Biology subjects

Houston, K.

Publications and source records attributed to Houston, K..

8 recordsLinked to original sources

bioRxiv2026

Pan-genomic and pan-transcriptomic analysis of the Heavy Metal ATPase family reveals diverse expression patterns and functional roles in barley

Heavy metals act as essential metalloprotein cofactors in numerous physiological processes but can become toxic when non-essential metals accumulate or when essential metals are in excess. As plants continuously encounter heavy metals through their roots, they have evolved complex homeostatic mechanisms to regulate metal uptake and distribution. The Heavy Metal ATPase (HMA) gene family encodes a group of heavy metal transporting P-type ATPases that have been linked to stress resistance and nutrient supply. Here, we used a bioinformatics approach to identify and characterise 13 HMA genes containing characteristic P1B-type ATPase domains and motifs in the barley Morex V3 reference genome. The genes are located on five of the seven barley chromosomes. Phylogenetic analysis revealed that they cluster into five sub-clades, including one clade unique to barley. Expression profiling across multiple datasets showed distinct temporal and tissue-specific expression patterns among HvHMAs, with several members exhibiting significant transcriptional responses to specific biotic and abiotic stresses. By utilising recently available pan-transcriptomic and pan-genomic resources, we have identified substantial allelic diversity and inter-accession variation in HvHMAs. Our findings suggest that HvHMAs have functions extending beyond canonical heavy metal homeostasis and warrant further investigation for their potential roles in broader physiological and stress-related processes.

plant biology↗

bioRxiv2025

Barley Can Utilise Algal Feriliser to Maintain Yield and Malt Quality Compared to Mineral Fertiliser

Background and AimsMineral fertilisers are essential for global crop productivity. However, their use is unsustainable due to high energy costs from sourcing and processing them, and nitrous oxide emissions after their application. An alternative proposition is the use of microalgal biomass as a nutrient source for fertilisation. To date, there is limited data on how the productivity of barley grown with microalgae would compare to barley grown with mineral fertilisers. Furthermore, the impact of the fertiliser source on suitability of grain for malting, one of barleys main end uses, should be considered. MethodsWe quantified the phenology, reflectance indices and yield components (including yield itself) of barley cv. Laureate grown with either Chlorella vulgaris powder or mineral fertiliser in three glasshouse trials in different soils, to assess the robustness of our findings under soil-to-soil variation. We extended this approach to carry out a field trial from which we malted the grain collected at the end of the season and quantified malt quality. ResultsWe hypothesised that there would be no statistically significant difference in plant performance when grown with microalgae or mineral fertiliser when nitrogen addition was equal. Both glasshouse trials and a field trial showed that plants grown with microalgae and mineral fertiliser do not significantly differ in any yield component, yield itself, or measure of malt quality except total malt nitrogen. ConclusionsSupplying the same amount of nitrogen to plants via microalgal biomass instead of mineral fertiliser produced barley with the same yield and malt quality as plants grown with mineral fertiliser.

plant biology↗

bioRxiv2022

MADS31 supports female germline development by repressing the post-fertilization program in cereal ovules

The female germline of flowering plants develops within a niche of somatic ovule cells, also referred to as the nucellus. How niche cells maintain their own somatic developmental program, yet support the development of adjoining germline cells, remains largely unknown. Here we report that MADS31, a conserved MADS-box transcription factor from the B-sister subclass, is a potent regulator of niche cell identity in barley. MADS31 is preferentially expressed in nucellar cells directly adjoining the germline, and loss-of-function mads31 mutants exhibit deformed and disorganized nucellar cells, leading to impaired germline development and partial female sterility. Molecular assays indicate that MADS31 encodes a potent transcriptional repressor, repressing genes in the ovule that are normally active in the seed. One prominent target of MADS31 is NRPD4b, a seed-expressed component of RNA polymerase IV/V that is involved in gene silencing via RNA directed DNA methylation. NRPD4b is directly repressed by MADS31 in vivo and is de-repressed in mads31 ovules, while overexpression of NRPD4b recapitulates the mads31 ovule phenotype. This coincides with specific changes in histone methylation and is consistent with NRPD4b being directly repressed by MADS31 to maintain ovule niche functionality. Our findings reveal a new mechanism by which somatic ovule tissues maintain their own identity before transitioning to the post-fertilization program.

