Cultivated Barley Genotypes Research Articles

LncRNA cis- and trans-regulation provides new insight into drought stress responses in wild barley.

Drought is one of the most common abiotic stresses that affect barley productivity. Long noncoding RNA (lncRNA) has been reported to be widely involved in abiotic stress, however, its function in the drought stress response in wild barley remains unclear. In this study, RNA sequencing was performed to identify differentially expressed lncRNAs (DElncRNA) among two wild barley and two cultivated barley genotypes. Then, the cis-regulatory networks were according to the chromosome position and the expression level correction. The GO annotation indicates that these cis-target genes are mainly involved in "ion transport transporter activity" and "metal ion transport transporter activity". Through weighted gene co-expression network analysis (WGCNA), 10 drought-related modules were identified to contract trans-regulatory networks. The KEGG annotation demonstrated that these trans-target genes were enriched for photosynthetic physiology, brassinosteroid biosynthesis, and flavonoid metabolism. In addition, we constructed the lncRNA-mediated ceRNA regulatory network by predicting the microRNA response elements (MREs). Furthermore, the expressions of lncRNAs were verified by RT-qPCR. Functional verification of a candidate lncRNA, MSTRG.32128, demonstrated its positive role in drought response and root growth and development regulation. Hormone content analysis provided insights into the regulatory mechanisms of MSTRG.32128 in root development, revealing its involvement in auxin and ethylene signal transduction pathways. These findings advance our understanding of lncRNA-mediated regulatory mechanisms in barley under drought stress. Our results will provide new insights into the functions of lncRNAs in barley responding to drought stress.

Differential reduction in cadmium accumulation in barley under cadmium-salt co-exposure involves specific HMA genes and antioxidative responses

Salinity and heavy metal accumulation adversely affect agricultural productivity and environmental sustainability. Little information exists about the combinatory effect of various stresses on plants, but it is assumed that stress interaction may trigger a specific response. Here, we assessed the combinatory effect of salinity and cadmium on various physiological and molecular traits in two cultivated barley genotypes with contrasting salinity tolerance; Rihane (RH, salt tolerant) and Lemsi (LM, salt sensitive). Studied genotypes were hydroponically exposed to CdCl2 (30 µM), NaCl (300 mM) or the combined Cd-NaCl stresses for 15 days. Salinity and to a lesser degree Cd-NaCl stress significantly reduced growth, leaf water content, chlorophyll pigments, and K uptake, and increased Na and Cl contents for both genotypes, with LM being more affected than RH. Cd content in roots was higher than in shoots for both genotypes either under Cd alone or when combined with NaCl. Interestingly, NaCl addition reduced Cd accumulation in both roots and shoots of the two barley genotypes, suggesting that the interaction of NaCl and Cd on their uptake and accumulation is antagonistic. The tolerant genotype (RH) accumulated lower Cd levels in shoots and roots than the salt-sensitive one (LM). Cd-NaCl stress significantly lowered H2O2 and MDA contents relative to NaCl treatment alone. The activity of several antioxidant enzymes was essentially higher in RH than in LM, under the different stresses. These responses were in concomitant with an enhanced expression of specific Heavy Metal ATPases (HvHMA) genes, mainly in RH, which can partially, explain the reduced Cd accumulation in this genotype. Overall, these findings suggest the possibility of cultivating salt-tolerant barley genotypes in saline soils slightly contaminated with Cd, whereas barley sensitive genotypes could be assessed for phytoremediation purposes.

Genomic resources for a historical collection of cultivated two-row European spring barley genotypes

Barley genomic resources are increasing rapidly, with the publication of a barley pangenome as one of the latest developments. Two-row spring barley cultivars are intensely studied as they are the source of high-quality grain for malting and distilling. Here we provide data from a European two-row spring barley population containing 209 different genotypes registered for the UK market between 1830 to 2014. The dataset encompasses RNA-sequencing data from six different tissues across a range of barley developmental stages, phenotypic datasets from two consecutive years of field-grown trials in the United Kingdom, Germany and the USA; and whole genome shotgun sequencing from all cultivars, which was used to complement the RNA-sequencing data for variant calling. The outcomes are a filtered SNP marker file, a phenotypic database and a large gene expression dataset providing a comprehensive resource which allows for downstream analyses like genome wide association studies or expression associations.

