Gabriella Lindgren

• Guest professor KU Leuven Assoc. prof SLU
• Lecturer at Swedish University of Agricultural Sciences

Physical and mental ability to compete is needed for trotters to be successful in harness racing. The ability to cope with a competition atmosphere and an elite training environment also influences the horses’ welfare, career longevity, as well as the safety of the humans handling them. Standardbred trotters have long been bred to be well suited fo...

Since their domestication, horses have accompanied mankind, and humans have constantly shaped horses according to their needs through stallion-centered breeding. Consequently, the male-specific portion of the Y chromosome (MSY) is extremely uniform in modern horse breeds. The majority of stallions worldwide carry MSY haplotypes (HT) attributed to a...

The Greying with age phenotype in horses involves loss of hair pigmentation whereas skin pigmentation is not reduced, and a predisposition to melanoma. The causal mutation was initially reported as a duplication of a 4.6 kb intronic sequence in Syntaxin 17. The speed of greying varies considerably among Grey horses. Here we demonstrate the presence...

Background The Icelandic horse and Exmoor pony are ancient, native breeds, adapted to harsh environmental conditions and they have both undergone severe historic bottlenecks. However, in modern days, the selection pressures on these breeds differ substantially. The aim of this study was to assess genetic diversity in both breeds through expected (H...

The control of transcription is crucial for homeostasis in mammals. A previous selective sweep analysis of horse racing performance revealed a 19.6 kb candidate regulatory region 50 kb downstream of the Endothelin3 (EDN3) gene. Here, the region was narrowed to a 5.5 kb span of 14 SNVs, with elite and sub-elite haplotypes analyzed for association to...

Horses revolutionized human history with fast mobility¹. However, the timeline between their domestication and their widespread integration as a means of transport remains contentious2–4. Here we assemble a collection of 475 ancient horse genomes to assess the period when these animals were first reshaped by human agency in Eurasia. We find that re...

Background In domesticated animals, many important traits are complex and regulated by a large number of genes, genetic interactions, and environmental influences. The ability of Icelandic horses to perform the gait ‘pace’ is largely influenced by a single mutation in the DMRT3 gene, but genetic modifiers likely exist. The aim of this study was to...

The Greying with age phenotype involves loss of hair pigmentation whereas skin pigmentation is not reduced and a predisposition to melanoma. The causal mutation was initially reported as a duplication of a 4.6 kb intronic sequence in Syntaxin 17. The speed of greying varies considerably among Grey horses. Here we demonstrate the presence of two dif...

The Icelandic horse has captured interest in many countries largely because of its unique ability to perform five gaits, including the lateral gaits tölt and flying pace. Despite the gait versatility characterizing the breed, the ability to perform flying pace varies widely between individuals and some seem to lack the ability to pace altogether. T...

Indigenous Iranian horse breeds were evolutionarily affected by natural and artificial selection in distinct phylogeographic clades, which shaped their genomes in several unique ways. The aims of this study were to evaluate the genetic diversity and genomewide selection signatures in four indigenous Iranian horse breeds. We evaluated 169 horses fro...

The Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence...

The horse is central to many Indigenous cultures across the American Southwest and the Great Plains. However, when and how horses were first integrated into Indigenous lifeways remain contentious, with extant models derived largely from colonial records. We conducted an interdisciplinary study of an assemblage of historic archaeological horse remai...

Gene expression differences can assist in characterizing important underlying genetic mechanisms between different phenotypic traits. However, when population-dense tissues are studied, the signals from scarce populations are diluted. Therefore, appropriately choosing a sample collection method that enriches a particular type of effector cells migh...

Indigenous Iranian horse breeds were evolutionarily affected by natural and artificial selection in distinct phylogeographic clades which shaped their genomes in several unique ways. The principal aims of this study were to evaluate genetic diversity and genome-wide selection signatures in four indigenous Iranian horse breeds. We evaluated 169 hors...

A previous selective sweep analysis of horse racing performance revealed a 19.6 kb candidate region approximately 50 kb downstream of the Endothelin 3 ( EDN3 ) gene. EDN3 and other endothelin family members are associated with blood pressure regulation in humans and other species, but similar association studies in horses are lacking. We hypothesiz...

The Icelandic horse has captured interest in many countries largely because of its superior gaiting ability, especially the symmetrical four-beat ambling gait called tölt. Tölt is a very smooth and comfortable gait to ride and the ability to tölt at a wide range of speed makes the Icelandic horse an excellent riding horse for leisure and competitio...

A high-quality reference genome assembly, a biobank of diverse equine tissues from the Functional Annotation of the Animal Genome (FAANG) initiative, and incorporation of long-read sequencing technologies, have enabled efforts to build a comprehensive and tissue-specific equine transcriptome. The equine FAANG transcriptome reported here provides up...