plant biology↗

bioRxiv2022

Ovule cell wall composition is a maternal determinant of grain size in barley

SummaryO_LIIn cereal species, seed and grain size is influenced by growth of the ovule integuments (seed coat), the spikelet hull (lemma and palea) and the filial endosperm. It has remained unclear whether a highly conserved ovule tissue, the nucellus, has any impact on grain size. C_LIO_LIImmunolabelling revealed that the barley nucellus comprises two distinct cell types that differ in terms of cell wall homogalacturonan (HG) accumulation. Transcriptional profiling of the nucellus identified two pectin methylesterase genes, OVULE PECTIN MODIFIER 1 (OPM1) and OPM2, which are expressed in the ovule but absent from the seed. C_LIO_LIOvules from an opm1 opm2 mutant, and plants expressing an ovule-specific pectin methylesterase inhibitor (PMEI), exhibit reduced HG accumulation. This results in changes to ovule cell size and shape, and ovules that are longer than wild-type controls. At grain maturity, this is manifested as significantly longer grain. C_LIO_LIThese findings indicate that cell wall composition during ovule development acts to limit ovule and seed growth. The investigation of ovule PME and PMEI activity reveals an unexpected role of maternal tissues in controlling grain growth prior to fertilisation, one that has been lacking from models exploring improvements in grain size. C_LI

plant biology↗

bioRxiv2020

The p-coumaroyl arabinoxylan transferase HvAT10 underlies natural variation in whole-grain cell wall phenolic acids in cultivated barley

Phenolic acids in cereal grains have important health-promoting properties and influence digestibility for industrial or agricultural uses. Here we identify alleles of a single BAHD p-coumaroyl arabinoxylan transferase gene, HvAT10, as responsible for the natural variation in cell wall-esterified p-coumaric and ferulic acid in whole grain of a collection of cultivated two-row spring barley genotypes. We show that HvAT10 is rendered non-functional by a premature stop codon mutation in approximately half of the genotypes in our mapping panel. The causal mutation is virtually absent in wild and landrace germplasm suggesting an important function for grain arabinoxylan p-coumaroylation pre-domestication that is dispensable in modern agriculture. Intriguingly, we detected detrimental impacts of the mutated locus on barley grain quality traits. We propose that HvAT10 could be a focus for future grain quality improvement or for manipulating phenolic acid content of wholegrain food products.

plant biology↗

bioRxiv2020

GWAS reveals the genetic complexity of fructan accumulation patterns in barley grain

