Genome-Wide Scans Reveal a Quantitative Trait Locus for Withers Height in Horses Near the ANKRD1 Gene

Genomic analyses of withers height and linear conformation traits in German Warmblood horses using imputed sequence-level genotypes

BACKGROUND

Body conformation, including withers height, is a major selection criterion in horse breeding and is associated with other important traits, such as health and performance. However, little is known about the genomic background of equine conformation. Therefore, the aim of this study was to use imputed sequence-level genotypes from up to 4891 German Warmblood horses to identify genomic regions associated with withers height and linear conformation traits. Furthermore, the traits were genetically characterised and putative causal variants for withers height were detected.

RESULTS

A genome-wide association study (GWAS) for withers height confirmed the presence of a previously known quantitative trait locus (QTL) on Equus caballus (ECA) chromosome 3 close to the LCORL/NCAPG locus, which explained 16% of the phenotypic variance for withers height. An additional significant association signal was detected on ECA1. Further investigations of the region on ECA3 identified a few promising candidate causal variants for withers height, including a nonsense mutation in the coding sequence of the LCORL gene. The estimated heritability for withers height was 0.53 and ranged from 0 to 0.34 for the conformation traits. GWAS identified significantly associated variants for more than half of the investigated conformation traits, among which 13 showed a peak on ECA3 in the same region as withers height. Genetic parameter estimation revealed high genetic correlations between these traits and withers height for the QTL on ECA3.

CONCLUSIONS

The use of imputed sequence-level genotypes from a large study cohort led to the discovery of novel QTL associated with conformation traits in German Warmblood horses. The results indicate the high relevance of the QTL on ECA3 for various conformation traits, including withers height, and contribute to deciphering causal mutations for body size in horses.

A Genome-Wide Association Study of the Chest Circumference Trait in Xinjiang Donkeys Based on Whole-Genome Sequencing Technology

Animal genotyping by means of genome-wide association studies is important for connecting phenotypes of interest with their underlying genetics in livestock. However, the use of whole genome sequencing to investigate chest circumference (CC) in donkeys has rarely been reported. We aimed to use the genome-wide association study approach to detect significant single nucleotide polymorphisms (SNPs) and key genes associated with chest circumference traits in Xinjiang donkeys. We assessed 112 Xinjiang donkeys in this study. The chest circumference of each was measured 2 h before milking. We re-sequenced blood samples from the Xinjiang donkeys, and genome-wide association study analyses were performed using a mixed model with the PLINK, GEMMA, and REGENIE programs. We tested 38 donkeys for candidate SNPs for genome-wide association study using three software programs. Additionally, 18 SNP markers reached genome-wide significance (p < 1.61 × 10^-9). On the basis of these, 41 genes were identified. Previously proposed candidate genes for CC traits were supported by this study, including NFATC2 (Nuclear Factor of Activated T Cells 2), PROP1 (PROP Paired-Like Homeobox 1), UBB (Ubiquitin B), and HAND2 (Heart and Neural Crest Derivatives Expressed 2). These promising candidates provide a valuable resource for validating potential meat production genes and will facilitate the development of high-yielding Xinjiang donkey breeds through marker-assisted selection or gene editing.

Fine-tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse

BACKGROUND

Estimating inbreeding, which is omnipresent and inevitable in livestock populations, is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding. Inbreeding coefficients have been historically estimated by using pedigree information; however, over the last decade, genome-base inbreeding coefficients have come to the forefront in this field. The Pura Raza Española (PRE) horse is an autochthonous Spanish horse breed which has been recognised since 1912. The total PRE population (344,718 horses) was used to estimate Classical (F), Ballou's ancestral, Kalinowski's ancestral, Kalinowski's new and the ancestral history coefficient values. In addition, genotypic data from a selected population of 805 PRE individuals was used to determine the individual inbreeding coefficient using SNP-by-SNP-based techniques (methods of moments -F_HOM-, the diagonal elements of the genomic -F_G-, and hybrid matrixes -F_H-) and ROH measures (F_RZ). The analyse of both pedigree and genomic based inbreeding coefficients in a large and robust population such as the PRE horse, with proven parenteral information for the last 40 years and a high degree of completeness (over 90% for the last 70 years) will allow us to understand PRE genetic variability better and the correlations between the estimations will give the data greater reliability.

