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Traditionally, pedigree-based relationship coefficients were used to manage inbreeding and control inbreeding depression that occurs within populations. The extensive incorporation of genomic data in livestock breeding creates the opportunity to develop and implement methods to manage populations at the genomic level. Consequently, the realized proportion of the genome that two individuals share can be more accurately estimated instead of using pedigree information to estimate the expected proportion of shared alleles. To make use of this improvement, in this study we evaluated the genomic inbreeding measures in the Polish conserved cold-blooded horse population and compared the data with the traditional measures of inbreeding. Additionally, an ancestry fractions/proportions from Admixture software were tested as an estimate of lineage (ancestry coefficient) used for horses qualifying for the conservation program. The highest correlation of pedigree-based (F PED ) and genomic inbreeding estimates was found for F ROH (runs of homozygosity-based F coefficient) and F UNI (F coefficient based on the correlation between uniting gametes). F ROH correlation with F PED tended to increase as the number of generations registered as pedigree increased. While lineage and gene contributions (Q) from Admixture software correlated, they showed poor direct compliance; hence, Q-value cannot be recommended as the estimate of pedigree-based lineage. All these findings suggest that the methods of genomics should be considered as an alternative or support in the analysis of population structure in conservative breeding that can help control inbreeding in rare horse populations.

This study reports runs of homozygosity (ROH) and heterozygosity (ROHet) distributed in a large population of Holstein cattle on the basis of two microarrays of medium (50k; 2163 animals; 54 609 SNPs) and high single nucleotide polymorphism (SNP) density (HD; 600 animals; 777 692 SNPs). To assess the inbreeding values of Holstein cattle, the ROH-based genomic inbreeding coefficient (FROH) was calculated. The comparison of SNP panels suggested that FROH values above 4 Mb should be considered for panels of medium densities as a relatively reliable measure of inbreeding. Moreover, ROH hotspots and coldspots were identified and compared between the HD and 50k SNP panels and were carefully examined for association with production and functional traits. The obtained results pinpointed genomic regions presumably under selection pressure in Holstein cattle. The regions overlapped with a large number of genes, including GHR, GBF1, SUMF1, CCL28, NIM1K, U6, BTRC and FABP1, many of which are involved in important Holstein cattle characteristics. We also found that some ROH hotspots and coldspots identified with the HD panel were not detected with the 50k panel, mainly because of insufficient SNP density in certain genomic regions. This suggests that using medium-density panels might not be the best choice when precise identification of ROH patterns is the main goal. In summary, in this work, we confirmed that a high-density SNP panel compared to a medium-density SNP panel allows for more precise identification of ROH patterns, especially in the case of short ROH that could be associated with ancestral inbreeding. [ABSTRACT FROM AUTHOR]

Simple Summary: In recent years, the concept of runs of homozygosity (ROH) has become increasingly important in the genetic studies of various animal species, due to its advantages in estimating inbreeding and identifying regions under selection pressure. In this study, ROH distribution in six horse breeds belonging to three horse types (primitive, light, and draft) was examined. The presented results showed diverse differences in the length, number, and frequency of ROH between the analyzed breeds. Moreover, genomic inbreeding coefficients (FROH) showed a higher level of inbreeding in light and primitive horses in comparison to draft horses. Regarding ROH islands, which are regions of the genome characterized by a high frequency of ROH and thus may represent signals of selection events, we observed several genes with confirmed effects on major horse breed characteristics. In addition, ROH regions of zero frequency were analyzed and these regions also spanned across genes involved in important breed characteristics. The presented results, especially regarding ROH islands and no-ROH regions, can be used as a basis for further research concerning the identification of genes and markers that determine important horse breed characteristics. The present study reports runs of homozygosity (ROH) distribution in the genomes of six horse breeds (571 horses in total) representing three horse types (primitive, light, and draft horses) based on the 65k Equine BeadChip assay. Of major interest was the length, quantity, and frequency of ROH characteristics, as well as differences between horse breeds and types. Noticeable differences in the number, length and distribution of ROH between breeds were observed, as well as in genomic inbreeding coefficients. We also identified regions of the genome characterized by high ROH coverage, known as ROH islands, which may be signals of recent selection events. Eight to fourteen ROH islands were identified per breed, which spanned multiple genes. Many were involved in important horse breed characteristics, including WFIKNN2, CACNA1G, STXBP4, NOG, FAM184B, QDPR, LCORL, and the zinc finger protein family. Regions of the genome with zero ROH occurrences were also of major interest in specific populations. Depending on the breed, we detected between 2 to 57 no-ROH regions and identified 27 genes in these regions that were common for five breeds. These genes were involved in, e.g., muscle contractility (CACNA1A) and muscle development (miR-23, miR-24, miR-27). To sum up, the obtained results can be furthered analyzed in the topic of identification of markers unique for specific horse breed characteristics. [ABSTRACT FROM AUTHOR]

