Differential gene expression during seed germination in barley (Hordeum vulgare L.)

A barley cDNA macroarray comprising 1,440 unique genes was used to analyze the spatial and temporal patterns of gene expression in embryo, scutellum and endosperm tissue during different stages of germination. Among the set of expressed genes, 69 displayed the highest mRNA level in endosperm tissue, 58 were up-regulated in both embryo and scutellum, 11 were specifically expressed in the embryo and 16 in scutellum tissue. Based on Blast X analyses, 70% of the differentially expressed genes could be assigned a putative function. One set of genes, expressed in both embryo and scutellum tissue, included functions in cell division, protein translation, nucleotide metabolism, carbohydrate metabolism and some transporters. The other set of genes expressed in endosperm encodes several metabolic pathways including carbohydrate and amino acid metabolism as well as protease inhibitors and storage proteins. As shown for a storage protein and a trypsin inhibitor, the endosperm of the germinating barley grain contains a considerable amount of residual mRNA which was produced during seed development and which is degraded during early stages of germination. Based on similar expression patterns in the endosperm tissue, we identified 29 genes which may undergo the same degradation process. Electronic Publication     

Several QTLs involved in osmotic-adjustment trait variation in barley (Hordeum vulgare L.)

 Osmotic adjustment (OA) was previously demonstrated to be an important adaptive mechanism of drought tolerance in cereals. In order to determine which genomic regions are involved in OA variation, 187 barley (Hordeum vulgare L.) recombinant inbred lines (RILs) derived from a cross between Tadmor (drought tolerant) and Er/Apm (susceptible) were studied in a growth chamber for their OA capacity (through correlated traits and by calculation), at an early growth stage and under two water treatments (soil moisture of 14% and 100% of field capacity). The continuous distribution of the traits and their broad-sense line heritabilities, ranging from 0.04 to 0.44, indicated that OA and related traits should have a polygenic nature. A subset of 167 RILs were also genotyped using 78 RFLP, 32 RAPD and three morphological markers and a linkage map was constructed. Despite strong environmental effects acting on the traits, interval mapping and single-marker ANOVA allowed the detection of three QTLs for relative water content (RWC), four QTLs for osmotic potential (ψ_π), two QTLs of osmotic potential at full turgor (ψ_π100) and one QTL for osmotic adjustment at a soil moisture of 14% field capacity. For the irrigated treatment, only two QTLs were detected: one for RWC and one for ψ_π100. Two chromosomal regions were involved in several OA-related trait variations and could be considered as regions controlling OA; these were present on chromosome 1 (7H) and chromosome 6 (6H), whereas other regions were specific for one trait. No major QTL was found. However, the genomic region involved in OA-related traits on chromosome 1 (7H) in barley seemed to be conserved for OA variation among cereals. Epistatic effects, with or without additive effects, acted on the traits. Received: 15 July 1997 / Accepted: 29 October 1997     

Mapping QTL controlling yield and yield components in a spring barley (Hordeum vulgare L.) cross using marker regression

An RFLP map constructed from 99 doubled haploid lines of a cross between two spring barley varieties (Blenheim × Kym) was used to localize quantitative trait loci (QTL) controlling grain yield and yield components by marker regression and single-marker analysis. Trials were conducted over three years. Genotype-by-year interaction was detected for plant grain weight and ear grain weight so they were analysed separately for each year. None was detected for thousand-grain weight and ear grain number so data were pooled over years. A total of eleven QTL were detected for plant grain weight over two years and fourteen for ear grain weight over three years. Seven QTL were detected for plot yield. The locus with the largest effect was on chromosome 2(2H)L and accounted for 19% of the variation in the progeny. Eight QTL were detected for thousand-grain weight and five for ear grain number. Many of the QTL detected were in comparable positions in each year. Yield and yield components were only partly correlated. Comparisons based on common RFLP markers showed that some QTL were found in positions similar to those identified in other studies. For a number of QTL the identification of linked markers provided suitable opportunities for marker-assisted selection and improvement of barley and reference markers with which to analyse the homoeologous chromosome regions of wheat and other cereals.     