RESULTS

The mean values of the pedigree-based inbreeding coefficients ranged from 0.01 (F for the last 3 generations -F3-) to 0.44 (ancestral history coefficient) and the mean values of genomic-based inbreeding coefficients varied from 0.05 (F_RZ for three generations, F_H and F_HOM) to 0.11 (F_RZ for nine generations). Significant correlations were also found between pedigree and genomic inbreeding values, which ranged between 0.58 (F3 with F_HOM) and 0.79 (F with F_RZ). In addition, the correlations between F_RZ estimated for the last 20 generations and the pedigree-based inbreeding highlight the fact that fewer generations of genomic data are required when comparing total inbreeding values, and the opposite when ancient values are calculated.

CONCLUSIONS

Ultimately, our results show that it is still useful to work with a deep and reliable pedigree in pedigree-based genetic studies with very large effective population sizes. Obtaining a satisfactory parameter will always be desirable, but the approximation obtained with a robust pedigree will allow us to work more efficiently and economically than with massive genotyping.

A genome-wide association study of mare fertility in the Pura Raza Español horse

Despite the economic importance of fertility for the horse industry, few efforts have been made to achieve a better understanding of the genetic mechanisms underlying its control. This is probably due to the difficulty of obtaining reliable phenotypes and the complexity of modelling the environmental and management factors. This work is novel in that we propose to use reproductive efficiency (RE) as an indicator of mare fertility. To achieve this, we performed a genome-wide association study in the Pura Raza Español horse aimed at identifying genomic variants, regions, and candidate genes associated with fertility in mares. The dataset included 819 animals genotyped with the Affymetrix Axiom™ Equine 670 K single-nucleotide polymorphisms (SNPs) Genotyping Array and the deregressed breeding values for RE trait, obtained using a ssBLUP model, employed as pseudo-phenotypic data. Our results showed 28 SNPs potentially associated with RE, which explained 87.19% of the genetic variance and 6.61% of the phenotypic variance. Those results were further validated in BayesB, showing a correlation between observed and predicted RE of 0.57. In addition, 15 candidate genes (HTRA3, SPIRE1, APOE, ERCC1, FOXA3, NECTIN-2, KLC3, RSPH6A, PDPK1, MEIOB, PAQR4, NM3, PKD1, PRSS21, IFT140) previously related to fertility in mammals were associated with the markers and genomic regions significantly associated with RE. To our knowledge, this is the first genome-wide association study performed on mare fertility.

Genomic Uniqueness of Local Sheep Breeds From Morocco

Sheep farming is a major source of meat in Morocco and plays a key role in the country's agriculture. This study aims at characterizing the whole-genome diversity and demographic history of the main Moroccan sheep breeds, as well as to identify selection signatures within and between breeds. Whole genome data from 87 individuals representing the five predominant local breeds were used to estimate their level of neutral genetic diversity and to infer the variation of their effective population size over time. In addition, we used two methods to detect selection signatures: either for detecting selective sweeps within each breed separately or by detecting differentially selected regions by contrasting different breeds. We identified hundreds of genomic regions putatively under selection, which related to several biological terms involved in local adaptation or the expression of zootechnical performances such as Growth, UV protection, Cell maturation or Feeding behavior. The results of this study revealed selection signatures in genes that have an important role in traits of interest and increased our understanding of how genetic diversity is distributed in these local breeds. Thus, Moroccan local sheep breeds exhibit both a high genetic diversity and a large set of adaptive variations, and therefore, represent a valuable genetic resource for the conservation of sheep in the context of climate change.

