This study assessed the effect of access to pasture, lactation number, and foals’ sex on the nutritional value of milk (79 samples) from nine mares. The following were analysed: content of dry matter, protein, fat, lactose, and ash; percentages of α-lactalbumin (α-La), β-lactoglobulin (β-Lg), serum albumin (SA), immunoglobulins (Ig), lactoferrin (Lf), and lysozyme (Lz) in the total protein; and the fatty acid profile. Mares without access to pastures were shown to produce milk with a higher dry matter content, including fat, lactose, and ash; higher percentages of β-Lg, α-La, Ig, and Lf; and a better fatty acid profile. The milk from mares with access to pasture contained more protein, including higher percentages of SA and Lz. Milk from mares in lactations 4–6 had the highest fat and protein concentrations and the lowest lactose concentration. The α-La level was highest in lactation 1, Lf in lactations 2–3, and Lz in lactations 4–6. Milk from mares in lactations 4–6 had the best fatty acid profile (the lowest concentration of saturated fatty acids (SFAs) and the highest concentration of monounsaturated fatty acids(MUFA) and polyunsaturated fatty acids (PUFA)). Milk from mothers of female offspring had higher dry matter, fat, and protein concentrations, a higher share of lysozyme, and a better fatty acid profile.

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.

Native breeds of farm animals, despite their unique characteristics and adaptability to diverse and often adverse environmental conditions, are at risk due to their lower profitability and corresponding declining use. According to FAO data, there are currently around 8800 livestock breeds in the world ( http://www.fao.org/dad-is/en/ update: 09.11.2019), of which 17% have been assessed to be endangered. The objective of the study was to develop a model for estimating the risk status of Polish native breeds. The proposed new model is based on 3 factors: demographic, genetic, and socioeconomic. The last factor is composed of 6 elements: geographical concentration, demographic trend over the last 5 years, cultural value of a breed, parentage control, ex situ conservation and anthropogenic factors. Using the factors and elements above, among the examined 30 breeds of cattle, horses, pigs, sheep and goats, 1 was assessed as being critically endangered; 24 were determined to be endangered and in need of conservation; 5 were less endangered, but in need of constant monitoring. Out of 35 populations of poultry 29 were assessed as endangered as they were being kept in only single public collections. Six flocks of ducks were given a critical risk status, due to a very low number of females.

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.

The study was carried out on milk from cold-blooded Sokólski mares and warm-blooded Polish Halfbred mares. Milk samples were analysed for content of solids, protein, fat, lactose, and ash; density; energy value; percentage of α-lactalbumin (α-La), β-lactoglobulin (β-Lg), serum albumin (SA), immunoglobulin (Ig), lactoferrin (Lf) and lysozyme (Lz) in the total protein; and fatty acid profile. Milk from cold-blooded mares was found to be similar in protein and fat content to that of warm-blooded mares, but had higher content of solids, including lactose and ash. It also had significantly (P≤0.01) higher content of α-La, SA and Lz, and lower content of β-Lg, Ig and Lf in comparison to milk from warm-blooded mares. Milk from Sokólski horses had a significantly (P≤0.01) higher proportion of SFA, including C10:0, C12:0, C14:0, C16:0 (P≤0.01) and C18:0 (P≤0.05), while the milk of warm-blooded mares had a significantly (P≤0.01) higher proportion of MUFA, including C16:1n-9 and C18:n-9, and PUFA, including C18:2n-6 and C18:3n3. The share of n-6 and n-3 PUFA was significantly (P≤0.01) higher in milk from warm-blooded horses, but their ratio (n-6/n-3) was lower (more favourable) in milk from cold-blooded mares. In addition, milk from warm-blooded horses had a lower (P≤0.01) share of HSFA and a higher proportion of DFA compared to cold-blooded horses, as well as lower values for AI and TI. Despite these minor differences in comparison with warmblooded mares (Polish Halfbred), milk from cold-blooded Sokólski mares was shown to be a food product of high nutritional value, which is one argument in favour of the use of this horse breed for dairy purposes.

The current role of the horse as a companion animal resulted in a decrease of interest in breeding and usage of draft horses. This meant that the population of cold-blooded horses in Poland has been dramatically reduced during the last decades. To avoid impoverishment of the gene pool of the local horse population, a conservation program was established which involves draft horses and other local horse breeds. The draft horses bred in Poland can be subdivided in a few horse types of which the most widespread and consolidated are Sztumski and Sokólski horses. These two subpopulations are phenotypically diversified, however, the overall level of their genetic differentiation seems to be relatively low and not precisely determined, especially with the use of molecular markers. In reference to this, in this study we used Illumina genotyping arrays to describe in detail the genetic differentiation of these two cold-blooded horse populations. We describe the genetic distance between them, as well as within-population variation, admixture patterns, and level of relatedness within populations. We also made an attempt to detect genome regions divergently selected between those horses by the detection of diversifying selection signals. The results of this study provide initial evidence supporting breeding decisions that were made during conservation breeding program design and answer questions raised by the breeders of Sokólski and Sztumski horses concerning the level of their genetic variation and differentiation.