Biology subjects

Stich, B.

Publications and source records attributed to Stich, B..

At least 19 recordsLinked to original sources

bioRxiv2026

A composited genome approach to analyse cistrome diversity in barley

Motivation: Functional regulatory variants are important determinants of heritable diversity, yet their systematic identification requires both genome-wide maps of transcription factor (TF) occupancy and suitable genome sequences for mapping. While chromosome-scale assemblies remain costly for large association panels, short-read sequencing data are widely available. We investigated whether draft genomes reconstructed from short reads are sufficient for comparative MOA-seq analyses of TF occupancy. Results: We generated genome-wide TF footprint maps for the barley cultivars Bowman, Morex, and Golden Promise, identifying approximately 240,000 loci per genotype. Roughly half of all footprints occurred in intergenic regions. Footprints conserved between genotypes were depleted for sequence variation and located closer to genes. Meanwhile, genotype-specific footprints were enriched for SNP-containing and gene-distal regions, highlighting the extensive diversity of regulatory landscapes among barley cultivars. We further compared two short-read-based draft genome assembly strategies: i) a SNP-replacement and ii) a Practical Haplotype Graph (PHG)-based composite genome approach, to enable MOA-seq analyses without chromosome-scale genome assemblies. Compared to the SNP-replacement strategy, the composite genome displayed 2.3-fold higher local sequence concordance for SNPs/INDELs relative to the published reference. Both draft genomes accurately reproduced MOA-seq profiles, recovering approximately 80 % of reference peak bases with per-base coverage correlations of 0.79-0.90 relative to the assembled reference. While the composite genome performed best across the genome overall, the simpler SNP-replacement strategy more accurately recovered TF occupancy within regulatory peaks due to fewer structural alignment artefacts. Availability: Pipelines consist of existing open-source tools, Bash, GAWK and Java, and are available at [zenodo; tbd].

genomics↗

bioRxiv2026

Genome-wide association study in a maize diversity panel dissects the genetic basis of lignocellulosic recalcitrance

Lignocellulosic biomass is an abundant, renewable resource for the production of biorenewable products. Its efficient utilization is largely hindered by the inherent recalcitrance of lignocellulose to degradation. Natural genetic variation in biomass saccharification efficiency and lignocellulose components across diverse maize germplasm provides a powerful resource to dissect the genetic basis of lignocellulosic recalcitrance. Here, we performed high-throughput profiling of lignocellulosic components and saccharification efficiency in mature stalks across a diverse panel of 239 field grown maize inbred lines, and identified extensive natural variation in biomass properties. Saccharification efficiency was strongly positively associated with matrix glucose content, moderately positively associated with the arabinose-to-xylose (Ara:Xyl) molar ratio and crystalline cellulose content, whereas saccharification efficiency was strongly negatively associated with xylose and lignin content. Genome-wide association studies (GWAS) were conducted to identify single nucleotide polymorphisms (SNPs) associated with saccharification efficiency and lignocellulosic components. Numerous significant single nucleotide polymorphisms (SNPs) were identified, defining 79 quantitative trait loci (QTLs) across all 10 maize chromosomes. The presence of pleiotropic SNPs and the extensive co-localization of QTLs for multiple traits highlight the complex genetic architecture and shared genetic basis of maize biomass properties. Our study reveals substantial natural variation in maize biomass digestibility and identifies multiple novel genetic loci underlying variation in saccharification efficiency and lignocellulose components.

plant biology↗

bioRxiv2026

HvbZIP33 and HvbZIP76 have overlapping roles in foliar transpiration in drought-stressed barley

Basic leucine zippers (bZIP) constitute one of the biggest protein families and evolutionarily conserved transcription factors (TFs) in plants. We obtained mutant lines for two bZIP TFs, HvbZIP33 and HvbZIP76, in the genetic background of the barley cultivar Golden Promise (GP) via targeted gene-specific mutagenesis using an RNA-guided Cas9 endonuclease. A comprehensive morphological, physiological and transcriptomic analysis was performed in wild-type GP compared with hvbzip33 and hvbzip76 mutants under drought stress. The morphological and physiological changes were similar in both mutants and in the wild-type GP. Most strikingly, the mutants exhibited accelerated wilting and increased water loss. This effect was primarily caused by higher stomatal conductance (gs) and transpiration rate (E) in mutants compared to wild-type GP under both control and drought conditions, which in turn had a detrimental effect on the mutants intrinsic water use efficiency (iWUE). Likewise, the transcriptome profiles of hvbzip33 and hvbzip76 were more similar to each other than those of wild-type GP. We found that the number of differentially regulated genes under control versus drought-stress conditions was higher in the mutants than in wild-type GP, suggesting that the mutants try to compensate for accelerated foliar water loss. The study highlights the essential roles of HvbZIP33 and HvbZIP76 in balancing water loss in barley. These findings provide a foundation for engineering enhanced drought tolerance in barley through targeted manipulation of these genes to optimize transpiration rates.

