Background: Genetic diversity is an essential resource for breeders to improve new cultivars with desirable characteristics. Recently, genotyping-by-sequencing (GBS), a next generation sequencing (NGS) technology that can simplify complex genomes, has now be used as a high-throughput and cost-effective molecular tool for routine breeding and screening in many crop species, including the species with a large genome. Results: We genotyped a diversity panel of 369 Iranian hexaploid wheat accessions including 270 landraces collected between 1931 and 1968 in different climate zones and 99 cultivars released between 1942 to 2014 using 16,506 GBS-based single nucleotide polymorphism (GBS-SNP) markers. The B genome had the highest number of mapped SNPs while the D genome had the lowest on both the Chinese Spring and W7984 references. Structure and cluster analyses divided the panel into three groups with two landrace groups and one cultivar group, suggesting a high differentiation between landraces and cultivars and between landraces. The cultivar group can be further divided into four subgroups with one subgroup was mostly derived from Iranian ancestor(s). Similarly, landrace groups can be further divided based on years of collection and climate zones where the accessions were collected. Molecular analysis of variance indicated that the genetic variation was larger between groups than within group. Conclusion: Obvious genetic diversity in Iranian wheat was revealed by analysis of GBS-SNPs and thus breeders can select genetically distant parents for crossing in breeding. The diverse Iranian landraces provide rich genetic sources of tolerance to biotic and abiotic stresses, and they can be useful resources for the improvement of wheat production in Iran and other countries.

Genotyping-by-sequencing (GBS) provides high SNP coverage and has recently emerged as a popular technology for genetic and breeding applications in bread wheat (Triticum aestivum L.) and many other plant species. Although GBS can discover millions of SNPs, a high rate of missing data is a major concern for many applications. Accurate imputation of those missing data can significantly improve the utility of GBS data. This study compared imputation accuracies among four genome references including three wheat references (Chinese Spring survey sequence, W7984, and IWGSC RefSeq v1.0) and one barley reference genome by comparing imputed data derived from low-depth sequencing to actual data from high-depth sequencing. After imputation, the average number of imputed data points was the highest in the B genome (~48.99%). The D genome had the lowest imputed data points (~15.02%) but the highest imputation accuracy. Among the four reference genomes, IWGSC RefSeq v1.0 reference provided the most imputed data points, but the lowest imputation accuracy for the SNPs with < 10% minor allele frequency (MAF). The W7984 reference, however, provided the highest imputation accuracy for the SNPs with < 10% MAF.

Background: Drought is most likely the most significant abiotic stress affecting wheat yield. The discovery of drought-tolerant genotypes is a promising strategy for dealing with the world’s rapidly diminishing water resources and growing population. A genome-wide association study (GWAS) was conducted on 298 Iranian bread wheat landraces and cultivars to investigate the genetic basis of yield, yield components, and drought tolerance indices in two cropping seasons (2018–2019 and 2019–2020) under rainfed and well-watered environments. Results: A heatmap display of hierarchical clustering divided cultivars and landraces into four categories, with high-yielding and drought-tolerant genotypes clustering in the same group. The results of the principal component analysis (PCA) demonstrated that selecting genotypes based on the mean productivity (MP), geometric mean productivity (GMP), harmonic mean (HM), and stress tolerance index (STI) can help achieve high-yield genotypes in the environment. Genome B had the highest number of significant marker pairs in linkage disequilibrium (LD) for both landraces (427,017) and cultivars (370,359). Similar to cultivars, marker pairs on chromosome 4A represented the strongest LD (r² = 0.32). However, the genomes D, A, and B have the highest LD, respectively. The single-locus mixed linear model (MLM) and multi-locus random-SNP-effect mixed linear model (mrMLM) identified 1711 and 1254 significant marker-trait association (MTAs) (-log10 P > 3) for all traits, respectively. A total of 874 common quantitative trait nucleotides (QTNs) were simultaneously discovered by both MLM and mrMLM methods. Gene ontology revealed that 11, 18, 6, and 11 MTAs were found in protein-coding regions (PCRs) for spike weight (SW), thousand kernel weight (TKW), grain number per spike (GN), and grain yield (GY), respectively. Conclusion: The results identified rich regions of quantitative trait loci (QTL) on Ch. 4A and 5A suggest that these chromosomes are important for drought tolerance and could be used in wheat breeding programs. Furthermore, the findings indicated that landraces studied in Iranian bread wheat germplasm possess valuable alleles, that are responsive to water-limited conditions. This GWAS experiment is one of the few types of research conducted on drought tolerance that can be exploited in the genome-mediated development of novel varieties of wheat.

