Barley Genome Research Articles

Identification of transcriptionally active transposons in Barley

BackgroundThe genomes of many major crops including barley (Hordeum vulgare) consist of numerous transposons. Despite their important roles in crop genome evolution and morphological variations, most of these elements are silent or truncated and unable to be mobile in host genomes. Thus far, only a very limited number of active transposons were identified in plants.ResultsWe analyzed the barley full-length cDNA (FLcDNA) sequences and detected 71 unique FLcDNAs exhibiting significant sequence similarity to the extant transposase proteins. These FLcDNAs were then used to search against the genome of a malting barley cultivar ‘Morex’, seven new intact transposons were identified. Sequence alignments indicated that six intact transposons contained the entire FLcDNAs whereas another one served as 3’ untranslated region (3’ UTR) of a barley gene. Our reverse transcription-PCR (RT-PCR) experiment further confirmed the expression of these six transposons and revealed their differential expression. We conducted genome-wide transposon comparisons and detected polymorphisms of three transposon families between the genomes of ‘Morex’ and other three genotypes including the wild barley (Hordeum spontaneum, B1K-04-12) and two cultivated barley varieties, ‘Golden Promise’ and ‘Lasa Goumang’. Lastly, we screened the transcripts of all annotated barley genes and found that some transposons may serve as the coding regions (CDSs) or UTRs of barley genes.ConclusionWe identified six newly expressed transposons in the barley genome and revealed the recent mobility of three transposon families. Our efforts provide a valuable resource for understanding the effects of transposons on barley genome evolution and for developing novel molecular tools for barley genetic improvement and other research.

Genomics and Physiology of Chlorophyll Fluorescence Parameters in Hordeum vulgare L. under Drought and Salt Stresses.

To map the genomic regions and control chlorophyll fluorescence attributes under normal, salinity-, and drought-stress conditions in barley (Hordeum vulgare L.) at the seedling stage, an experiment was conducted in 2019-2020 using 106 F8 lines resulting from the cross between Badia × Kavir. Initially, the different chlorophyll fluorescence parameters were evaluated. Under drought stress, the highest decrease was related to REo/CSm (59.56%), and the highest increase was related to dV/dto (77.17%). Also, under salinity stress, the highest decrease was related to Fv/Fo (59.56%), and the highest increase was related to DIo/RC (77.17%). Linkage maps were prepared using 152 SSR polymorphic markers, 72 ISSR alleles, 7 IRAP alleles, 29 CAAT alleles, 27 Scot alleles, and 15 iPBS alleles. The obtained map accounted for 999.2 centi-Morgans (cM) of the barley genome length (92% of the whole barley genome). The results indicated the importance of chromosomes 3, 2, and 7 in controlling ABS/CSm, Area, ETo/CSm, Fm, Fv, and ETo/RC under drought stress. qEToRCD-7, as a major QTL, controlled 18.3% of ETo/RC phenotypic variation under drought stress. Under salinity stress, the regions of chromosomes 2 and 7 (102 cM and 126 cM) controlled the parameters ABS/CSo, Fm, Fo, Fv, TRo/SCo, Area, ETo/CSm, and ETo/CSo. The results showed that chlorophyll fluorescence is an important parameter in the study of drought and salinity effects on barley. This is the first report of the investigation of changes in the genetic structure of quantitative genes controlling the fluorescence parameters associated with barley response to drought and salinity stresses in the Iranian barley RILs population. According to the obtained results, it is possible to use HVPLASC1B and EBmac0713 in normal conditions, ISSR21-2 and ISSR30-4 in drought conditions, and Bmac0047, Scot5-B, CAAT6-C, and ISSR30iPBS2076-4 in saline stress conditions to select genotypes with higher photosynthetic capacity in marker-assisted selection programs.

Genome wide identification and expression profiling of PYL genes in barley

PYLs (pyrabactin resistance1/PYR1-like) sense ABA, an essential phytohormone that regulates plant growth and stress responses. PYLs act as the main controllers of ABA stress signaling in plants. In this study, a total of 10 HvPYLs were discovered in the barley genome using an in silico genome search technique. These HvPYLs were then grouped into 3 subfamilies based on a phylogenetic analysis that compared them to the genomes of Arabidopsis, Brachypodium, rice, and maize. These HvPYLs demonstrated conserved motif compositions and identical protein structures across clades. Additionally, this study includes detailed investigations of gene structure variations, chromosomal distributions, cis-regulatory elements, protein-protein interactions, expression profiles in different tissues, and stress responses. We identified various cis-elements in the HvPYL promoter regions related to plant development and stresses indicating their potential roles in development and stress management. Our analysis of the interaction network has identified that HvPYLs can interact with key components of the ABA signaling pathway, demonstrating the critical regulatory functions of HvPYL genes in managing stress and growth in barley. These findings provide a basis for future research aimed at exploring the functions of PYL genes, with the ultimate goal of enhancing stress tolerance in barley and other related species.

