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Among horses selected for speed, the racing line of Quarter Horses is characterized by high performance in sprint races, with these animals being considered the fastest horses in the world. However, few studies have investigated in more detail the polymorphisms and genes that act on this trait. The objective of this study was to analyze exomes and UTRs in regions previously associated with this trait by GWAS in Quarter Horse racehorses with contrasting maximum speed index (SImax), prospecting causal gene polymorphisms that are related to or are in strong linkage disequilibrium with racing performance. Genotypic and phenotypic records from 360 animals of the racing line of Quarter Horses, previously genotyped with an SNP chip to obtain individual genomic estimated breeding values for performance, were used for the formation and sequencing of two groups of animals with contrasting racing performance (20 animals with superior SImax and 20 with inferior SImax). Two rapid runs were performed using two pools of libraries containing 20 and 19 samples randomly chosen among the 40 samples with contrasting SIs. A total of 1203 variants (1105 SNPs and 93 InDels) were identified in 33 regions of interest obtained previously by GWAS. Twenty-nine of the polymorphisms (24 SNPs and 5 InDels) were considered to be important based on three different and independent approaches: SIFT scores classified as deleterious (< 0.05), degree of impact on the consensus region of each polymorphism, and different allele frequencies identified by Fisher's exact test (p < 0.01) between the groups of horses with contrasting SImax. Thus, eight genes described as functional and positional candidates in previous studies (ABCG5, COL11A1, GEN1, SOCS3, MICAL1, SPTBN1, EPB41L3, and SHQ1) and nine new candidate genes (AKNA, ARMC2, FKBP15, LHX1, NOL10, TMEM192, ZFP37, FIG4, and HNRNPU), some of them with known function, were related to racing performance in Quarter Horses.

Background: The detection of signatures of selection in genomic regions provides insights into the evolutionary process, enabling discoveries regarding complex phenotypic traits. In this research, we focused on identifying genomic regions affected by different selection pressures, mainly highlighting the recent positive selection, as well as understanding the candidate genes and functional pathways associated with the signatures of selection in the Mangalarga Marchador genome. Besides, we seek to direct the discussion about genes and traits of importance in this breed, especially traits related to the type and quality of gait, temperament, conformation, and locomotor system. Results: Three different methods were used to search for signals of selection: Tajima's D (TD), the integrated haplotype score (iHS), and runs of homozygosity (ROH). The samples were composed of males (n = 62) and females (n = 130) that were initially chosen considering well-defined phenotypes for gait: picada (n = 86) and batida (n = 106). All horses were genotyped using a 670 k Axiom® Equine Genotyping Array​ (Axiom MNEC670). In total, 27, 104 (chosen), and 38 candidate genes were observed within the signatures of selection identified in TD, iHS, and ROH analyses, respectively. The genes are acting in essential biological processes. The enrichment analysis highlighted the following functions: anterior/posterior pattern for the set of genes (GLI3, HOXC9, HOXC6, HOXC5, HOXC4, HOXC13, HOXC11, and HOXC10); limb morphogenesis, skeletal system, proximal/distal pattern formation, JUN kinase activity (CCL19 and MAP3K6); and muscle stretch response (MAPK14). Other candidate genes were associated with energy metabolism, bronchodilator response, NADH regeneration, reproduction, keratinization, and the immunological system. Conclusions: Our findings revealed evidence of signatures of selection in the MM breed that encompass genes acting on athletic performance, limb development, and energy to muscle activity, with the particular involvement of the HOX family genes. The genome of MM is marked by recent positive selection. However, Tajima's D and iHS results point also to the presence of balancing selection in specific regions of the genome. [ABSTRACT FROM AUTHOR]

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Simple Summary: Whorls have been used to indicate the temperaments of domestic animals; however, little is known about the biological events that drive this association. The present study is the first that aims to find the main genomic regions that influence the whorl traits in livestock, with horses as a model. Genes related to hair follicle growth were found. Interestingly, some of these genes also influence psychiatric diseases and neurological disorders, thus evidencing a consistent biological explanation for the association. The position and number of hair whorls have been associated with the behavior, temperament, and laterality of horses. The easy observation of whorls assists in the prediction of reactivity, and thus permits the development of better measures of handling, training, mounting, and riding horses. However, little is known about the genetics involved in the formation of hair whorls. Therefore, the aim of this study was to perform a genome-wide association analysis to identify chromosome regions and candidate genes associated with hair whorl traits. Data from 342 Quarter Horses genotyped for approximately 53,000 SNPs were used in an association study using a single-step procedure. The following traits were analyzed: vertical position of hair whorl on the head, number of whorls on the head, and number of whorls on the left and right sides of the neck. The traits had between one and three genomic windows associated. Each of them explained at least 4% of the additive variance. The windows accounted for 20–80% of additive variance for each trait analyzed. Many of the prospected genes are related to hair follicle growth. Some of these genes exert a pleiotropic effect on neurological and behavioral traits. This is the first indication of biological and physiological activity that might explain the association of hair whorls and temperament. [ABSTRACT FROM AUTHOR]