A QTL for conformation of back and croup influences lateral gait quality in Icelandic horses

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 performance in multiple horse breeds, where the back and croup conformation plays a significant role. The conformation of back and croup plays an important role on riding ability in Icelandic horses. However, the genes behind this trait are still unknown. Therefore, the aim of this study was to identify genomic regions associated with conformation of back and croup in Icelandic horses and to investigate their effects on riding ability. One hundred seventy-seven assessed Icelandic horses were included in the study. A genome-wide association analysis was performed using the 670 K+ Axiom Equine Genotyping Array, and the effects of different haplotypes in the top associated region were estimated for riding ability and additional conformation traits assessed during breeding field tests.

RESULTS

A suggestive quantitative trait loci (QTL) for the score of back and croup was detected on Equus caballus (ECA) 22 (p-value = 2.67 × 10- 7). Haplotype analysis revealed two opposite haplotypes, which resulted in higher and lower scores of the back and croup, respectively (p-value < 0.001). Horses with the favorable haplotype were more inclined to have a well-balanced backline with an uphill conformation and had, on average, higher scores for the lateral gaits tölt (p-value = 0.02) and pace (p-value = 0.004). This genomic region harbors three genes: C20orf85, ANKRD60 and LOC100056167. ANKRD60 is associated with body height in humans. C20orf85 and ANKRD60 are potentially linked to adolescent idiopathic scoliosis in humans.

CONCLUSIONS

Our results show that the detected QTL for conformation of back and croup is of importance for quality of lateral gaits in Icelandic horses. These findings could result in a genetic test to aid in the selection of breeding horses, thus they are of major interest for horse breeders. The results may also offer a gateway to comparative functional genomics by potentially linking both motor laterality and back inclination in horses with scoliosis in humans.

A selection signatures study among Middle Eastern and European sheep breeds

Selection, both natural and artificial, leaves patterns on the genome during domestication of animals and leads to changes in allele frequencies among populations. Detecting genomic regions influenced by selection in livestock may assist in understanding the processes involved in genome evolution and discovering genomic regions related to traits of economic and ecological interests. In the current study, genetic diversity analyses were conducted on 34,206 quality-filtered SNP positions from 450 individuals in 15 sheep breeds, including six indigenous breeds from the Middle East, namely Iranian Balouchi, Afshari, Moghani, Qezel, Karakas and Norduz, and nine breeds from Europe, namely East Friesian Sheep, Ile de France, Mourerous, Romane, Swiss Mirror, Spaelsau, Suffolk, Comisana and Engadine Red Sheep. The SNP genotype data generated by the Illumina OvineSNP50 Genotyping BeadChip array were used in this analysis. We applied two complementary statistical analyses, F_ST (fixation index) and xp-EHH (cross-population extended haplotype homozygosity), to detect selection signatures in Middle Eastern and European sheep populations. F_ST and xp-EHH detected 629 and 256 genes indicating signatures of selection, respectively. Genomic regions identified using F_ST and xp-EHH contained the CIDEA, HHATL, MGST1, FADS1, RTL1 and DGKG genes, which were reported earlier to influence a number of economic traits. Both F_ST and xp-EHH approaches identified 60 shared genes as the signatures of selection, including four candidate genes (NT5E, ADA2, C8A and C8B) that were enriched for two significant Gene Ontology (GO) terms associated with the adenosine metabolic procedure. Knowledge about the candidate genomic regions under selective pressure in sheep breeds may facilitate identification of the underlying genes and enhance our understanding on these genes role in local adaptation.

Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony

Background

Body size is considered as one of the most fundamental properties of an organism. Due to intensive breeding and artificial selection throughout the domestication history, horses exhibit striking variations for heights at withers and body sizes. Debao pony (DBP), a famous Chinese horse, is known for its small body size and lives in Guangxi mountains of southern China. In this study, we employed comparative population genomics to study the genetic basis underlying the small body size of DBP breed based on the whole genome sequencing data. To detect genomic signatures of positive selection, we applied three methods based on population comparison, fixation index (F_ST), cross population composite likelihood ratio (XP-CLR) and nucleotide diversity (θπ), and further analyzed the results to find genomic regions under selection for body size-related traits.