Runs of homozygosity (ROH) are continuous segments of the genome that arose as a result of inbreeding, resulting in the inheritance of identical haplotypes from both parents who shared a common ancestor. In the present study, we performed a detailed characterization and comparison of ROH in four pig breeds, including intensively selected Polish Landrace as well as native unselected animals of Puławska and two Złotnicka breeds (White and Spotted). We used a medium‐density PorcineSNP60 BeadChip assay (Illumina) and cgaTOH software to detect ROH covering a minimum of 30 adjacent SNPs and maintaining a size over 1 Mb. By analysing ROH distribution and frequency across the genome, we also identified genomic regions with high ROH frequency (so‐called "ROH hotspots"). The obtained results showed that the analysed conserved breeds were characterized by a higher ROH span and higher ROH‐based inbreeding coefficients (FROH), which likely result from past population bottlenecks, increasing the overall inbreeding level within these populations. The analysis of ROH distribution across the genomes revealed the presence of both shared and breed‐specific ROH hotspots. These hotspots, presumably representing genome regions under selection, overlapped with a variety of genes associated with processes connected with immune system functioning, reproduction, glucose homeostasis and metabolism. The genome regions with ROH hotspots overlapping in all analysed populations, located on SSC4 (51.9–55.9 Mb) and 13 (92.6–97.8 Mb), covered thirty‐one different genes, including MMP16, SLC7A13, ATP6V0D2, CNGB3, WWiP1, RiMDN1 and CPNE3. These genes are primarily associated with biological regulation and metabolism, processes that could be responsible for the variety of the selected production and functional features. [ABSTRACT FROM AUTHOR]

• Analyzed breeds have distinct genetic profiles with clear signs of admixture. • Świniarka breed is characterized by low N e and high level of genomic inbreeding. • The most pronounced selection signal was at RXFP2 gene responsible for horn size/type in sheep. Since their domestication, sheep breeds have been a subject of artificial selection directed towards production of wool, meat and milk as well as natural selection associated with regional climates and nutritional conditions. These selection pressures created a large diversity of sheep breeds and the opportunity to study their genetic differentiation. Despite the existence of several studies on genetic variation and selection signatures in sheep, information on the genetic background and variability of local sheep populations, especially on a genome wide-level, is still incomplete. This is mostly due to the large number of local sheep breeds and populations in existence. Several of these populations are under conservative breeding because of their largely primitive character, which is not suitable for the modern intensive animal production. In this study we analysed population parameters and quantified genetic differentiation among seven Polish conserved sheep breeds or local sheep populations, namely: Black-headed (BH; n=104), Polish Merino of coloured variety (MPC; n=59), 'Old type' Merino (MPOT; n=50), Polish Mountain Sheep (PMS; n=103), Świniarka (SW; n=100), Uhruska (UHR; n=69) and Wrzosówka (WRZ; n=90). The breeds represent mainly multipurpose production type with the emphasize on meat, wool and skin. Based on the data from OvineSNP50 BeadChip array (Illumina), we found that the genetic structures of the populations are not heavily affected, despite the bottlenecks in their recent breeding history. The only exception seems to be the SW breed in which we found very low effective population size (30.7) and high level of genomic inbreeding (17% as shown by F ROH). Average MAF across breeds was high and ranged from 0.285 in MPC to 0.297 in PMS. The average observed heterozygosity per breed ranged from 0.378 in SW to 0.398 in UHR. The admixture patterns analysis showed that the analysed breeds have distinct genetic profiles with clear signs of common origin and admixture, similar to other worldwide sheep populations. By using F ST statistics we also identified loci of the genome with the strongest divergence between the analysed breeds, presumably responsible for the fixed genetic differences among them which were created by artificial selection. The most pronounced of these results was selection signal at the locus of RXFP2 gene which is responsible for horn size/type in sheep. This analysis also allowed for genomic localization of genetic differences between the analysed breeds, providing a basis for further studies aimed at identification of sources of genetic variation in these sheep breeds. [ABSTRACT FROM AUTHOR]