Gene expression and activity of antioxidant enzymes in barley (Hordeum vulgare L.) under controlled severe drought

The objective of the present study was to determine the activity of antioxidant enzymes: superoxide dismutase (SOD), ascorbate peroxidase (APX), and catalase (CAT) and the expression of their genes in two barley genotypes under controlled severe drought. To fulfill this objective, 21-day-old barley plants of two genotypes: Rum and Yarmouk were exposed to controlled severe drought (25% field capacity) for 2, 9, and 16 days. The activity of SOD was significantly high in Rum genotype after 2 days of drought treatment. In Yarmouk genotype, the activity of APX was significantly high after 2 and 9 days of drought treatment. In Rum genotype, CAT2 was upregulated after 9 days of drought treatment and SOD and APX were upregulated after 16 days of drought treatment, whereas CAT2, SOD, and APX were upregulated in Yarmouk genotype after 2 days of drought treatment. The results indicate a unique pattern of activity and gene expression of the antioxidant enzymes in the two barley genotypes under controlled severe drought. Moreover, the data suggest that each genotype utilizes different molecular and biochemical responses under the same drought conditions.     

Acrotrisomic analysis in linkage mapping in barley (Hordeum vulgare L.)

Summary Three acrotrisomic lines, Triplo IL^1S, 3L^3S, and 4L^4S, each carrying an extra acrocentric chromosome, were used for cytogenetic linkage mapping of barley chromosomes. The cytological structures of the acrocentric chromosome of the three acrotrisomic lines were studied with an improved Giemsa N-banding technique. The long (1L) and short arm (1S) of chromosome 1 had deficiencies of approximately 38% and 65%, respectively. The percentages of deficiencies were 0 and 77.8% for 3L and 3S, and 31.7 and 59.3% for 4L and 4S, respectively. All three genes tested (br, f _c , gs3) in 1S and all three genes tested, f8, n and 1k2 in 1L showed a disomic ratio indicating that they are located in the deficient segments. Two genes (a _c , yst2) located in the middle segment of 3S in linkage map showed a trisomic ratio, and two others a _n , x _s showed a disomic ratio. The only gene(f9) tested in 4L showed a trisomic ratio. Two genes (1g4, g1) located in the proximal segment of 4S in the linkage map showed a trisomic ratio, whereas two genes (br2, g13) located distally in 4S showed a disomic ratio, indicating that the breakage occurred between g1 and br2. This experiment demonstrates a new method for physical localization of genes on chromosome segments in material such as barley in which pachytene analysis can not be effectively used for accurate determination of break points in structural changes. Problems associated with this new technique are discussed.Contribution from the Department of Agronomy and published with the approval of the Director of Colorado State University Experiment Station as Scientific Series Paper No. 2823. Supported by USDA/SEA Competitive Research Grant Nos. 5901-0410-9-0334-0 and 82-CRCR-1-1020 and USDA-CSU Cooperative Research Grant 58-9AHZ-2-265     

Association between SCMV Resistance and Macroarray-based Expression Patterns in Maize Inbreds

Recent advances in RNA profiling offer an opportunity to establish functional links between genotype and phenotype for complex traits such as SCMV resistance. The change of RNA profiles was monitored on a macroarray containing SSH (suppression subtractive hybridization) clones. The number of differentially expressed genes (SCMV infected vs. non-infected) in individual lines was 177, 163, 165, 62, 47, 37, and 93, for FAP1360A, D21, D32, Pa405, F7, D145, and D408, respectively. All inbreds were divided into two groups by hierarchical cluster analysis: D32, D21, FAP1360A and D408 formed one; Pa405, D145, and F7 another group. Due to the genetic structure among the seven inbreds, genetic background and resistance response are confounded. With or without the resistant U.S. inbred line Pa405, 22 and 112 genes were identified by t tests between resistant (D21, D32, and FAP1360A) and susceptible (D145, D408, and F7) inbred lines, respectively. The 112 candidate genes were divided into three clusters by K-means clustering and analyzed in more detail, e.g., five genes were in silico mapped surrounding Scmv2 QTLs. These candidate genes provide a better understanding of signal transduction pathway for SCMV resistance and have the potential to develop functional markers to distinguish resistant and susceptible genotypes.     

Parameters influencing transient and stable transformation of barley (Hordeum vulgare L.) protoplasts

