Transboundary Breeds Research Articles

Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka.

Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on ZFST, hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits.

Genetic diversity and population structure analysis of Philippine native pigs highlight five priority populations for conservation.

The Philippine native pig (PhNP) is a unique genetic resource composed of multiple domesticated Sus scrofa lineages and interspecific hybrids. No prior study has determined the population structure and genetic diversity of PhNPs on multiple islands and provinces, which is essential for establishing conservation priorities. In this study, we explore the population structure and genetic diversity of various PhNP populations in Luzon and the Visayas, Philippines, to identify conservation priorities. We analyzed seven PhNP populations (n = 20-27 samples each; Benguet [B], Kalinga [K], Nueva Vizcaya [N], Isabela [I], Quezon [Q], Marinduque [M], and Samar [S]) and four transboundary breeds present in the Philippines (n = 9-11 samples each; Duroc, Large White, Landrace, and Berkshire). The pigs were compared against a panel of 20 microsatellite markers recommended by the ISAG-FAO. We tested for population structure at the island, region, and province levels. Strong genetic differentiation between native and transboundary breeds was confirmed by Bayesian clustering (k = 2) and Nei's D A genetic distance (100% bootstrap support for the PhNP cluster). PhNP exhibited high heterozygosity (Ho: 0.737), a high allele count (Na: 7.771), and a low inbreeding coefficient (Fis: -0.040-0.125). Bayesian clustering supported genetic differentiation at the island (k = 2; North Luzon and South Luzon-Visayas cluster), region (k = 3), and population (k = 8) levels. The pairwise F'st between PhNP populations ranged from 0.084 (N and I) to 0.397 (Q and K), confirming that some PhNP populations exhibited sufficient genetic distance to be considered separate populations. This study shows that native pigs from B, K, I, Q, M, and S are unique genetic units for conservation. Furthermore, the small effective population sizes of B, I, Q, M, and S (Ne: 3.9, 19.1, 14.2, 44.7, and 22.5, respectively) necessitate immediate conservation actions, such as incentivizing PhNP farming.

Genetic Structure Analysis of 155 Transboundary and Local Populations of Cattle (Bos taurus, Bos indicus and Bos grunniens) Based on STR Markers.

Every week, 1-2 breeds of farm animals, including local cattle, disappear in the world. As the keepers of rare allelic variants, native breeds potentially expand the range of genetic solutions to possible problems of the future, which means that the study of the genetic structure of these breeds is an urgent task. Providing nomadic herders with valuable resources necessary for life, domestic yaks have also become an important object of study. In order to determine the population genetic characteristics, and clarify the phylogenetic relationships of modern representatives of 155 cattle populations from different regions of the world, we collected a large set of STR data (10,250 individuals), including unique native cattle, 12 yak populations from Russia, Mongolia and Kyrgyzstan, as well as zebu breeds. Estimation of main population genetic parameters, phylogenetic analysis, principal component analysis and Bayesian cluster analysis allowed us to refine genetic structure and provided insights in relationships of native populations, transboundary breeds and populations of domestic yak. Our results can find practical application in conservation programs of endangered breeds, as well as become the basis for future fundamental research.

Genetic diversity of modern lines of hybrid pigs based on variations in mitochondrial DNA sequence

Genetic diversity of modern lines of hybrid pigs based on variations in mitochondrial DNA sequence

Animal Genetic Resources (AnGR) Diversity in India

The history of farm Animal Genetic Resources (AnGR) is about 12 to 14 thousand years old; started with the domestication of the animals for companion, food, fur and hide purposes. Among 40 non-carnivores livestock species domesticated by human being, till date, only cattle, sheep, goat, pig and chicken are highly prevalent and known as ‘Big five’. Other species like buffalo, dromedaries and Bactrian camel, llama, alpaca, yak, and mithun are region specific. At present, about one-fifth of the global food is of animal origin in the world. A vast genetic diversity of AnGR has been generated during hundreds of years through culmination of various evolutionary forces, including intensive selection and preferred mating by human for various utilization purposes. Initial domestication modulated the wild ancestors to adapt to human habitation and making themselves more useful for the human being. Migration of animals by humans across the continents further disseminated the germplasm, initiating the diversification of the farm animals across the globe. However, artificial selection for different needs and likings by the human is the chief element for development of large-scale genetic diversity, in form of distinct breeds and populations. These breeds as well as specialized populations have been evolved for a specific need or utilization pattern like milk, draft, meat, fibre, carting, riding etc. Today, the world possesses more than eight thousand livestock and poultry breeds, evolved from only few founder populations and catering various needs of human society around the world. As per Global data bank on Animal Genetic Resources of FAO, a total of 8774 breeds of 38 species were reported, worldwide (data from 182 countries) in 2014. Among these, 7718 are local breeds (in one country) and 510 are regional transboundary breeds (in one region) and 546 are international transboundary breeds (in more than one region).