Stomatal Responses of Two Drought-Tolerant Barley Varieties with Different ROS Regulation Strategies under Drought Conditions.

Drought stress is a major obstacle to agricultural production. Stomata are central to efforts to improve photosynthesis and water use. They are targets for manipulation to improve both processes and the balance between them. An in-depth understanding of stomatal behavior and kinetics is important for improving photosynthesis and the WUE of crops. In this study, a drought stress pot experiment was performed, and a transcriptome analysis of the leaves of three contrasting, cultivated barley genotypes Lumley (Lum, drought-tolerant), Golden Promise (GP, drought-sensitive), and Tadmor (Tad, drought-tolerant), generated by high-throughput sequencing, were compared. Lum exhibited a different WUE at the leaf and whole-plant levels and had greater CO2 assimilation, with a higher gs under drought stress. Interestingly, Lum showed a slower stomatal closure in response to a light-dark transition and significant differences compared to Tad in stomatal response to the exogenous application of ABA, H2O2, and CaCl2. A transcriptome analysis revealed that 24 ROS-related genes were indeed involved in drought response regulation, and impaired ABA-induced ROS accumulation in Lum was identified using ROS and antioxidant capacity measurements. We conclude that different stomatal ROS responses affect stomatal closure in barley, demonstrating different drought regulation strategies. These results provide valuable insight into the physiological and molecular basis of stomatal behavior and drought tolerance in barley.

Single-Nucleotide Polymorphisms in Bmy1 Intron III Alleles Conferring the Genotypic Variations in β-Amylase Activity under Drought Stress between Tibetan Wild and Cultivated Barley

β-amylase activity is related to the polymorphisms of Bmy1 intron III; however, no attention has been given to such relationships under environmental stresses such as drought. In this study, 73 cultivated barley genotypes and 52 Tibetan wild barley accessions were used to test the association between Bmy1 gene intron III polymorphisms and β-amylase activity under drought stress. Our results showed that three alleles, Bmy1.a, Bmy1.b, and Bmy1.c, existed in the examined barley genotypes. Tibetan wild barley had a higher proportion of Bmy1.b, whereas cultivated barley showed a higher proportion of Bmy1.a. Impressively, barley genotypes with Bmy1.b showed a significant increase in β-amylase activity under drought stress, compared with those with Bmy1.a or Bmy1.c, indicating that the Bmy1.b allele might provide more chances for developing barley cultivars with higher β-amylase activity under water stress than both the Bmy1.a and Bmy1.c alleles. Furthermore, the Tibetan wild barley XZ147, belonging to the Bmy1.b allele type, showed significantly higher β-amylase activity than Triumph under drought stress. This might be the result of the unique amino acid substitution M527 or the amino acid composition of R115, D165, A233, S347, and M527 of XZ147.

Comparative Analysis of Transcriptome Profiles Reveals the Mechanisms in the Difference of Low Potassium Tolerance among Cultivated and Tibetan Wild Barleys

Potassium (K) deficiency is a bottleneck for crop production. Thus, developing low K (LK)-tolerant crop cultivars to relieve the issue is extremely urgent. Our previous studies had found that Tibetan annual wild barley accessions showed a higher LK tolerance than the cultivated barley. In this study, RNA-sequencing was performed on three barley genotypes, wild (XZ153, LK tolerance; XZ141, LK sensitivity) and cultivated (ZD9, LK sensitivity) barley genotypes, to compare the transcriptome profiles of their shoots at two time points after LK stress. In total, 4832 genes displayed differential expression at 48 h and 15 d among three genotypes after K stress treatment, with XZ153 having much more differentially expressed genes (DEGs) at 48 h than 15 d, but it was the opposite in ZD9. Meanwhile, GO annotation analysis and KEGG pathway enrichment were implemented on 555 and 814 LK tolerance-associated DEGs at 48 h and 15 d after LK stress, respectively. Three barley genotypes differed significantly in transcriptional level after LK treatment. The high tolerance in wild genotype XZ153 could be attributed to many factors, mainly including K channels, Ca2+ signaling pathway, ethylene biosynthesis process, TCA cycle, glycolysis, pentose phosphate pathway, and photosynthesis. Furthermore, some candidate genes identified in this study may be used to improve the LK tolerance of barley.