We profiled the grain oligosaccharide content of 154 two-row spring barley genotypes and quantified 27 compounds, mainly fructans, that exhibited differential abundance. Clustering revealed two major profile groups where the ‘high’ set contained greater amounts of sugar monomers, sucrose and overall fructans, but lower fructosylraffinose. GWAS identified a significant association for the variability of two fructan types; neoseries-DP7 and inulin-DP9 which showed increased strength when a compound-ratio GWAS was applied. Gene models within this region included five fructan biosynthesis genes, of which three (fructan:fructan 1-fructosyltransferase, sucrose:sucrose 1-fructosyltransferase, and sucrose:fructan 6-fructosyltransferase) have already been described. The remaining two, 6(G)-fructosyltransferase and vacuolar invertase1 have not previously been linked to fructan biosynthesis in barley and showed expression patterns distinct from those of the other three genes, including exclusive expression of 6(G)-fructosyltransferase in outer grain tissues at the storage phase. From exome capture data several SNPs related to inulin- and neoseries-type fructan variability were identified in fructan:fructan 1-fructosyltransferase and 6(G)-fructosyltransferase genes Co-expression analyses uncovered potential regulators of fructan biosynthesis including transcription factors. Our results provide evidence for the distinct biosynthesis of neoseries-type fructans during barley grain maturation plus new gene candidates likely involved in the differential biosynthesis of the various fructan types.Highlight Grain fructan profiles in barley are more complex than previously expected and variations in a diversity panel relate to a genomic region where fructan biosynthesis genes cluster.Abbreviations1-FFTfructan:fructan 1-fructosyltransferase1-SSTsucrose:sucrose 1-fructosyltransferase6-SFTsucrose:fructan 6-fructosyltransferase6G-FFT6(G)-fructosyltransferaseDAPdays after pollinationDPdegree of polymerisationDMdry matterELSDevaporative light scattering detectionFDRfalse discovery rateFOSfructooligosaccharidesFPKMfragments per kilobase, per million mapped readsGWAgenome wide associationGWASgenome wide association studyHAIhours after imbibitionHPAEC–PADhigh pH anion exchange chromatography with pulsed amperometric detectionHPLChigh performance liquid chromatographyKPkestopentaoseKTkestotetraoseLCliquid chromatographyLDlinkage disequilibriumLODlogarithm of oddsMAFminimum allele frequencyMSmass spectrometryNGNeural GasNSneoseries-type fructanPprobability valuePEGpolyethylene glycolQTLquantitative trait lociRFOraffinose family oligosaccharidesRTretention timeSNPsingle nucleotide polymorphismsSPEsolid phase extractionTFAtrifluoroacetic acidTPMtranscripts per millionVI-1vacuolar invertase1View Full Text

plant biology↗

bioRxiv2020

Targeted mutation of barley (1,3;1,4)-β-glucan synthases reveals complex relationships between the storage and cell wall polysaccharide content

Barley (Hordeum vulgare L) grain is comparatively rich in (1,3;1,4)-{beta}-glucan, a source of fermentable dietary fibre that protects against various human health conditions. However, low grain (1,3;1,4)-{beta}-glucan content is preferred for brewing and distilling. We took a reverse genetics approach, using CRISPR/Cas9 to generate mutations in members of the Cellulose synthase-like (Csl) gene superfamily that encode known (HvCslF6 and HvCslH1) and putative (HvCslF3 and HvCslF9) (1,3;1,4)-{beta}-glucan synthases. Resultant mutations ranged from single amino acid (aa) substitutions to frameshift mutations causing premature stop codons, and led to specific differences in grain morphology, composition and (1,3;1,4)-{beta}-glucan content. (1,3;1,4)-{beta}-Glucan was absent in the grain of cslf6 knock-out lines whereas cslf9 knock-out lines had similar (1,3;1,4)-{beta}-glucan content to WT. However, cslf9 mutants showed changes in the abundance of other cell wall-related monosaccharides compared to WT. Thousand grain weight (TGW), grain length, width and surface area were altered in cslf6 knock-outs and to a lesser extent TGW in cslf9 knock-outs. cslf3 and cslh1 mutants had no effect on grain (1,3;1,4)-{beta}-glucan content. Our data indicate that multiple members of the CslF/H family fulfil important functions during grain development but, with the exception of HvCslF6, do not impact the abundance of (1,3;1,4)-{beta}-glucan in mature grain.

plant biology↗

bioRxiv2020

A Grain of Salt

We quantified grain sodium (Na+) content across a barley GWAS panel grown under optimal conditions. We identified a strong association with a region containing two low and one high Na+ accumulating haplotypes of a Class 1 HIGH-AFFINITY POTASSIUM TRANSPORTER (HKT1;5) known to be involved in regulating plant Na+ homeostasis. The haplotypes exhibited an average 1.8-fold difference in grain Na+ content. We show that an L189P substitution disrupts Na+ transport in the high Na+ lines, disturbs the plasma membrane localisation typical of HKT1;5 and induces a conformational change in the protein predicted to compromise function. Under NaCl stress, lines containing P189 accumulate high levels of Na+, but show no significant difference in biomass. P189 increases in frequency from wild-species to elite cultivars leading us to speculate that the compromised haplotype is undergoing directional selection possibly due to the value of Na+ as a functional nutrient in non-saline environments.

genetics↗