A Matrilineal Study on the Origin and Genetic Relations of the Ecuadorian Pillareño Creole Pig Population through D-Loop Mitochondrial DNA Analysis.

Simple SummaryMitochondrial DNA (mtDNA) analysis is a tool in assessing the maternal origin, phylogeny, and population structure of domestic animals. The Ecuadorian Pillareño Creole pig is a creole breed that comes from the descendants of Iberian pig introduced to Ecuador by the Spanish conquerors. This creole population represents important reservoirs of genetic diversity that are very essential to preserve; however, the introduction of new breeds of pigs has displaced this creole pig from Ecuador to the background. The objective of the mitochondrial DNA analysis was to identify the Ecuadorian Pillareño Creole pig populations, their origins, and their maternal lines. For this study, DNA samples from 34 Ecuadorian Pillareño Creole pigs were used, with the animals belonging to seven rural regions of Ecuador. The haplogroup network suggested that the Pillareño creole pig population can be grouped into a single haplotype and that it belongs to the European pig clades. The genetic relationship between the Ecuadorian Pillareño Creole and the European pigs, particularly the Iberian pigs from Spain, can be used to establish of an official breeding program for the conservation and valuation of these creole populations, with this genetic mitochondrial analysis potentially providing a better approach for the rescue of the Ecuadorian Pillareño Creole pig populations.Domestic pig breeds reached America on the second Columbus trip; from this date, Iberian pig genetic resources were disseminated throughout the continent, forming diverse creole breeds. These Ecuadorian Creole pigs are important for food production but have been genetically eroded since the introduction of transboundary breeds. In this study, we sought to characterize this erosion more thoroughly through mitochondrial DNA D-Loop analysis of Ecuadorian Pillareño Creole pigs from seven regions of Ecuador. To allow comparison, we also included in our analysis sequences from wild species, commercial lines, and domestic pigs, which were obtained from the NCBI GenBank database. Creole pigs’ population showed overall moderate Hd values and low π values, and a negative value of Tajima’s D was observed. The greatest differentiation from the Ecuadorian Pillareño Creole pigs was observed between Asian wild and Asian domestic pigs. The haplotype analysis revealed three different phylogenetic clades (A, E I, and E II) and 65 haplotypes. Ecuadorian Creole populations were grouped into nine haplotypes for Clade E I and E II, which have not previously been reported for Creole Pillareño populations. Our analysis indicates that in the establishment of Creole Pillareño pigs, individuals most likely separated from the Asian pig population and appear to be genetically influenced by European and Iberian populations raised in Spain.

PSXII-1 Tracing the historical genetic components in turano-mongolian cattle breeds based on the microsatellite analysis of modern and museum samples

