Genome-Wide Homozygosity Patterns and Evidence for Selection in a Set of European and Near Eastern Horse Breeds

Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies

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 (HE) and observed heterozygosity (HO) and effective population size (Ne). Furthermore, we aimed to identify runs of homozygosity (ROH) to estimate and compare genomic inbreeding and signatures of selection in the breeds.

RESULTS

HO was estimated at 0.34 and 0.33 in the Icelandic horse and Exmoor pony, respectively, aligning closely with HE of 0.34 for both breeds. Based on genomic data, the Ne for the last generation was calculated to be 125 individuals for Icelandic horses and 42 for Exmoor ponies. Genomic inbreeding coefficient (FROH) ranged from 0.08 to 0.20 for the Icelandic horse and 0.12 to 0.27 for the Exmoor pony, with the majority of inbreeding attributed to short ROHs in both breeds. Several ROH islands associated with performance were identified in the Icelandic horse, featuring target genes such as DMRT3, DOCK8, EDNRB, SLAIN1, and NEURL1. Shared ROH islands between both breeds were linked to metabolic processes (FOXO1), body size, and the immune system (CYRIB), while private ROH islands in Exmoor ponies were associated with coat colours (ASIP, TBX3, OCA2), immune system (LYG1, LYG2), and fertility (TEX14, SPO11, ADAM20).

CONCLUSIONS

Evaluations of genetic diversity and inbreeding reveal insights into the evolutionary trajectories of both breeds, highlighting the consequences of population bottlenecks. While the genetic diversity in the Icelandic horse is acceptable, a critically low genetic diversity was estimated for the Exmoor pony, which requires further validation. Identified signatures of selection highlight the differences in the use of the two breeds as well as their adaptive trait similarities. The results provide insight into genomic regions under selection pressure in a gaited performance horse breed and various adaptive traits in small-sized native horse breeds. This understanding contributes to preserving genetic diversity and population health in these equine populations.

Using high-density SNP data to unravel the origin of the Franches-Montagnes horse breed

BACKGROUND

The Franches-Montagnes (FM) is the last native horse breed of Switzerland, established at the end of the 19th century by cross-breeding local mares with Anglo-Norman stallions. We collected high-density SNP genotype data (Axiom™ 670 K Equine genotyping array) from 522 FM horses, including 44 old-type horses (OF), 514 European Warmblood horses (WB) from Sweden and Switzerland (including a stallion used for cross-breeding in 1990), 136 purebred Arabians (AR), 32 Shagya Arabians (SA), and 64 Thoroughbred (TB) horses, as introgressed WB stallions showed TB origin in their pedigrees. The aim of the study was to ascertain fine-scale population structures of the FM breed, including estimation of individual admixture levels and genomic inbreeding (FROH) by means of Runs of Homozygosity.

RESULTS

To assess fine-scale population structures within the FM breed, we applied a three-step approach, which combined admixture, genetic contribution, and FROH of individuals into a high-resolution network visualization. Based on this approach, we were able to demonstrate that population substructures, as detected by model-based clustering, can be either associated with a different genetic origin or with the progeny of most influential sires. Within the FM breed, admixed horses explained most of the genetic variance of the current breeding population, while OF horses only accounted for a small proportion of the variance. Furthermore, we illustrated that FM horses showed high TB admixture levels and we identified inconsistencies in the origin of FM horses descending from the Arabian stallion Doktryner. With the exception of WB, FM horses were less inbred compared to the other breeds. However, the relatively few but long ROH segments suggested diversity loss in both FM subpopulations. Genes located in FM- and OF-specific ROH islands had known functions involved in conformation and behaviour, two traits that are highly valued by breeders.

CONCLUSIONS

The FM remains the last native Swiss breed, clearly distinguishable from other historically introgressed breeds, but it suffered bottlenecks due to intensive selection of stallions, restrictive mating choices based on arbitrary definitions of pure breeding, and selection of rare coat colours. To preserve the genetic diversity of FM horses, future conservation managements strategies should involve a well-balanced selection of stallions (e.g., by integrating OF stallions in the FM breeding population) and avoid selection for rare coat colours.

Population structure and genomic diversity of the Einsiedler horse

The breeding history of the Einsiedler horse is closely connected with the Benedictine cloister Einsiedeln. In the mid-nineteenth century, it was decided to use European Warmblood stallions for cross-breeding and to abandon the selection of stallions. Since that time, it has only been possible to trace back the origin of Einsiedler horses using maternal ancestry information. Here, we collected high-density genotype data for European Warmblood horses (Selle Français, Swiss Warmblood and Einsiedler) and Franches-Montagnes horses, the last native Swiss horse breed, to unravel the current population structure of the Einsiedler horse. Using commonly applied methods to ascertain fine-scale population structures, it was not possible to clearly differentiate the Einsiedler from other European Warmblood horses. However, by means of runs of homozygosity (ROH) we were able to detect breed-specific ROH islands for the Einsiedler horse, including genes involved in domestication and adaptation to high altitude. Therefore, future breeding activities should involve the screening of these breed-specific ROH segments, the revival of cryopreserved sperm and the selection of Einsiedler stallions.