• Mangalarga Marchador gaited horses raised in Brazil of marcha batida and marcha picada belong to the same population; • This fact that should be taken into consideration in genetic population studies of the breed; • There are marked LD decay at short distances in the genome and the effective size; • There are population substructures more related to important sires of the breed rather than to the type of gait. The Mangalarga Marchador is the Brazilian saddle horse. It has two characteristic gaits, marcha batida and marcha picada, that provide greater comfort to the rider during cavalcade and work. This horse breed is mainly used for work on beef cattle farms and different modalities of equestrian sports. The objective of this study was to characterize the linkage disequilibrium (LD), calculated by r², of Brazilian Mangalarga Marchador horses raised in Brazil using large-scale SNP genotyping. We also investigated the effective size (Ne) of the population, as well as its structure and relationships. A total of 240 Mangalarga Marchador horses of both sexes, registered with the Brazilian breeders association (ABCCMM), were used. The number of informative SNPs was 377,308. Principal component analysis showed that Mangalarga Marchador horses of the two different gait types belong to the same population, i.e., these groups did not segregate significantly within the breed. This finding should be taken into consideration in genetic population studies. The estimated genomic r² was 0.096 ± 0.166. The LD declined considerably at distances greater than 15 and 20 kb, with values lower than 0.3 and 0.2, respectively. The current Ne was 99 animals. There was a marked reduction in this parameter when the estimated Ne of 16 generations ago was considered, which was 650 animals. These results may be linked to a broad and partially open genetic base and to increasing selection pressures in the breed. Finally, we observed defined population substructures that were more related to the breed's important sires rather than to the type of gait. [ABSTRACT FROM AUTHOR]

• Bayesian threshold models are feasible for genetic analysis of gait type. • Gait type is the most relevant trait for Mangalarga Marchador breeding. • Simplest models outperformed the other ones in terms of prediction ability. Mangalarga Marchador (MM) is a very important Brazilian gaited horse breed. These animals show two gait types, differing in proportion of lateral or diagonal movements. Thus, it is possible to consider the gait type as a binary categorical trait in our statistical models. Threshold models (TM) are strongly recommended to handle binary traits for genetic evaluation purposes. However, TM are susceptible to the extreme categorical problem (ECP). ECP is usually observed due to the absence of variation within subclasses for a given systematic effect and can be avoided after handling this effect as random or by combining different systematic effects in the model. In this context, we aimed to find the most suitable systematic effect (based on goodness-of-fit and predictive ability) to be included in Bayesian threshold model for the genetic evaluation of gait type in MM horses. The dataset consisted of 1,231 gait type records and 3,172 animals in the pedigree file. Phenotypic record associated with gait type was treated as a categorical trait (MP = 0 and MB = 1). In summary, models with small complexity were benefited by smaller bias and average prediction errors. Additionally, these models showed higher heritability estimates. ECP was an important issue, and should always be approached when using threshold models for genetic evaluation. [ABSTRACT FROM AUTHOR]

• Gait determination is associated with metabolism changes in MM horses. • Perception of sternal stimuli is related to the type of gait. • Large-effects markers can assist selection to gait type. • This study presents a basis to justify genotyping and phenotyping for new studies. The ECA23:22999655C>A DMRT3 variant has been described as a causative region for the four-beat gait in horses, however it remains uncertain for the two distinct gait types observed in the Brazilian Mangalarga Marchador (MM) breed. This study aimed to perform a single-step GWAS, prospecting the genetic architecture of the marcha batida (MB) and marcha picada (MP) in MM horses. Phenotypic records from 1,230 animals in a pedigree file containing 3172 individuals were considered in the current analysis. A total of 192 (86 MB and 106 MP) horses were genotyped with the 670 k equine genotyping array (Thermo Fisher Scientific), and 48 horses were imputed from 65k (Illumina) to 670k. The GWAS was conducted in a Bayesian approach. For the estimation of SNP effects, three iterations were performed. The position from SNPs that explained more than 1% of the additive genetic variance were used to prospect genomic regions in windows of 250 kb. From the 69 identified genes, 39 were not annotated in horses and were blasted against the NCBI database. The enrichment analysis revealed that eight metabolic pathways might be involved with the gait type since most were related to the metabolism of amino acid, energy, and immune system. The found genes were associated with differences in the energetic metabolism between animals from the marcha batida or marcha picada groups, as well as with metabolic changes after gait exercise. [ABSTRACT FROM AUTHOR]