Abstract In their centuries-long history, the nomads of the south of Russia developed the local cattle breeds, which are well adapted to the harsh steppe conditions. In 20th century, the population size of such cattle breeds was dramatically decreased. At the same time, intensive cross breeding with high-producing transboundary breeds had been practiced on the small remaining part of population. The aim of our study was to trace the historical genetic components in modern populations of local cattle breeds of the turano-mongolian origin. The historical specimens of Kalmyk (n = 10), Kyrgyz (n = 11) and Kazakh (n = 3) cattle dated by the first quarter of the 20th century were derived from the craniological collection of the E.F. Liskun Museum for Animal Husbandry and subjected to the study. The modern representatives of Kalmyk (n = 28), Kyrgyz (n = 20), Kazakh White-headed (n = 30), Hereford (n = 26), and Mongolian (n = 41) cattle were used for comparison. All works with historical samples were performed in dedicated facility of the L.K. Ernst research Center for Animal Husbandry. The samples were genotyped for 11 microsatellite loci (BM1818, BM2113, BM1824, ETH10, ETH225, INRA023, SPS115, TGLA53, TGLA122, TGLA126, and TGLA227). For historical samples, the PCR reactions were carried out in five replicates to determine the consensus genotypes. In total, 132 alleles were identified, including 97 alleles in historical samples and 124 alleles in modern samples. The values of unbiased expected heterozygosity were 0.767–0.776 and 0.653–0.778 for the historical and modern samples, respectively. The STRUCTURE clustering showed the visible differences in genetic structure between the historical and modern populations of Kalmyk, Kyrgyz and Kazakh cattle breeds; however, the historical genetic components were still maintained in modern representatives of all of studied breeds. The research results will be useful for the sustainable breeding and conservation of valuable local genetic resources. The study was funded by the RSF No. 19-76-20012.

ELEMENT OF SELECTION – STATE BOOKS OF BREEDING ANIMALS IN UKRAINE FOR THE PERIOD 2002–2010 YEARS

The issue of registration of breeding animals of different breeds is dealt with by organizations that keep state books of breeding animals. In Ukraine, the functions of keeping state books of breeding animals in cattle breeding, pig breeding, sheep breeding and horse breeding belong to the powers of the minister, which ensures the formation of state policy in the field of animal husbandry. The issue of animal breeding books is relevant because it is an ongoing process that requires a set of measures aimed at registration, maintenance and promotion of domestic breeding livestock.
 The purpose of research. To monitor the state books of breeding animals (SBBA) in dairy and meat cattle breeding, sheep breeding and pig breeding for the period 2002–2010. Also, establish the number of potential females that could be entered in the stud books.
 Materials and methods of research. The material for the study was data on the presence of breeding cows of dairy and meat production, sows and ewes of breeds registered in the State Register of Breeding Subjects in Animal Husbandry (until 2009, the State Breeding Register, SBR) during 2002–2019.
 The results of research. According to the SBR, 15 dairy breeds of cattle have been registered in Ukraine. During the study period, 15 volumes of SBBA of four breeds of dairy cattle were published in Ukraine, which included information on 12331 breeding animals, including 11477 cows. The largest number of recorded breeding animals of the Ukrainian Black-and-White dairy cattle, of which 144 breeding bulls and 4989 cows, are concentrated in six volumes. In second place is the Ukrainian Red-and-White dairy cattle, namely 4554 animals. Then there is the Simmental with 871 animals, of which 809 cows, and the red steppe 1773 heads, including 1609 cows.
 It is established that 48.7% of breeding animals were born in the period from 1990 to 1999. A small proportion, namely 0.3%, are animals born before 1979, and only 24% after 2000. Younger animals are recorded in the breeding books of Ukrainian Black-and-White dairy cattle and Ukrainian Red-and-White dairy cattle, and older – in the books of the red steppe.
 Of the 14 meat breeds used in Ukraine, only 5 have breeding animals that are registered with the SBBA. The total number of meat-producing animals recorded in the SBBA is 5586, including 4649 cows.
 Of the twelve breeds of pigs bred in Ukraine, only seven breeds, namely the Ukrainian white steppe (1451 heads) and Ukrainian spotted steppe (974), Myrhorod breed (123), Great Black (181), Landrace (727), Poltava meat breed (290) and Ukrainian meat breed (300) during the study period were published state pedigree books. Half (50.7%) of all recorded breeding pigs have a year of birth before 2000. Young (born in 2000) animals are recorded in the breeding books of the Landrace breed and the Ukrainian white steppe, Ukrainian meat breed and Poltava meat breed, where their share varies from 64 to 98%.
 During the study period, 9 volumes of state books of breeding sheep were published. In addition to Tsigai (884 goals), Askanian Karakul (700), fine-wool (1168), meat-wool with crossbred wool (1917) and Sokol (443), in 2003, 2004 and 2009 3 volumes of SBBA sheep of the Prekos breed were published.
 The calculation of potential females that could be recorded in the state breeding books revealed the presence of 1251102 breeding animals, including 100796 ewes, 70678 sows, 71341 beef cows and 1008287 dairy cows.
 The largest number of potential females of different breeds in cattle breeding, sheep breeding and pig breeding in the regions of Ukraine showed a certain pattern, namely the centers for dairy cattle breeding – Vinnytsia (83395 heads), Kyiv (111650), Khmelnytsky (64667), Cherkasy (68035) regions, beef cattle breeding – Volyn (13.466 head), Chernihiv (10.907 head), sheep breeding – Kherson (13.837), Odessa (19078) and pig breeding – Dnipropetrovsk (6452), Poltava (4621).
 The main goal for calculating potential females was to try to determine the size of the breed in dairy and beef cattle, sheep breeding and pigs breeding. Because the more animals included in the breeding model, the better the results of genetic improvement. In addition, it is possible to address the dynamics of the development of breeding traits, identify successful methods of selection and selection, assessment of population and genetic parameters over time and the creation of breeding programs with breeds of farm animals.
 Conclusion. State books of breeding animals are an important element of selection. Animal information databases help to estimate the populations of domestic and transboundary breeds in general by a set of characteristics, to determine the population-genetic parameters over time and to develop programs for the improvement of farm animals. Studies have identified a significant number (1251102 heads) of breeding cows, ewes and sows, which at one time could be recorded in the breeding books of the respective breeds.

