ALLELIC VARIATIONS OF SOS, HVNHX AND SDO GENES IN SOME BARLEY (Hordeum Vulgare L.) GENOTYPES

This study has been carried out at the Biotechnology Lab., Department of Field Crops, Faculty of Agriculture, Damascus University during the growing season 2019 - 2020, in order to detect the variations of SOS, HVNHX and SDO genes in different barley genotypes. Clear variations in the SOS, HVNHX and SDO genes, which are responsible for salinity tolerance were found among the investigated genotypes. It has been found that the variation in the amplicon size between loci per gene was very high in some cases, while there was a high degree of symmetry in other cases, and could be easily distinguished on 2% Agarose gel. The PCR results for the SOS genes (SOS1, SOS2, SOS3), HVNHX genes (HVNHX1, HVNHX2, HVNHX3) and SDO genes (Cu/Zn SODII, Cu/Zn SODI, CAT, GRI , APXIII) have shown only one morphological pattern in most of the studied genotypes, while revealed two patterns for the SOS3 gene, but the rest of genes (HVNHX1, HVNHX2, HVNHX3 Cu/Zn SODI, CAT) exhibited only one morphological pattern. The SOS3 was superior in the number of polymorphic patterns, as the number of total patterns was 14 in all the studied genotypes, but the Cu/Zn SODI showed the least number of polymorphic patterns with only 1 pattern, while the largest number (7 patterns) was detected in the genotype (H9), but the two genotypes Fourat9 and Fourat7 showed only one polymorphic pattern.

Uncoupling differential water usage from drought resistance in a dwarf Arabidopsis mutant

Understanding the molecular and physiological mechanisms of how plants respond to drought is paramount to breeding more drought resistant crops. Certain mutations or allelic variations result in plants with altered water-use requirements. To correctly identify genetic differences which confer a drought phenotype, plants with different genotypes must therefore be subjected to equal levels of drought stress. Many reports of advantageous mutations conferring drought resistance do not control for soil water content variations across genotypes and may therefore need to be re-examined. Here, we reassessed the drought phenotype of the Arabidopsis thaliana dwarf mutant, chiquita1-1 (also called cost1), by growing mutant seedlings together with the wild type to ensure uniform soil water availability across genotypes. Our results demonstrate that the dwarf phenotype conferred by loss of CHIQ1 function results in constitutively lower water usage, but not increased drought resistance.

Flor Yeasts Rewire the Central Carbon Metabolism During Wine Alcoholic Fermentation

The identification of natural allelic variations controlling quantitative traits could contribute to decipher metabolic adaptation mechanisms within different populations of the same species. Such variations could result from human-mediated selection pressures and participate to the domestication. In this study, the genetic causes of the phenotypic variability of the central carbon metabolism of Saccharomyces cerevisiae were investigated in the context of the enological fermentation. The genetic determinism of this trait was found out by a quantitative trait loci (QTL) mapping approach using the offspring of two strains belonging to the wine genetic group of the species. A total of 14 QTL were identified from which 8 were validated down to the gene level by genetic engineering. The allelic frequencies of the validated genes within 403 enological strains showed that most of the validated QTL had allelic variations involving flor yeast specific alleles. Those alleles were brought in the offspring by one parental strain that contains introgressions from the flor yeast genetic group. The causative genes identified are functionally linked to quantitative proteomic variations that would explain divergent metabolic features of wine and flor yeasts involving the tricarboxylic acid cycle (TCA), the glyoxylate shunt and the homeostasis of proton and redox cofactors. Overall, this work led to the identification of genetic factors that are hallmarks of adaptive divergence between flor yeast and wine yeast in the wine biotope. These results also reveal that introgressions originated from intraspecific hybridization events promoted phenotypic variability of carbon metabolism observed in wine strains.

A 646C > G (rs41423247) polymorphism of the glucocorticoid receptor as a risk factor for hyperglycaemia diagnosed in pregnancy—data from an observational study

Aim Hyperglycaemia diagnosed in pregnancy (HiP) is a serious and frequent complication of pregnancy, increasing the risk for adverse maternal and neonatal outcomes. Investigate whether allelic variations of the glucocorticoid receptor are related to an increased risk of HiP. Method The following polymorphisms of the glucocorticoid receptor (GR) were investigated in the cohort study of N = 197 pregnant women with HiP and N = 133 normoglycemic pregnant controls: 646C > G (rs41423247), N363S (rs6195), ER23/22EK (rs6190, rs6189). Results A GG variant of the rs41423247 polymorphism was associated with a significantly higher risk for HiP: OR 1.94 (1.18; 3.18), p = 0.009. The relationship remained significant after controlling for maternal age and prepregnancy BMI: OR 3.09 (1.25; 7.64), p = 0.014. Conclusions The allelic GG variant of the 646C > G (rs41423247) polymorphism is associated with an increased risk for hyperglycaemia in pregnancy.