Spotting the Pattern: A Review on White Coat Color in the Domestic Horse

Traits such as shape, size, and color often influence the economic and sentimental value of a horse. Around the world, horses are bred and prized for the colors and markings that make their unique coat patterns stand out from the crowd. The underlying genetic mechanisms determining the color of a horse's coat can vary greatly in their complexity. For example, only two genetic markers are used to determine a horse's base coat color, whereas over 50 genetic variations have been discovered to cause white patterning in horses. Some of these white-causing mutations are benign and beautiful, while others have a notable impact on horse health. Negative effects range from slightly more innocuous defects, like deafness, to more pernicious defects, such as the lethal developmental defect incurred when a horse inherits two copies of the Lethal White Overo allele. In this review, we explore, in detail, the etiology of white spotting and its overall effect on the domestic horse to Spot the Pattern of these beautiful (and sometimes dangerous) white mutations.

The Genetic Diversity of Horse Native Breeds in Russia

Horses were domesticated later than other farm animals. Horse breeds have been selectively developed by humans to satisfy different needs and purposes. The factory and indigenous breeds are of particular interest, having been bred in purity for many centuries without the addition of foreign blood. Data from 31 stud farms, as well as ranches, located in fifteen regions of the Russian Federation were used in this work. DNA was sampled from 102 stallions of 11 breeds: Arabian, Akhal-Teke, Don, Orlov Trotter, Vladimir Heavy Draft, Russian Heavy Draft, Soviet Heavy Draft, Kabardin, Yakut, Tuva, and Vyatka. Data on the origin of each animal from which the material was collected were taken into account. DNA genotyping was carried out using GGP Equine 70 k ® array chips (Thermo Fisher Scientific, USA). Genetic diversity of horse breeds was estimated using Admixture 1.3. and PLINK 1.9 software. FROH inbreeding was computed via the R detectRUNS package. The minimum length for ROH was set at 1 Mb to reduce the occurrence of false positives. We conducted PCA analysis using PLINK 1.9, and used the ggplot2 library in R for visualizing the results. Indigenous equine breeds, such as Vyatka, Tuva, and Yakut, are very hardy, and well adapted to local environmental and climatic conditions. They are employed as draft power, as well as for milk and meat. Both the Akhal-Teke breed and the Arabian breed have retained a minimum effective population size over many generations. We note significant accumulations of homozygosity in these breeds. In equestrian sports, performance is a top priority. ADMIXTURE and PCA analyses showed similarities between Don equine breeds and Kabardin, as well as some Arabian breed animals. Earlier research indicated the presence of thoroughbred traits in Don stallions. The Orlov Trotter breed stands out as a separate cluster in the structural and PCA analyses. Considering the small population size of this breed, our study found high FROH in all tested animals. The general reduction in the diversity of the horse breed gene pool, due to numerous crosses for breed improvement with thoroughbreds, has lead to a decline in the differences between the top sporting breeds. Our study presents new opportunities for exploring the genetic factors that influence the formation of adaptive traits in indigenous breeds, and for finding ways to preserve genetic diversity for effective population reproduction.

Genomic inbreeding estimation, runs of homozygosity, and heterozygosity-enriched regions uncover signals of selection in the Quarter Horse racing line

With the advent of genomics, significant progress has been made in the genetic improvement of livestock species, particularly through increased accuracy in predicting breeding values for selecting superior animals and the possibility of performing a high-resolution genetic scan throughout the genome of an individual. The main objectives of this study were to estimate the individual genomic inbreeding coefficient based on runs of homozygosity (FROH ), to identify and characterize runs of homozygosity and heterozygosity (ROH and ROHet, respectively; length and distribution) throughout the genome, and to map selection signatures in relevant chromosomal regions in the Quarter Horse racing line. A total of 336 animals registered with the Brazilian Association of Quarter Horse Breeders (ABQM) were genotyped. One hundred and twelve animals were genotyped using the Equine SNP50 BeadChip (Illumina, USA), with 54,602 single nucleotide polymorphisms (SNPs; 54K). The remaining 224 samples were genotyped using the Equine SNP70 BeadChip (Illumina, USA) with 65,157 SNPs (65K). To ensure data quality, we excluded animals with a call rate below 0.9. We also excluded SNPs located on non-autosomal chromosomes, as well as those with a call rate below 0.9 or a p-value below 1 × 10-5 for Hardy-Weinberg equilibrium. The results indicate moderate to high genomic inbreeding, with 46,594 ROH and 16,101 ROHet detected. In total, 30 and 14 candidate genes overlap with ROH and ROHet regions, respectively. The ROH islands showed genes linked to crucial biological processes, such as cell differentiation (CTBP1, WNT5B, and TMEM120B), regulation of glucose metabolic process (MAEA and NKX1-1), heme transport (PGRMC2), and negative regulation of calcium ion import (VDAC1). In ROHet, the islands showed genes related to respiratory capacity (OR7D19, OR7D4G, OR7D4E, and OR7D4J) and muscle repair (EGFR and BCL9). These findings could aid in selecting animals with greater regenerative capacity and developing treatments for muscle disorders in the QH breed. This study serves as a foundation for future research on equine breeds. It can contribute to developing reproductive strategies in animal breeding programs to improve and preserve the Quarter Horse breed.

Genetic characterisation of the Connemara pony and the Warmblood horse using a within-breed clustering approach

BACKGROUND

The Connemara pony (CP) is an Irish breed that has experienced varied selection by breeders over the last fifty years, with objectives ranging from the traditional hardy pony to an agile athlete. We compared these ponies with well-studied Warmblood (WB) horses, which are also selectively bred for athletic performance but with a much larger census population. Using genome-wide single nucleotide polymorphism (SNP) and whole-genome sequencing data from 116 WB (94 UK WB and 22 European WB) and 36 CP (33 UK CP and 3 US CP), we studied the genomic diversity, inbreeding and population structure of these breeds.

