Dataset Information

The horse Y chromosome as an informative marker for tracing sire lines.

ABSTRACT: Analysis of the Y chromosome is the best-established way to reconstruct paternal family history in humans. Here, we applied fine-scaled Y-chromosomal haplotyping in horses with biallelic markers and demonstrate the potential of our approach to address the ancestry of sire lines. We de novo assembled a draft reference of the male-specific region of the Y chromosome from Illumina short reads and then screened 5.8 million basepairs for variants in 130 specimens from intensively selected and rural breeds and nine Przewalski's horses. Among domestic horses we confirmed the predominance of a young'crown haplogroup' in Central European and North American breeds. Within the crown, we distinguished 58 haplotypes based on 211 variants, forming three major haplogroups. In addition to two previously characterised haplogroups, one observed in Arabian/Coldblooded and the other in Turkoman/Thoroughbred horses, we uncovered a third haplogroup containing Iberian lines and a North African Barb Horse. In a genealogical showcase, we distinguished the patrilines of the three English Thoroughbred founder stallions and resolved a historic controversy over the parentage of the horse 'Galopin', born in 1872. We observed two nearly instantaneous radiations in the history of Central and Northern European Y-chromosomal lineages that both occurred after domestication 5,500 years ago.

SUBMITTER: Felkel S

PROVIDER: S-EPMC6465346 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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The horse Y chromosome as an informative marker for tracing sire lines.

Felkel Sabine S Vogl Claus C Rigler Doris D Dobretsberger Viktoria V Chowdhary Bhanu P BP Distl Ottmar O Fries Ruedi R Jagannathan Vidhya V Janečka Jan E JE Leeb Tosso T Lindgren Gabriella G McCue Molly M Metzger Julia J Neuditschko Markus M Rattei Thomas T Raudsepp Terje T Rieder Stefan S Rubin Carl-Johan CJ Schaefer Robert R Schlötterer Christian C Thaller Georg G Tetens Jens J Velie Brandon B Brem Gottfried G Wallner Barbara B

Scientific reports 20190415 1

Analysis of the Y chromosome is the best-established way to reconstruct paternal family history in humans. Here, we applied fine-scaled Y-chromosomal haplotyping in horses with biallelic markers and demonstrate the potential of our approach to address the ancestry of sire lines. We de novo assembled a draft reference of the male-specific region of the Y chromosome from Illumina short reads and then screened 5.8 million basepairs for variants in 130 specimens from intensively selected and rural b ...[more]

PMID: 30988347

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Project description:The Thoroughbred horse is a highly valued domestic animal population under strong selection for athletic phenotypes. Here we present a high resolution genomics-based analysis of inbreeding in the population that may form the basis for evidence-based discussion amid concerns in the breeding industry over the increasing use of small numbers of popular sire lines, which may accelerate a loss of genetic diversity. In the most comprehensive globally representative sample of Thoroughbreds to-date (n?=?10,118), including prominent stallions (n?=?305) from the major bloodstock regions of the world, we show using pan-genomic SNP genotypes that there has been a highly significant decline in global genetic diversity during the last five decades (FIS R2?=?0.942, P?=?2.19?×?10-13; FROH R2?=?0.88, P?=?1.81?×?10-10) that has likely been influenced by the use of popular sire lines. Estimates of effective population size in the global and regional populations indicate that there is some level of regional variation that may be exploited to improve global genetic diversity. Inbreeding is often a consequence of selection, which in managed animal populations tends to be driven by preferences for cultural, aesthetic or economically advantageous phenotypes. Using a composite selection signals approach, we show that centuries of selection for favourable athletic traits among Thoroughbreds acts on genes with functions in behaviour, musculoskeletal conformation and metabolism. As well as classical selective sweeps at core loci, polygenic adaptation for functional modalities in cardiovascular signalling, organismal growth and development, cellular stress and injury, metabolic pathways and neurotransmitters and other nervous system signalling has shaped the Thoroughbred athletic phenotype. Our results demonstrate that genomics-based approaches to identify genetic outcrosses will add valuable objectivity to augment traditional methods of stallion selection and that genomics-based methods will be beneficial to actively monitor the population to address the marked inbreeding trend.