Genome-wide Identification of HvPP2C Genes and Expression Profiling in Response to Cold and Heat Stresses in Barley (Hordeum vulgare L.)

Background: Protein phosphatases (PP2Cs) are the main classes of protein phosphatases in plants, having pivotal functions in different plant stages and abiotic stresses. The PP2C genes are suggested to have critical roles in barley by exposure to heat and cold treatments. Objectives: We surveyed HvPP2C genes from the barley genome in the present study. Phylogenetic analysis, functional annotation, synteny analysis, chromosomal distribution, prediction of cis-elements, and gene expression of HvPP2Cs under abiotic stresses were studied. Methods: In this study, HvPP2Cs of barley were surveyed using bioinformatics tools, and HvPP2C gene expression profiles under cold and heat stresses in 3 tissues (root, leaf, and stem) were analyzed. Results: In this study, 61 HvPP2C genes were detected from barley, and a phylogenetic tree was divided into 13 subfamilies. The results of chromosomal distribution showed that the HvPP2C genes were located on 7 chromosomes. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis of HvPP2Cs showed that they were largely expressed in different tissues (root, stem, and leaf) in the Azaran and Jolge barley cultivars. In Azaran, the HvPP2C gene expression increased in response to cold stress, whereas, in the Jolge cultivar, the HvPP2C gene expression increased in response to heat stress. The analysis of synteny revealed that HvPP2C24b with HvPP2C24a, HvPP2C24 with HvPP2C24a and HvPP2C24b; HvPP2C5 with HvPP2C5a, and HvPP2C41 with HvPP2C41a were paralogous. Conclusions: Results revealed a broad understanding of the HvPP2C gene family in barley, which can be valuable for the functional description of HvPP2Cs in plant response to abiotic stresses.

High-quality wild barley genome assemblies and annotation with Nanopore long reads and Hi-C sequencing data

Wild barley, from “Evolution Canyon (EC)” in Mount Carmel, Israel, are ideal models for cereal chromosome evolution studies. Here, the wild barley EC_S1 is from the south slope with higher daily temperatures and drought, while EC_N1 is from the north slope with a cooler climate and higher relative humidity, which results in a differentiated selection due to contrasting environments. We assembled a 5.03 Gb genome with contig N50 of 3.53 Mb for wild barley EC_S1 and a 5.05 Gb genome with contig N50 of 3.45 Mb for EC_N1 using 145 Gb and 160.0 Gb Illumina sequencing data, 295.6 Gb and 285.35 Gb Nanopore sequencing data and 555.1 Gb and 514.5 Gb Hi-C sequencing data, respectively. BUSCOs and CEGMA evaluation suggested highly complete assemblies. Using full-length transcriptome data, we predicted 39,179 and 38,373 high-confidence genes in EC_S1 and EC_N1, in which 93.6% and 95.2% were functionally annotated, respectively. We annotated repetitive elements and non-coding RNAs. These two wild barley genome assemblies will provide a rich gene pool for domesticated barley.

Professor Andreas Graner: driven by the quest to unlock crop plant genomes for conservation and utilization of germplasm for breeding.

Professor Andreas Graner stands as a towering figure in international crop plant genomics research, leaving an indelible imprint on the field over the past four decades. As we commemorate the 80th anniversary of Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany and Professor Graner's retirement in September 2023, here we celebrate and acknowledge his profound impact on crop genome analyses and genebank genomics. His trailblazing work extends from developing the first integrated RFLP map of barley, establishing the foundation of barley genome sequencing, and advancing functional genomics of malting quality, to pioneering the use of high-throughput phenomics. As the dedicated custodian of Germany's largest ex situ genebank at IPK Gatersleben, Professor Graner has fortified the institution's collection management and crop research, thereby contributing significantly to global efforts on conservation and utilization of plant genetic resources through genomics approaches. Alongside his impressive array of scientific achievements, Professor Graner's inspiring mentorship has nurtured a new generation of scientists, including us, leaving a lasting legacy in the field. This tribute underscores his enduring influence and celebrates his unwavering dedication to the scientific community.