Osteochondrosis (OC) is an important skeletal disease causing profound welfare concerns in horses. Although numerous studies have explored the genetics underlying OC in various breeds, the Belgian Warmblood (BW) remains unstudied despite having a concerning prevalence of 32.0%. As a result, this study aimed to conduct genome-wide association (GWA)...

Since the first Spanish settlers brought horses to America centuries ago, several local varieties and breeds have been established in the New World. These were generally a consequence of the admixture of the different breeds arriving from Europe. In some instances, local horses have been selectively bred for specific traits, such as appearance, end...

Abstract Background In horses, the autoimmune disease vitiligo is characterized by the loss of melanocytes and results in patchy depigmentation of the skin around the eyes, muzzle and the perianal region. Vitiligo-like depigmentation occurs predominantly in horses displaying the grey coat colour and is observed at a prevalence level of 26.0–67.0% i...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Background: The back plays a vital role in horse locomotion, where the spine functions as a spring during the stride cycle. A complex interaction between the spine and the muscles of the back contribute to locomotion soundness, gait ability, and performance of riding and racehorses. Conformation is commonly used to select horses for breeding and p...

Infrared thermography (IRT) is a popular technology used for the detection of thermal changes given its non-invasive nature and lack of direct contact with the individual. Accordingly, the maximal eye temperature (MaxET) measured with IRT has been extensively applied in equine research. However, there is little information available about the poten...

Abstract For centuries humans have been fascinated by the natural beauty of horses in motion and their different gaits. Gait classification (GC) is commonly performed through visual assessment and reliable, automated methods for real-time objective GC in horses are warranted. In this study, we used a full body network of wireless, high sampling-rat...

Domestic animal populations are often characterised by high rates of inbreeding and low effective population sizes due to selective breeding practices. These practices can result in otherwise rare recessive deleterious alleles drifting to high frequencies, resulting in reduced fertility rates. This study aimed to identify potential recessive lethal...

Equine skin diseases are common, causing increased costs and reduced welfare of affected horses.Genetic testing, if available, can complement early detection, disease diagnosis, and clinical treatment and offers horse breeders the possibility to rule out carrier status. The mechanisms of complex disease can be investigated by using the latest state...

Recessive lethal variants often segregate at low frequencies in animal populations, such that two randomly selected individuals are unlikely to carry the same mutation. However, the likelihood of an individual inheriting two copies of a recessive lethal mutation is dramatically increased by inbreeding events. Such occurrences are particularly commo...

There is a lack of research on the benefits and risks of shoeing conditions in harness racing. Our objectives were thus to: 1) investigate whether velocity times (VT; s/km) are affected by racing unshod (N=76,932 records on 5247 horses); 2) determine the potential risks of galloping, being penalized and disqualification when competing unshod (N=111...

Disorders of sex development (DSD) and reproduction are not uncommon among horses, though knowledge about their molecular causes is sparse. Here we characterized a ~200 kb homozygous deletion in chromosome 29 at 29.7–29.9 Mb. The region contains AKR1C genes which function as ketosteroid reductases in steroid hormone biosynthesis, including androgen...

The roan coat color in horses is characterized by dispersed white hair and dark points. This phenotype segregates in a broad range of horse breeds, while the underlying genetic background is still unknown. Previous studies mapped the roan locus to the KIT gene on equine chromosome 3 (ECA3). However, this association could not be validated across di...

Abstract Background Since the 1950s, the Norwegian–Swedish Coldblooded trotter (NSCT) has been intensively selected for harness racing performance. As a result, the racing performance of the NSCT has improved remarkably; however, this improved racing performance has also been accompanied by a gradual increase in inbreeding level. Inbreeding in NSCT...

Abstract Background Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds may be candidates for population-specific selection. However, CNV differentiation, selection and its...

Background Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds may be candidates for population-specific selection. However, CNV differentiation, selection and its populatio...

Background Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds may be candidates for population-specific selection. However, CNV differentiation, selection and its populatio...

Background Dynamic laryngeal collapse (DLC) associated with poll flexion is the most common disorder of the upper respiratory tract (URT) in the Norwegian‐Swedish Coldblooded Trotter (NSCT). The disorder, which has also been diagnosed in other breeds of trotters and gaited horses, appears to be related to anatomic phenotypes and only occurs during...

Background A growing demand for improved physical skills and mental attitude in modern sport horses has led to strong selection for performance in many warmblood studbooks. The aim of this study was to detect genomic regions with low diversity, and therefore potentially under selection, in Swedish Warmblood horses (SWB) by analysing high-density SN...

The Estonian Native Horse (ENH) is a medium-size pony found mainly in the western islands of Estonia and is well-adapted to the harsh northern climate and poor pastures. The ancestry of the ENH is debated, including alleged claims about direct descendance from the extinct Tarpan. Here we conducted a detailed analysis of the genetic makeup and relat...

