Biology & Life Sciences
Domestic Animal Genetics
Domestication of wild animal and plant species may be considered the largest genetic experiment in human history. Human selection for specific traits and targeted breeding over hundreds or thousands of generations has shaped very special populations that provide unique opportunities for research. Domestic animal genetics contributes to technological advances facilitating a more sustainable, environment- and climate-friendly food production that respects changing societal expectations related to ethical and animal welfare issues. Domestic animal genetics also enables fundamental insights into gene functions and provides animal models for biomedical research.
In this collection, curated by Associate Editor Tosso Leeb, we present a selection of PLOS Genetics research that exemplifies recent progress in domestic animal genetics and areas for future development.
Editorial
Monogenic traits, new genotype-phenotype correlations, in vivo function of genes
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PLOS Genetics Whole genome variant association across 100 dogs identifies a frame shift mutation in DISHEVELLED 2 which contributes to Robinow-like syndrome in Bulldogs and related screw tail dog breeds
Domestic dog breeds exhibit remarkable morphological variations that result from centuries of artificial selection and breeding.…
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PLOS Genetics ANLN truncation causes a familial fatal acute respiratory distress syndrome in Dalmatian dogs
Acute respiratory distress syndrome (ARDS) is the leading cause of death in critical care medicine. The syndrome is typified by an…
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PLOS Genetics The evolution of Sex-linked barring alleles in chickens involves both regulatory and coding changes in CDKN2A
Sex-linked barring is a fascinating plumage pattern in chickens recently shown to be associated with two non-coding and two missense…
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PLOS Genetics A de novo variant in the ASPRV1 gene in a dog with ichthyosis
Ichthyoses are a heterogeneous group of inherited cornification disorders characterized by generalized dry skin, scaling and/or…
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PLOS Genetics MKLN1 splicing defect in dogs with lethal acrodermatitis
Lethal acrodermatitis (LAD) is a genodermatosis with monogenic autosomal recessive inheritance in Bull Terriers and Miniature Bull…
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PLOS Genetics A nonsense variant in Rap Guanine Nucleotide Exchange Factor 5 (RAPGEF5) is associated with equine familial isolated hypoparathyroidism in Thoroughbred foals
Idiopathic hypocalcemia in Thoroughbred (TB) foals causes tetany and seizures and is invariably fatal. Based upon the similarity of this…
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PLOS Genetics Characterisation of canine KCNIP4: A novel gene for cerebellar ataxia identified by whole-genome sequencing two affected Norwegian Buhund dogs
A form of hereditary cerebellar ataxia has recently been described in the Norwegian Buhund dog breed. This study aimed to identify the…
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PLOS Genetics Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility
Cattle are ideally suited to investigate the genetics of male reproduction, because semen quality and fertility are recorded for all…
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PLOS Genetics PEA15 loss of function and defective cerebral development in the domestic cat
Cerebral cortical size and organization are critical features of neurodevelopment and human evolution, for which genetic investigation in…
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PLOS Genetics TSEN54 missense variant in Standard Schnauzers with leukodystrophy
We report a hereditary leukodystrophy in Standard Schnauzer puppies. Clinical signs occurred shortly after birth or started at an age of…
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PLOS Genetics Deletion of the SELENOP gene leads to CNS atrophy with cerebellar ataxia in dogs
We investigated a hereditary cerebellar ataxia in Belgian Shepherd dogs. Affected dogs developed uncoordinated movements and intention…
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PLOS Genetics The genetics and evolution of eye color in domestic pigeons (Columba livia)
The eye color of birds, generally referring to the color of the iris, results from both pigmentation and structural coloration. Avian iris…
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PLOS Genetics Bovine and murine models highlight novel roles for SLC25A46 in mitochondrial dynamics and metabolism, with implications for human and animal health
Neuropathies are neurodegenerative diseases affecting humans and other mammals. Many genetic causes have been identified so far, including…
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PLOS Genetics Progressive ataxia of Charolais cattle highlights a role of KIF1C in sustainable myelination
Hereditary spastic paraplegias (HSPs) are clinically and genetically heterogeneous human neurodegenerative diseases. Amongst the…
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PLOS Genetics Direct-to-consumer DNA testing of 6,000 dogs reveals 98.6-kb duplication associated with blue eyes and heterochromia in Siberian Huskies
Consumer genomics enables genetic discovery on an unprecedented scale by linking very large databases of personal genomic data with…
