Biology subjects

Domoney, C.

Publications and source records attributed to Domoney, C..

6 recordsLinked to original sources

bioRxiv2026

Postprandial profiling of the duodenal microbiome reveals the impact of food structure and association with luminal metabolite and gut hormone responses

The human duodenum harbours a complex, dynamic microbial community that is challenging to study due to inaccessibility, particularly postprandially when nutrient-rich chyme and fluctuating metabolites create unique microbial niches. We used naso-duodenal intubation to longitudinally sample duodenal luminal contents following pea-based meals of differing food structure, alongside parallel blood collection. Shotgun metagenomic sequencing, comprehensive metabolomic profiling and gut hormone measurements were combined to explore microbe-metabolite-hormone interactions. Food structure significantly affected postprandial bacterial composition, with saccharolytic oral taxa increasing after meals with intact structure. Alpha diversity was influenced by structure type (P = 0.025), with whole pea seeds promoting greater diversity than pea flour. Network analysis revealed complex interactions between the duodenal microbiome, luminal metabolites and gut hormones, with most microbial associations linked to glucose-dependent insulinotropic polypeptide (GIP) rather than glucagon-like peptide-1 (GLP-1). Metabolic profiling showed meal-dependent changes in amino acid metabolism, including shifts in D/L amino acid ratios over time consistent with microbial metabolism. The duodenal microbiome showed close phylogenetic relationships with the oral microbiome, with composition influenced by food structuring and swallowing. These findings reveal dynamic microbe-metabolite interplay in the human duodenum during digestion and its relationship to gut hormone responses.

microbiology↗

bioRxiv2025

Pea-Saving Partners: Bacillus and Pseudomonas combat downy mildew in pea crops

Downy mildew (DM) is a destructive disease that significantly reduces the yield and quality of important pulses (legumes) and horticultural crops, particularly during humid and cool seasons. This disease is caused by obligate and host-specific oomycete pathogens. Controlling the pathogen is challenging due to its long-term survival as spores and its rapid mutation. Use of chemical pesticides has been the most effective method to control DM pathogens, but their environmental hazards are a global concern. Current research is focused on exploring the potential of microbial biological control agents (MBCA), particularly rhizobacteria strains of the genera Bacillus and Pseudomonas, which have shown suppression of plant pathogens. However, to date, no MBCA has been reported to be effective against DM pathogens in pulses. We investigated the effectiveness of Bacillus and Pseudomonas strains as potential biopesticides against the pea downy mildew pathogen Peronospora viciae f. sp. pisi (Pvp). In our study, in vitro bioassays showed 100% inhibition of Pvp spore germination compared to the control. In planta antagonism assays further demonstrated significant suppression (>80%) of Pvp sporulation in pea plants sprayed with strains of Bacillus velezensis or P. fluorescens or their filtrates. The drench application also showed significant effects where either a Pseudomonas or cold-adapted Bacillus strain was used. We observed a synergistic effect for the dual foliar application of the microbes compared to individual application (27.6 to 46.7% suppression). Furthermore, the results from the molecular biomass analysis were consistent with the results of the sporulation assays. This demonstrates the strong interactive and promotive benefits of using Bacillus and Pseudomonas as biocontrol agents Based on these results, we conclude that these MBCAs could be effective in combatting Pvp infections in the field.

plant biology↗

bioRxiv2024

Identification of significant genome-wide associations and QTL underlying variation in seed protein composition in pea (Pisum sativum L.)

Pea seeds are a valuable source of plant proteins for human and animal nutrition and have various industrial applications. The relative abundance of different seed storage proteins affects protein quality, including digestibility and functional properties of protein extracts. Thus, understanding the genetic basis of seed protein composition is crucial to enhance protein quality and nutritional value through breeding. In this study, we employed two complementary approaches, Genome-Wide Association Study (GWAS) and Quantitative Trait Locus (QTL) mapping, to identify genetic loci underlying seed protein composition in pea. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was used to separate the seed proteins, and their relative abundance was quantified using densitometric analysis. For GWAS, we analysed a diverse panel of 209 accessions genotyped with an 84,691 SNP array and identified genetic loci significantly associated with globulins, such as convicilin, vicilin, legumins; and non-globulins, including lipoxygenase, late embryogenesis abundant protein (LEA), and annexin-like protein. Additionally, using QTL mapping with 96 recombinant inbred lines (RILs), we mapped 11 QTL, including five that overlapped with regions identified by GWAS for the same proteins. Within these regions, we identified structural genes for seed proteins and other genes with predicted functions in protein biosynthesis, trafficking, and modification. This comprehensive genetic mapping study serves as a foundation for future breeding efforts to improve protein quality in pea and other legumes.