Project description:The study of selection signatures helps to find genomic regions that have been under selective pressure and might host genes or variants that modulate important phenotypes. Such knowledge improves our understanding of how breeding programmes have shaped the genomes of livestock. In this study, 942 stallions were included from four, exemplarily chosen, German warmblood breeds with divergent historical and recent selection focus and different crossbreeding policies: Trakehner (N = 44), Holsteiner (N = 358), Hanoverian (N = 319) and Oldenburger (N = 221). Those breeds are nowadays bred for athletic performance and aptitude for show-jumping, dressage or eventing, with a particular focus of Holsteiner on the first discipline. Blood samples were collected during the health exams of the stallion preselections before licensing and were genotyped with the Illumina EquineSNP50 BeadChip. Autosomal markers were used for a multi-method search for signals of positive selection. Analyses within and across breeds were conducted by using the integrated Haplotype Score (iHS), cross-population Extended Haplotype Homozygosity (xpEHH) and Runs of Homozygosity (ROH). Oldenburger and Hanoverian showed very similar iHS signatures, but breed specificities were detected on multiple chromosomes with the xpEHH. The Trakehner clustered as a distinct group in a principal component analysis and also showed the highest number of ROHs, which reflects their historical bottleneck. Beside breed specific differences, we found shared selection signals in an across breed iHS analysis on chromosomes 1, 4 and 7. After investigation of these iHS signals and shared ROH for potential functional candidate genes and affected pathways including enrichment analyses, we suggest that genes affecting muscle functionality (TPM1, TMOD2-3, MYO5A, MYO5C), energy metabolism and growth (AEBP1, RALGAPA2, IGFBP1, IGFBP3-4), embryonic development (HOXB-complex) and fertility (THEGL, ZPBP1-2, TEX14, ZP1, SUN3 and CFAP61) have been targeted by selection in all breeds. Our findings also indicate selection pressure on KITLG, which is well-documented for influencing pigmentation.

Project description:BackgroundGenomic selection has become a standard tool in dairy cattle breeding. However, for other animal species, implementation of this technology is hindered by the high cost of genotyping. One way to reduce the routine costs is to genotype selection candidates with an SNP (single nucleotide polymorphism) panel of reduced density. This strategy is investigated in the present paper. Methods are proposed for the approximation of SNP positions, for selection of SNPs to be included in the low-density panel, for genotype imputation, and for the estimation of the accuracy of genomic breeding values. The imputation method was developed for a situation in which selection candidates are genotyped with an SNP panel of reduced density but have high-density genotyped sires. The dams of selection candidates are not genotyped. The methods were applied to a sire line pig population with 895 German Piétrain boars genotyped with the PorcineSNP60 BeadChip.ResultsGenotype imputation error rates were 0.133 for a 384 marker panel, 0.079 for a 768 marker panel, and 0.022 for a 3000 marker panel. Error rates for markers with approximated positions were slightly larger. Availability of high-density genotypes for close relatives of the selection candidates reduced the imputation error rate. The estimated decrease in the accuracy of genomic breeding values due to imputation errors was 3% for the 384 marker panel and negligible for larger panels, provided that at least one parent of the selection candidates was genotyped at high-density.Genomic breeding values predicted from deregressed breeding values with low reliabilities were more strongly correlated with the estimated BLUP breeding values than with the true breeding values. This was not the case when a shortened pedigree was used to predict BLUP breeding values, in which the parents of the individuals genotyped at high-density were considered unknown.ConclusionsGenomic selection with imputation from very low- to high-density marker panels is a promising strategy for the implementation of genomic selection at acceptable costs. A panel size of 384 markers can be recommended for selection candidates of a pig breeding program if at least one parent is genotyped at high-density, but this appears to be the lower bound.

Dataset Information

The horse Y chromosome as an informative marker for tracing sire lines.

Publications

The horse Y chromosome as an informative marker for tracing sire lines.

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