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PLOS Genetics An ABCA4 loss-of-function mutation causes a canine form of Stargardt disease
Autosomal recessive retinal degenerative diseases cause visual impairment and blindness in both humans and dogs. Currently, no standard…
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PLOS Genetics NME5 frameshift variant in Alaskan Malamutes with primary ciliary dyskinesia
Primary ciliary dyskinesia (PCD) is a hereditary defect of motile cilia in humans and several domestic animal species. Typical clinical…
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PLOS Genetics A RAPGEF6 variant constitutes a major risk factor for laryngeal paralysis in dogs
Laryngeal paralysis (LP) is the inability to abduct the arytenoid cartilages during inspiration, resulting in a partial to complete airway…
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PLOS Genetics Recessive missense LAMP3 variant associated with defect in lamellar body biogenesis and fatal neonatal interstitial lung disease in dogs
Neonatal interstitial lung diseases due to abnormal surfactant biogenesis are rare in humans and have never been reported as a spontaneous…
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PLOS Genetics Molecular parallelisms between pigmentation in the avian iris and the integument of ectothermic vertebrates
Birds exhibit striking variation in eye color that arises from interactions between specialized pigment cells named chromatophores. The…
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PLOS Genetics A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia)
Rock pigeons (Columba livia) display an extraordinary array of pigment pattern variation. One such pattern, Almond, is characterized by a…
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PLOS Genetics A loss-of-function mutation in RORB disrupts saltatorial locomotion in rabbits
Saltatorial locomotion is a type of hopping gait that in mammals can be found in rabbits, hares, kangaroos, and some species of rodents.…
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PLOS Genetics An ADAMTS3 missense variant is associated with Norwich Terrier upper airway syndrome
In flat-faced dog breeds, air resistance caused by skull conformation is believed to be a major determinant of Brachycephalic Obstructive…
Complex traits
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PLOS Genetics A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle
Clinical mastitis (CM) is an inflammatory disease occurring in the mammary glands of lactating cows. CM is under genetic control, and a…
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PLOS Genetics Beyond the MHC: A canine model of dermatomyositis shows a complex pattern of genetic risk involving novel loci
Juvenile dermatomyositis (JDM) is a chronic inflammatory myopathy and vasculopathy driven by genetic and environmental influences. Here,…
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PLOS Genetics Balancing selection on a recessive lethal deletion with pleiotropic effects on two neighboring genes in the porcine genome
Livestock populations can be used to study recessive defects caused by deleterious alleles. The frequency of deleterious alleles including…
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PLOS Genetics Analysis of large versus small dogs reveals three genes on the canine X chromosome associated with body weight, muscling and back fat thickness
Domestic dog breeds display significant diversity in both body mass and skeletal size, resulting from intensive selective pressure during…
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PLOS Genetics Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows
Cattle and other ruminants produce large quantities of methane (~110 million metric tonnes per annum), which is a potent greenhouse gas…
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PLOS Genetics The genetic architecture of helminth-specific immune responses in a wild population of Soay sheep (Ovis aries)
Much of our knowledge of the drivers of immune variation, and how these responses vary over time, comes from humans, domesticated…
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PLOS Genetics Identification and validation of genetic variants predictive of gait in standardbred horses
Several horse breeds have been specifically selected for the ability to exhibit alternative patterns of locomotion, or gaits. A premature…
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PLOS Genetics Novel protective and risk loci in hip dysplasia in German Shepherds
Canine hip dysplasia is a common, non-congenital, complex and hereditary disorder. It can inflict severe pain via secondary osteoarthritis…
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PLOS Genetics A functional regulatory variant of MYH3 influences muscle fiber-type composition and intramuscular fat content in pigs
Muscle development and lipid accumulation in muscle critically affect meat quality of livestock. However, the genetic factors underlying…
Cancer genetics
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PLOS Genetics Multi-omics approach identifies germline regulatory variants associated with hematopoietic malignancies in retriever dog breeds
Histiocytic sarcoma is an aggressive hematopoietic malignancy of mature tissue histiocytes with a poorly understood etiology in humans. A…
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PLOS Genetics Naturally-occurring canine invasive urothelial carcinoma harbors luminal and basal transcriptional subtypes found in human muscle invasive bladder cancer