Results

A number of protein-coding genes in windows with the top 1% values of F_ST (367 genes), XP-CLR (681 genes), and log₂ (θπ ratio) (332 genes) were identified. The most significant signal of positive selection was mapped to the NELL1 gene, probably underlies the body size and development traits, and may also have been selected for short stature in the DBP population. In addition, some other loci on different chromosomes were identified to be potentially involved in the development of body size.

Conclusions

Results of our study identified some positively selected genes across the horse genome, which are possibly involved in body size traits. These novel candidate genes may be useful targets for clarifying our understanding of the molecular basis of body size and as such they should be of great interest for future research into the genetic architecture of relevant traits in horse breeding program.

Signatures of selection analysis using whole-genome sequence data reveals novel candidate genes for pony and light horse types

Natural selection and domestication have shaped modern horse populations, resulting in a vast range of phenotypically diverse breeds. Horse breeds are classified into three types (pony, light, and draft) generally based on their body type. Understanding the genetic basis of horse type variation and selective pressures related to the evolutionary trend can be particularly important for current selection strategies. Whole-genome sequences were generated for 14 pony and 32 light horses to investigate the genetic signatures of selection of the horse type in pony and light horses. In the overlapping extremes of the fixation index and nucleotide diversity results, we found novel genomic signatures of selective sweeps near key genes previously implicated in body measurements including C4ORF33, CRB1, CPN1, FAM13A, and FGF12 that may influence variation in pony and light horse types. This study contributes to a better understanding of the genetic background of differences between pony and light horse types.

Whole genome detection of sequence and structural polymorphism in six diverse horses

The domesticated horse has played a unique role in human history, serving not just as a source of animal protein, but also as a catalyst for long-distance migration and military conquest. As a result, the horse developed unique physiological adaptations to meet the demands of both their climatic environment and their relationship with man. Completed in 2009, the first domesticated horse reference genome assembly (EquCab 2.0) produced most of the publicly available genetic variations annotations in this species. Yet, there are around 400 geographically and physiologically diverse breeds of horse. To enrich the current collection of genetic variants in the horse, we sequenced whole genomes from six horses of six different breeds: an American Miniature, a Percheron, an Arabian, a Mangalarga Marchador, a Native Mongolian Chakouyi, and a Tennessee Walking Horse, and mapped them to EquCab3.0 genome. Aside from extreme contrasts in body size, these breeds originate from diverse global locations and each possess unique adaptive physiology. A total of 1.3 billion reads were generated for the six horses with coverage between 15x to 24x per horse. After applying rigorous filtration, we identified and functionally annotated 17,514,723 Single Nucleotide Polymorphisms (SNPs), and 1,923,693 Insertions/Deletions (INDELs), as well as an average of 1,540 Copy Number Variations (CNVs) and 3,321 Structural Variations (SVs) per horse. Our results revealed putative functional variants including genes associated with size variation like LCORL gene (found in all horses), ZFAT in the Arabian, American Miniature and Percheron horses and ANKRD1 in the Native Mongolian Chakouyi horse. We detected a copy number variation in the Latherin gene that may be the result of evolutionary selection impacting thermoregulation by sweating, an important component of athleticism and heat tolerance. The newly discovered variants were formatted into user-friendly browser tracks and will provide a foundational database for future studies of the genetic underpinnings of diverse phenotypes within the horse.