RESULTS

The k-means clustering approach divided both the CP and WB populations into four genetic groups, among which the CP genetic group 1 (C1) associated with non-registered CP, C4 with US CP, WB genetic group 1 (W1) with Holsteiners, and W3 with Anglo European and British WB. Maximum and mean linkage disequilibrium (LD) varied significantly between the two breeds (mean from 0.077 to 0.130 for CP and from 0.016 to 0.370 for WB), but the rate of LD decay was generally slower in CP than WB. The LD block size distribution peaked at 225 kb for all genetic groups, with most of the LD blocks not exceeding 1 Mb. The top 0.5% harmonic mean pairwise fixation index (FST) values identified ontology terms related to cancer risk when the four CP genetic groups were compared. The four CP genetic groups were less inbred than the WB genetic groups, but C2, C3 and C4 had a lower proportion of shorter runs of homozygosity (ROH) (74 to 76% < 4 Mb) than the four WB genetic groups (80 to 85% < 4 Mb), indicating more recent inbreeding. The CP and WB genetic groups had a similar ratio of effective number of breeders (Neb) to effective population size (Ne).

CONCLUSIONS

Distinct genetic groups of individuals were revealed within each breed, and in WB these genetic groups reflected population substructure better than studbook or country of origin. Ontology terms associated with immune and inflammatory responses were identified from the signatures of selection between CP genetic groups, and while CP were less inbred than WB, the evidence pointed to a greater degree of recent inbreeding. The ratio of Neb to Ne was similar in CP and WB, indicating the influence of popular sires is similar in CP and WB.

Genome-Wide Single-Nucleotide Polymorphism-Based Genomic Diversity and Runs of Homozygosity for Selection Signatures in Equine Breeds

The horse, one of the most domesticated animals, has been used for several purposes, like transportation, hunting, in sport, or for agriculture-related works. Kathiawari, Marwari, Manipuri, Zanskari, Bhutia, Spiti, and Thoroughbred are the main breeds of horses, particularly due to their agroclimatic adaptation and role in any kind of strong physical activity, and these characteristics are majorly governed by genetic factors. The genetic diversity and phylogenetic relationship of these Indian equine breeds using microsatellite markers have been reported, but further studies exploring the SNP diversity and runs of homozygosity revealing the selection signature of breeds are still warranted. In our study, the identification of genes that play a vital role in muscle development is performed through SNP detection via the whole-genome sequencing approach. A total of 96 samples, categorized under seven breeds, and 620,721 SNPs were considered to ascertain the ROH patterns amongst all the seven breeds. Over 5444 ROH islands were mined, and the maximum number of ROHs was found to be present in Zanskari, while Thoroughbred was confined to the lowest number of ROHs. Gene enrichment of these ROH islands produced 6757 functional genes, with AGPAT1, CLEC4, and CFAP20 as important gene families. However, QTL annotation revealed that the maximum QTLs were associated with Wither's height trait ontology that falls under the growth trait in all seven breeds. An Equine SNP marker database (EqSNPDb) was developed to catalogue ROHs for all these equine breeds for the flexible and easy chromosome-wise retrieval of ROH along with the genotype details of all the SNPs. Such a study can reveal breed divergence in different climatic and ecological conditions.

The Characteristics, Distribution, Function, and Origin of Alternative Lateral Horse Gaits

This article traces the characteristics, origin, distribution, and function of alternative lateral horse gaits, i.e., intermediate speed lateral-sequence gaits. Such alternative lateral gaits (running walk, rack, broken pace, hard pace, and broken trot) are prized by equestrians today for their comfort and have been found in select horse breeds for hundreds of years and even exhibited in fossil equid trackways. After exploring the evolution and development of alternative lateral gaits via fossil equid trackways, human art, and historical writings, the functional and genetic factors that led to the genesis of these gaits are discussed. Such gaited breeds were particularly favored and spread by the Scythians, Celts, Turks, and Spaniards. Fast and low-swinging hard pacing gaits are common in several horse breeds of mountainous areas of East and North Asia; high-stepping rack and running walk gaits are often displayed in European and North and South American breeds; the broken pace is found in breeds of Central Asia, Southeast Asia, West Asia, Western North America, and Brazil in South America; and the broken trot occurs in breeds of North Asia, South Asia, the Southern United States, and Brazil in South America, inhabiting desert or marshy areas.

The Genetic Diversity of Stallions of Different Breeds in Russia

The specifics of breeding and selection significantly affect genetic diversity and variability within a breed. We present the data obtained from the genetic analysis of 21 thoroughbred and warmblood horse breeds. The most detailed information is described from the following breeds: Arabian, Trakehner, French Trotter, Standardbred, and Soviet Heavy Horse. The analysis of 509,617 SNP variants in 87 stallions from 21 populations made it possible to estimate the genetic diversity at the genome-wide level and distinguish the studied horse breeds from each other. In this study, we searched for heterozygous and homozygous ROH regions, evaluated inbreeding using FROH analysis, and generated a population structure using Admixture 1.3 software. Our findings indicate that the Arabian breed is an ancestor of many horse breeds. The study of the full-genome architectonics of breeds is of great practical importance for preserving the genetic characteristics of breeds and managing breeding. Studies were carried out to determine homozygous regions in individual breeds and search for candidate genes in these regions. Fifty-six candidate genes for the influence of selection pressure were identified. Our research reveals genetic diversity consistent with breeding directions and the breeds' history of origin.