Meta‐analysis of the genetics of resistance to Fusarium head blight and deoxynivalenol accumulation in barley and considerations for breeding

AbstractFusarium head blight (FHB) or scab is a devastating disease of barley that severely reduces the yield and quality of the grain. Additionally, mycotoxins produced by the causal Fusarium species can contaminate harvested grain, resulting in food safety concerns and further economic losses. In the Upper Midwest region of the United States, Fusarium graminearum is the primary causal agent, and deoxynivalenol (DON) is the main mycotoxin associated with Fusarium infection. Deployment of resistant cultivars is an important component of an integrated strategy to manage this disease. Unfortunately, few good sources of FHB resistance have been identified from the evaluation of large collections of Hordeum germplasm. Over the past 25 years, many barley mapping populations have been developed with selected resistance sources to identify the number, chromosomal position and allelic effect of quantitative trait loci (QTL) contributing to FHB resistance and DON accumulation. To consolidate the genetic data generated from 14 mapping studies that included 22 bi‐ or tri‐parental mapping populations and three genome‐wide association (GWAS) mapping panels, a consensus map was constructed that includes 4145 SNP, SSR, RFLP and AFLP markers. A meta‐analysis based on this consensus map revealed 96 QTL for FHB resistance and 57 for DON accumulation scattered across the barley genome. Many of the QTL explained a low percentage (<10%) of variation for the traits and were often found significant in only one or a few environments in multi‐year/multi‐location field trials. Moreover, many of the FHB/DON QTL mapped to chromosomal positions coincided with various agro‐morphological traits that could influence the level of disease (e.g. heading date, height, spike density, and spike angle), raising the important question of whether the former are true resistance factors or are simply the result of pleiotropy with the latter. Considering the magnitude of effect, consistency of detection across environments and independence from agro‐morphological traits, only three of 96 QTL for FHB and five of 57 QTL for DON were considered priority targets for marker‐assisted selection (MAS). In spite of the challenge for having a limited number of useful QTL for breeding, genomic selection holds promise for increasing the efficiency of developing FHB‐resistant barley cultivars, an essential component of the overall management strategy for the disease.

Genetic portrait of polyamine transporters in barley: insights in the regulation of leaf senescence.

Nitrogen (N) is one of the most expensive nutrients to supply, therefore, improving the efficiency of N use is essential to reduce the cost of commercial fertilization in plant production. Since cells cannot store reduced N as NH3 or NH4 +, polyamines (PAs), the low molecular weight aliphatic nitrogenous bases, are important N storage compounds in plants. Manipulating polyamines may provide a method to increase nitrogen remobilization efficiency. Homeostasis of PAs is maintained by intricate multiple feedback mechanisms at the level of biosynthesis, catabolism, efflux, and uptake. The molecular characterization of the PA uptake transporter (PUT) in most crop plants remains largely unknown, and knowledge of polyamine exporters in plants is lacking. Bi-directional amino acid transporters (BATs) have been recently suggested as possible PAs exporters for Arabidopsis and rice, however, detailed characterization of these genes in crops is missing. This report describes the first systematic study to comprehensively analyze PA transporters in barley (Hordeum vulgare, Hv), specifically the PUT and BAT gene families. Here, seven PUTs (HvPUT1-7) and six BATs (HvBAT1-6) genes were identified as PA transporters in the barley genome and the detailed characterization of these HvPUT and HvBAT genes and proteins is provided. Homology modeling of all studied PA transporters provided 3D structures prediction of the proteins of interest with high accuracy. Moreover, molecular docking studies provided insights into the PA-binding pockets of HvPUTs and HvBATs facilitating improved understanding of the mechanisms and interactions involved in HvPUT/HvBAT-mediated transport of PAs. We also examined the physiochemical characteristics of PA transporters and discuss the function of PA transporters in barley development, and how they help barley respond to stress, with a particular emphasis on leaf senescence. Insights gained here could lead to improved barley production via modulation of polyamine homeostasis.

Genome-wide identification of WD40 transcription factors and their regulation of the MYB-bHLH-WD40 (MBW) complex related to anthocyanin synthesis in Qingke (Hordeum vulgare L. var. nudum Hook. f.)