Characterizing the Mitochondrial Diversity of Arbi Goats from Tunisia.

Arbi is one of the main local goat breeds in Tunisia, representing an important economic resource in arid and hot areas where cattle and sheep cannot thrive successfully. In the current work, we have characterized the mitochondrial diversity of 26 Arbi goats by partially sequencing the mitochondrial D-loop region. These sequences plus 10 retrieved from GenBank were analyzed with the DnaSP v.5.10.1, evidencing the existence of 12 different haplotypes. Nucleotide and haplotype diversities were 0.02 and 0.96. Moreover, median-joining network analysis showed that all D-loop sequences from Arbi goats correspond to haplogroup A and that in general they do not cluster with sequences from other goat breeds. The high diversity that has been observed in North African goats is compatible with the maritime diffusion of the Neolithic package 10,000-7000 YBP. Moreover, there are evidences that local Tunisian breeds have been extensively crossed with highly productive transboundary breeds in order to improve meat and milk yields. These uncontrolled crossing practices may lead to the loss of alleles that play key roles in the adaptation of Tunisian local breeds to a harsh environment.

ACTIVE PART OF POPULATIONS OF TRANSBOUNDARY AND DOMESTIC BREEDS OF DAIRY AND COMBINED CATTLE BREEDING OF UKRAINE

Today in Ukraine, according to the State Register of Breeding Subjects, 13 dairy cattle breeds have been registered in animal husbandry. Conventionally, they can be divided into transboundary ones, such as Ayrshire, Angler, Holstein, Simmental, Brown Swiss and Red Polish, and domestic – Ukrainian Whiteheaded, Lebedyn, Red Steppe, Ukrainian Brown Dairy, Red, Black-and-White and Red-and-White Dairy cattle.
 The breeding part of the dairy cattle population is 299908 breeding animals, including 129557 cows, which are concentrated in 321 breeding subjects. The share of domestic breeds is at the level of 67.9%. A tendency towards an increase in the number of animals in the population of transboundary breeds by 56724 animals was noted, with a simultaneous reduction in domestic breeds by 221980 animals. The main part of the transboundary breeds is Holstein (83%) and Simmental (11%), and in the domestic breed population, it is Ukrainian Black-and-White (71.5%) and Red-and-White (19.8%) dairy cattle. Local domestic breeds (Lebedyn, Red Steppe, Ukrainian Brown Dairy) occupy 2.8%.
 The level of milk yield of the studied cows of the breeding part of the population of domestic and transboundary breeds is quite high and is in the range of 7242 ... 4309 kg. During the study period, there is a gradual increase from 2002 to 2019 for the milking, fat content and the amount of milk fat in cows of a population of transboundary and domestic breeds, which is respectively 3382.1 kg 0.16%; 140.7 kg and 3052 kg 0.06%; 118.1 kg. In 2019, the highest milk yield in the population of transboundary breeds was noted among Holstein cows (8679 kg) and Brown Swiss (8789) breeds, and in domestic – Ukrainian Black-and-White (7514 kg) and Red-and-White (7005 kg) dairy breads. The fat content in milk is more than 4% in cows of local breeds of Ukraine.
 An analysis of the level of milk yield of cows for the studied periods showed a decrease in the number of farms with a yield of 5 thousand kg or less. So, in 2002, the share of farms breeding transboundary breeds was 70%, then in 2019 only 13%, and in domestic from 83% to 16%. The average milk yield of cows of more than 10000 kg was recorded in 17 breeding farms.