Whole Genome Screening Procures a Holistic Hold of the Russian Chicken Gene Pool Heritage and Demographic History

A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th-19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn (WL), were used along with other breeds representing the Russian gene pool. The characteristics of the genetic diversity and phylogenetic relationships of the native breeds of chickens were represented in comparison with foreign breeds. It was established that the studied native breeds demonstrate their own genetic structure that distinguishes them from foreign breeds, and from each other. For example, we previously made an assumption on what could cause the differences between two RW populations, RW1 and RW2. From the data obtained here, it was verified that WL was additionally crossed to RW2, unlike RW1. Thus, inherently, RW1 is a purer population of this improved Russian breed. A significant contribution of the gene pool of native breeds to the global genetic diversity of chickens was shown. In general, based on the results of a multilateral survey of this sample of breeds, it can be concluded that phylogenetic relationships based on their genetic structure and variability robustly reflect the known, previously postulated and newly discovered patterns of evolution of native chickens. The results herein presented will aid selection and breeding work using this gene pool.

New genomic insights into the conformation of Lipizzan horses

Conformation traits are important selection criteria in equine breeding, as they describe the exterior aspects of the horse (height, joint angles, shape). However, the genetic architecture of conformation is not well understood, as data of these traits mainly consist of subjective evaluation scores. Here, we performed genome-wide association studies on two-dimensional shape data of Lipizzan horses. Based on this data, we identified significant quantitative trait loci (QTL) associated with cresty neck on equine chromosome (ECA)16 within the MAGI1 gene, and with type, hereby differentiating heavy from light horses on ECA5 within the POU2F1 gene. Both genes were previously described to affect growth, muscling and fatty deposits in sheep, cattle and pigs. Furthermore, we pin-pointed another suggestive QTL on ECA21, near the PTGER4 gene, associated with human ankylosing spondylitis, for shape differences in the back and pelvis (roach back vs sway back). Further differences in the shape of the back and abdomen were suggestively associated with the RYR1 gene, involved in core muscle weakness in humans. Therefore, we demonstrated that horse shape space data enhance the genomic investigations of horse conformation.

The coefficients of inbreeding revealed by ROH study among inbred individuals belonging to each type of the first cousin marriage: A preliminary report from North India

BACKGROUND

Genome-wide runs of homozygosity (ROH) are appropriate to estimate genomic inbreeding, determine population history, unravel the genetic architecture of complex traits and disorders.

OBJECTIVE

The study sought to investigate and compare the actual proportion of homozygosity or autozygosity in the genomes of progeny of four subtypes of first cousin mating in humans, using both pedigree and genomic measures for autosomes and sex chromosomes.

METHODS

For this purpose, Illumina Global Screening Array-24 v1.0 BeadChip followed by cyto-ROH analysis through Illumina Genome Studio was used to characterise the homozygosity in five participants from North Indian state (Uttar Pradesh). PLINK v.1.9 software was used to estimate the genomic inbreeding coefficients viz. ROH-based inbreeding estimate (F_ROH) and homozygous loci-based inbreeding estimate (F_HOM).

RESULTS

A total of 133 ROH segments were detected with maximum number and genomic coverage in Matrilateral Parallel (MP) type and minimum in outbred individual. ROH pattern revealed that MP type has a higher degree of homozygosity than other subtypes. The comparison of F_ROH, F_HOM, and pedigree-based inbreeding estimate (F_PED) showed some difference in theoretical and realised proportion of homozygosity for sex-chromosomal loci but not for autosome for each type of consanguinity.

CONCLUSIONS

This is the very first study to compare and estimate the pattern of homozygosity among the kindreds of first cousin unions. However, a greater number of individuals from each type of marriage is required for statistical inference of no difference between theoretical and realized homozygosity among different degrees of inbreeding prevalent in humans worldwide.

Identification of runs of homozygosity in Western honey bees (Apis mellifera) using whole-genome sequencing data

Runs of homozygosity (ROH) are continuous homozygous segments that arise through the transmission of haplotypes that are identical by descent. The length and distribution of ROH segments provide insights into the genetic diversity of populations and can be associated with selection signatures. Here, we analyzed reconstructed whole-genome queen genotypes, from a pool-seq data experiment including 265 Western honeybee colonies from Apis mellifera mellifera and Apis mellifera carnica. Integrating individual ROH patterns and admixture levels in a dynamic population network visualization allowed us to ascertain major differences between the two subspecies. Within A. m. mellifera, we identified well-defined substructures according to the genetic origin of the queens. Despite the current applied conservation efforts, we pinpointed 79 admixed queens. Genomic inbreeding (F ROH) strongly varied within and between the identified subpopulations. Conserved A. m. mellifera from Switzerland had the highest mean F ROH (3.39%), while queens originating from a conservation area in France, which were also highly admixed, showed significantly lower F ROH (0.45%). The majority of A. m. carnica queens were also highly admixed, except 12 purebred queens with a mean F ROH of 2.33%. Within the breed-specific ROH islands, we identified 14 coding genes for A. m. mellifera and five for A. m. carnica, respectively. Local adaption of A. m. mellifera could be suggested by the identification of genes involved in the response to ultraviolet light (Crh-BP, Uvop) and body size (Hex70a, Hex70b), while the A. m. carnica specific genes Cpr3 and Cpr4 are most likely associated with the lighter striping pattern, a morphological phenotype expected in this subspecies. We demonstrated that queen genotypes derived from pooled workers are useful tool to unravel the population dynamics in A. mellifera and provide fundamental information to conserve native honey bees.