BackgroundWD40 transcription factors, a large gene family in eukaryotes, are involved in a variety of growth regulation and development pathways. WD40 plays an important role in the formation of MYB-bHLH-WD (MBW) complexes associated with anthocyanin synthesis, but studies of Qingke barley are lacking.ResultsIn this study, 164 barley HvWD40 genes were identified in the barley genome and were analyzed to determine their relevant bioinformatics. The 164 HvWD40 were classified into 11 clusters and 14 subfamilies based on their structural and phylogenetic protein profiles. Co-lineage analysis revealed that there were 43 pairs between barley and rice, and 56 pairs between barley and maize. Gene ontology (GO) enrichment analysis revealed that the molecular function, biological process, and cell composition were enriched. The Kyoto Encyclopedia of Genes and Genomes (KEGG) results showed that the RNA transport pathway was mainly enriched. Based on the identification and analysis of the barley WD40 family and the transcriptome sequencing (RNA-seq) results, we found that HvWD40-140 (WD40 family; Gene ID: r1G058730), HvANT1 (MYB family; Gene ID: HORVU7Hr1G034630), and HvANT2 (bHLH family; Gene ID: HORVU2Hr1G096810) were important components of the MBW complex related to anthocyanin biosynthesis in Qingke, which was verified via quantitative real-time fluorescence polymerase chain reaction (qRT-PCR), subcellular location, yeast two-hybrid (Y2H), and bimolecular fluorescent complimentary (BiFC) and dual-luciferase assay analyses.ConclusionsIn this study, we identified 164 HvWD40 genes in barley and found that HvnANT1, HvnANT2, and HvWD40-140 can form an MBW complex and regulate the transcriptional activation of the anthocyanin synthesis related structural gene HvDFR. The results of this study provide a theoretical basis for further study of the mechanism of HvWD40-140 in the MBW complex related to anthocyanin synthesis in Qingke.

Genetic diversity and population structure assessment of Western Canadian barley cooperative trials.

Studying the population structure and genetic diversity of historical datasets is a proposed use for association analysis. This is particularly important when the dataset contains traits that are time-consuming or costly to measure. A set of 96 elite barley genotypes, developed from eight breeding programs of the Western Canadian Cooperative Trials were used in the current study. Genetic diversity, allelic variation, and linkage disequilibrium (LD) were investigated using 5063 high-quality SNP markers via the Illumina 9K Barley Infinium iSelect SNP assay. The distribution of SNPs markers across the barley genome ranged from 449 markers on chromosome 1H to 1111 markers on chromosome 5H. The average polymorphism information content (PIC) per locus was 0.275 and ranged from 0.094 to 0.375. Bayesian clustering in STRUCTURE and principal coordinate analysis revealed that the populations are differentiated primarily due to the different breeding program origins and ear-row type into five subpopulations. Analysis of molecular variance based on PhiPT values suggested that high values of genetic diversity were observed within populations and accounted for 90% of the total variance. Subpopulation 5 exhibited the most diversity with the highest values of the diversity indices, which represent the breeding program gene pool of AFC, AAFRD, AU, and BARI. With increasing genetic distance, the LD values, expressed as r2, declined to below the critical r2 = 0.18 after 3.91 cM, and the same pattern was observed on each chromosome. Our results identified an important pattern of genetic diversity among the Canadian barley panel that was proposed to be representative of target breeding programs and may have important implications for association mapping in the future. This highlight, that efforts to identify novel variability underlying this diversity may present practical breeding opportunities to develop new barley genotypes.

