The Winter-Type Allele of HvCEN Is Associated With Earliness Without Severe Yield Penalty in Icelandic Spring Barley (Hordeum vulgare L.).
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ABSTRACT:
SUBMITTER: Goransson M
PROVIDER: S-EPMC8500236 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundAluminium (Al) toxicity is the main factor limiting the crop production in acid soils and barley (Hordeum vulgare L.) is one of the most Al-sensitive of the small-grained cereals. The major gene for Al tolerance in barley is HvAACT1 (HvMATE) on chromosome 4H which encodes a multidrug and toxic compound extrusion (MATE) protein. The HvAACT1 protein facilitates the Al-activated release of citrate from root apices which protects the growing cells and enables root elongation to continue. A 1 kb transposable element-like insert in the 5' untranslated region (UTR) of HvAACT1 is associated with increased gene expression and tolerance and a PCR-based marker is available to score for this insertion.ResultsWe screened a wide range of barley genotypes for Al tolerance and identified a moderately tolerant Chinese genotype named CXHKSL which did not show the typical allele in the 5' UTR of HvAACT1 associated with tolerance. We investigated the mechanism of Al tolerance in CXHKSL and concluded it also relies on the Al-activated release of citrate from roots. Quantitative trait loci (QTL) analysis of double haploid lines generated with CXHKSL and the Al-sensitive variety Gairdner mapped the tolerance locus to the same region as HvAACT1 on chromosome 4H.ConclusionsOur results show that the Chinese barley genotype CXHKSL possesses a novel allele of the major Al tolerance gene HvAACT1.
| S-EPMC4779196 | biostudies-literature
Project description:Association analysis based on linkage disequilibrium has become a common and powerful approach for detection of QTLs underlying complex agronomic traits including drought tolerance. To determine marker/trait association, 148 modern European spring barley cultivars were evaluated under drought stress. Associations of morphological traits with AFLP/SSR markers were investigated based on the mixed linear model using the TASSEL3.0. Population structure was estimated using various methods including Bayesian clustering model by STRUCTURE software, PCoA analysis, NJ dendrogram and Hierarchical Clustering. Linkage disequilibrium patterns were explored among the whole genome and each chromosome separately. All the analysis for population structure divided the population into two sub-groups. Linkage disequilibrium analysis showed that by increasing genetic distance, LD decreases. Totally, 167 significant marker trait associations were found which delineated into 65 QTLs in both treatments. Two stable QTLs on 5H at 86.880 cM were detected for Internode Length and on 3H at 126.421 cM for flag leaf length in drought stress treatment. Fourteen QTLs were co-localized with previously reported QTLs and others were novel. The results indicate that these putative genomic regions contain genes that have pleiotropic effects on morphological traits in drought condition.
| S-EPMC6160164 | biostudies-literature
Project description:Key messageIdentification and allele-specific marker development of a functional SNP of HvLox - 1 which associated with barley lipoxygenase activity. Improving the stability of the flavor of beer is one of the main objectives in breeding barley for malting, and lipoxygenase-1 (LOX-1) is a key enzyme controlling this trait. In this study, a modified LOX activity assay was used for null LOX-1 mutant screening. Four barley landraces with no detected level of LOX-1 activity were screened from 1,083 barley germplasm accessions from China. The genomic sequence diversity of the HvLox-1 gene of the four null LOX-1 Chinese landraces was compared with that of a further 76 accessions. A total of 104 nucleotide polymorphisms were found, which contained 83 single-nucleotide polymorphisms (SNPs), 7 multiple-nucleotide polymorphisms, and 14 insertions and deletions. Most notably, we found a rare C/G mutation (SNP-61) in the second intron which led to null LOX-1 activity through an altered splicing acceptor site. In addition, an allele-specific polymerase chain reaction marker was developed for the genotyping of SNP-61, which could be used in breeding programs for barley to be used for malting. The objective was to improve beer quality.