Common protein-coding variants influence the racing phenotype in galloping racehorse breeds

Selection for system-wide morphological, physiological, and metabolic adaptations has led to extreme athletic phenotypes among geographically diverse horse breeds. Here, we identify genes contributing to exercise adaptation in racehorses by applying genomics approaches for racing performance, an end-point athletic phenotype. Using an integrative genomics strategy to first combine population genomics results with skeletal muscle exercise and training transcriptomic data, followed by whole-genome resequencing of Asian horses, we identify protein-coding variants in genes of interest in galloping racehorse breeds (Arabian, Mongolian and Thoroughbred). A core set of genes, G6PC2, HDAC9, KTN1, MYLK2, NTM, SLC16A1 and SYNDIG1, with central roles in muscle, metabolism, and neurobiology, are key drivers of the racing phenotype. Although racing potential is a multifactorial trait, the genomic architecture shaping the common athletic phenotype in horse populations bred for racing provides evidence for the influence of protein-coding variants in fundamental exercise-relevant genes. Variation in these genes may therefore be exploited for genetic improvement of horse populations towards specific types of racing.

Assessing Genetic Diversity and Searching for Selection Signatures by Comparison between the Indigenous Livni and Duroc Breeds in Local Livestock of the Central Region of Russia

Indigenous pig breeds are mainly associated with the adaptive capacity that is necessary to respond adequately to climate change, food security, and livelihood needs, and natural resources conservation. Livni pigs are an indigenous fat-type breed farmed in a single farm in the Orel region and located in the Central European part of the Russian Federation. To determine the genomic regions and genes that are affected by artificial selection, we conducted the comparative study of two pig breeds with different breeding histories and breeding objectives, i.e., the native fat-type Livni and meat-type Duroc breeds using the Porcine GGP HD BeadChip, which contains ~80,000 SNPs. To check the Livni pigs for possible admixture, the Landrace and the Large White breeds were included into the study of genetic diversity as these breeds participated in the formation of the Livni pigs. We observed the highest level of genetic diversity in Livni pigs compared to commercial breeds (UHE = 0.409 vs. 0.319–0.359, p < 0.001; AR = 1.995 vs. 1.894–1.964, p < 0.001). A slight excess of heterozygotes was found in all of the breeds. We identified 291 candidate genes, which were localized within the regions under putative selection, including 22 and 228 genes, which were specific for Livni and Duroc breeds, respectively, and 41 genes common for both breeds. A detailed analysis of the molecular functions identified the genes, which were related to the formation of meat and fat traits, and adaptation to environmental stress, including extreme temperatures, which were different between breeds. Our research results are useful for conservation and sustainable breeding of Livni breed, which shows a high level of genetic diversity. This makes Livni one of the valuable national pig genetic resources.

Whole-genome sequence analysis reveals selection signatures for important economic traits in Xiang pigs

Xiang pig (XP) is one of the best-known indigenous pig breeds in China, which is characterized by its small body size, strong disease resistance, high adaptability, favorite meat quality, small litter sizes, and early sexual maturity. However, the genomic evidence that links these unique traits of XP is still poorly understood. To identify the genomic signatures of selection in XP, we performed whole-genome resequencing on 25 unrelated individual XPs. We obtained 876.70 Gb of raw data from the genomic libraries. The LD analysis showed that the lowest level of linkage disequilibrium was observed in Xiang pig. Comparative genomic analysis between XPs and other breeds including Tibetan, Meishan, Duroc and Landrace revealed 3062, 1228, 907 and 1519 selected regions, respectively. The genes identified in selected regions of XPs were associated with growth and development processes (IGF1R, PROP1, TBX19, STAC3, RLF, SELENOM, MSTN), immunity and disease resistance (ZCCHC2, SERPINB2, ADGRE5, CYP7B1, STAT6, IL2, CD80, RHBDD3, PIK3IP1), environmental adaptation (NR2E1, SERPINB8, SERPINB10, SLC26A7, MYO1A, SDR9C7, UVSSA, EXPH5, VEGFC, PDE1A), reproduction (CCNB2, TRPM6, EYA3, CYP7B1, LIMK2, RSPO1, ADAM32, SPAG16), meat quality traits (DECR1, EWSR1), and early sexual maturity (TAC3). Through the absolute allele frequency difference (ΔAF) analysis, we explored two population-specific missense mutations occurred in NR6A1 and LTBP2 genes, which well explained that the vertebrae numbers of Xiang pigs were less than that of the European pig breeds. Our results indicated that Xiang pigs were less affected by artificial selection than the European and Meishan pig breeds. The selected candidate genes were mainly involved in growth and development, disease resistance, reproduction, meat quality, and early sexual maturity. This study provided a list of functional candidate genes, as well as a number of genetic variants, which would provide insight into the molecular basis for the unique traits of Xiang pig.

Genome-wide survey on three local horse populations with a focus on runs of homozygosity pattern

Purosangue Orientale Siciliano, Sanfratellano and Siciliano represent the Sicilian equine genetic resource. This study aimed to investigate the genetic diversity, population structure and the pattern of autozygosity of Sicilian horse populations using genome‐wide single‐nucleotide polymorphism (SNP) data generated with the Illumina Equine SNP70 array. The genotyping data of 17 European and Middle East populations were also included in the study. The patterns of genetic differentiation, model‐based clustering and Neighbour‐Net showed the expected positioning of Sicilian populations within the wide analysed framework and the close connections between the Purosangue Orientale Siciliano and the Arab as well as between Sanfratellano, Siciliano and Maremmano. The highest expected heterozygosity (H_e) and contemporary effective population size (cNe) were reported in Siciliano (H_e = 0.323, cNe = 397), and the lowest were reported in Purosangue Orientale Siciliano (H_e = 0.277, cNe = 10). The analysis of the runs of homozygosity and the relative derived inbreeding revealed high internal homogeneity in Purosangue Orientale Siciliano and Arab horses, intermediate values in Maremmano and Sanfratellano and high heterogeneity in the Siciliano population. The genome‐wide SNP analysis showed the selective pressure on Purosangue Orientale Siciliano towards traits related to endurance performance. Our results underline the importance of planning adequate conservation and exploitation programmes to reduce the level of inbreeding and, therefore, the loss of genetic diversity.