Metal tolerance gene family in barley: an in silico comprehensive analysis

Metal-tolerance proteins (MTPs) are divalent cation transporters that play critical roles in metal tolerance and ion homeostasis in plants. However, a comprehensive study of MTPs is still lacking in crop plants. The current study aimed to comprehensively identify and characterize the MTP gene family in barley (Hordeum vulgare, Hv), an important crop. In total, 12 HvMTPs were identified in the barley genome in this study. They were divided into three phylogenetic groups (Zn-cation diffusion facilitator proteins [CDFs], Fe/Zn-CDFs, and Mn-CDFs) and further subdivided into seven groups (G1, G5, G6, G7, G8, G9, and G12). The majority of MTPs were hydrophobic proteins found in the vacuolar membrane. Gene duplication analysis of HvMTPs revealed one pair of segmental-like duplications in the barley genome. Evolutionary analysis suggested that barley MTPs underwent purifying natural selection. Additionally, the HvMTPs were analyzed in the pan-genome sequences of barley (20 accessions), which suggests that HvMTPs are highly conserved in barley evolution. Cis-acting regulatory elements, microRNA target sites, and protein–protein interaction analysis indicated the role of HvMTPs in a variety of biological processes. Expression profiling suggests that HvMTPs play an active role in maintaining barley nutrient homeostasis throughout its life cycle, and their expression levels were not significantly altered by abiotic stresses like cold, drought, or heat. The expression of barley HvMTP genes in the presence of heavy metals such as Zn2+, Cu2+, As3+, and Cd2+ revealed that these MTPs were induced by at least one metal ion, implying their involvement in metal tolerance or transportation. The identification and comprehensive investigation of MTP gene family members will provide important gene resources for the genetic improvement of crops for metal tolerance, bioremediation, or biofortification of staple crops.

Reprogramming of Fundamental miRNA and Gene Expression during the Barley-Piriformospora indica Interaction.

The interactions between plants and microorganisms, which are widely present in the microbial-dominated rhizosphere, have been studied. This association is highly beneficial to the organisms involved, as plants benefit soil microorganisms by providing them with metabolites, while microorganisms promote plant growth and development by promoting nutrient uptake and/or protecting the plant from biotic and abiotic stresses. Piriformospora indica, an endophytic fungus of Sebacinales, colonizes the roots of a wide range of host plants and establishes various benefits for the plants. In this work, an interaction between barley and the P. indica was established to elucidate microRNA (miRNA)-based regulatory changes in miRNA profiles and gene expression that occurred during the symbiosis. Growth promotion and vigorous root development were confirmed in barley colonized by P. indica. The genome-wide expression profile analysis of miRNAs in barley root showed that 7,798,928, 6,418,039 and 7,136,192 clean reads were obtained from the libraries of mock, 3 dai and 7 dai roots, respectively. Sequencing of the barley genome yielded in 81 novel miRNA and 450 differently expressed genes (DEGs). Additionally, 11, 24, 6 differentially expressed microRNAs (DEMs) in barley were found in the three comparison groups, including 3 dai vs. mock, 7 dai vs. mock and 7 dai vs. 3 dai, respectively. The predicted target genes of these miRNAs are mainly involved in transcription, cell division, auxin signal perception and transduction, photosynthesis and hormone stimulus. Transcriptome analysis of P. indica identified 667 and 594 differentially expressed genes (DEG) at 3 dai and 7 dai. Annotation and GO (Gene Ontology) analysis indicated that the DEGs with the greatest changes were concentrated in oxidoreductase activity, ion transmembrane transporter activity. It implies that reprogramming of fundamental miRNA and gene expression occurs both in barley and P. indica. Analysis of global changes in miRNA profiles of barley colonized with P. indica revealed that several putative endogenous barley miRNAs expressed upon colonization belonging to known micro RNA families involved in growth and developmental regulation.

Exome-wide variation in a diverse barley panel reveals genetic associations with ten agronomic traits in Eastern landraces

Barley (Hordeum vulgare ssp. vulgare) is one of the first crops to be domesticated and is adapted to a wide range of environments. Worldwide barley germplasm collections possess valuable allelic variations that could further improve barley productivity. Although barley genomics has offered a global picture of allelic variation among varieties and its association with various agronomic traits, polymorphisms from East Asian varieties remain scarce. In this study, we analyze exome polymorphisms in a panel of 274 barley varieties collected worldwide, including 137 varieties from East Asian countries and Ethiopia. We reveal the underlying population structure and conduct genome-wide association studies for 10 agronomic traits. Moreover, we examin genome-wide associations for traits related to grain size such as awn length and glume length. Our results demonstrate the value of diverse barley germplasm panels containing Eastern varieties, highlighting their distinct genomic signatures relative to Western subpopulations.

Genome-Wide Identification and Expression Analysis of Kinesin Family in Barley (Hordeum vulgare).

