Fine-scale population structure analysis of seven local Swiss sheep breeds using genome-wide SNP data

Assessing the levels of intraspecific admixture and interspecific hybridization in Iberian wild goats (Capra pyrenaica)

Iberian wild goats (Capra pyrenaica, also known as Iberian ibex, Spanish ibex, and Spanish wild goat) underwent strong genetic bottlenecks during the 19th and 20th centuries due to overhunting and habitat destruction. From the 1970s to 1990s, augmentation translocations were frequently carried out to restock Iberian wild goat populations (very often with hunting purposes), but they were not systematically planned or recorded. On the other hand, recent data suggest the occurrence of hybridization events between Iberian wild goats and domestic goats (Capra hircus). Augmentation translocations and interspecific hybridization might have contributed to increase the diversity of Iberian wild goats. With the aim of investigating this issue, we have genotyped 118 Iberian wild goats from Tortosa-Beceite, Sierra Nevada, Muela de Cortes, Gredos, Batuecas, and Ordesa and Monte Perdido by using the Goat SNP50 BeadChip (Illumina). The analysis of genotypic data indicated that Iberian wild goat populations are strongly differentiated and display low diversity. Only three Iberian wild goats out from 118 show genomic signatures of mixed ancestry, a result consistent with a scenario in which past augmentation translocations have had a limited impact on the diversity of Iberian wild goats. Besides, we have detected eight Iberian wild goats from Tortosa-Beceite with signs of domestic goat introgression. Although rare, hybridization with domestic goats could become a potential threat to the genetic integrity of Iberian wild goats; hence, measures should be taken to avoid the presence of uncontrolled herds of domestic or feral goats in mountainous areas inhabited by this iconic wild ungulate.

An Overview of the Use of Genotyping Techniques for Assessing Genetic Diversity in Local Farm Animal Breeds

Simple Summary

The number of local farm animal breeds is declining worldwide. However, these breeds have different degrees of genetic diversity. Measuring genetic diversity is important for the development of conservation strategies and, therefore, various genomic analysis techniques are available. The aim of the present work was to shed light on the use of these techniques in diversity studies of local breeds. In summary, a total of 133 worldwide studies that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that over time, almost all available genomic techniques were used and various diversity parameters were calculated. Therefore, the present results provide a comprehensive overview of the application of these techniques in the field of local breeds. This can provide helpful insights into the advancement of the conservation of breeds with high genetic diversity.

Abstract

Globally, many local farm animal breeds are threatened with extinction. However, these breeds contribute to the high amount of genetic diversity required to combat unforeseen future challenges of livestock production systems. To assess genetic diversity, various genotyping techniques have been developed. Based on the respective genomic information, different parameters, e.g., heterozygosity, allele frequencies and inbreeding coefficient, can be measured in order to reveal genetic diversity between and within breeds. The aim of the present work was to shed light on the use of genotyping techniques in the field of local farm animal breeds. Therefore, a total of 133 studies across the world that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that diversity of cattle was most often investigated with microsatellite use as the main technique. Furthermore, a large variety of diversity parameters that were calculated with different programs were identified. For 15% of the included studies, the used genotypes are publicly available, and, in 6%, phenotypes were recorded. In conclusion, the present results provide a comprehensive overview of the application of genotyping techniques in the field of local breeds. This can provide helpful insights to advance the conservation of breeds.

Ear type in sheep is associated with the MSRB3 locus

Ear morphology is an important determinant of sheep breeds. It includes different variable traits such as ear size and erectness, suggesting a polygenic architecture. Here, we performed a comprehensive genome-wide analysis to identify regions under selection for ear morphology in 515 sheep from 17 breeds fixed for diverse ear phenotypes using 34k SNP genotyping data. GWASs for two ear type traits, size and erectness, revealed a single genome-wide significant association on ovine chromosome 3. The derived marker alleles were enriched in sheep with large and/or floppy ears. The GWAS signal harboured the MSRB3 gene encoding methionine sulphoxide reductase B3, which has already been found to be associated with different ear types in other species. We attempted whole-genome resequencing to identify causal variant(s) within a 1 Mb interval around MSRB3. This experiment excluded major copy number variants in the interval, but failed to identify a compelling candidate causal variant. Fine-mapping suggested that the causal variant for large floppy ears most likely resides in a 175 kb interval downstream of the MSRB3 coding region.

Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran

The development of camel husbandry for good production in a desert climate is very important, thus we need to understand the genetic basis of camels and give attention to genomic analysis. We assessed genome-wide diversity, linkage disequilibrium (LD), effective population size (Ne) and relatedness in 96 dromedaries originating from five different regions of the central desert of Iran using genotyping-by-sequencing (GBS). A total of 14,522 Single Nucleotide Polymorphisms (SNPs) with an average minor allele frequency (MAF) of 0.19 passed quality control and filtering steps. The average observed heterozygosity in the population was estimated at 0.25 ± 0.03. The mean of LD at distances shorter than 40 kb was low (r² = 0.089 ± 0.234). The camels sampled from the central desert of Iran exhibited higher relatedness than Sudanese and lower than Arabian Peninsula dromedaries. Recent Ne of Iran's camels was estimated to be 89. Predicted Tajima's D (1.28) suggested a bottleneck or balancing selection in dromedary camels in the central desert of Iran. A general decrease in effective and census population size poses a threat for Iran's dromedaries. This report is the first SNP calling report on nearly the chromosome level and a first step towards understanding genomic diversity, population structure and demography in Iranian dromedaries.

On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools

Background

In the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly and northwesterly directions. Reconstruction of these migrations and subsequent genetic events requires a more detailed characterization of the current phylogeographic differentiation.

Results

We collected 50 K single nucleotide polymorphism (SNP) profiles of Balkan sheep that are currently found near the major Neolithic point of entry into Europe, and combined these data with published genotypes from southwest-Asian, Mediterranean, central-European and north-European sheep and from Asian and European mouflons. We detected clines, ancestral components and admixture by using variants of common analysis tools: geography-informative supervised principal component analysis (PCA), breed-specific admixture analysis, across-breed \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$f_{4}$$\end{document}f4 profiles and phylogenetic analysis of regional pools of breeds. The regional Balkan sheep populations exhibit considerable genetic overlap, but are clearly distinct from the breeds in surrounding regions. The Asian mouflon did not influence the differentiation of the European domestic sheep and is only distantly related to present-day sheep, including those from Iran where the mouflons were sampled. We demonstrate the occurrence, from southeast to northwest Europe, of a continuously increasing ancestral component of up to 20% contributed by the European mouflon, which is assumed to descend from the original Neolithic domesticates. The overall patterns indicate that the Balkan region and Italy served as post-domestication migration hubs, from which wool sheep reached Spain and north Italy with subsequent migrations northwards. The documented dispersal of Tarentine wool sheep during the Roman period may have been part of this process. Our results also reproduce the documented 18th century admixture of Spanish Merino sheep into several central-European breeds.

Conclusions

Our results contribute to a better understanding of the events that have created the present diversity pattern, which is relevant for the management of the genetic resources represented by the European sheep population.

Population structure of five native sheep breeds of Sweden estimated with high density SNP genotypes

BACKGROUND

Native Swedish sheep breeds are part of the North European short-tailed sheep group; characterized in part by their genetic uniqueness. Our objective was to study the population structure of native Swedish sheep. Five breeds were genotyped using the 600 K SNP array. Dalapäls and Klövsjö sheep are from the middle of Sweden; Gotland and Gute sheep from Gotland, an island in the Baltic Sea; and Fjällnäs sheep from northern Sweden. We studied population structure by: principal component analysis (PCA), cluster-based analysis of admixture, and an estimated population tree.

RESULTS

The analyses of the five Swedish breeds revealed that these breeds are five distinct breeds, while Gute and Gotland are more closely related to each other as seen in all analyses. All breeds had long branch lengths in the population tree indicating they've been subjected to drift. We repeated our analyses using 39 K SNP and including 50 K SNP genotypes from other European and southwestern Asian breeds from the Sheep HapMap project and 600 K SNP genotypes from a dataset of French sheep. Results arranged breeds into five groups: south-west Asia, south-west Europe, central Europe, north Europe and north European short-tailed sheep. Within this last group, Norwegian and Icelandic breeds, Finn and Romanov sheep, Scottish breeds, and Gute and Gotland sheep were more closely related while the remaining Swedish breeds and Ouessant sheep were distinct from all breeds and had longer branches in the population tree.

CONCLUSIONS

We showed population structure of five Swedish breeds and their structure within European and southwestern Asian breeds. Swedish breeds are unique, distinct breeds that have been subjected to drift but group with other north European short-tailed sheep.