genetics↗

bioRxiv2025

Highly polygenic control of photosynthetic responses to nighttime temperature in Arabidopsis studied by genomic prediction

O_LIRising nighttime temperature (Tnight) can reduce crop yields, while low Tnight may restrict plant growth and development. Despite these quantifiable effects of Tnight, the genetic basis underlying plant responses to Tnight remains unclear. We investigated natural variation in long-term response of effective photosynthetic efficiency (Fq/Fm) to Tnight among Arabidopsis accessions. C_LIO_LIGenome-wide association study (GWAS) was conducted for Fq/Fm of the accessions grown under 15{degrees}C or 20{degrees}C Tnight. The associated single nucleotide polymorphisms (SNPs) were identified and incorporated in genomic prediction (GP) models to assess the improvement of prediction accuracy. The predictions were experimentally validated in an independent, genetically diverse population. C_LIO_LIGWAS revealed highly polygenic architecture of Fq/Fm, with associated SNPs varying across Tnight conditions and measurement days. Notably, 15{degrees}C Tnight stabilized the contributions of a subset of associated SNPs, whereas 20{degrees}C Tnight enhanced day-to-day variations in SNP-trait associations. The GWAS-derived SNPs significantly improved the prediction accuracy of GP models, indicating their collective influence. The validation experiment confirmed the identification of low-Fq/Fm accessions in 15{degrees}C Tnight. C_LIO_LIThe results uncover the genetic underpinnings of long-term Fq/Fm response to cool vs warm nights and establish a framework for leveraging GWAS and GP to explore complex traits, such as photosynthesis, toward breeding climate-resilient crops. C_LI

plant biology↗

bioRxiv2025

An Axiom SNP genotyping array for potato: development, evaluation and applications

Potato is a versatile food crop and a major component of human nutrition worldwide. Genomic-assisted breeding methods have the potential to increase the gain of selection. We report the development and validation of a high-density Axiom-based SNP array for potato (Solanum tuberosum L.). Whole-genome 10X Genomics based sequencing of 108 diverse clones representing landraces, improved cultivars, and wild relatives identified around 23.8 million sequence variants, from which 929,127 variants, alongside with 18,718 markers from a previously developed Illumina Infinium 21K array (GGP3), were tiled on the array. The array demonstrated high reproducibility, with replicate samples showing an average concordance of 99.88% in genotype calls for PotatoTools specific variants, compared to 99.93% for the Illumina Infinium 21K array variants. A panel of 1,247 diploid and tetraploid clones was genotyped with the developed array. Genotype calling, considering allele dosage, was realized using fitpoly and yielded 852,793 calls. The array informativeness was optimized by applying Euclidean distance, heterozygous strength offset metrics, call rate, minor allele frequency filtering, and diploid-based allele correction, yielding a final set of 206,616 robust and informative markers. The filtered marker set enables precise characterization of genetic variation across diverse germplasm, thereby supporting robust analyses of population structure, genome-wide association studies (GWAS), and genomic prediction in potato. Population structure analysis genotyped clones revealed clear subpopulation differentiation consistent with known ploidy groups. In addition, our discriminant analysis of principal components revealed a weak but structured diversity among clones of different market segments. GWAS analysis of 998 potato clones identified sequence variants significantly associated with polyphenol oxidase (PPO) activity, confirming the platforms efficacy for trait mapping. For the same trait, genomic prediction accuracies of 0.72-0.86 have been observed. The developed potato SNP array provides a robust platform for high-throughput genotyping, supporting genetic diversity studies, association mapping, and genomic-assisted breeding in this important crop.

plant biology↗

bioRxiv2025

Assessment of segregation variance estimates from derivation, simulations, and empirical data in autotetraploid species exemplified in potato