Background: Pre-harvest sprouting (PHS) refers to a phenomenon, in which the physiologically mature seeds are germinated on the spike before or during the harvesting practice owing to high humidity or prolonged period of rainfall. Pre-harvest sprouting (PHS) remarkably decreases seed quality and yield in wheat; hence it is imperative to uncover genomic regions responsible for PHS tolerance to be used in wheat breeding. A genome-wide association study (GWAS) was carried out using 298 bread wheat landraces and varieties from Iran to dissect the genomic regions of PHS tolerance in a well-irrigated environment. Three different approaches (RRBLUP, GBLUP and BRR) were followed to estimate prediction accuracies in wheat genomic selection. Results: Genomes B, A, and D harbored the largest number of significant marker pairs (MPs) in both landraces (427,017, 328,006, 92,702 MPs) and varieties (370,359, 266,708, 63,924 MPs), respectively. However, the LD levels were found the opposite, i.e., genomes D, A, and B have the highest LD, respectively. Association mapping by using GLM and MLM models resulted in 572 and 598 marker-trait associations (MTAs) for imputed SNPs (− log10 P > 3), respectively. Gene ontology exhibited that the pleitropic MPs located on 1A control seed color, α-Amy activity, and PHS. RRBLUP model indicated genetic effects better than GBLUP and BRR, offering a favorable tool for wheat genomic selection. Conclusions: Gene ontology exhibited that the pleitropic MPs located on 1A can control seed color, α-Amy activity, and PHS. The verified markers in the current work can provide an opportunity to clone the underlying QTLs/genes, fine mapping, and genome-assisted selection.Our observations uncovered key MTAs related to seed color, α-Amy activity, and PHS that can be exploited in the genome-mediated development of novel varieties in wheat.

Water deficit stress exposure frequently constrains plant and agri-food production globally. Biostimulants (BSs) can be considered a new tool in mitigating water deficit stress. This study aimed to understand how BSs influence water deficit stress perceived by savory plants (Satureja hortensisL.), an important herb used for nutritional and herbal purposes in the Middle East. Three BS treatments, including bio-fertilizers, humic acid and foliar application of amino acid (AA), were implemented. Each treatment was applied to savory plants using three irrigation regimes (low, moderate and severe water deficit stress FC100, FC75 and FC50, respectively). Foliar application of AA increased dry matter yield, essential oil (EO) content and EO yield by 22%, 31% and 57%, respectively. The greatest EO yields resulted from the moderate (FC75) and severe water deficit stress (FC50) treatments treated with AA. Primary EO constituents included carvacrol (39–43%), gamma-terpinene (27–37%), alpha-terpinene (4–7%) andp-cymene (2–5%). Foliar application of AA enhanced carvacrol, gamma-terpinene, alpha-terpinene andp-cymene content by 6%, 19%, 46% and 18%, respectively. Physiological characteristics were increased with increasing water shortage and application of AA. Moreover, the maximum activities of superoxide dismutase (3.17 unit mg⁻¹ min⁻¹), peroxidase (2.60 unit mg⁻¹ min⁻¹) and catalase (3.08 unit mg⁻¹ min⁻¹) were obtained from plants subjected to severe water deficit stress (FC50) and treated with AA. We conclude that foliar application of AA under water deficit stress conditions would improve EO quantity and quality in savory.