B. J. A. Hayes

Haplotype-based insights into the genetic architecture of net blotch resistance in barley

This study identifies 40 QTL for net blotch resistance in barley using haplotype analysis, revealing shared and distinct genetic mechanisms between two disease forms.

Comparison of localGEBV and Optimal Haplotype Stacking Fitness Functions using a Novel R Package: HapSelect

The paper compares localGEBV and OHS fitness functions for parent selection in inbred crops using a novel R package, finding similar long-term genetic gains with dosage-based localGEBV offering simpler workflows.

Short communication: Oral microbiome as a potential proxy for grazing livestock methane emissions

This study investigates whether oral microbiome profiles can serve as a non-invasive proxy for estimating methane emissions in grazing cattle, finding that microbial function explains a meaningful proportion of methane variation.

Advancing rust resistance in elite wheat with haplotype mapping and a novel introgression strategy

This study identifies haploblocks associated with rust resistance in wheat and develops a selection index to improve breeding for durable resistance.

The potential to breed for genetic legacy effects in sustainable farming systems

This study shows that mungbean genotypes significantly influence subsequent wheat yield through legacy effects, suggesting opportunities to breed for system-level productivity in sustainable farming.

Local genomic estimates provide a powerful framework for haplotype discovery

This paper introduces localGEBV, a haplotype-based method that improves QTL discovery and phenotypic prediction compared to traditional GWAS approaches in barley.

Stacking haplotypes from the Vavilov wheat collection to accelerate breeding for multiple disease resistance

This paper identifies haploblocks associated with multiple disease resistance in wheat using a diversity panel and demonstrates their potential to improve resistance through haplotype stacking.

Evolutionary computing to assemble standing genetic diversity and achieve long-term genetic gain

This paper compares selection strategies for crop breeding, finding that optimal haplotype selection (OHS) maintains more genetic diversity and achieves higher long-term gains than truncation selection or optimal cross selection.

Genomic mate-allocation strategies exploiting additive and non-additive genetic effects to maximise total clonal performance in sugarcane

The paper compares mate-allocation strategies in sugarcane breeding that use additive and non-additive genetic effects to maximize clonal performance and reduce inbreeding.

genomicSimulation: fast R functions for stochastic simulation of breeding programs

The paper introduces genomicSimulation, a fast R tool for stochastic simulation of breeding programs using real genotypes, showing it accurately reproduces key population features.

The genome of tropically adapted Brahman cattle (Bos taurus indicus) reveals novel genome variation in production animals

The paper presents a high-quality genome assembly of Brahman cattle using long-read sequencing and identifies structural variants and gene copy number variations associated with immune function.

In-situ genomic prediction using low-coverage Nanopore sequencing

This paper demonstrates that low-coverage Oxford Nanopore sequencing can accurately predict genomic breeding values in cattle, comparable to SNP array-based methods, with potential for on-farm or clinical use.

Correlation scan: identifying genomic regions that affect genetic correlations applied to fertility traits

This paper introduces a framework to identify genomic regions affecting genetic correlations between male and female fertility traits in cattle using high-density SNP data.

Prowler: A novel trimming algorithm for Oxford Nanopore sequence data

Prowler improves Oxford Nanopore sequence data quality by retaining phase and read length information, leading to better alignment accuracy but slightly reduced assembly contiguity.

Analysis Of Polycerate Mutants Reveals The Evolutionary Co-Option Of HOXD1 To Determine The Number And Topology Of Horns In Bovidae

The paper identifies POLYCERATE alleles in sheep and goats linked to defective HOXD1 function, showing haploinsufficiency causes horn bud splitting and highlights HOXD1's role in headgear patterning in Bovidae.

Using prior information from humans to prioritize genes and gene-associated variants for complex traits in livestock

This study uses human height GWAS data to prioritize genes and variants for cattle stature, finding some overlap but no added benefit over within-species data.

Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits

The paper identifies sequence variants with regulatory and evolutionary significance in cattle and ranks them using a Functional-And-Evolutionary Trait Heritability score to improve genomic prediction.

Genome-wide profiling of microRNAs and prediction of mRNA targets in 17 bovine tissues

This study identifies microRNA expression and target sites in 17 bovine tissues, revealing tissue-specific regulation and genomic features of microRNA-target interactions.

Genome variants associated with RNA splicing variation in bovine are extensively shared between tissues

The paper identifies bovine sQTLs associated with RNA splicing variation and shows they are shared across tissues and linked to complex traits.

Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits

The paper maps bovine TADs and CTCF binding motifs using genomic synteny and shows they reduce the search space for regulatory variants associated with complex traits.

Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics and epigenetics data

The paper develops a computational method to predict regulatory regions in mammals using human genomics data, and applies it to cattle to prioritize variants and identify genome editing targets.