The optimal choice of parents and crosses and, therefore, the prediction of the segregation variance are of high relevance to maximize genetic gain in breeding programs. Several methods have been developed for the prediction of segregation variance, including correlation with genotypic diversity, progeny simulations, or algebraic derivations in case of a diploid inheritance. To the best of our knowledge, no algebraic derivation using parental genotypic information is available to predict segregation variance for autotetraploid species. The objectives of our study were to (1) derive algebraic derivation based on linkage disequilibrium (LD) between linked loci to predict the segregation variance in autotetraploid species; (2) compare the performance of segregation variance estimated based on simulated progenies and the algebraic derivation; (3) investigate by simulations how experimental parameters affect the accuracy of segregation variance prediction; and (4) compare the segregation variance estimated in empirical data of potato and the one based on the algebraic derivation. The segregation variance estimated by the developed derivations showed very high correlations with the one observed in large simulated progenies, but those were lower when phased parental haplotypes were not available or family size decreased. The correlation between segregation variance estimated by the developed derivation and the empirical data was low. This could be attributed to the small family size used in the study, which we could show to increase LD between unlinked loci. The proposed algebraic derivations promise to be a precise alternative to simulations to help breeders in optimizing their family choices and sizes considering the segregation variance.

genetics↗

bioRxiv2025

Contemporary hybridization among Arabis floodplain species creates opportunities for adaptation

Hybridization between closely related species is increasingly recognized as a major source of biodiversity. Yet, whether it can create advantageous trait combinations while purging harmful alleles remains unknown. We studied Arabis nemorensis and A. sagittata, two endangered species that currently hybridize in a single hotspot. We measured 22 phenotypic traits and mapped their genetic basis in an F2 population, after generating high quality genome assemblies for both species. In total, 58 QTLs were identified for 20 traits, with additive and dominance effects best fitting Gaussian and logistic distributions, respectively. Six large-effect QTLs were linked to significant hybrid fitness loss. Two genomic regions showed strong transmission bias favoring A. sagittata alleles, potentially accelerating their introgression. However, 48% of QTLs were unlinked to reduced fitness or segregation distortion and may generate genotypes exceeding parental performance. Notably, a major QTL affecting flowering time explained 23% of phenotypic variation and implicated TFL1 as a candidate gene for life history adaptation. While most QTLs lacked overlap with past selective sweeps, indicating limited recent positive selection, 5 of 7 QTLs for rosette size overlapped with sweep signatures in the parental lineages. Overall, our findings offer unique insights into incipient stages of hybridization.

evolutionary biology↗

bioRxiv2025

Conserved spatial patterning of gene expression in independent lineages of C4 plants

O_LIC4 photosynthesis enhances carbon fixation efficiency by reducing photorespiration through the use of an oxygen-insensitive carboxylase and spatial separation of photosynthesis between mesophyll and bundle sheath cells. The C4 pathway has evolved independently in more than sixty plant lineages but molecular mechanisms underpinning this convergence remain unclear. To explore this, we generated high-resolution transcriptome atlases for two independently evolved C4 dicotyledonous species - Gynandropsis gynandra (NAD-ME subtype) and Flaveria bidentis (NADP-ME subtype). C_LIO_LIWe used both single-cell and single-nucleus RNA sequencing to capture gene expression profiles from individual leaf cells, enabling detailed comparison of cell types and transcriptional signatures. C_LIO_LIBoth approaches produced biologically comparable data for major leaf cell types, transcriptomes from single-nucleus sequencing showed lower stress signatures and were more representative of tissue proportions in the leaf. The single-nucleus data revealed that bundle sheath cells from both C4 species share a gene expression pattern associated with mesophyll cells of C3 plants. A conserved set of transcription factors, including members of the C2H2 and DOF families, was identified in the bundle sheath cells of both species. C_LIO_LIThis study presents the first single-cell-resolution transcriptomes for two independent C4 dicot lineages and provides a valuable resource, including a web-based portal for data visualization. C_LI