The domesticated horse played a unique role in human history, serving not just as a source of dietary animal protein, but also as a catalyst for long-distance migration and military conquest. As a result, the horse developed unique physiological adaptations to meet the demands of both their climatic environment and their relationship with man. Although the completion of the horse reference genome allowed for the discovery of many genetic variants, the remarkable diversity across breeds of horse calls for additional effort to quantify the complete span of genetic polymorphism within this unique species. In this work, we present genome re-sequencing and variant detection analysis for six horses belonging to six different breeds representing different morphology, origins and vary in their physiological demands and response. We identified and annotated not just single nucleotide polymorphisms (SNPs), but also insertions and deletions (INDELs), copy number variations (CNVs) and structural variations (SVs). Our results illustrate novel sources of polymorphism and highlight potentially impactful variations for phenotypes of body size and conformation. We also detected a copy number loss in the Latherin gene that could be the result of an evolutionary selection affecting thermoregulation through sweating. Our newly discovered variants were formatted into easy-to-use tracks that can be easily accessed by researchers around the globe.

Heterozygotes for ACAN dwarfism alleles in horses have reduced stature

Homozygous and compound heterozygous Miniature horses for ACAN alleles D1, D2, D3* and D4 exhibit chondrodysplastic dwarfism (OMIA 001271-9796). In a previous study, the carrier rate for these four alleles, combined, was 26.2%. The purpose of this study was to investigate whether carriers of these dwarfism-causing alleles had a shorter withers height than non-carriers. A total of 245 Miniature horses were tested for these four ACAN alleles and also were measured for withers height. Of these horses, 98 were carriers and 147 were non-carriers. A statistically significant difference of 1.43 inches was observed with the carriers being shorter (P = 1.72E - 11). The range of heights for the two groups overlapped, indicating that other factors, including genes, have an impact on withers height. However, the high carrier rate of these dwarfism-causing variants may be due to selection for decreased height.

Adaptive introgression from indicine cattle into white cattle breeds from Central Italy

Cattle domestication occurred at least twice independently and gave rise to the modern taurine and indicine cattle breeds. European cattle diversity is generally dominated by taurine cattle, although elevated levels of indicine ancestry have been recorded in several breeds from southern Europe. Here we use genome-wide high-density SNP genotyping data to investigate the taurine and indicine ancestry in southern European cattle, based on a dataset comprising 508 individuals from 23 cattle breeds of taurine, indicine and mixed ancestry, including three breeds from Central Italy known to exhibit the highest levels of indicine introgression among southern European breeds. Based on local genomic ancestry analyses, we reconstruct taurine and indicine ancestry genome-wide and along chromosomes. We scrutinise local genomic introgression signals and identify genomic regions that have introgressed from indicine into taurine cattle under positive selection, harbouring genes with functions related to body size and feed efficiency. These findings suggest that indicine-derived traits helped enhance Central Italian cattle through adaptive introgression. The identified genes could provide genomic targets for selection for improved cattle performance. Our findings elucidate the key role of adaptive introgression in shaping the phenotypic features of modern cattle, aided by cultural and livestock exchange among historic human societies.

A genome-wide scan for diversifying selection signatures in selected horse breeds

The genetic differentiation of the current horse population was evolutionarily created by natural or artificial selection which shaped the genomes of individual breeds in several unique ways. The availability of high throughput genotyping methods created the opportunity to study this genetic variation on a genome-wide level allowing detection of genome regions divergently selected between separate breeds as well as among different horse types sharing similar phenotypic features. In this study, we used the population differentiation index (FST) that is generally used for measuring locus-specific allele frequencies variation between populations, to detect selection signatures among six horse breeds maintained in Poland. These breeds can be classified into three major categories, including light, draft and primitive horses, selected mainly in terms of type (utility), exterior, performance, size, coat color and appearance. The analysis of the most pronounced selection signals found in this study allowed us to detect several genomic regions and genes connected with processes potentially important for breed phenotypic differentiation and associated with energy homeostasis during physical effort, heart functioning, fertility, disease resistance and motor coordination. Our results also confirmed previously described association of loci on ECA3 (spanning LCORL and NCAPG genes) and ECA11 (spanning LASP1 gene) with the regulation of body size in our draft and primitive (small size) horses. The efficiency of the applied FST-based approach was also confirmed by the identification of a robust selection signal in the blue dun colored Polish Konik horses at the locus of TBX3 gene, which was previously shown to be responsible for dun coat color dilution in other horse breeds. FST-based method showed to be efficient in detection of diversifying selection signatures in the analyzed horse breeds. Especially pronounced signals were observed at the loci responsible for fixed breed-specific features. Several candidate genes under selection were proposed in this study for traits selected in separate breeds and horse types, however, further functional and comparative studies are needed to confirm and explain their effect on the observed genetic diversity of the horse breeds.

