Ben J. Hayes

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

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.

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.

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

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.

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

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.

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.

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

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 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.

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.

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

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.

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.

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.

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

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

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.