plant biology↗

bioRxiv2025

Genetic architecture and cellular basis of flag leaf size variation in barley

Flag leaf is the major contributor of photosynthetic assimilates to developing grains. We investigated the genetic architecture and cellular basis of flag leaf length (FLL) and width (FLW) in a multi-parent population comprised of 45 recombinant inbred line (RIL) populations (HvDRR) in barley. Fine mapping of a major quantitative trait locus (QTL) was performed as a first step to isolate the causal gene. Natural variation of FLL and FLW across multi-environment was highly heritable and genotypes adapted to warm climate produced longer and wider flag leaf than those adapted to cooler regions. The variation in flag leaf size was quantitatively inherited and influenced by 24 consensus QTLs of which 17 have not been reported earlier. Further, validation of QTL qHvDRR-FLS-8 and qHvDRR-FLS-17 in nearly isogenic RILs demonstrated that these QTLs also controlled length and width of leaves older than flag leaf. The number of epidermal cells primarily determined the differences in FLL and FLW. In addition, we identified the previously unknown effect of genic- and epiallele at Vrn-H1 on flag leaf size variation in spring barley. Furthermore, we fine-mapped qHvDRR-FLS-8, narrowing the interval from 8.7 to 3.5 Mb. In conclusion, our study identified the genomic regions associated with morphological and anatomical variation for leaf size and set the stage to uncover causal genes.

genetics↗

bioRxiv2025

Regulatory Analysis of Root Architectural and Anatomical Adaptation to Nitrate and Ammonium in Brachypodium distachyon

Root system architecture plays an important role in nitrate and ammonium uptake, the two primary nitrogen (N) forms essential for plant growth. Plants deploy different strategies to optimize the N uptake by roots, based on a complicated regulatory network that controls root phenotype and physiology. Here, we studied the response of root architecture to varying N applications in the model species Brachypodium distachyon. Using a combination of phenotypic and transcriptomic analyses, we examined how different forms and concentrations of ammonium and nitrate affect root growth, biomass allocation, and N uptake. N concentrations significantly influence root traits such as root length, root hair development, and aerenchyma formation in response to nitrate and ammonium. Plants grown in ammonium conditions had thin but highly branched roots, whereas nitrate application resulted in shorter, thicker roots with denser root hair at higher nitrate concentrations. Furthermore, using advanced co-expression network analysis, we identified an Atypical Aspartic Protease (APs) gene encoding an aspartyl protease family protein and a phosphoenolpyruvate carboxylase 1 (PEPC1) gene in brachypodium, which potentially control the root architectural and anatomical adaptions to different N form. APs expression showed a positive correlation with total root length and lateral root development, along with a negative correlation with root hair density. In contrast, PEPC1 exhibited positive correlations with cortex, stele, root cross-sectional areas, and root hair density, while showing a negative correlation with total root length. These genes likely play an important role in the transcriptional regulatory networks involved in these adaptive responses, which highlight the complex interplay between root morphology, nitrogen metabolism, and environmental nutrient conditions.

plant biology↗

bioRxiv2024

Investigating the barley methylome, its variation and association with genomic, transcriptomic, and phenotypic variation

Epigenetic variation contributes to explaining the missing heritability of complex traits. In order to understand the genome-wide methylation variation in spring barley, our objectives were to gain fundamental insight into the barley methylome through whole genome bisulfite sequencing, characterizing methylation variation among 23 parental inbreds of a community resource for genetic mapping of phenotypic traits, and assessing the association of differentially methylated regions (DMRs) with single nucleotide polymorphisms (SNPs) and gene expression variation. Compared to other angiosperms, barley was found to have a highly methylated genome with an average genome wide methylation level of 88.6%, 58.1%, and 1.4% in the CpG, CHG, and CHH sequence context, respectively. We identified just below 500 000 differentially methylated regions (DMRs) among the inbreds. About 64%, 64%, and 83% of the DMRs were not associated with genomic variation in the CpG, CHG, and CHH context, respectively. The methylation level of around 6% of all DMRs was significantly associated with gene expression, where the directionality of the correlation was depended on the relative location of the DMR to the respective gene with a recognizable pattern. Notably, this pattern was much more specific and spatially confined than the association of methylation with gene expression across genes in a singular inbred line. We exemplified this association between DNA methylation and gene expression on the known flowering promoting gene VRN-H1 and identified a highly methylated epiallele associated with earlier flowering time. Finally, methylation was shown to improve the prediction abilities of genomic prediction models for a variety of traits over models using solely SNPs and gene expression as predictors. These observations highlight the independence of DNA methylation to sequence variation and their difference in information content. Our discoveries suggest that epigenetic variation provides a layer of information likely not predictable by other means and is therefore a valuable addition to genomic prediction models.

plant biology↗

bioRxiv2024

The role of methylation and structural variants in shaping the recombination landscape of barley

