A novel polymorphism in the 5′ UTR of HvDEP1 is associated with grain length and 1000-grain weight in barley (Hordeum vulgare)

The gene HvDEP1, on barley (Hordeum vulgare L.) chromosome 5H, encodes a γ-subunit of the heterotrimeric G-protein complex and was previously determined to be a candidate gene underlying a major quantitative trait locus for grain length. In the present study, we identified a 9 bp indel (insertion–deletion mutation) at position –84 bp from the start codon within a reported upstream open reading frame located in the 5′ UTR (untranslated region) and developed a diagnostic molecular marker. We also identified a 13 bp indel (–514 bp) in linkage disequilibrium that bridges an important regulatory motif. Using a doubled-haploid population and a barley diversity panel, we were able to show that the effects of these indels were environmentally stable and consistently delineated phenotypic groups based on grain length and 1000-grain weight. Genotypes represented by deletions at these two positions relative to the reference cv. Morex had consistently shorter grains, by 3.69–3.96%, and lower 1000-grain weight, by 2.38–4.21%, in a doubled-haploid population studied. Additionally, a diversity panel was tested but consistent differences were observed only for grain length, reinforcing literature indicating the importance of this gene for grain-length regulation. The frequency of the longer and heavier grained reference allele was higher in modern cultivars, suggesting that indirect selection for longer grain may have occurred through direct selection for grain yield via grain-weight improvement. These results indicate that grain length and 1000-grain weight in barley can be manipulated by targeting variation in gene promoters through marker-assisted selection

Early growth stages salinity stress tolerance in CM72 x Gairdner doubled haploid barley population

A doubled haploid (DH) population of barley (Hordeum vulgare L.) generated from salinity tolerant genotype CM72 and salinity sensitive variety Gairdner was studied for salinity stress tolerance at germination, seedling emergence and first leaf full expansion growth stages. Germination study was conducted with deionized water, 150 mM and 300 mM NaCl treatments. Seedling stage salinity tolerance was conducted with three treatments: control, 150 mM NaCl added at seedling emergence and first leaf full expansion growth stages. Results from this study revealed transgressive phenotypic segregations for germination percentage and biomass at seedling stage. Twelve QTL were identified on chromosomes 2H–6H each explaining 10–25% of the phenotypic variations. A QTL located at 176.5 cM on chromosome 3H was linked with fresh weight per plant and dry weight per plant in salinity stress induced at first leaf full expansion growth stage, and dry weight per plant in salinity stress induced at seedling emergence. A stable QTL for germination at both 150 and 300 mM salinity stress was mapped on chromosome 2H but distantly located from a QTL linked with seedling stage salinity stress tolerance. QTL, associated markers and genotypes identified in this study play important roles in developing salinity stress tolerant barley varieties

Multi-locus genome-wide association studies reveal novel alleles for flowering time under vernalisation and extended photoperiod in a barley MAGIC population

Optimal flowering time has a major impact on grain yield in crop species, including the globally important temperate cereal crop barley (Hordeum vulgare L.). Understanding the genetics of flowering is a key avenue to enhancing yield potential. Although bi-parental populations were used intensively to map genes controlling flowering, their lack of genetic diversity requires additional work to obtain desired gene combinations in the selected lines, especially when the two parental cultivars did not carry the genes. Multi-parent mapping populations, which use a combination of four or eight parental cultivars, have higher genetic and phenotypic diversity and can provide novel genetic combinations that cannot be achieved using bi-parental populations. This study uses a Multi-parent advanced generation intercross (MAGIC) population from four commercial barley cultivars to identify genes controlling flowering time in different environmental conditions. Genome-wide association studies (GWAS) were performed using 5,112 high-quality markers from Diversity Arrays Technology sequencing (DArT-seq), and Kompetitive allele-specific polymerase chain reaction (KASP) genetic markers were developed. Phenotypic data were collected from fifteen different field trials for three consecutive years. Planting was conducted at various sowing times, and plants were grown with/without additional vernalisation and extended photoperiod treatments. This study detected fourteen stable regions associated with flowering time across multiple environments. GWAS combined with pangenome data highlighted the role of CEN gene in flowering and enabled the prediction of different CEN alleles from parental lines. As the founder lines of the multi-parental population are elite germplasm, the favourable alleles identified in this study are directly relevant to breeding, increasing the efficiency of subsequent breeding strategies and offering better grain yield and adaptation to growing conditions