Runs of Homozygosity and NetView analyses provide new insight into the genome-wide diversity and admixture of three German cattle breeds

Angler (RVA) and Red-and-White dual-purpose (RDN) cattle were in the past decades crossed with influential Red Holstein (RH) sires. However, genome-wide diversity studies in these breeds are lacking. The objective of the present study was to elucidate the genome-wide diversity and population structure of the three German cattle breeds. Using 40,851 single nucleotide polymorphism markers scored in 337 individuals, runs of homozygosity (ROH) were analysed in each breed. Clustering and a high-resolution network visualisation analyses were performed on an extended dataset that included 11 additional (outgroup) breeds. Genetic diversity levels were high with observed heterozygosity above 0.35 in all three breeds. Only RVA had a recent past effective population size (Ne) estimate above 100 at 5 generations ago. ROH length distribution followed a similar pattern across breeds and the majority of ROH were found in the length class of >5 to 10 Mb. Estimates of average inbreeding calculated from ROH (FROH) were 0.021 (RVA), 0.045 (RDN) and 0.053 (RH). Moderate to high positive correlations were found between FROH and pedigree inbreeding (FPED) and between FROH and inbreeding derived from the excess of homozygosity (FHOM), while the intercept of the regression of FROH on FPED was above zero. The population structure analysis showed strong evidence of admixture between RVA and RH. Introgression of RDN with RH genes was minimally detected and for the first time, the study uncovered Norwegian Red Cattle ancestry in RVA. Highly heterogeneous genetic background was found for RVA and RH and as expected, the breeds of the extended dataset effectively differentiated mostly based on geographical origin, validating our findings. The results of this study confirm the impact of RH sires on RVA and RDN populations. Furthermore, a close monitoring is suggested to curb further reduction of Ne in the breeds.

Identification of two TYRP1 loss-of-function alleles in Valais Red sheep

The Valais Red sheep breed is a local breed of the Swiss canton Valais. Although the breed is characterised by its brown colour, black animals occasionally occur and the objective of this study was to identify the causative genetic variants responsible for the obvious difference. A GWAS using high-density SNP data to compare 51 brown and 38 black sheep showed a strong signal on chromosome 2 at the TYRP1 locus. Haplotype analyses revealed three different brown-associated alleles. The WGS of three sheep revealed four protein-changing variants within the TYRP1 gene. Three of these variants were associated with the recessively inherited brown coat colour. This includes the known missense variant TYRP1:c.869G>T designated as b^{S oay} and two novel loss-of-function variants. We propose to designate the frame-shift variant TYRP1:c.86_87delGA as b^{VS 1} and the nonsense variant TYRP1:c.1066C>T as b^{VS 2} . Interestingly, the b^{VS 1} allele occurs only in local breeds of Switzerland whereas the b^{VS 2} allele seems to be more widespread across Europe.

Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds

A dataset consisting of 787 animals with high-density SNP chip genotypes (346 774 SNPs) and 939 animals with medium-density SNP chip genotypes (33 828 SNPs) from eight indigenous Swiss sheep breeds was analyzed to characterize population structure, quantify genomic inbreeding based on runs of homozygosity and identify selection signatures. In concordance with the recent known history of these breeds, the highest genetic diversity was observed in Engadine Red sheep and the lowest in Valais Blacknose sheep. Correlation between F_PED and F_ROH was around 0.50 and thereby lower than that found in similar studies in cattle. Mean F_ROH estimates from medium-density data and HD data were highly correlated (0.95). Signatures of selection and candidate gene analysis revealed that the most prominent signatures of selection were found in the proximity of genes associated with body size (NCAPG, LCORL, LAP3, SPP1, PLAG1, ALOX12, TP53), litter size (SPP1), milk production (ABCG2, SPP1), coat color (KIT, ASIP, TBX3) and horn status (RXFP2). For the Valais Blacknose sheep, the private signatures in proximity of genes/QTL influencing body size, coat color and fatty acid composition were confirmed based on runs of homozygosity analysis. These private signatures underline the genetic uniqueness of the Valais Blacknose sheep breed. In conclusion, we identified differences in the genetic make-up of Swiss sheep breeds, and we present relevant candidate genes responsible for breed differentiation in locally adapted breeds.