Cat gene expression has been investigated following PEG-mediated plasmid uptake into barley protoplasts. The uptake conditions optimised for transient expression were employed for stable transformation. Transformed protoplast-derived calli of the cvs. Dissa and Igri, were selected on medium containing G418 at 40 g ml^–1 or kanamycin sulphate at 250 g ml^–1. Absolute transformation frequencies of 28.9×10^–5 and 21.3×10^–5 were recorded for Dissa with kanamycin sulphate and G418 selection, respectively. The frequency for Igri was 11.5×10^–5 with G418 selection. Antibiotic resistant protoplast-derived colonies expressed NPTII activity; Southern hybridisation confirmed integration of the nptII gene into barley genomic DNA.Abbreviations ABA abscisic acid - AC-CAP acetylated chloramphenicol - BAP 6-benzylaminopurine - cat chloramphenicol acetyltransferase gene - CAT chloramphenicol acetyltransferase activity - CaMV cauliflower mosaic virus - CAP chloramphenicol, 2,4-d-2,4-dichlorophenoxyacetic acid - GA₃ gibberellic acid - G418 Geneticin - gus -glucuronidase gene - HEPES (N[2-hydroxyethyl] piperazine-N-[2-ethanesulphonic acid]) - IAA indole acetic acid - MES 2-N-morpholinoethane sulphonic acid - NAA -naphthaleneacetic acid - npt II neomycin phosphotransferase gene - NPTH neomycin phosphotransferase activity - PEG polyethylene glycol - SCV settled cell volume     

Localising QTLs for leaf rust resistance and agronomic traits in barley (Hordeum vulgare L.)

The Hordeum vulgare accession ’HOR 1063’ was crossed with the barley cultivar Krona, and 220 doubled haploid lines were produced based on this cross. A molecular map was constructed based on RFLP markers. Field trials were performed over 2 years and at two locations. In field trials, resistance to leaf rust by means of artificial infection, heading date, plant height and Kernel weight were assessed. For leaf rust resistance, 4 QTLs were localised, that explained 96.1% of the genetic variation. One QTL on chromosome 4H confirmed a position found in another genetic background and one mapped to the same position as Rph16 on chromosome 2H. All digenic effects decreased the effects of the respective QTLs. In addition to the denso-locus and the hex-v locus, other QTLs influencing heading date, plant length and kernel weight were found in this cross. Received: 16 July 1999 / Accepted: 7 September 1999     

Isolation and characterization of aleurone protoplasts from a malting variety of barley (Hordeum vulgare L.)

Summary A procedure has been developed to isolate protoplasts from mature aleurone layers of the malting variety Alexis and four other barley genotypes. It combines induction of endogenous cell wall degrading enzymes together with use of Onuzuka cellulase R 10 and driselase and results in better yields for two varieties than can be obtained with the huskless variety Himalaya. The viability of the freshly isolated protoplasts is greater than 90% and in spite of the presence of gibberellic acid during isolation procedures, most of the protoplasts are at an early developmental stage, as judged by ultrastructure. Gibberellic acid-induced changes in protoplast structure resemble those reported for Himalaya protoplasts. The protoplasts secrete both -amylase (EC 3.2.1.1) and (1-3, 1-4)--glucanase (EC 3.2.1.73) into the surrounding medium. Transfection studies using a low pI -amylase promoter to direct chloramphenicol acetyltransferase expression in aleurone protoplasts from Alexis and Himalaya revealed significant differences in their hormone responsiveness. In the absence of hormones, low levels of expression of the reporter enzyme were obtained in Alexis protoplasts, while high levels were characteristic for Himalaya protoplasts. An 8-fold increase in the expression of the reporter gene was induced by supplying the transfected Alexis protoplasts with gibberellin A₃, whereas expression in Himalaya protoplasts remained unchanged. When Himalaya protoplasts were isolated from aleurone layers that had not been incubated with GA₃ during the initial stages of protoplasting (the classical procedure), the hormone response of the promoter was 2.5-fold. It is thus possible to optimize the aleurone protoplast isolation procedure for different barley genotypes and mutants of interest in studies of transgenic gene expression and hormone induced secretion of proteins from this unique secretory plant tissue.Abbreviations ABA abscisic acid - APIM aleurone protoplast isolation medium - CAT chloramphenicol acetyltransferase - EDTA ethylenediamine tetraacetic acid - ER endoplasmic reticulum - GA₃ gibberellin A₃ - IgG immunoglobulin G - MES 2-(N-morpholino)-ethanesulfonic acid - PAGE polyacrylamide gel electrophoresis - PEG polyethylene glycol - pI isoelectric point - PIPES piperazine N,N-bis-(diethanesulfonic acid) - SDS sodium dodecyl sulfate     

Genetic analysis of the components of winterhardiness in barley (Hordeum vulgare L.)