Hybridisation-based target enrichment of phenology genes to dissect the genetic basis of yield and adaptation in barley

Barley (Hordeum vulgare L.) is a major cereal grain widely used for livestock feed, brewing malts and human food. Grain yield is the most important breeding target for genetic improvement and largely depends on optimal timing of flowering. Little is known about the allelic diversity of genes that underlie flowering time in domesticated barley, the genetic changes that have occurred during breeding, and their impact on yield and adaptation. Here we report a comprehensive genomic assessment of a worldwide collection of 895 barley accessions based on the targeted resequencing of phenology genes. A versatile target‐capture method was used to detect genome‐wide polymorphisms in a panel of 174 flowering time‐related genes, chosen based on prior knowledge from barley, rice, and Arabidopsis thaliana. Association studies identified novel polymorphisms that accounted for observed phenotypic variation in phenology and grain yield, and explained improvements in adaptation as a result of historical breeding of Australian barley cultivars. We found that 50% of genetic variants associated with grain yield, and 67% of the plant height variation was also associated with phenology. The precise identification of favourable alleles provides a genomic basis to improve barley yield traits and to enhance adaptation for specific production areas

Exploration and Utilization of Genetic Diversity Exotic Germplasm for Barley Improvement

Research reports show high genetic diversity in exotic germplasm, which include landraces and wild barley, and low genetic diversity in commercial cultivars. However, exotic germplasm have been reported to be underutilized in barley cultivar development. This is probably due to consumer demand on high yield and high-quality barley cultivars especially for malting purposes, and poor agronomic and quality traits in exotic germplasm. Nevertheless, exotic germplasm have genes that can help reduce the damage caused by biotic and abiotic stress factors. Mass screening and evaluation helped to identify important genotypes that contributed to the development of commercial cultivars. To increase the efficiency of identifying genotypes with important genes from barley germplasm conserved ex situ worldwide, systematic approaches need to be used. The Core-Collection concept, based on agromorphologic traits, and the Focused Identification of Germplasm Strategy (FIGS), based on ecological data of collection site matched with the ecology of the stress factors, can play useful roles. Although such approaches can substantially reduce the number of germplasm for evaluation, they have their own shortcomings that may limit their uses

Frost tolerance and genetic improvement in barley

Frost is an important stress factor both at vegetative and reproductive stages of barley. Frost, otherwise known as low temperature stress, damages leaf and stem, causes floret sterility, increases screenings, and reduces grain yield and germination causing substantial loses. To curb these problems, numerous studies have been undertaken elsewhere on frost tolerance in barley both at vegetative and reproductive stages. These studies used field or controlled environments, or a combination of field and controlled environments to understand response of barley genotypes to frost. At the vegetative stage, percentage survival, electrolyte leakage, ABA content, cold induced protein contents, and molecular markers as diagnostic tools have been used to distinguish between barley cultivars for frost tolerance. Reproductive stage traits used to distinguish between barley genotypes for frost tolerance include floret sterility, grain damage, and grain yield and associated molecular markers. Measurement for frost tolerance at reproductive stages has been reported to be complex. Despite substantial research efforts to understand frost tolerance in barley, improvement for this stress at the reproductive stage of development remains challenging. This is in contrast to vegetative stage frost tolerance in winter barleys that not only tolerate but also require low temperature to transit from the vegetative stage to the reproductive stage. Recent developments in barley genomics may help to exploit high genotypic variation in barley for frost tolerance at the reproductive stage. Frost tolerance genes already mapped on various chromosomes would play key roles in improving commercial barley varieties for reproductive stage frost tolerance. This chapter is an overview of barley genotypic variation, methods used in frost tolerance studies, and genetic factors reported elsewhere to be associated with frost tolerance

Quantitative trait loci mapping for vigour and survival traits of barley seedlings after germinating under salinity stress