genetics↗

bioRxiv2024

Genomic and Genetic Insights into Mendel's Pea Genes

Pea, Pisum sativum, is an excellent model system through which Gregor Mendel established the foundational principles of inheritance. Surprisingly, till today, the molecular nature of the genetic differences underlying the seven pairs of contrasting traits that Mendel studied in detail remains partially understood. Here, we present a genomic and phenotypic variation map, coupled with haplotype-phenotype association analyses across a wide range of traits in a global Pisum diversity panel. We focus on a genomics-enabled genetic dissection of each of the seven traits Mendel studied, revealing many previously undescribed alleles for the four characterized genes, R, Le, I and A, and elucidating the gene identities and mutations for the remaining three uncharacterized traits. Notably, we identify: (1) a ca. 100kb deletion upstream of the Chlorophyll synthase (ChlG) gene, which generates aberrant transcripts and confers the yellow pod phenotype of gp mutants; (2) an in-frame premature stop codon mutation in a Dodeca-CLE41/44 signalling peptide which explains the parchmentless mutant phenotype corresponding to p; and (3) a 5bp in-frame deletion in a CIK-like receptor kinase gene corresponding to the fasciated stem phenotype fa, which Mendel described in terms of flower position, and we postulate the existence of a Modifier of fa (Mfa) locus that masks this meristem defect. Mendel noted the pleiotropy of the a mutation, including inhibition of axil ring anthocyanin pigmentation, a trait we found to be controlled by allelic variants of the gene D within an R2R3-MYB gene cluster. Furthermore, we characterize and validate natural variation of a quantitative genetic locus governing both pod width and seed weight, characters that Mendel deemed were not sufficiently demarcated for his analyses. This study establishes a cornerstone for fundamental research, education in biology and genetics, and pea breeding practices.

genetics↗

bioRxiv2018

Speed breeding in growth chambers and glasshouses for crop breeding and model plant research

1.To meet the challenge of feeding a growing population, breeders and scientists are continuously looking for ways to increase genetic gain in crop breeding. One way this can be achieved is through \"speed breeding\" (SB), which shortens the breeding cycle and accelerates research studies through rapid generation advancement. The SB method can be carried out in a number of ways, one of which involves extending the duration of a plants daily exposure to light (photoperiod) combined with early seed harvest in order to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral crops. Here we present glasshouse and growth chamber-based SB protocols with supporting data from experimentation with several crop species. These protocols describe the growing conditions, including soil media composition, lighting, temperature and spacing, which promote rapid growth of spring and winter bread wheat, durum wheat, barley, oat, various members of the Brassica family, chickpea, pea, grasspea, quinoa and the model grass Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale-up plant numbers for single seed descent (SSD) purposes. Conversely, instructions on how to perform SB on a small-scale by creating a benchtop SB growth cabinet that enables optimization of parameters at a low cost are provided. We also outline the procedure for harvesting and germinating premature wheat, barley and pea seed to reduce generation time. Finally, we provide troubleshooting suggestions to avoid potential pitfalls.

plant biology↗

bioRxiv2017

Speed breeding: a powerful tool to accelerate crop research and breeding

The growing human population and a changing environment have raised significant concern for global food security, with the current improvement rate of several important crops inadequate to meet future demand [1]. This slow improvement rate is attributed partly to the long generation times of crop plants. Here we present a method called speed breeding, which greatly shortens generation time and accelerates breeding and research programs. Speed breeding can be used to achieve up to 6 generations per year for spring wheat (Triticum aestivum), durum wheat (T. durum), barley (Hordeum vulgare), chickpea (Cicer arietinum), and pea (Pisum sativum) and 4 generations for canola (Brassica napus), instead of 2-3 under normal glasshouse conditions. We demonstrate that speed breeding in fully-enclosed controlled-environment growth chambers can accelerate plant development for research purposes, including phenotyping of adult plant traits, mutant studies, and transformation. The use of supplemental lighting in a glasshouse environment allows rapid generation cycling through single seed descent and potential for adaptation to larger-scale crop improvement programs. Cost-saving through LED supplemental lighting is also outlined. We envisage great potential for integrating speed breeding with other modern crop breeding technologies, including high-throughput genotyping, genome editing, and genomic selection, accelerating the rate of crop improvement.

plant biology↗