Winterhardiness in cereals is the consequence of a number of complex and interacting component characters: cold tolerance, vernalization requirement, and photoperiod sensitivity. An understanding of the genetic basis of these component traits should allow for more-effective selection. Genome map-based analyses hold considerable promise for dissecting complex phenotypes. A 74-point linkage map was developed from 100 doubled haploid lines derived from a winter x spring barley cross and used as the basis for quantitative trait locus (QTL) analyses to determine the chromosome location of genes controlling components of winterhardiness. Despite the greater genome coverage provided by the current map, a previously-reported interval on chromosome 7 remains the only region where significant QTL effects for winter survival were detected in this population. QTLs for growth habit and heading date, under 16 h and 24 h light, map to the same region. A QTL for heading date under these photoperiod regimes also maps to chromosome 2. Contrasting alleles at these loci interact in an epistatic fashion. A distinct set of QTLs mapping to chromosomes 1, 2, 3, and 5 determined heading date under 8 h of light. Under field conditions, all QTLs identified under controlled environment conditions were determinants of heading date. Patterns of differential QTL expression, coupled with additive and additive x additive QTL effects, underscore the complexity of winterhardiness. The presence of unique phenotype combinations in the mapping population suggests that coincident QTLs for heading date and winter survival represent the effects of linkage rather than pleiotropy.     

Mapping of chromosome regions conferring boron toxicity tolerance in barley (Hordeum vulgare L.)

 Boron toxicity has been recognised as an important problem limiting production in the low-rainfall regions of southern Australia, West Asia and North Africa. Genetic variation for boron toxicity tolerance in barley has been characterised but the mode of inheritance and the location of genes controlling tolerance were not previously known. A population of 150 doubled-haploid lines from a cross between a boron toxicity tolerant Algerian landrace, Sahara 3771, and the intolerant Australian cultivar Clipper was screened in four tolerance assays. An RFLP linkage map of the Clipper×Sahara population was used to identify chromosomal regions associated with boron tolerance in barley. Interval regression-mapping allowed the detection of four chromosomal regions involved in the boron tolerance traits measured. A region on chromosome 2H was associated with leaf-symptom expression, a region on chromosome 3H was associated with a reduction of the affect of boron toxicity on root growth suppression, a region on chromosome 6H was associated with reduced boron uptake, and a region on chromosome 4H was also associated with the control of boron uptake as well as being associated with root-length response, dry matter production and symptom expression. The benefits and potential of marker-assisted selection for boron toxicity tolerance are discussed. Received: 18 December 1997 / Accepted: 28 November 1998     

Microarray analysis of gene expression in germinating barley embryos (Hordeum vulgare L.)

A cDNA library containing approximately 5,000 clones from germinating barley embryos was constructed and used to examine the variation in gene expression patterns during the first 4 days postimbibition. The expression profiles of embryos (including scutellum) from 4 to 96 h postimbibition were compared to a reference profile from 24 h postimbibition using microarray analysis. A subset of clones exhibiting tenfold or greater differential expression patterns was sequenced to elucidate function. All of the sequenced clones could be identified to at least EST level with 64% exhibiting homology to published protein sequences. Almost 95% of the library exhibited similar expression levels at the 4 h time point as at the 24 h reference point. From 24 to 96 h, however, considerable fluctuations in gene expression occurred. The observed patterns of gene expression for the classified genes are consistent with the expected genetic changes required to prepare an embryo for germinative development. A replicate set of clones for the 23-kDa jasmonate-induced protein was identified. The current data not only provides conclusive evidence for the expression patterns of this abundant stress-response protein in germinating embryos, but also serves to validate previous research into JIP-23 isoforms, function and the relationship between timing of mRNA upregulation and protein abundance.     

Marker-assisted analysis of three grain yield QTL in barley (Hordeum vulgare L.) using near isogenic lines

Three previously identified grain yield quantitative trait loci (QTL) on chromosomes 2S(2HS), 3C(3HC) and 5L(1HL), designated QTL-2S, QTL-3 and QTL-5L, respectively, were evaluated for their potential to increase yields of high-quality malting barley without disturbing their favorable malting quality profile. QTL mapping of yield related traits was performed and near-isogenic lines (NILs) were developed. QTL for plant height, head shattering, seed weight and number of rachis nodes/spike were detected in the QTL-3 region. NILs developed by introgressing QTL-3 from the high-yielding cv. Steptoe to the superior malting quality, moderate-yielding cv. Morex acquired reduced height, lodging and head shattering features of Steptoe without major changes in malting quality. The yield of NILs, measured by minimizing the losses due to lodging and head shattering, did not exceed that of Morex. Steptoe NILs, with the Morex QTL-2S region, flowered 10 days later than Steptoe but the grain yield was not changed. None of the 3 QTL studied altered the measured yield of the recipient genotype, per se, although QTL 2S and QTL-3 affected yield-related traits. We conclude that these yield QTL must interact with other genes for full expression. Alternatively, they affect the harvestable yield through reduced lodging, head shattering, and/or altered flowering time.     