Meiotic recombination is not only a key mechanism for sexual adaptation in eukaryotes but crucial for the accumulation of beneficial alleles in breeding populations. The effective manipulation of recombination requires, however, a better understanding of the mechanisms regulating the rate and distribution of recombination events in genomes. Here, we identified the genomic features that best explain the recombination variation among a diverse set of segregating populations of barley at a resolution of 1 Mbp and investigated how methylation and structural variants determine recombination hotspots and coldspots at a high-resolution of 10 kb. Hotspots were found to be in proximity to genes and the genetic effects not assigned to methylation were found to be the most important factor explaining differences in recombination rates among populations along with the methylation and the parental sequence divergence. Interestingly, the inheritance of a highly-methylated genomic fragment from one parent only was enough to generate a coldspot, but both parents must be equally low methylated at a genomic segment to allow a hotspot. The parental sequence divergence was shown to have a sigmoidal correlation with recombination indicating an upper limit of mismatch among homologous chromosomes for CO formation. Structural variants (SVs) were shown to suppress COs, and their type and size were not found to influence that effect. Methylation and SVs act jointly determining the location of coldspots in barley and the weight of their relative effect depends on the genomic region. Our findings suggest that recombination in barley is highly predictable, occurring mostly in multiple short sections located in the proximity to genes and being modulated by local levels of methylation and SV load.

genomics↗

bioRxiv2024

Optimal implementation of genomic selection in clone breeding programs - exemplified in potato: II. Effect of selection strategy and cross-selection method on long-term genetic gain

Different cross-selection (CS) methods incorporating genomic selection (GS) have been used in diploid species to improve long-term genetic gain and preserve diversity. However, their application to heterozygous and autotetraploid crops such as potato is lacking so far. The objectives of our study were to (i) assess how different CS methods incorporating GS with or without consideration of genetic variability affect both short- and long-term genetic gains compared to strategies using phenotypic selection (PS); (ii) evaluate the changes in genetic variability and the efficiency of converting diversity into genetic gain across different CS methods; and (iii) investigate the interaction effects between different genetic architectures and CS methods on long-term genetic gain. In our simulation results, implementing GS with optimal selection intensities had a higher short- and long-term genetic gain compared to any PS strategy. The CS method considering additive and dominance effects to predict progeny mean based on simulated progenies (MEGV-O) reached the highest long-term genetic gain among the assessed mean-based CS methods. Compared to MEGV-O and usefulness criteria (UC), the linear combination of UC and genome-wide diversity (called EUCD) kept the same level of genetic gain but resulted in a higher diversity and a lower number of fixed QTL. Moreover, EUCD had a relatively high efficiency in converting diversity into genetic gain. However, choosing the most appropriate weight to account for diversity in EUCD depends on the genetic architecture of the target trait and the breeders objectives. Our results provide breeders with concrete methods to improve their potato breeding programs. Key messageCross-selection method considering progeny mean performance and genetic variability can improve long-term genetic gain and keep genetic diversity in clone breeding.

genetics↗

bioRxiv2024

Morphological, physiological and metabolic responses of diverse barley inbreds to dry down and moderate drought stress

Drought stress alters the metabolic activity, physiological processes, and plant growth and such responses might differ with the intensity of stress. We evaluated the genotypic diversity on plant morphology, photosynthetic responses, metabolite shift and their relationship in diverse barley inbreds under dry down (DD) and moderate drought (MD) stress using 23 genetically diverse parental inbreds of genetic mapping population of barley. MD stress caused a strong growth reduction, while DD stress triggered inhibition of photosynthetic health. We observed that the induced changes occurred in a genotype-dependent manner. Compared to control conditions, the metabolism of simple sugars and polyhydroxy acids increased in MD and DD, while the maximum accumulation of amino acid, lipids and phosphates occurred in DD stress. Accumulation of hexose and metabolites with unknown classification was the metabolic signature of drought tolerant inbreds. The inbreds tolerant to MD originated from the temperate regions while those tolerant to both MD and DD came from semi-arid regions. Low stomata density, reduced water loss and retarded growth under drought stress were the key features of inbreds with better survival capacity under severe dehydration. We identified drought tolerant barley inbreds and our study offers resources for future genetic research on various drought tolerance strategies.

plant biology↗

bioRxiv2023

Exploring natural genetic variation in photosynthesis-related traits of barley in the field