| S-EPMC4180031 | biostudies-literature
Project description:The powdery mildew fungus, Blumeria graminis f. sp. hordei is a worldwide threat to barley (Hordeum vulgare L. ssp. vulgare) production. One way to control the disease is by the development and deployment of resistant cultivars. A genome-wide association study was performed in a Nordic spring barley panel consisting of 169 genotypes, to identify marker-trait associations significant for powdery mildew. Powdery mildew was scored during three years (2012-2014) in four different locations within the Nordic region. There were strong correlations between data from all locations and years. In total four QTLs were identified, one located on chromosome 4H in the same region as the previously identified mlo locus and three on chromosome 6H. Out of these three QTLs identified on chromosome 6H, two are in the same region as previously reported QTLs for powdery mildew resistance, whereas one QTL appears to be novel. The top NCBI BLASTn hit of the SNP markers within the novel QTL predicted the responsible gene to be the 26S proteasome regulatory subunit, RPN1, which is required for innate immunity and powdery mildew-induced cell death in Arabidopsis. The results from this study have revealed SNP marker candidates that can be exploited for use in marker-assisted selection and stacking of genes for powdery mildew resistance in barley.
| S-EPMC5694554 | biostudies-literature
Project description:Image-based phenotyping is a non-invasive method that permits the dynamic evaluation of plant features during growth, which is especially important for understanding plant adaptation and temporal dynamics of responses to environmental cues such as water deficit or drought. The aim of the present study was to use high-throughput imaging in order to assess the variation and dynamics of growth and development during drought in a spring barley population and to investigate associations between traits measured in time and yield-related traits measured after harvesting. Plant material covered recombinant inbred line population derived from a cross between European and Syrian cultivars. After placing the plants on the platform (28th day after sowing), drought stress was applied for 2 weeks. Top and side cameras were used to capture images daily that covered the visible range of the light spectrum, fluorescence signals, and the near infrared spectrum. The image processing provided 376 traits that were subjected to analysis. After 32 days of image phenotyping, the plants were cultivated in the greenhouse under optimal watering conditions until ripening, when several architecture and yield-related traits were measured. The applied data analysis approach, based on the clustering of image-derived traits into groups according to time profiles of statistical and genetic parameters, permitted to select traits representative for inference from the experiment. In particular, drought effects for 27 traits related to convex hull geometry, texture, proportion of brown pixels and chlorophyll intensity were found to be highly correlated with drought effects for spike traits and thousand grain weight.
| S-EPMC7296146 | biostudies-literature
Project description:Gene expression in plastids of higher plants is dependent on two different transcription machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. The division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear due to a lack of comprehensive information on promoter usage. Here we present a thorough investigation into the distribution of PEP and NEP promoters within the plastid genome of barley (Hordeum vulgare L). Using a novel differential RNA sequencing approach, which discriminates between primary and processed transcripts, we obtained a genome-wide map of transcription start sites in plastids of mature first leaves. PEP-lacking plastids of the albostrians mutant allowed for the unambiguous identifications of NEP promoters. We observed that the chloroplast genome contains many more promoters than genes. According to our data, most genes (including genes coding for photosynthesis proteins) have both PEP and NEP promoters. We also detected numerous transcription start sites within operons indicating transcriptional uncoupling of genes in polycistronic gene clusters. Moreover, we mapped many transcription start sites in intergenic regions, as well as opposite to annotated genes demonstrating the existence of numerous non-coding RNA candidates.
2011-11-23 | GSE33773 | GEO
Project description:IntroductionReducing plant height has played an important role in improving crop yields. The success of a breeding program relies on the source of dwarfing genes. For a dwarfing or semi-dwarfing gene to be successfully used in a breeding program, the gene should have minimal negative effects on yield and perform consistently in different environments.MethodsIn this study, 182 doubled haploid lines, generated from a cross between TX9425 and Naso Nijo, were grown in six different environments to identify quantitative trait loci (QTL) controlling plant height and investigate QTL × environments interaction.ResultsA QTL for plant was identified on 7H. This QTL showed no significant effects on other agronomic traits and yield components and consistently expressed in the six environments. A sufficient allelic effect makes it possible for this QTL to be successfully used in breeding programs.