Molecular diversity of Azerbaijani wild and cultivated barley genotypes

In this study the genetic diversity of Azerbaijan barley, nuclear genomes of 13 cultivated and 9 wild barley accessions were analyzed at population and individual levels using twenty ISSR primers. In total, 304 fragments were amplified, of which 263 were found to be polymorphic. High genetic diversity indices for ISSR markers (0.714) suggested that this method was equally effective in determining genetic variation in barley accessions. The highest and the lowest similarity indexes were equal to 0.92 and 0.20, respectively. Cluster analysis based on Nei’s genetic distance values showed that genotypes could be grouped into seven main clusters. Furthermore, no differences between the wild and cultivated barley accessions were revealed. Screening a higher number of anonymous loci in barley using ISSR markers will enable the selection of the best parent cultivars for the development of novel varieties

Rhizosphere Soil Quality of Different Cultivated and Wild Barley Genotypes as Evaluated Using Physical and Chemical Indicators

Rhizosphere Soil Quality of Different Cultivated and Wild Barley Genotypes as Evaluated Using Physical and Chemical Indicators

Differential Changes in D1 Protein Content and Quantum Yield of Wild and Cultivated Barley Genotypes Caused by Moderate and Severe Drought Stress in Relation to Oxidative Stress

The aim of this study was to investigate the effects of drought stress on oxidative damage and efficiency of PSII photochemistry in barley and compare the varietal response of different genotypes including Yusof (tolerant), Moroc9-75 (sensitive), and wild barley (HS) to drought. Plants were subjected to different levels of soil water availability including control, moderate, and severe drought stress. Exposure to drought stress led to decrease in leaf water potential, biomass production, and stomatal conductance (gs) in all genotypes. Drought induced an increase in H2O2 content followed by increase in malondialdehyde (MDA) as a final result of lipid peroxidation. Drought stress also resulted in reduction of D1 protein content in all genotypes and decreased the maximal quantum yield of PSII photochemistry (FV/FM). These parameters were more affected in Moroc9-75 cultivar by drought stress compare to Yusof and HS genotype. Based on our results, drought-induced reactive oxygen species may decrease PSII photochemistry either through peroxidation of thylakoid membranes or interfering with D1 protein synthesis, necessary for proper function of PSII.

Identification of molecular markers for starch content in barley (Hordeum vulgare L.) by genome-wide association studies based on bulked samples

AbstractStarch content is an important trait in barley. To evaluate the genetic diversity and identify molecular markers of starch content in barley, 40 cultivated barley genotypes collected from different regions, including genotypes whose starch content is at either the high or low end of the spectrum (15), were used in this study. All the genotypes were re-sequenced by the double-digest-restriction associated DNA sequencing method, and a total of 299,103 single-nucleotide polymorphism (SNP) markers were obtained. The genotypes were divided into four sub-populations based on FASTSTRUCTURE, principal component analysis and neighbour-joining tree analysis. All four sub-populations had a high linkage disequilibrium, especially group 3, whose members were recently bred for malting in the Jiangsu coastal area. The starch content of the barley lines was evaluated during three growing seasons (2014–2017), and the average values of starch content across the three growing seasons at the low and high ends were 51.5 and 55.0%, respectively. The starch content was affected by population structure, the barley in group 2 had a low starch content, while the barley in group 4 had a high starch content. Twenty-six SNP markers were identified as being significantly associated with starch content (P ⩽ 0.001) based on the average values across the three growing seasons using the mixed linear model method. These SNP markers were located on chromosomes 1H and 4H, and were considered loci of qSC1-1 and qSC4-1, respectively. The major identified QTLs for starch content are helpful for further research on carbohydrates and for barley breeding.