Seed germination and seedling establishment are the most critical stages in the barley (Hordeum vulgare ssp. vulgare L.) life cycle that contribute substantially to grain yield. These two phases are exposed to several forms of environmental stresses such as salinity due to high level of salt accumulation in the soil rhizosphere where seed germination takes place and seedlings emerge from. Previously, we have reported genotypic variability and independent QTLs associated with salinity tolerance at seedling and germination stages. However, genotypic studies on revival of a seedling germinating under salinity stress are yet to close the lack of information between germination and seedling stages. Here, we attempt to close the genetic gap by targeting early seedling survival traits in barley after germination under salinity (NaCl) stress and the various seedling vigour indices. Seedling vigour parameters formed the basis for Quantitative trait locus (QTL) linkage mapping in 103 Doubled Haploid (DH) lines of CM72/Gairdner population, and validated the phenotypic response using a selected diverse panel of 85 barley germplasm. The results indicate that 150 mM NaCl stress significantly reduced all the recorded phenotypic traits compared to 75, 90 and 120 mM NaCl. In both DH population and diversity panel barley germplasm, the highest percentage reduction was recorded in shoot length (65.6% and 50.3%) followed by seedling vigour index length (56.5% and 41.0%), while root length (28.6% and 15.8%) and root dry weight (29.3% and 28.0%) were least reduced when control was compared to150 mM NaCl stress treatment. Six QTLs containing 13 significant markers were detected in the DH population, 3 on chromosomes 1H, 8 on 3H and 2 on 4H with LOD values ranging from 3 to 8 associated with seedling survival traits under salinity stress. Three QTLs one on 1H and two on 3H with closely linked significant markers (Bmac0032, bPb-9418 and bPb-4741), (bPb-4576 and bPb-9624) and (bPb-3623, bPb-5666 and bPb-6383) for 1H and two on 3H respectively formed the regions with high possibility of candidate genes. A QTL on 3H flanked with markers bPb-4576 and bPb-9624 that were detected in more than one salinity survival trait and were closely linked to each other will form a basis for detailed studies leading to gene functional analysis, genetic transformation and marker assisted selection (MAS)

Polymorphism of floral type gene Cly1 and its association with thermal stress in barley

Cleistogamy refers to a type of sexual breeding system with closed flowers. Cleistogamous flowers shed their pollen before flower opening, which leads to autogamy. Two SNPs in the open reading frame region of the Cly1 gene are associated with floral type. In the present study, we investigated the floral type of 436 barley accessions. Molecular markers were developed to genotype these barley accessions based on the two SNPs in the Cly1 gene region. The molecular markers explained floral type in 90% of the accessions. The Cly1 gene was sequenced in accessions with inconsistent genotype and phenotype. Thirteen SNPs were detected with ten new SNPs in the gene region. We further investigated whether floral type was associated with temperature stress tolerance in four field trials. One site experienced frost stress with a minimum temperature of -3.4°C during flowering. Grain fertility rates as low as 85% were observed at this site but ranged from 92–96% at the other three sites. The relationship between grain fertility rate and floral type under temperature stress was inconclusive. Some lines with higher grain fertility rates were identified under frost stress, and would be useful for frost stress studies in barley

Salinity tolerance in barley during germination—homologs and potential genes

Salinity affects more than 6% of the world’s total land area, causing massive losses in crop yield. Salinity inhibits plant growth and development through osmotic and ionic stresses; however, some plants exhibit adaptations through osmotic regulation, exclusion, and translocation of accumulated Na+ or Cl-. Currently, there are no practical, economically viable methods for managing salinity, so the best practice is to grow crops with improved tolerance. Germination is the stage in a plant’s life cycle most adversely affected by salinity. Barley, the fourth most important cereal crop in the world, has outstanding salinity tolerance, relative to other cereal crops. Here, we review the genetics of salinity tolerance in barley during germination by summarizing reported quantitative trait loci (QTLs) and functional genes. The homologs of candidate genes for salinity tolerance in Arabidopsis, soybean, maize, wheat, and rice have been blasted and mapped on the barley reference genome. The genetic diversity of three reported functional gene families for salt tolerance during barley germination, namely dehydration-responsive element-binding (DREB) protein, somatic embryogenesis receptor-like kinase and aquaporin genes, is discussed. While all three gene families show great diversity in most plant species, the DREB gene family is more diverse in barley than in wheat and rice. Further to this review, a convenient method for screening for salinity tolerance at germination is needed, and the mechanisms of action of the genes involved in salt tolerance need to be identified, validated, and transferred to commercial cultivars for field production in saline soil