Simple Summary: Runs of homozygosity (ROH) regions are known to be common in the genomes of cattle and have become a subject of interest of various research in recent years. ROH can be used as a valuable tool to estimate inbreeding, which needs to be controlled in livestock populations. Moreover, analysis of ROH is considered to be an effective method of identifying genome regions that are a subject of selection pressure, which may help in understanding the genetic aspects of production traits under selection. In this study, we analyzed ROH characteristics of 11 cattle breeds, both commercial and native, maintained in Poland. We presented distinct differences in the length, quantity and frequency of ROH between the analyzed breeds as well as in the levels of genomic inbreeding. Higher levels of inbreeding were characteristic for commercial breeds, especially beef breeds. In addition, within ROH islands, we observed a number of genes with a confirmed influence on the level of production traits. The presented results and identified genes can be a basis for further research focused on the identification of genes and markers essential in the determination of the most important production traits in cattle. In the presented research, BovineSNP50 microarrays (Illumina) were applied to determine runs of homozygosity in the genomes of 11 cattle breeds maintained in Poland. These cattle breeds represent three basic utility types: milk, meat and dual purpose. Analysis of runs of homozygosity allowed the evaluation of the level of autozygosity within each breed in order to calculate the genomic inbreeding coefficient (FROH), as well as to identify regions of the genome with a high frequency of ROH occurrence, which may reflect traces of directional selectin left in their genomes. Visible differences in the length and distribution of runs of homozygosity in the genomes of the analyzed cattle breeds have been observed. The highest mean number and mean sums of lengths of runs of homozygosity were characteristic for Hereford cattle and intermediate for the Holstein-Friesian Black-and-White variety, Holstein-Friesian Red-and-White variety, Simmental, Limousin, Montbeliarde and Charolais breeds. However, lower values were observed for cattle of conserved breeds. Moreover, the selected livestock differed in the level of inbreeding estimated using the FROH coefficient. In regions of the genome with a high frequency of ROH occurrence, which may reflect the impact of directional selection, a number of genes were observed that can be potentially related to the production traits which are under selection pressure for specific production types. The most important detected genes were GHR, MSTN, DGAT1, FABP4, and TRH, with a known influence on the milk and meat traits of the studied cattle breeds. [ABSTRACT FROM AUTHOR]

Runs of homozygosity (ROH) are defined as contiguous homozygous regions of the genome where the two haplotypes inherited from the parents are identical. It has been shown that the length and frequency of ROH may describe the history of the population in which an individual occurs; they may also reveal the level of inbreeding within populations, recent population bottlenecks or signatures of positive selection. In this study, BovineSNP50 whole-genome genotyping assay was used to analyse the lengths and distributions of the ROH found in the genomes of four cattle breeds maintained in Poland (Holstein, Polish Red, Limousin and Simmental) to assess both the level of autozygosity of each breed and to identify the genomic regions most commonly associated with ROH that may reflect directional selection pressure. Visible differences in the length and distribution of homozygous regions across the genome between selected breeds were observed. The breeds also varied in the level of autozygosity (inbreeding) estimated by F ROH , which was lower for unselected cattle. Moreover, within the regions of the genome most commonly associated with ROH that may reveal signatures of recent selection a number of genes potentially connected with different production features characteristic for individual breeds were detected. [ABSTRACT FROM AUTHOR]