Expression pattern and physiological roles of Plastid Terminal Oxidase (PTOX) in wild and cultivated barley genotypes under drought stress

Plastid terminal oxidase (PTOX) is a plastid-localized protein that acts as plastoquinol oxidase. The objective of this study was to determine the role of plastid terminal oxidase in response to drought stress and examine the differential response of PTOX pathway in both cultivated (Yousef and Morocco) and tolerant wild barley (spantaneum; HS) genotypes. Plants were subjected to different levels of soil water availability including control, mild and severe drought stress. Decrease in leaf relative water content as a result of progressive drought stressed led to decrease in stomatal conductance and increased enzymatic antioxidant machinery in all genotypes. Drought stress did not affect the PTOX transcript and protein level in cultivated genotypes Yousef and Morocco. However, PTOX gene expression and protein content significantly increased in HS genotype under severe drought. Assessment of PTOX activity via fast fluorescence induction curve in presence of PTOX specific inhibitor revealed that PTOX could efficiently oxidize plastoquinon pool and acts as alternative electron pathway in HS genotype. Results indicated that the role of PTOX in stress response was more significant in the wild barley than the cultivated barley varieties, where the emphasis has been on the desirable agronomic traits.

A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication

BackgroundIt has become clear in recent years that many genes in a given species may not be found in a single genotype thus using sequences from a single genotype as reference may not be adequate for various applications.ResultsIn this study we constructed a pan-transcriptome for barley by de novo assembling 288 sets of RNA-seq data from 32 cultivated barley genotypes and 31 wild barley genotypes. The pan-transcriptome consists of 756,632 transcripts with an average N50 length of 1240 bp. Of these, 289,697 (38.2%) were not found in the genome of the international reference genotype Morex. The novel transcripts are enriched with genes associated with responses to different stresses and stimuli. At the pan-transcriptome level, genotypes of wild barley have a higher proportion of disease resistance genes than cultivated ones.ConclusionsWe demonstrate that the use of the pan-transcriptome dramatically improved the efficiency in detecting variation in barley. Analysing the pan-transcriptome also found that, compared with those in other categories, disease resistance genes have gone through stronger selective pressures during domestication.

Assembly and analysis of a qingke reference genome demonstrate its close genetic relation to modern cultivated barley.

Summary Qingke, the local name of hulless barley in the Tibetan Plateau, is a staple food for Tibetans. The availability of its reference genome sequences could be useful for studies on breeding and molecular evolution. Taking advantage of the third‐generation sequencer (PacBio), we de novo assembled a 4.84‐Gb genome sequence of qingke, cv. Zangqing320 and anchored a 4.59‐Gb sequence to seven chromosomes. Of the 46,787 annotated ‘high‐confidence’ genes, 31 564 were validated by RNA‐sequencing data of 39 wild and cultivated barley genotypes with wide genetic diversity, and the results were also confirmed by nonredundant protein database from NCBI. As some gaps in the reference genome of Morex were covered in the reference genome of Zangqing320 by PacBio reads, we believe that the Zangqing320 genome provides the useful supplements for the Morex genome. Using the qingke genome as a reference, we conducted a genome comparison, revealing a close genetic relationship between a hulled barley (cv. Morex) and a hulless barley (cv. Zangqing320), which is strongly supported by the low‐diversity regions in the two genomes. Considering the origin of Morex from its breeding pedigree, we then demonstrated a close genomic relationship between modern cultivated barley and qingke. Given this genomic relationship and the large genetic diversity between qingke and modern cultivated barley, we propose that qingke could provide elite genes for barley improvement.

Transposon-based genetic diversity assessment in wild and cultivated barley

Transposable element-based molecular markers can be utilized to investigate genetic diversity and to create genetic linkage maps. In this study, Class I and class II transposons were employed to obtain a comparative account of genetic diversity between wild and cultivated barley genotypes. Three types of PCR-based techniques were used: IMP (Inter MITE Polymorphism), IRAP (Inter-Retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism). Specific primer pairs for IMP, IRAP, and REMAP detected a total of 200 bands with an average of 20 bands per marker. The mean polymorphic information content (PIC) and discrimination power (D) values in all 47 genotypes from these three types of transposon-based polymorphisms were 0.910 and 0.935, respectively. Unweighted Pair Group Method with Arithmetic mean (UPGMA)-based cluster analysis classified all 47 genotypes, both wild and cultivated, into separate groups consistent with their geographical origins. Sequencing followed by chromosome location of polymorphic bands enables precise gene introgression from wild gene pool to cultivated barley. The highly polymorphic nature of these marker systems makes them suitable for use in varietal identification and MAS-based breeding programs in barley and other cereals.