Whole-genome sequencing reveals the artificial selection and local environmental adaptability of pigeons (Columba livia)

To meet human needs, domestic pigeons (Columba livia) with various phenotypes have been bred to provide genetic material for our research on artificial selection and local environmental adaptation. Seven pigeon breeds were resequenced and can be divided into commercial varieties (Euro-pigeon, Shiqi, Shen King, Taishen, and Silver King), ornamental varieties (High Fliers), and local varieties (Tarim pigeon). Phylogenetic analysis based on population resequencing showed that one group contained local breeds and ornamental pigeons from China, whereas all commercial varieties were clustered together. It is revealed that the traditional Chinese ornamental pigeon is a branch of Tarim pigeon. Runs of homozygosity (ROH) and linkage disequilibrium (LD) analyses revealed significant differences in the genetic diversity of the three types of pigeons. Genome sweep analysis revealed that the selected genes of commercial breeds were related to body size, reproduction, and plumage color. The genomic imprinting genes left by the ornamental pigeon breeds were mostly related to special human facial features and muscular dystrophy. The Tarim pigeon has evolved genes related to chemical ion transport, photoreceptors, oxidative stress, organ development, and olfaction in order to adapt to local environmental stress. This research provides a molecular basis for pigeon genetic resource evaluation and genetic improvement and suggests that the understanding of adaptive evolution should integrate the effects of various natural environmental characteristics.

DPF3, A Putative Candidate Gene For Melanoma Etiopathogenesis in Gray Horses

Melanoma prevalence in gray horses reaches up to 50% and more. Several studies have documented a genetic melanoma predisposition which is referred to the 4.6 kb duplication in intron 6 of STX17 and its surrounding haplotype. However, the genetic background and mechanisms responsible for differences in etiopathogenesis of equine dermal melanomatosis still remain unknown. In the current study, we performed a genome wide association analysis in 141 Lipizzan horses and subsequently identified one candidate gene on chromosome 24 putatively involved in melanoma pathogenesis in gray horses. The associated SNP was located in the intronic region of DPF3, a gene which is involved in humans in cell growth, proliferation, apoptosis and motility of cancer cells. The replication study in 1210 horses from seven breeds demonstrated, that the G/G genotype of the DPF3 associated SNP exhibits putative melanoma suppression effects. As a conclusion DPF3 represents a candidate gene, which might play an essential role for gray horses coping with high genetic melanoma related tumor load.

Runs of homozygosity analysis reveals population characteristics of yellow-feathered chickens using re-sequencing data

1. To evaluate the inbreeding of yellow-feathered chickens (YFCs) and identify genes related to their unique characteristics, whole-genome re-sequencing data were applied to detect runs of homozygosity (ROH) in the genomes of ten YFC breeds. The number, length, distribution of ROH, and inbreeding coefficient in different YFC populations were calculated. Genomic regions with high frequency in ROH were annotated.2. In total, 25,547 ROH with an average length of 335 kb were detected, with most being <1 Mb. The domination of short ROH reflected the long breeding history of this chicken. The number, length, frequency, and distribution of ROH varied among chicken populations, and high genetic diversity was maintained.3. Numerous genes related to YFC characteristics were identified in the high-frequency ROH regions. Among these, IFNA, IFNB, IL11RA, IL22RA1, IFNLR1, and TRIF genes were involved in disease resistance. The AMY, G6PC, SDHB, GCNT4, and ACO genes were associated with energy material metabolism; and FABPL, AQP7, ACAA2, and RYR2 were related to meat quality and flavour. The KITLG, CREB3, RYR2, and LGR4 genes, related to pigmentation, were detected.4. This ROH-based inbreeding evaluation laid the foundation for breeding and conservation of YFC populations, and the candidate genes identified can be used for marker-assisted selection.

Equine vitiligo-like depigmentation in grey horses is related to genes involved in immune response and tumor metastasis

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% in grey horses compared with only 0.8–3.5% in non-grey horses. While the polygenetic background of this complex disease is well documented in humans, the underlying candidate genes for this skin disorder in horses remain unknown. In this study we aim to perform a genome-wide association study (GWAS) for identifying putative candidate loci for vitiligo-like depigmentation in horses.

Methods

In the current study, we performed a GWAS analysis using high-density 670 k single nucleotide polymorphism (SNP) data from 152 Lipizzan and 104 Noriker horses, which were phenotyped for vitiligo-like depigmentation by visual inspection. After quality control 376,219 SNPs remained for analyses, the genome-wide Bonferroni corrected significance level was p < 1.33e-7.

Results

We identified seven candidate genes on four chromosomes (ECA1, ECA13, ECA17, ECA20) putatively involved in vitiligo pathogenesis in grey horses. The highlighted genes PHF11, SETDB2, CARHSP1 and LITAFD, are associated with the innate immune system, while the genes RCBTB1, LITAFD, NUBPL, PTP4A1, play a role in tumor suppression and metastasis. The antagonistic pathogenesis of vitiligo in relation to cancer specific enhanced cell motility and/or metastasis on typical melanoma predilection sites underlines a plausible involvement of RCBTB1, LITAFD, NUBPL, and PTP4A1.

