Lee Thomas Hickey

High-throughput sequencing of unmethylated DNA (UMR-seq) reveals extensive epigenetic variation in the hypomethylome of diverse plant species

UMR-seq reveals epigenetic variation in plant hypomethylomes, showing UMRs are enriched in regulatory loci and improve genomic prediction and trait association mapping in wheat.

Leveraging synthetic environmental covariates to explore crop genotype by environment interactions

The paper introduces a method to analyze genotype by environment interactions by examining environmental effects across growth stages, finding that early grain fill stages have the greatest impact on yield variance.

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.

Trait stability of diverse kabuli chickpea germplasm from delayed sowing in a rainfed environment

This study evaluates the impact of delayed sowing on grain yield in kabuli chickpea germplasm, identifying genomic regions associated with seed number and phenology that could improve yield.

Identifying water stress response haplotypes in barley using latent environmental covariates

This paper identifies water stress response haplotypes in barley by integrating environmental covariates with genetic analysis to uncover adaptive genomic regions.

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.

The PIN2 ortholog in barley modifies root gravitropism and architecture without impacting the shoot

This study shows that knocking out PIN2 in barley alters root gravitropism and architecture without affecting shoot growth.

Phenotyping the hidden half: Combining UAV phenotyping and machine learning to predict barley root traits in the field

This paper uses UAV phenotyping and machine learning to predict barley root traits in the field, identifying genetic drivers of root gravitropism.

Envirotyping Facilitates Understanding of Genotype x Environment Interactions and Highlights the Potential of Stay-green Traits in Wheat

This study uses envirotyping to analyze genotype x environment interactions in wheat, showing stay-green traits improve yield across environments.

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.

Extensive somatic nuclear exchanges shape global populations of the wheat leaf rust pathogen Puccinia triticina

The paper shows that somatic nuclear exchange in Puccinia triticina generates genetic diversity, leading to new strains through repeated shuffling of haploid nuclei between clonal lineages.

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.

Physiological and genetic drivers underpinning canopy development are associated with durum wheat yield in rainfed environments

This study identifies QTL associated with canopy closure timing in durum wheat that improve yield in rainfed environments without yield penalties.