Fine mapping of a major QTL for awn length in barley using a multiparent mapping population

Key messageAwn length was mapped using a multiparent population derived from cv. Morex and four wild accessions. One QTL was fine mapped and candidate genes were identified in NILs by RNA-seq.Barley awns are photosynthetically active and contribute to grain yield. Awn length is variable among both wild and cultivated barley genotypes and many mutants with alterations in awn length have been identified. Here, we used a multiparent mapping population derived from cv. Morex and four genetically diverse wild barley lines to detect quantitative trait loci (QTLs) for awn length. Twelve QTLs, distributed over the barley genome, were identified with the most significant one located on chromosome arm 7HL (QTL AL7.1). The effect of AL7.1 was confirmed using near isogenic lines (NILs) and fine-mapped in two independent heterogeneous inbred families to a < 0.9 cM interval. With exception of a small effect on grain width, no other traits such as plant height or flowering time were affected by AL7.1. Variant calling on transcripts obtained from RNA sequencing reads in NILs was used to narrow down the list of candidate genes located in the interval. This data may be used for further characterization and unravelling of the mechanisms underlying natural variation in awn length.

The relationship of limit dextrinase, limit dextrinase inhibitor and malt quality parameters in barley and their genetic analysis

Limit dextrinase (LD) and limit dextrinase inhibitor (LDI) are the two important traits affecting malt quality. The genetic variation and controlling of LD activity and LDI content in barley grains and malt are not well understood. In this study, we measured LD activity and LDI content in both grains and malt of 68 cultivated barley genotypes. The results show that there is a wide difference among barley genotypes in both LD activity and LDI content. LD in malt is not correlated with LD in grains, but negatively correlated with LDI in malt. LD in malt is positively correlated with diastatic power (DP), Kolbach index (KI) and soluble nitrogen content (SN), and negatively correlated with viscosity (VC). LDI in malt is positively correlated with DP and total nitrogen (TN), and negatively correlated with KI. Association analysis identifies 5 QTLs associated with LD and 3 QTLs associated with LDI in malt. Three major QTLs controlling LD in malt account for 35.7%, 35.7% and 28.4% of phenotypic variation, respectively. A total of 17 QTLs associated with malt quality are identified. The current results address the importance of both LD and LDI in affecting malt quality and the identified QTLs could be useful in barley breeding.

The genotypic difference in the effect of water stress after anthesis on the malt quality parameters in barley

It is well known that water stress is a major abiotic factor causing barley yield loss and unstable malt quality. However it is not quite clear about the altered pattern of the main malt quality traits for the barley genotypes differing in water stress tolerance. In this study, the effect of water stress during grain filling stage on grain weight, β-glucan content, β-amylase and limit dextrinase (LD) activities of three Tibetan wild and two cultivated barley genotypes were investigated. The results showed that water stress reduced biomass accumulation and grain weight of all genotypes, and increased protein content, but the reduced or increased extent differed significantly among genotypes, with XZ147 being less affected. In general, water stress increased β-amylase activity, reduced β-glucan content, had little effect on LD activity, which are attributed to increased protein and hordein contents, reduced grain weight, and its ineffective form in grains, respectively. Tibetan wild barley XZ147 is characterized by little change in grain weight and β-glucan content, dramatically increase of β-amylase activity under water stress, indicating its great potential for use in developing barley cultivars with high tolerance to water stress and high malt quality.