Equine insect bite hypersensitivity (IBH) is a pruritic skin allergy caused primarily by biting midges, Culicoides spp. IBH susceptibility has polygenic inheritance and occurs at high frequencies in several horse breeds worldwide, causing increased costs and reduced welfare of affected horses. The aim of this study was to identify and validate sing...

Insect bite hypersensitivity (IBH), which is a cutaneous allergic reaction to antigens from Culicoides spp., is the most prevalent skin disorder in horses. Misdiagnosis is possible, as IBH is usually diagnosed based on clinical signs. Our study is the first to employ IgE levels against several recombinant Culicoides spp. allergens as an objective,...

The breeding goals for Icelandic horses comprise various conformation and riding ability traits. To aid the subjective conformation assessments in breeding field tests, 13 objective body measures (height, length and circumference) are recorded. Genetics has previously been shown to play a major role in conformation traits. Height at withers is the...

The process of horse domestication, followed by intensified selective breeding during the last hundreds years is associated with increased homozygosity at loci controlling valuable traits. Behavior and learning capacity likely contributed to the cognitive and social changes associated with domestication. Assuming the individual genome as a mosaic o...

Intensive artificial and natural selection have shaped substantial variation among European horse breeds. Whereas most equine selection signature studies employ divergent genetic population structures in order to derive specific inter-breed targets of selection, we screened a total of 1476 horses originating from 12 breeds for the loss of genetic d...

Background Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds may be candidates for population-specific selection. However, CNV differentiation, selection and its populatio...

Analysis of the Y chromosome is the best-established way to reconstruct paternal family history in humans. Here, we applied fine-scaled Y-chromosomal haplotyping in horses with biallelic markers and demonstrate the potential of our approach to address the ancestry of sire lines. We de novoassembled a draft reference of the male-specific region of t...

[This corrects the article DOI: 10.1371/journal.pone.0202584.].

Colombian trot and gallop horse performing Colombian trot gait. Reprinted under a CC BY license, with permission from Héctor Barriga Torres, original copyright [2018]. (MP4)

Background Horses have been strongly selected for speed, strength, and endurance-exercise traits since the onset of domestication. As a result, highly specialized horse breeds have developed with many modern horse breeds often representing closed populations with high phenotypic and genetic uniformity. However, a great deal of variation still exist...

Copy Number Variants (CNVs −gain or loss of genomic material) are a common form of genetic variation underlying phenotypic diversity across a wide range of species. It has previously been hypothesized that high frequency CNV differentiation between breeds may be linked to population-specific selection; and highly inbred populations may also accumul...

Norwegian-Swedish Coldblooded Trotters can participate in premie races as two year olds, where prize money is awarded for finishing the race within a specific time interval rather than winning. In this study, the association with premie race participation and future competitive racing success was evaluated. Analyses including all raced horses born...

Background: Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations betwe...

Background: Although harness racing is of high economic importance to the global equine industry, significant genomic resources have yet to be applied to mapping harness racing success. To identify genomic regions associated with harness racing success, the current study performs genome-wide association analyses with three racing performance trait...

The horse breeding sector has to meet the growing demand of horses for high level competitions, while guaranteeing good health standards. Knowledge of the genetic background of sport-related traits could benefit the selection process. Recent advances in genome mapping are paving the way to further explore effects of selection. Strong selective pres...

The Colombian paso horse, the most important horse breed in Colombia, performs specific and particular gaits (paso fino, trocha, and Colombian trot), which display different footfall patterns and stride frequencies. The breed has been selected for gait and conformation for more than 50 years and we hypothesize that this selection has led to kinemat...

Colombian trot and gallop horse performing Colombian trot gait. Reprinted under a CC BY license, with permission from Héctor Barriga Torres, original copyright [2018]. (MP4)

Colombian paso fino horse performing paso fino gait. Reprinted under a CC BY license, with permission from Héctor Barriga Torres, original copyright [2018]. (MP4)

Colombian trot and gallop horse performing gallop. Reprinted under a CC BY license, with permission from Héctor Barriga Torres, original copyright [2018]. (MP4)

Mean and variation for kinematic parameters by horse group and sex in a sample of Colombian paso horse breed. (DOCX)

Genetic structure analysis based on microsatellites of the Colombian paso horse sample. Inferred ancestry of individuals (Y-axis) per horse (bar columns) in the CPH groups (X-axis). 1) Colombian trot and gallop group. 2) Colombian trocha and gallop group. 3) Colombian trocha group. 4) Colombian paso fino group. (TIF)

Colombian trocha horse performing trocha gait. Reprinted under a CC BY license, with permission from Héctor Barriga Torres, original copyright [2018]. (MP4)

Background Studies of large racing populations have established clear differences in the career profile of stallions, mares and geldings. Multiple studies have also demonstrated positive effects on racing careers for horses that commence racing at a younger age. However, the applicability of these studies to small, native racing populations is unkn...