Martin Johnsson

This paper estimates variant intolerance scores for cattle genes and predicts protein domains, finding similar patterns to other species and moderate correlation with human orthologs.

The paper shows that BMP2 and retinoic acid together activate a meiotic-entry program in chicken primordial germ cells, unlike retinoic acid alone.

This study evaluates two-tower machine learning models for predicting reproductive outcomes and sex-specific fertility liabilities using simulated genomic data.

This study develops a 72k SNP array to assess BKD resistance in Arctic charr and finds genomic prediction is feasible with moderate accuracy.

The paper estimates recent population history of Swedish cattle breeds using linkage disequilibrium methods and finds a recent population decline following the start of systematic breeding.

The paper estimates genetic parameters and sex-specific architecture of fertility traits in Arctic charr, identifying genetic correlations and trade-offs affecting reproductive success.

The paper models how large-effect damaging alleles spread in small populations, finding that balancing selection and influential parents can lead to their commonality.

This study identifies miR-2954 as a male-essential microRNA critical for avian sex chromosome dosage compensation, showing its role in balancing gene expression in males and females.

This study simulates dairy cattle breeding programs to assess how accounting for mitochondrial DNA variation affects the accuracy of breeding values and genetic gain.

This study examines bone properties in laying hens under different housing systems, finding environmental effects on bone strength but limited genetic associations.

This study evaluates the benefits of using whole-genome sequence data for genomic prediction in pigs, finding small improvements over marker arrays in some scenarios.

The paper identifies rare and population-specific functional variants in commercial pig lines and assesses their impact on production traits and genomic prediction.

The paper profiles open chromatin in developing pig muscle to identify regulatory regions and provides a resource for genome regulation studies and variant filtering in pig breeding.

This study estimates recombination rate variation in pigs using multiocus iterative peeling across 150,000 pigs, identifies heritability, and finds three genomic regions associated with recombination.

This study shows genomic data can improve genetic evaluation accuracy in smallholder dairy farms with small herds and weak genetic connections.

This study simulates genome editing and selection strategies to reduce deleterious load in animal breeding, finding that editing multiple recessive variants is more effective than selection against carriers.

The paper identifies three haplotypes with putatively recessive lethal alleles in Irish beef cattle and shows their pleiotropic effects on economically important traits.

The paper shows that index hopping and reference allele bias have minimal impact on genotype calls from low-coverage sequencing, but pruning low-support haplotypes introduces a significant reference allele bias.

The paper analyzes sequence variation, constraint, and selection in the CD163 gene in pigs, finding no knock-out variants and evidence of positive selection but no recent selective sweeps.

The paper identifies five candidate genes affecting quantitative red colouration variation in chickens using QTL mapping and genetical genomics.

This study identifies genes affecting social reinstatement behavior in chickens using QTL and eQTL analysis, finding TTRAP as a strong candidate gene and suggesting clustered genetic modules drive domestication.

This study maps genes controlling brain mass and body mass variation in domestic chickens, showing they have separate genetic architectures and domestication increases body mass and absolute brain mass.