Molecular markers based genetic relatedness studies in tissue culture propagated Japanese plum cultivars Santa Rosa and Frontier

Santa Rosa and Frontier are the major Japanese plum cultivars grown throughout the world. The present investigation was performed to understand the genetic relatedness among in vitro propagated plum cultivars Santa Rosa and Frontier using PCR based molecular markers. For the study, three arbitrary markers viz. RAPD (Random amplified Polymorphic DNA), ISSR (Inter-Simple Sequence Repeats) and SCoT (Start Codon Targeted) were used. In RAPD analysis, 18 primers out of 28 amplified and generated 33 scorable bands. The allelic variations when analysed, revealed 84 percent similarity between these two cultivars with highest polymorphic information content of 0.78. Similarly, 15 ISSR primers produced 73 amplicons with an average of 4.86 amplicon per primer and similarity coefficient ranging from 62 to 67 percent. Seven SCoT primers out of 26 resulted in a total of twenty- six scorable bands with 24 polymorphic bands. Cluster analysis from all the three markers used broadly divided plum cultivars santa rosa and frontier into two major clusters containing in vitro shoots, their progenies and mother trees of respective genotypes. The study concluded that these three marker systems were found to be effective in revealing genetic relationship of these two commercially important plum cultivars.

Effect of TRPV1 and TRPV4 genes polymorphisms on the development of airway hyperresponsiveness in patients with asthma

Introduction. A change in the level of relative humidity of the inhaled air can lead to the appearance of symptoms of airway hyperresponsiveness (AHR) in patients with asthma. Allelic variations of the TRPV genes encoding osmotic receptors may serve as an internal factor predisposing to the development of respiratory manifestations in response to an osmotic trigger.Aim. The aim of the study was to establish the contribution of some single nucleotide polymorphisms (SNPs) of TRPV1 and TRPV4 to the development of osmotic AHR in asthma patients.Materials and methods. Three hundred patients with mild and moderate asthma were enrolled in the study. Osmotic AHR was diagnosed using bronchoprovocation tests with inhalation of distilled water, hypertonic saline (4.5% NaCl) or by treadmill exercise challenge test. Three SNPs (rs222747, rs224534 и rs8065080) of TRPV1 and two SNPs (rs6606743, rs7971845) of TRPV4 were geno- typed.Results. Carriage of the AA genotype for rs6606743 was associated with a lower probability of developing hypo-osmotic-induced bronchospasm. This result was confirmed in recessive (OR 0.43 95% CI [0.19; 0.94], p=0.02) and Logadditive (OR 0.62 95% CI [0.4; 0.96], p=0.03) inheritance models. Besides, in patients with the AA genotype, a less pronounced decrease in all basic parameters of lung function was observed as compared with GG and ΔG genotypes (ΔFVC, ΔPEF and ΔFEF75 - p<0.01; ΔFEV1 ΔFEV1/FVC, ΔFEF50 and ΔMMEF - p<0.001).Conclusion. A protective effect of the AA genotype for rs6606743 of TRPV4 was revealed in relation to the formation of hypoosmotic AHR.

Development of an Aus-Derived Nested Association Mapping (Aus-NAM) Population in Rice

A genetic resource for studying genetic architecture of agronomic traits and environmental adaptation is essential for crop improvements. Here, we report the development of a rice nested association mapping population (aus-NAM) using 7 aus varieties as diversity donors and T65 as the common parent. Aus-NAM showed broad phenotypic variations. To test whether aus-NAM was useful for quantitative trait loci (QTL) mapping, known flowering genes (Ehd1, Hd1, and Ghd7) in rice were characterized using single-family QTL mapping, joint QTL mapping, and the methods based on genome-wide association study (GWAS). Ehd1 was detected in all the seven families and all the methods. On the other hand, Hd1 and Ghd7 were detected in some families, and joint QTL mapping and GWAS-based methods resulted in weaker and uncertain peaks. Overall, the high allelic variations in aus-NAM provide a valuable genetic resource for the rice community.

Development and Exploitation of KASP Assays for Genes Underpinning Drought Tolerance Among Wheat Cultivars From Pakistan

High-throughput genotyping for functional markers offers an excellent opportunity to effectively practice marker-assisted selection (MAS) while breeding cultivars. We developed kompetitive allele-specific PCR (KASP) assays for genes conferring drought tolerance in common wheat (Triticum aestivum L.). In total, 11 KASP assays developed in this study and five already reported assays were used for their application in wheat breeding. We investigated alleles at 16 loci associated with drought tolerance among 153 Pakistani hexaploid wheat cultivars released during 1953–2016; 28 diploid wheat accessions (16 for AA and 12 for BB) and 19 tetraploid wheat (AABB) were used to study the evolutionary history of the studied genes. Superior allelic variations of the studied genes were significantly associated with higher grain yield. Favored haplotypes of TaSnRK2.3-1A, TaSnRK2.3-1B, TaSnRK2.9-5A, TaSAP-7B, and TaLTPs-1A predominated in Pakistani wheat germplasm indicating unconscious pyramiding and selection pressure on favorable haplotypes during selection breeding. TaSnRK2.8-5A, TaDreb-B1, 1-feh w3, TaPPH-7A, TaMOC-7A, and TaPARG-2A had moderate to low frequencies of favorable haplotype among Pakistani wheat germplasm pointing toward introgression of favorable haplotypes by deploying functional markers in marker-assisted breeding. The KASP assays were compared with gel-based markers for reliability and phenotypically validated among 62 Pakistani wheat cultivars. Association analyses showed that the favorable allelic variations were significantly associated with grain yield-contributing traits. The developed molecular marker toolkit of the genes can be instrumental for the wheat breeding in Pakistan.