Assessment of genetic diversity among Jordanian wild barley (Hordeum spontaneum) genotypes revealed by SSR markers

Wild barley, Hordeum spontaneum is the progenitor of cultivated barley. The center of diversity is in the Fertile Crescent in the Near East, where wild barley grows under a wide range of environmental and climatic conditions. Jordan wild barley is expected to harbor important genes that could be used for the improvement of the cultivated varieties especially in their tolerance to drought. To assess genetic diversity and allelic variation of Jordanian wild barley, 103 wild barley genotypes collected from different parts of Jordan along with 29 cultivated barley genotypes were analyzed for diversity by means of Simple Sequence Repeats (SSR). The spontaneum genotypes were grouped into six populations according to their longitude, latitude, altitude, and rainfall zone of the sites from where they have been collected, and the cultivated in one population. All barley genotypes were analyzed with 11 SSR markers with known sequences and chromosomal locations. The 11 microsatellite markers revealed 237 alleles, with an average of 21.5 alleles per locus. In spontaneum genotypes, 209 alleles were identified with an average of 19 alleles per locus, whereas, cultivated genotypes had 95 alleles with an average of 8.6 alleles per locus. Moreover, 52 alleles were identified in spontaneum (22 %) of the total alleles and 22 alleles in cultivated barley (9 %). The level of genetic diversity was very high; in fact, mean in total gene diversity (Ht) was 0.86 ranging from 0.72 to 0.94. Average gene diversity (H) was 0.79 ranging from 0.74 to 0.82. Genetic variation within population was much higher than among populations at molecular levels: this was also supported by the finding that morphological characters such as awn length, plant height, days to maturity, peduncle length, peduncle extrusion and tillering number, showed higher variation within populations than among populations. Clustering of populations was according to their ecological geographical pattern.

Variation in β-amylase activity and thermostability in Tibetan annual wild and cultivated barley genotypes.

β-Amylase activity (BAA) and thermostability (BAT) are important traits for malt quality. In this study, 138 Tibetan annual wild barley accessions and 20 cultivated genotypes differing in BAA were planted and analyzed in 2009 and 2012. Significant differences were detected among genotypes in BAA and BAT. The cultivated genotypes had a mean BAA of 1137.6 U/g and a range of from 602.1 to 1407.5 U/g, while the wild accessions had a mean of 1517.9 U/g and a range of from 829.7 to 2310.0 U/g. The cultivated genotypes had a mean relative residual β-amylase activity (RRBAA) of 61.6% and a range of from 22.2% to 82.3%, while the wild barleys had a mean of 57.8% and a range of from 21.9% to 96.1%. Moreover, there was a significant difference among genotypes in the response of RRBAA to the temperature and duration of heat treatment. The wild barleys had wider variation in BAA and BAT than cultivated genotypes.

The influence of salinity on cell ultrastructures and photosynthetic apparatus of barley genotypes differing in salt stress tolerance

A hydroponic experiment was conducted to elucidate the difference in growth and cell ultrastructure between Tibetan wild and cultivated barley genotypes under moderate (150 mM NaCl) and high (300 mM NaCl) salt stress. The growth of three barley genotypes was reduced significantly under salt stress, but the wild barley XZ16 (tolerant) was less affected relative to cultivated barley Yerong (moderate tolerant) and Gairdner (sensitive). Meanwhile, XZ16 had lower Na+ and higher K+ concentrations in leaves than other two genotypes. In terms of photosynthetic and chlorophyll fluorescence parameters, salt stress reduced maximal photochemical efficiency (F v/F m), net photosynthetic rate (Pn), stomatal conductance (Gs), and intracellular CO2 concentration (Ci). XZ16 showed relatively smaller reduction in comparison with the two cultivated barley genotypes. The observation of transmission electron microscopy found that fundamental cell ultrastructure changes happened in both leaves and roots of all barley genotypes under salt NaCl stress, with chloroplasts being most changed. Moreover, obvious difference could be detected among the three genotypes in the damage of cell ultrastructure under salt stress, with XZ16 and Gairdner being least and most affected, respectively. It may be concluded that high salt tolerance in XZ16 is attributed to less Na+ accumulation and K+ reduction in leaves, more slight damage in cell ultrastructure, which in turn caused less influence on chloroplast function and photosynthesis.