There is growing evidence that molecular subtypes (e.g. luminal and basal subtypes) affect the prognosis and treatment response in…
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PLOS Genetics Somatic inactivating PTPRJ mutations and dysregulated pathways identified in canine malignant melanoma by integrated comparative genomic analysis
Canine malignant melanoma, a significant cause of mortality in domestic dogs, is a powerful comparative model for human melanoma, but…
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PLOS Genetics A synonymous germline variant in a gene encoding a cell adhesion molecule is associated with cutaneous mast cell tumour development in Labrador and Golden Retrievers
Mast cell tumours are the most common type of skin cancer in dogs, representing a significant concern in canine health. The molecular…
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PLOS Genetics Identification of common predisposing loci to hematopoietic cancers in four dog breeds
Histiocytic sarcoma (HS) is a rare but aggressive cancer in both humans and dogs. The spontaneous canine model, which has clinical,…
Domestication genetics
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PLOS Genetics The genetic consequences of dog breed formation—Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels
Selective breeding for desirable traits in strictly controlled populations has generated an extraordinary diversity in canine morphology…
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PLOS Genetics Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle
Selection on complex traits can rapidly drive evolution, especially in stressful environments. This polygenic selection does not leave…
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PLOS Genetics Selection and hybridization shaped the rapid spread of African honey bee ancestry in the Americas
Recent biological invasions offer ‘natural’ laboratories to understand the genetics and ecology of adaptation, hybridization, and range…
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PLOS Genetics Selection signatures in goats reveal copy number variants underlying breed-defining coat color phenotypes
Domestication and human selection have formed diverse goat breeds with characteristic phenotypes. This process correlated with the…
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PLOS Genetics Balancing selection at a premature stop mutation in the myostatin gene underlies a recessive leg weakness syndrome in pigs
Balancing selection provides a plausible explanation for the maintenance of deleterious alleles at moderate frequency in livestock,…
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PLOS Genetics Genetics of adaptation in modern chicken
We carried out whole genome resequencing of 127 chicken including red jungle fowl and multiple populations of commercial broilers and…
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PLOS Genetics Loss of function mutations in essential genes cause embryonic lethality in pigs
Lethal recessive alleles cause pre- or postnatal death in homozygous affected individuals, reducing fertility. Especially in small size…
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PLOS Genetics Genetic analysis of the modern Australian labradoodle dog breed reveals an excess of the poodle genome
The genomic diversity of the domestic dog is an invaluable resource for advancing understanding of mammalian biology, evolutionary…
Molecular tools, computational methods, and resources for domestic animal genetics
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PLOS Genetics Frequency and distribution of 152 genetic disease variants in over 100,000 mixed breed and purebred dogs
Knowledge on the genetic epidemiology of disorders in the dog population has implications for both veterinary medicine and sustainable…
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PLOS Genetics A high resolution atlas of gene expression in the domestic sheep (Ovis aries)
Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene…
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PLOS Genetics Inferring sex-specific demographic history from SNP data
The relative female and male contributions to demography are of great importance to better understand the history and dynamics of…
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PLOS Genetics Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies
Genomic resources for the domestic dog have improved with the widespread adoption of a 173k SNP array platform and updated reference…
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PLOS Genetics Prioritizing sequence variants in conserved non-coding elements in the chicken genome using chCADD
The availability of genomes for many species has advanced our understanding of the non-protein-coding fraction of the genome. Comparative…
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PLOS Genetics Using prior information from humans to prioritize genes and gene-associated variants for complex traits in livestock
Genome-Wide Association Studies (GWAS) in large human cohorts have identified thousands of loci associated with complex traits and…
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PLOS Genetics A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism
The domestic cat (Felis catus) numbers over 94 million in the USA alone, occupies households as a companion animal, and, like humans,…