| S-EPMC3938599 | biostudies-literature
Project description:BackgroundBarley (Hordeum vulgare L.) is a major cereal crop, which is cultivated under variable environmental conditions and abiotic stresses in marginal areas around the globe. In this study, we evaluated 150 Jordanian landraces obtained from ICARDA Gene Bank and four local checks for yield and yield components related-traits in two locations across Jordan for three growing seasons under rainfed conditions. The study aims to identify superior Jordanian barley genotypes under dry conditions, to understand the genotype × environment (G × E) interactions, to analyze stability parameters and to identify markers associated with yield and yield components under rainfed conditions.ResultsThe barley accessions exhibited significant variation for all traits studied. Three accessions with high yield, cultivar superiority and stability under specific environments were identified with accession G69 is the highest yielding and superior for Madaba and overall environments and G144 is the highest yielding at Ramtha. Accession G123 was high yielding in all environments and was stable across different environments. At the genetic level, the Jordanian landraces were found to be diverse with a clustering that was based on row-type. The GWAS analysis identified 77 significant markers-traits associations for multiple traits including grain yield (GY) with three significant QTLs located at 1H, 2H and 7H, which seem important for dry environments.ConclusionUtilizing Jordanian barley landraces can effectively improve and adapt the current barley cultivars for cultivation under environmental stresses in dry regions. Utilization of markers associated with important agronomical traits and their incorporation in breeding using marker assisted selection can improve barley tolerance to drought stress.
| S-EPMC5668982 | biostudies-literature
Project description:BACKGROUND: Endogenous phytase plays a crucial role in phytate degradation and is thus closely related to nutrient efficiency in barley products. The understanding of genetic information of phytase in barley can provide a useful tool for breeding new barley varieties with high phytase activity. METHODOLOGY/PRINCIPAL FINDINGS: Quantitative trait loci (QTL) analysis for phytase activity was conducted using a doubled haploid population. Phytase protein was purified and identified by the LC-ESI MS/MS Shotgun method. Purple acid phosphatase (PAP) gene was sequenced and the position was compared with the QTL controlling phytase activity. A major QTL for phytase activity was mapped to chromosome 5 H in barley. The gene controlling phytase activity in the region was named as mqPhy. The gene HvPAP a was mapped to the same position as mqPhy, supporting the colinearity between HvPAP a and mqPhy. CONCLUSIONS/SIGNIFICANCE: It is the first report on QTLs for phytase activity and the results showed that HvPAP a, which shares a same position with the QTL, is a major phytase gene in barley grains.
| S-EPMC3080886 | biostudies-literature
Project description:Heading date (HD) of cereals is an important trait for adaptation to diverse environments and is critical for determining yield and quality and the number of genes and gene combinations that confer earliness in barley under short days is limited. In our study, a QTL for early flowering was identified from the cross between an Australian malting barley cultivar and a Chinese landrace. Four sets of near isogenic lines (NILs) were developed with a QTL located on chromosome 5H at the interval of 122.0-129.0 cM. Further experiments were conducted to investigate how this gene was regulated by photoperiod using the NILs with three sowing dates from autumn to summer. The NILs carrying the earliness allele were significantly earlier than the late genotype at all sowing dates. This gene was different from previously reported vernalisation genes that are located at a similar position as no vernalisation was required for all the NILs. The difference between this gene and Eam5 (HvPHYC) locus which also located between two co-segregated markers (3398516S5, 122.5 cM, and 4014046D5, 126.1 cM), is that with the existence of Ppd-H1 (Eam1), Eam5 has no effect on ear emergence under long days while the gene from TX9425 still reduced the time to ear emergency. The locus showed no pleiotropic effects on grain pasting properties and agronomic traits except for spike length and number of spikelets per spike, and thus can be effectively used in breeding programs. The array of early heading dates caused by interactions of Eam5 gene with other maturity genes provides an opportunity to better fine tune heading dates with production environments, which can be critical factor in barley breeding.
| S-EPMC6049932 | biostudies-literature