Optimizing photosynthesis is considered an important strategy for improving crop yields to ensure food security. To evaluate the potential of using photosynthesis-related parameters in crop breeding programs, we measured chlorophyll fluorescence along with growth-related and morphological traits of 23 barley inbreds across different developmental stages in field conditions. The photosynthesis-related parameters were highly variable, changing with light intensity and developmental progression of plants. Yet, the variations in photosystem II (PSII) quantum yield observed among the inbreds in the field largely reflected the variations in CO2 assimilation properties in controlled climate chamber conditions, confirming that the chlorophyll fluorescence-based technique can provide proxy parameters of photosynthesis to explore genetic variations under field conditions. Heritability (H2) of the photosynthesis-related parameters in the field ranged from 0.16 for the quantum yield of non-photochemical quenching to 0.78 for the fraction of open PSII center. Two parameters, the maximum PSII efficiency in light-adapted state ( H2 0.58) and the total non-photochemical quenching ( H2 0.53), showed significant positive and negative correlations, respectively, with yield-related traits (dry weight per plant and net straw weight) in the barley inbreds. These results indicate the possibility of improving crop yield through optimizing photosynthetic light use efficiency by conventional breeding programs.

plant biology↗

bioRxiv2023

Phenotypic variation in maize can be largely explained by genetic variation at transcription factor binding sites

Comprehensive maps of functional variation at transcription factor (TF) binding sites (cis-elements) are crucial for elucidating how genotype shapes phenotype. Here we report the construction of a pan-cistrome of the maize leaf under well-watered and drought conditions. We quantified haplotype-specific TF footprints across a pan-genome of 25 maize hybrids and mapped over two-hundred thousand genetic variants (termed binding-QTL) linked to cis-element occupancy. Three lines of evidence support the functional significance of binding-QTL: i) they coincide with numerous known causative loci that regulate traits, including VGT1, Trehalase1, and the MITE transposon near ZmNAC111 under drought; ii) their footprint bias is mirrored between inbred parents and by ChIP-seq; iii) partitioning genetic variation across genomic regions demonstrates that binding-QTL capture the majority of heritable trait variation across [~]70% of 143 phenotypes. Our study provides a promising approach to make previously hidden cis-variation more accessible for genetic studies and multi-target engineering of complex traits.

genomics↗

bioRxiv2023

A genomic panel for studying C3-C4 intermediate photosynthesis in the Brassiceae tribe

Research on C4 and C3-C4 photosynthesis has attracted significant attention because the understanding of the genetic underpinnings of this trait will support the introduction of its characteristics into commercially relevant crop species. We used a panel of 19 taxa of 18 Brassiceae species with different photosynthesis characteristics (C3 and C3-C4) with the following objectives: (i) create draft genome assemblies and annotations, (ii) quantify the level of orthology using synteny maps between all pairs of taxa, (iii) describe the phylogenetic relatedness across all the species, and (iv) track the evolution of C3-C4 intermediate photosynthesis in the Brassiceae tribe. Our results indicate that the draft de novo genome assemblies are of high quality and cover at least 90% of the gene space. Therewith we more than doubled the sampling depth of genomes of the Brassiceae tribe that comprises commercially important as well as biologically interesting species. The gene annotation generated high-quality gene models, and for most genes extensive upstream sequences are available for all taxa, yielding potential to explore variants in regulatory sequences. The genome-based phylogenetic tree of the Brassiceae contained two main clades and indicated that the C3-C4 intermediate photosynthesis has evolved five times independently. Furthermore, our study provides the first genomic support of the hypothesis that Diplotaxis muralis is a natural hybrid of D. tenuifolia and D. viminea. Altogether, the de novo genome assemblies and the annotations reported in this study are a valuable resource for research on the evolution of C3-C4 intermediate photosynthesis.

genomics↗

bioRxiv2023

Genetic mapping reveals new loci and alleles for flowering time and plant height using the double round-robin population of barley

Flowering time and plant height are two critical determinants of yield potential in barley (Hordeum vulgare). Although their role as key traits, a comprehensive understanding of the genetic complexity of flowering time and plant height regulation in barley is still lacking. Through a double round-robin population originated from the crossings of 23 diverse parental inbred lines, we aimed to determine the variance components in the regulation of flowering time and plant height in barley as well as identify new genetic variants by single and multi-population quantitative trait loci (QTL) analyses and allele mining. Despite similar genotypic variance, we observed higher environmental variance components for plant height than flowering time. Furthermore, we detected one new QTL for flowering time and two new QTL for plant height. Finally, we identified a new functional allelic variant of the main regulatory gene Ppd-H1. Our results show that the genetic architecture of flowering time and plant height might be more complex than reported earlier and that a number of undetected, small effect or low frequency, genetic variants underlie the control of these two traits.

genetics↗