Kinesin, as a member of the molecular motor protein superfamily, plays an essential function in various plants' developmental processes. Especially at the early stages of plant growth, including influences on plants' growth rate, yield, and quality. In this study, we did a genome-wide identification and expression profile analysis of the kinesin family in barley. Forty-two HvKINs were identified and screened from the barley genome, and a generated phylogenetic tree was used to compare the evolutionary relationships between Rice and Arabidopsis. The protein structure prediction, physicochemical properties, and bioinformatics of the HvKINs were also dissected. Our results reveal the important regulatory roles of HvKIN genes in barley growth. We found many cis- elements related to GA3 and ABA in homeopathic elements of the HvKIN gene and verified them by QRT-PCR, indicating their potential role in the barley kinesin family. The current study revealed the biological functions of barley kinesin genes in barley and will aid in further investigating the kinesin in other plant species.

Deciphering the genomic regions governing major agronomic traits and blast resistance using genome wide association mapping in finger millet

Finger millet (Eleusine coracana L.) is climate resilient minor millet of Asia and Africa with wide adaptation and unparallel nutritional profile. To date, genomic resources available in finger millet are scanty and genetic control of agronomic traits remains elusive. Here, a collection of eco-geographically diverse 186 genotypes was quantified for variation in 13 agronomic traits and reaction to blast to identify marker-trait associations (MTAs) using genotyping-by-sequencing (GBS) and genome-wide association study (GWAS). GBS generated 2977 high quality single nucleotide polymorphism (SNPs) markers and identified three subpopulations with varying admixture levels. General linear and mixed model approaches of GWAS to correct for population structure and genetic relatedness identified 132 common MTAs for agronomic traits across the years. The phenotypic variance explained by the makers varied from 4.8% (TP692389-flag leaf width) to 20% (TP714446-green fodder weight). Of these, 26 MTAs showed homology with candidate genes having role in plant growth, development and photosynthesis in the genomes of foxtail millet, rice, maize, wheat and barley. We also found 4 common MTAs for neck blast resistance, which explained 5.9–15.1% phenotypic variance. Three MTAs for neck blast resistance showed orthologues in related genera having putative functions in pathogen defense in plants. The results of this work lay a foundation for understanding the genetic architecture of agronomic traits and blast resistance in finger millet and provide a framework for genomics assisted breeding.

Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley.

Divergent selection of populations in contrasting environments leads to functional genomic divergence. However, the genomic architecture underlying heterogeneous genomic differentiation remains poorly understood. Here, we de novo assembled two high-quality wild barley (Hordeum spontaneum K. Koch) genomes and examined genomic differentiation and gene expression patterns under abiotic stress in two populations. These two populations had a shared ancestry and originated in close geographic proximity but experienced different selective pressures due to their contrasting micro-environments. We identified structural variants that may have played significant roles in affecting genes potentially associated with well-differentiated phenotypes such as flowering time and drought response between two wild barley genomes. Among them, a 29-bp insertion into the promoter region formed a cis-regulatory element in the HvWRKY45 gene, which may contribute to enhanced tolerance to drought. A single SNP mutation in the promoter region may influence HvCO5 expression and be putatively linked to local flowering time adaptation. We also revealed significant genomic differentiation between the two populations with ongoing gene flow. Our results indicate that SNPs and small SVs link to genetic differentiation at the gene level through local adaptation and are maintained through divergent selection. In contrast, large chromosome inversions may have shaped the heterogeneous pattern of genomic differentiation along the chromosomes by suppressing chromosome recombination and gene flow. Our research offers novel insights into the genomic basis underlying local adaptation and provides valuable resources for the genetic improvement of cultivated barley.

The Complete Nucleotide Sequence of Barley Yellow Dwarf Virus-PAV from Wheat in Turkey

ABSTRACTWe report the sequence of an assembled genome of Barley yellow dwarf virus-PAV (BYDV-PAV) from Turkey. This 5,672 nucleotide RNA encodes seven known open reading frames and a possible eighth. This genome from wheat is closely related to BYDV-PAVs in Pakistan, Brazil, and Australia, including one sequenced 34 years ago.