Conclusions

The proposed candidate genes for equine vitiligo-like depigmentation, indicate an antagonistic relation between vitiligo and tumor metastasis in a horse population with higher incidence of melanoma. Further replication and expression studies should lead to a better understanding of this skin disorder in horses.

Genome-wide scans for signatures of selection in Mangalarga Marchador horses using high-throughput SNP genotyping

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.

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by F_ST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding.

Genotyping and Whole-Genome Resequencing of Welsh Sheep Breeds Reveal Candidate Genes and Variants for Adaptation to Local Environment and Socioeconomic Traits

Background

Advances in genetic tools applied to livestock breeding has prompted research into the previously neglected breeds adapted to harsh local environments. One such group is the Welsh mountain sheep breeds, which can be farmed at altitudes of 300 m above sea level but are considered to have a low productive value because of their poor wool quality and small carcass size. This is contrary to the lowland breeds which are more suited to wool and meat production qualities, but do not fare well on upland pasture. Herein, medium-density genotyping data from 317 individuals representing 15 Welsh sheep breeds were used alongside the whole-genome resequencing data of 14 breeds from the same set to scan for the signatures of selection and candidate genetic variants using haplotype- and SNP-based approaches.

Results

Haplotype-based selection scan performed on the genotyping data pointed to a strong selection in the regions of GBA3, PPARGC1A, APOB, and PPP1R16B genes in the upland breeds, and RNF24, PANK2, and MUC15 in the lowland breeds. SNP-based selection scan performed on the resequencing data pointed to the missense mutations under putative selection relating to a local adaptation in the upland breeds with functions such as angiogenesis (VASH1), anti-oxidation (RWDD1), cell stress (HSPA5), membrane transport (ABCA13 and SLC22A7), and insulin signaling (PTPN1 and GIGFY1). By contrast, genes containing candidate missense mutations in the lowland breeds are related to cell cycle (CDK5RAP2), cell adhesion (CDHR3), and coat color (MC1R).

Conclusion

We found new variants in genes with potentially functional consequences to the adaptation of local sheep to their environments in Wales. Knowledge of these variations is important for improving the adaptative qualities of UK and world sheep breeds through a marker-assisted selection.

The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events

Background

Water buffalo is one of the most important livestock species in the world. Two types of water buffalo exist: river buffalo (Bubalus bubalis bubalis) and swamp buffalo (Bubalus bubalis carabanensis). The buffalo genome has been recently sequenced, and thus a new 90 K single nucleotide polymorphism (SNP) bead chip has been developed. In this study, we investigated the genomic population structure and the level of inbreeding of 185 river and 153 swamp buffaloes using runs of homozygosity (ROH). Analyses were carried out jointly and separately for the two buffalo types.

Results

The SNP bead chip detected in swamp about one-third of the SNPs identified in the river type. In total, 18,116 ROH were detected in the combined data set (17,784 SNPs), and 16,251 of these were unique. ROH were present in both buffalo types mostly detected (~ 59%) in swamp buffalo. The number of ROH per animal was larger and genomic inbreeding was higher in swamp than river buffalo. In the separated datasets (46,891 and 17,690 SNPs for river and swamp type, respectively), 19,760 and 10,581 ROH were found in river and swamp, respectively. The genes that map to the ROH islands are associated with the adaptation to the environment, fitness traits and reproduction.

Conclusions

Analysis of ROH features in the genome of the two water buffalo types allowed their genomic characterization and highlighted differences between buffalo types and between breeds. A large ROH island on chromosome 2 was shared between river and swamp buffaloes and contained genes that are involved in environmental adaptation and reproduction.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00616-3.

Homozygosity Mapping Reveals Population History and Trait Architecture in Self-Incompatible Pear (Pyrus spp.)

Runs of homozygosity (ROH) have been widely used to study population history and trait architecture in humans and livestock species, but their application in self-incompatible plants has not been reported. The distributions of ROH in 199 accessions representing Asian pears (45), European pears (109), and interspecific hybrids (45) were investigated using genotyping-by-sequencing in this study. Fruit phenotypes including fruit weight, firmness, Brix, titratable acidity, and flavor volatiles were measured for genotype-phenotype analyses. The average number of ROH and the average total genomic length of ROH were 6 and 11 Mb, respectively, in Asian accessions, and 13 and 30 Mb, respectively, in European accessions. Significant associations between genomic inbreeding coefficients (F_ROH) and phenotypes were observed for 23 out of 32 traits analyzed. An overlap between ROH islands and significant markers from genome-wide association analyses was observed. Previously published quantitative trait loci for fruit traits and disease resistances also overlapped with some of the ROH islands. A prominent ROH island at the bottom of linkage group 17 overlapped with a recombination-supressed genomic region harboring the self-incompatibility locus. The observed ROH patterns suggested that systematic breeding of European pears would have started earlier than of Asian pears. Our research suggest that F_ROH would serve as a novel tool for managing inbreeding in gene-banks of self-incompatible plant species. ROH mapping provides a complementary strategy to unravel the genetic architecture of complex traits, and to evaluate differential selection in outbred plants. This seminal work would provide foundation for the ROH research in self-incompatible plants.