Combined QTL and Genome Scan Analyses With the Help of 2b-RAD Identify Growth-Associated Genetic Markers in a New Fast-Growing Carp Strain

Common carp is one of the oldest and most popular cultured freshwater fish species both globally and in China. In a previous study, we used a carp strain with a long breeding tradition in China, named Huanghe, to create a new fast-growing strain by selection for fast growth for 6 years. The growth performance at 8 months of age has been improved by 20.84%. To achieve this, we combined the best linear unbiased prediction with marker-assisted selection techniques. Recent progress in genome-wide association studies and genomic selection in livestock breeding inspired common carp breeders to consider genome-based breeding approaches. In this study, we developed a 2b-RAD sequence assay as a means of investigating the quantitative trait loci in common carp. A total of 4,953,017,786 clean reads were generated for 250 specimens (average reads/specimen = 19,812,071) with BsaXI Restriction Enzyme. From these, 56,663 SNPs were identified, covering 50 chromosomes and 3,377 scaffolds. Principal component analysis indicated that selection and control groups are relatively clearly distinct. Top 1% of Fst values was selected as the threshold signature of artificial selection. Among the 244 identified loci, genes associated with sex-related factors and nutritional metabolism (especially fat metabolism) were annotated. Eighteen QTL were associated with growth parameters. Body length at 3 months of age and body weight (both at 3 and 8 months) were controlled by polygenic effects, but body size (length, depth, width) at 8 months of age was controlled mainly by several loci with major effects. Importantly, a single shared QTL (IGF2 gene) partially controlled the body length, depth, and width. By merging the above results, we concluded that mainly the genes related to neural pathways, sex and fatty acid metabolism contributed to the improved growth performance of the new Huanghe carp strain. These findings are one of the first investigations into the potential use of genomic selection in the breeding of common carp. Moreover, our results show that combining the Fst, QTL mapping and CRISPR–Cas9 methods can be an effective way to identify important novel candidate molecular markers in economic breeding programs.

Genome data uncover four synergistic key regulators for extremely small body size in horses

Background

Miniature size in horses represents an extreme reduction of withers height that originated after domestication. In some breeds, it is a highly desired trait representing a breed- or subtype-specific feature. The genomic changes that emerged due to strong-targeted selection towards this distinct type remain unclear.

Results

Comparisons of whole-genome sequencing data from two Miniature Shetland ponies and one standard-sized Shetland pony, performed to elucidate genetic determinants for miniature size, revealed four synergistic variants, limiting withers height to 34.25 in. (87 cm). Runs of homozygosity regions were detected spanning these four variants in both the Miniature Shetland ponies and the standard-sized Shetland pony. They were shown to be characteristic of the Shetland pony breed, resulting in a miniature type under specific genotypic combinations. These four genetic variants explained 72% of the size variation among Shetland ponies and related breeds. The length of the homozygous regions indicate that they arose over 1000 years ago. In addition, a copy number variant was identified in DIAPH3 harboring a loss exclusively in ponies and donkeys and thus representing a potential height-associated variant.

Conclusion

This study reveals main drivers for miniature size in horses identified in whole genome data and thus provides relevant candidate genes for extremely short stature in mammals.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4877-5) contains supplementary material, which is available to authorized users.