therefore, these genomic regions at 2H and 7H can be targeted to select for improved seedling development and seed germination under nTiO2 stress in soils. These results improve understanding the genetic control of seed germination and seedling development under high levels of nTiO2 that can support plant breeding and crop improvement programmes.

Exploring natural diversity reveals alleles to enhance antioxidant system in barley under salt stress.

Soil salinity stress causes osmotic/ionic imbalances and induces oxidative stress that causes cellular structure damage, perturbs metabolism, antioxidant system (comprising enzymatic and non-enzymatic components) and hence inhibits plant growth performance. In this study, we used genome-wide association scan (GWAS) in 174 diverse spring barley accessions which were exposed to salt stress under field conditions at the vegetative stage to uncover the genetic basis of antioxidant components and agronomic traits. High activities of enzymatic and content of non-enzymatic antioxidants were observed under salt stress compared to control conditions. Under salt stress, all the agronomic and yield-related traits were significantly reduced. Six genomic regions were associated with antioxidants and agronomic traits under salt stress conditions which were found to be linked with candidate genes. Several significant associations were physically located inside or near genes which are potentially involved in antioxidants. Two candidate genes at 2H (40,659,364 bp) and 7H (416,743,127 bp) were found to be involved in Dihydroflavonol 4-reductase/flavanone protein and Glyceraldehyde-3-phosphate dehydrogenase, respectively. The allelic variation at SNP of BK_07 at 7H inside the GAPDH gene demonstrates a negative selection of accessions carrying A allele. This allele appears in cultivars with lower activity of enzymatic antioxidants e.g. superoxide dismutase and catalases under salt stress conditions. These accessions are predominantly two-rowed, cultivars, originated from Europe, and carrying photoperiod sensitive alleles. The detected associated molecular markers in this work are considered as an important source for selection of increased amount of antioxidant compounds in barley under stress conditions.

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

Drought induces several challenges for plant development, growth, and production. These challenges become more severe, in particular, in arid and semiarid countries like Egypt. In terms of production, barley ranks fourth after wheat, maize, and rice. Seed germination and seedling stages are critical stages for plant establishment and growth. In the current study, 60 diverse barley genotypes were tested for drought tolerance using two different treatments: control (0-PEG) and drought (20%-PEG). Twenty-two traits were estimated for seed germination and seedling parameters. All traits were reduced under drought stress, and a significant variation was found among genotypes under control and stress conditions. The broad-sense heritability estimates were very high under both control and drought for all traits. It ranged from 0.63 to 0.97 under the control condition and from 0.89 to 0.97 under drought, respectively. These high heritabilities suggested that genetic improvement of drought tolerance in barley at both stages is feasible. The principal component analysis revealed that root-related parameters account for the largest portion of phenotypic variation in this collection. The single-marker analysis (SMA) resulted in 71 quantitative trait loci (QTLs) distributed across the seven chromosomes of barley. Thirty-three QTLs were detected for root-length-related traits. Many hotspots of QTLs were detected for various traits. Interestingly, some markers controlled many traits in a pleiotropic manner; thus, they can be used to control multiple traits at a time. Some QTLs were constitutive, i.e., they are mapped under control and drought, and targeting these QTLs makes the selection for drought tolerance a single-step process. The results of gene annotation analysis revealed very potential candidate genes that can be targeted to select for drought tolerance.

Natural Variation Uncovers Candidate Genes for Barley Spikelet Number and Grain Yield under Drought Stress.

Drought stress can occur at any growth stage and can affect crop productivity, which can result in large yield losses all over the world. In this respect, understanding the genetic architecture of agronomic traits under drought stress is essential for increasing crop yield potential and harvest. Barley is considered the most abiotic stress-tolerant cereal, particularly with respect to drought. In the present study, worldwide spring barley accessions were exposed to drought stress beginning from the early reproductive stage with 35% field capacity under field conditions. Drought stress had significantly reduced the agronomic and yield-related traits such as spike length, awn length, spikelet per spike, grains per spike and thousand kernel weight. To unravel the genetic factors underlying drought tolerance at the early reproductive stage, genome-wide association scan (GWAS) was performed using 121 spring barley accessions and a 9K single nucleotide polymorphisms (SNPs) chip. A total number of 101 significant SNPs, distributed over all seven barley chromosomes, were found to be highly associated with the studied traits, of which five genomic regions were associated with candidate genes at chromosomes 2 and 3. On chromosome 2H, the region between 6469300693-647258342 bp includes two candidate drought-specific genes (HORVU2Hr1G091030 and HORVU2Hr1G091170), which are highly associated with spikelet and final grain number per spike under drought stress conditions. Interestingly, the gene expression profile shows that the candidate genes were highly expressed in spikelet, grain, spike and leaf organs, demonstrating their pivotal role in drought tolerance. To the best of our knowledge, we reported the first detailed study that used GWAS with bioinformatic analyses to define the causative alleles and putative candidate genes underlying grain yield-related traits under field drought conditions in diverse barley germplasm. The identified alleles and candidate genes represent valuable resources for future functional characterization towards the enhancement of barley cultivars for drought tolerance.

Genetic basis of drought tolerance during seed germination in barley.

Drought is one of the harshest abiotic stresses hindering seed germination, plant growth, and crop productivity. A high rate and uniformity of germination under stressful conditions are vital for crop establishment and growth; thus, for productivity. A better understanding of the genetic architecture of seed germination under drought stress is a prerequisite for further increasing yield potential. Barley is considered one of the most abiotic stresses-tolerant cereals. Elucidating the drought tolerance of barley during seed germination would indeed pave the way towards improving the performance of all cereals. However, we still know relatively little about the genetic control of drought tolerance during the seed germination phase. In our study, 218 worldwide spring barley accessions were subjected to PEG-induced drought during seed germination. Induced drought stress "20% PEG" significantly reduced the seed germination parameters and seedling related traits. A genome-wide association scan (GWAS) was used to identify genomic regions associated with our trait of interest. In total, 338 single nucleotide polymorphisms (SNPs) were found to be associated with several traits distributed across seven barley chromosomes, of which 26 genomic regions were associated with candidate genes. The current study found some of the quantitative trait loci (QTL) that have previously been reported to be linked to seed germination-related traits under drought conditions, as well as some new associations. Noteworthy, the identified QTL colocalized with a number of genes (within interval ±0.5 Mbp) that are exclusively distributed on chromosomes 1H, 2H, and 5H. The annotation of these genes in barley shows their roles in drought tolerance through encoding different transcription factors. The function of the identified genes during seed germination was also confirmed by the annotation of their counterparts in Arabidopsis. The current analyses show the power of the GWAS both for identifying putative candidate genes and for improving plant adaptive traits in barley.