Structural variants in the barley gene pool: precision and sensitivity to detect them using short-read sequencing and their association with gene expression and phenotypic variation

Key messageStructural variants (SV) of 23 barley inbreds, detected by the best combination of SV callers based on short-read sequencing, were associated with genome-wide and gene-specific gene expression and, thus, were evaluated to predict agronomic traits.In human genetics, several studies have shown that phenotypic variation is more likely to be caused by structural variants (SV) than by single nucleotide variants. However, accurate while cost-efficient discovery of SV in complex genomes remains challenging. The objectives of our study were to (i) facilitate SV discovery studies by benchmarking SV callers and their combinations with respect to their sensitivity and precision to detect SV in the barley genome, (ii) characterize the occurrence and distribution of SV clusters in the genomes of 23 barley inbreds that are the parents of a unique resource for mapping quantitative traits, the double round robin population, (iii) quantify the association of SV clusters with transcript abundance, and (iv) evaluate the use of SV clusters for the prediction of phenotypic traits. In our computer simulations based on a sequencing coverage of 25x, a sensitivity > 70% and precision > 95% was observed for all combinations of SV types and SV length categories if the best combination of SV callers was used. We observed a significant (P < 0.05) association of gene-associated SV clusters with global gene-specific gene expression. Furthermore, about 9% of all SV clusters that were within 5 kb of a gene were significantly (P < 0.05) associated with the gene expression of the corresponding gene. The prediction ability of SV clusters was higher compared to that of single-nucleotide polymorphisms from an array across the seven studied phenotypic traits. These findings suggest the usefulness of exploiting SV information when fine mapping and cloning the causal genes underlying quantitative traits as well as the high potential of using SV clusters for the prediction of phenotypes in diverse germplasm sets.

Mapping of QTLs controlling barley agronomic traits (Hordeum vulgare L.) under normal conditions and drought and salinity stress at reproductive stage

The present study is focused on mapping the genomic regions for controlling some agronomic traits in the reproductive stage of barley under normal, drought and saline conditions. In this regard, a total of 103 samples of F8 families derived from the cross of two cultivars of Badia×Kavir were planted in a completely randomized design in the crop year 2018–2019. The research procedure has been accomplished in the greenhouse of Gonbad Kavous University in three replications. In this case, transgressive segregation was observed for the evaluated traits. This situation indicated the difference between allelic interactions in the parents. Also, linkage maps were prepared using 152 SSR polymorphic markers, 72 ISSR alleles, 7 IRAP alleles, 29 CAAT alleles, 27 SCoT alleles, and 15 iPBS alleles. These markers were assigned to the seven barley chromosomes. Thus, the obtained map covered 999.29 centiMorgans (cM) of the barley genome length, and the average distance between two flanking markers was 3.387 cM. In this study, the most significant QTL under normal conditions have been identified on chromosomes 1, 5, and 6. In the drought conditions, four major QTLs were detected for spike diameter, awn weight, flag leaf weight (qPPT-7, qAWW-7, qFLW-4a and qFLW-5). Under salinity stress conditions, two major QTLs were identified for the number of leaves qLEN-6a and shoot diameter qSHT-6b. In this case, the values of R2 were 18.3 and 17.6, respectively. The major QTLs that control the effect of the desired traits and the markers associated with them can be used in marker-assisted selection programs.

Temporal Expression Analysis of Barley Disproportionating Enzyme 1 (DPE1) during Grain Development and Malting

Disproportionating enzyme (D-enzyme) is a 4-α-glucanotransferase (EC 2.4.1.25) that disproportionates α-glucans and maltooligosaccharides and preferentially disproportionates maltotriose into maltopentaose and glucose. Maltotriose is a maltooligosaccharide that accumulates in barley malt and wort without being digested further by starch degrading enzymes. Furthermore, not all brewer’s yeast strains can ferment maltotriose. This research was undertaken to determine if D-enzyme is expressed in developing and/or malting barley grains and thus providing evidence of an inherent enzymatic mechanism capable of disproportionating maltotriose into maltopentaose that can be further degraded into fermentable sugars by amylolytic enzymes such as β-amylase. A partial genomic sequence of barley disproportionating enzyme 1 (DPE1) was obtained that was comprised of 16 exons and 15 introns totaling 4680 bp. The 5’ region of the DPE1 gene was recalcitrant to Sanger sequencing owing to its localization in a highly repetitive region of the barley genome. The DPE1 gene is expressed during grain development and the protein stored in the mature grain. Additionally, the DPE1 gene is de novo expressed during malting in both a 2- and 6-row malting cultivar with significant variation observed amongst 13 elite malting cultivars representing spring and winter growth habits. During grain development, DPE1 mRNA levels peak at 17 days after anthesis, which coincides with a large increase in proteins that react to anti-DPE1 polyclonal antibodies. These proteins appear as a doublet on immunoblots during initial stages of malting and as a singlet as malting progresses indicating proteolytic processing (e.g., transit peptide removal) or differential isoform/splice variant expression.