A WebGIS platform for the monitoring of Farm Animal Genetic Resources (GENMON)

BACKGROUND

In 2007, the Food and Agriculture Organization of the United Nations (FAO) initiated the Global plan of action for Farm Animal Genetic Resources (FAnGR). The main goal of this plan is to reduce further loss of genetic diversity in farm animals, so as to protect and promote the diversity of farm animal resources. An important step to reach this goal is to monitor and prioritize endangered breeds in the context of conservation programs.

METHODOLOGY/WEB PORTAL IMPLEMENTATION

The GENMON WebGIS platform is able to monitor FAnGR and to evaluate the degree of endangerment of livestock breeds. The system takes into account pedigree and introgression information, the geographical concentration of animals, the cryo-conservation plan and the sustainability of breeding activities based on socio-economic data as well as present and future land use conditions. A multi-criteria decision tool supports the aggregation of the multi-thematic indices mentioned above using the MACBETH method, which is based on a weighted average using satisfaction thresholds. GENMON is a monitoring tool to reach subjective decisions made by a government agency. It relies on open source software and is available at http://lasigsrv2.epfl.ch/genmon-ch.

RESULTS/SIGNIFICANCE

GENMON allows users to upload pedigree-information (animal ID, parents, birthdate, sex, location and introgression) from a specific livestock breed and to define species and/or region-specific weighting parameters and thresholds. The program then completes a pedigree analysis and derives several indices that are used to calculate an integrated score of conservation prioritization for the breeds under investigation. The score can be visualized on a geographic map and allows a fast, intuitive and regional identification of breeds in danger. Appropriate conservation actions and breeding programs can thus be undertaken in order to promote the recovery of the genetic diversity in livestock breeds in need. The use of the platform is illustrated by means of an example based on three local livestock breeds from different species in Switzerland.

Genetic diversity analyses reveal first insights into breed-specific selection signatures within Swiss goat breeds

We used genotype data from the caprine 50k Illumina BeadChip for the assessment of genetic diversity within and between 10 local Swiss goat breeds. Three different cluster methods allowed the goat samples to be assigned to the respective breed groups, whilst the samples of Nera Verzasca and Tessin Grey goats could not be differentiated from each other. The results of the different genetic diversity measures show that Appenzell, Toggenburg, Valais and Booted goats should be prioritized in future conservation activities. Furthermore, we examined runs of homozygosity (ROH) and compared genomic inbreeding coefficients based on ROH (F_ROH ) with pedigree-based inbreeding coefficients (F_PED ). The linear relationship between F_ROH and F_PED was confirmed for goats by including samples from the three main breeds (Saanen, Chamois and Toggenburg goats). F_ROH appears to be a suitable measure for describing levels of inbreeding in goat breeds with missing pedigree information. Finally, we derived selection signatures between the breeds. We report a total of 384 putative selection signals. The 25 most significant windows contained genes known for traits such as: coat color variation (MITF, KIT, ASIP), growth (IGF2, IGF2R, HRAS, FGFR3) and milk composition (PITX2). Several other putative genes involved in the formation of populations, which might have been selected for adaptation to the alpine environment, are highlighted. The results provide a contemporary background for the management of genetic diversity in local Swiss goat breeds.

Inference and Analysis of Population Structure Using Genetic Data and Network Theory

Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition's modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of prior conditions. The method is implemented in the software NetStruct (available at https://giligreenbaum.wordpress.com/software/).

SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data

Effective population size (N_e) is a key population genetic parameter that describes the amount of genetic drift in a population. Estimating N_e has been subject to much research over the last 80 years. Methods to estimate N_e from linkage disequilibrium (LD) were developed ~40 years ago but depend on the availability of large amounts of genetic marker data that only the most recent advances in DNA technology have made available. Here we introduce SNeP, a multithreaded tool to perform the estimate of N_e using LD using the standard PLINK input file format (.ped and.map files) or by using LD values calculated using other software. Through SNeP the user can apply several corrections to take account of sample size, mutation, phasing, and recombination rate. Each variable involved in the computation such as the binning parameters or the chromosomes to include in the analysis can be modified. When applied to published datasets, SNeP produced results closely comparable with those obtained in the original studies. The use of SNeP to estimate N_e trends can improve understanding of population demography in the recent past, provided a sufficient number of SNPs and their physical position in the genome are available. Binaries for the most common operating systems are available at https://sourceforge.net/projects/snepnetrends/.