Identification of quantitative trait loci for ion homeostasis and salt tolerance in barley (Hordeum vulgare L.)

Ion homeostasis is considered to be one of the most important mechanisms underlying salt stress tolerance. We used the Steptoe × Morex barley doubled haploid population to screen for genetic variation in response to salinity stress at an early development stage in a hydroponics system, focusing on ion homeostasis. Salinity induced a strong adverse effect on growth of the parents and their derived population, with Steptoe as the more tolerant parent. Steptoe maintained higher concentrations of K⁺, Na⁺ and Cl^? in the roots and a similar shoot/root ion ratio (<1) under stress conditions compared to control conditions. In contrast, Morex had higher concentrations of these ions in the shoots under stress and a doubled shoot/root ion ratio relative to control conditions, indicating that salt exclusion might contribute to the higher tolerance of Steptoe. Correlation and path analysis demonstrated that shoot Cl^? contents most strongly affected salt tolerance and suggest that both Na⁺ and Cl^? contents are important for salinity stress tolerance in barley. We identified 11 chromosomal regions involved in the control of the variation observed for salt tolerance and various salt stress response traits, including Na⁺, Cl^? and K⁺ contents in shoots. Two specific regions on chromosomes 2H and 3H were found controlling ion contents and salt tolerance, pointing to genes involved in ion homeostasis that contribute to salt tolerance.     

Expression of XET-related genes and its relation to elongation in leaves of barley (Hordeum vulgare L.)

Five cDNA clones were isolated from barley (Hordeum vulgare L.) that encoded mRNAs related to xyloglucan endotransglycosylase (XET). One of the clones encoded a protein with XET activity in vitro. Sequence comparisons revealed five families of XET-related sequences, one of which (containing two of the barley genes) was novel. Hybridization studies using clone-specific probes indicated that the corresponding genes were represented once, or possibly twice, in the barley genome. Treatment of dwarf mutants with gibberellic acid (GA₃), or homozygosity at the ‘slender’ (sln1) locus, resulted in a 2.5-fold (approximately) stimulation of blade elongation rate. Three of the five clones detected mRNAs that were maximally expressed towards the base of the blade, and present in greater quantities in GA₃-treated or slender seedlings. The remaining two clones detected mRNAs that were maximally expressed in the middle of the blade. Relative elemental growth rate (REGR) profiles of leaves growing with or without GA₃ treatment revealed similar maximal REGR values despite a 2.5-fold difference in leaf elongation rate. Segments of GA₃-treated leaves attained their maximal REGR values more rapidly, this being associated with enhanced expression of the three ‘basal’ XET-related mRNAs. Highest XET activities were detected in the base of the elongation zone, and in GA₃-treated seedlings a second activity peak was observed near the distal end of the elongation zone. We conclude that there are likely to be several XET isoenzymes with different expression patterns, and identify those XET-related proteins potentially involved in leaf elongation.     

The allene oxide cyclase of barley (Hordeum vulgare L.)--cloning and organ-specific expression

The naturally occurring enantiomer of the various octadecanoids and jasmonates is established in a biosynthetic step catalyzed by the allene oxide cyclase (AOC). The AOC converts an allene oxide formed by an allene oxide synthase (AOS). Here, we show cloning and characterization of cDNAs encoding the AOC and a third AOS, respectively, in addition to the two AOSs previously published (Plant J. 21, 199-213, 2000). The ORF of the AOC-cDNA of 717 bp codes for a protein of 238 amino acid residues carrying a putative chloroplast target sequence. Overexpression without chloroplast target sequence revealed AOC activity. The AOC was found to be a single copy gene which mapped on chromosome 6H. AOC mRNA accumulation appeared in leaf segments upon treatment with various jasmonates, octadecanoids and ABA or during stress such as treatment with sorbitol or glucose solutions. Infection with powdery mildew activated AOC expression in susceptible and resistant lines of barley which correlated with PR1b expression. Among different tissues of barley seedlings, the scutellar node and leaf base accumulated AOC mRNA preferentially which correlated with accumulation of mRNAs for other biosynthetic enzymes (lipoxygenases, AOSs). AOC mRNA accumulation appeared also abundantly in parts of the root containing the tip and correlated with elevated levels of jasmonates. The data suggest a link of AOC expression and JA formation and support role of JA in stress responses and development of barley.