Genomics and the Evolutionary History of Equids

The equid family contains only one single extant genus, Equus, including seven living species grouped into horses on the one hand and zebras and asses on the other. In contrast, the equine fossil record shows that an extraordinarily richer diversity existed in the past and provides multiple examples of a highly dynamic evolution punctuated by several waves of explosive radiations and extinctions, cross-continental migrations, and local adaptations. In recent years, genomic technologies have provided new analytical solutions that have enhanced our understanding of equine evolution, including the species radiation within Equus; the extinction dynamics of several lineages; and the domestication history of two individual species, the horse and the donkey. Here, we provide an overview of these recent developments and suggest areas for further research.

Equine Genotyping Arrays

High-quality genomic tools have been integral in understanding genomic architecture and function in the modern-day horse. The equine genetics community has a long tradition of pooling resources to develop genomic tools. Since the equine genome was sequenced in 2006, several iterations of high throughput genotyping arrays have been developed and released, enabling rapid and cost-effective genotyping. This review highlights the design considerations of each iteration, focusing on data available during development and outlining considerations in selecting the genetic variants included on each array. Additionally, we outline recent applications of equine genotyping arrays as well as future prospects and applications.

Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data

Simple Summary

The Bardigiano horse is a native Italian breed bred for living in rural areas, traditionally used in agriculture. The breed counts about 3000 horses, and it is nowadays mainly used for recreational purposes. The relatively small size and the closed status of the breed raise the issue of monitoring genetic diversity. We therefore characterized the breed’s genetic diversity based on molecular data. We showed a critical reduction of genetic variability mainly driven by past bottlenecks. We also highlighted homozygous genomic regions that might be the outcome of directional selection in recent years, in line with the conversion of Bardigiano horses from agricultural to riding purposes.

Abstract

Horses are nowadays mainly used for sport and leisure activities, and several local breeds, traditionally used in agriculture, have been exposed to a dramatic loss in population size and genetic diversity. The loss of genetic diversity negatively impacts individual fitness and reduces the potential long-term survivability of a breed. Recent advances in molecular biology and bioinformatics have allowed researchers to explore biodiversity one step further. This study aimed to evaluate the loss of genetic variability and identify genomic regions under selection pressure in the Bardigiano breed based on GGP Equine70k SNP data. The effective population size based on Linkage Disequilibrium (N_e) was equal to 39 horses, and it showed a decline over time. The average inbreeding based on runs of homozygosity (ROH) was equal to 0.17 (SD = 0.03). The majority of the ROH were relatively short (91% were ≤2 Mbp long), highlighting the occurrence of older inbreeding, rather than a more recent occurrence. A total of eight ROH islands, shared among more than 70% of the Bardigiano horses, were found. Four of them mapped to known quantitative trait loci related to morphological traits (e.g., body size and coat color) and disease susceptibility. This study provided the first genome-wide scan of genetic diversity and selection signatures in an Italian native horse breed.

A Genome-Wide Association Analysis in Noriker Horses Identifies a SNP Associated With Roan Coat Color

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 different horse breeds. Performing a genome-wide association analysis (GWAS) in Noriker horses, we identified a single nucleotide polymorphism (SNP) (ECA3:g.79,543.439 A > G) in the intron 17 of the KIT gene. The G -allele of the top associated SNP was present in other roan horses, namely Quarter Horse, Murgese, Slovenian, and Belgian draught horse, while it was absent in a panel of 15 breeds, including 657 non-roan horses. In further 379 gray Lipizzan horses, eight animals exhibited a heterozygous genotype (A/G). Comparative whole-genome sequence analysis of the KIT region revealed two deletions in the downstream region (ECA3:79,533,217_79,533,224delTCGTCTTC; ECA3:79,533,282_79,533,285delTTCT) and a 3 bp deletion combined with 17 bp insertion in intron 20 of KIT (ECA3:79,588,128_79,588,130delinsTTATCTCTATAGTAGTT). Within the Noriker sample, these loci were in complete linkage disequilibrium (LD) with the identified top SNP. Based upon pedigree information and historical records, we were able to trace back the genetic origin of roan coat color to a baroque gene pool. Furthermore, our data suggest allelic heterogeneity and the existence of additional roan alleles in ponies and breeds related to the English Thoroughbred. In order to study the roan phenotype segregating in those breeds, further association and verification studies are required.

HMGA Genes and Proteins in Development and Evolution

HMGA (high mobility group A) (HMGA1 and HMGA2) are small non-histone proteins that can bind DNA and modify chromatin state, thus modulating the accessibility of regulatory factors to the DNA and contributing to the overall panorama of gene expression tuning. In general, they are abundantly expressed during embryogenesis, but are downregulated in the adult differentiated tissues. In the present review, we summarize some aspects of their role during development, also dealing with relevant studies that have shed light on their functioning in cell biology and with emerging possible involvement of HMGA1 and HMGA2 in evolutionary biology.

Signatures of selection in the genome of Swedish warmblood horses selected for sport performance

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 SNP data. To investigate if such signatures could be the result of selection for equestrian sport performance, we compared our SWB SNP data with those from Exmoor ponies, a horse breed not selected for sport performance traits.

Results

The genomic scan for homozygous regions identified long runs of homozygosity (ROH) shared by more than 85% of the genotyped SWB individuals. Such ROH were located on ECA4, ECA6, ECA7, ECA10 and ECA17. Long ROH were instead distributed evenly across the genome of Exmoor ponies in 77% of the chromosomes. Two population differentiation tests (F_ST and XP-EHH) revealed signatures of selection on ECA1, ECA4, and ECA6 in SWB horses.

Conclusions

Genes related to behaviour, physical abilities and fertility, appear to be targets of selection in the SWB breed. This study provides a genome-wide map of selection signatures in SWB horses, and ground for further functional studies to unravel the biological mechanisms behind complex traits in horses.