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis.

Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses-calculation of fixation index (FST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals-were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4-25.1 Mbp and on BTA 16 at 42.5-43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74-5.36 Mbp, BTA 15 at 17.80-18.77 Mbp, and BTA 17 at 45.59-45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40-81.69 Mbp, BTA 15 at 16.04-16.62 Mbp, and BTA 18 at 0.19-1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds.

Evaluation of haploid diversity of sows of the Large White breed of the pedigree factory of the State enterprise “Experimental enterprise “imeni 9 Sіchnja”

The development and use of effective selection programs accelerated the genetic improvement of breeds, advances in feeding technology allowed for optimal nutrition, and the creation of identical and strictly controlled production conditions, a uniform and strictly controlled production environment led to the replacement of local pig breeds with highly productive transboundary breeds. This development of the industry has led to increased concern about the erosion of genetic resources. The number of purebred boars of the Large White breed in 1973 amounted to 98.3 % of the total number of boars of this breed, and sows - 38.9 %. These data allow us to assume that significant haploid diversity could persist in the individual pedigree factory of the Large White breed. Thus, the subject of our study was the assessment of the haploid diversity of the Large White sows of the pedigree factory of the State enterprise “Experimental enterprise “imeni 9 Sіchnja”, the Institute of Pig Breeding and AIP NAAS of Ukraine. For the study, samples of the bristles of 25 sows of the Large White breed of the SE "Experimental enterprise "imeni 9 Sіchnja" of the Institute of Pig Breeding and AIP NAAS of Ukraine, representing all families. DNA isolation from bristles was performed using a Chelex-100 ion exchange resin. Mitochondrial haplotypes were determined using PCR-RFLP analysis according K. F. Pochernyaev (2016). Among the sample of breeding pigs of the Large White breed of the SE “Experimental enterprise “imeni 9 Sіchnja”, mitochondrial haplotypes B1, B2, C, G, and J1 were identified. In previous studies, seven mitochondrial haplotypes were found among pigs of the Large White breed of Ukraine, which were found with different frequencies. The haplotypes G (14.1 %), J1 (13.3 %) and N (5.91 %) were found with the highest frequency; much less often - haplotypes A (0.3 %), B1 (1.9 %), C (9.2 %) and L (2.2 %). Thus, our studies have shown that the mitochondrial haplotypes B1, B2, C, G, J1 found in the sample of breeding pigs of the Large White breed of the SE «Experimental enterprise «imeni 9 Sіchnja» typical for pigs of the Large White breed of Ukraine except haplotype B2. Important for the restoration of the Mirgorod breed of pigs is the existence in the herd of pigs of the Large White breed of the SE “Experimental entewrprise“imeni 9 Sіchnja” animals having haplotype B1 inherent to Myrgorod breed. Thus, our studies have shown that in sows of the Large White breed breeding farm SE “Experimental enterprise “imeni 9 Sіchnja”, significant haploid diversity remains, which must be maintained at a high level in the future. Key words: pigs, the Large White breed, haplotype, mitochondrial genome, PCR-RFLP.

Cryoconservation of Animal Genetic Resources in Europe and Two African Countries: A Gap Analysis

Cryoconservation is one of the main strategies to conserve farm animal genetic resources, providing opportunities for genetic improvement and adaptation to changes in production environments and consumer demands. In this study, we combine livestock breed-related data from the Domesticated Animal Diversity Information System (DAD-IS) and information provided by gene banks from 15 European and 2 non-European countries on material stored for livestock breeds to analyze the gaps in cryomaterial collections according to species, countries and various breed categories. Out of the 2949 breeds registered in DAD-IS for these countries, 15.9% have been reported to have material stored in gene banks, but only 4.3% have material sufficient to allow breed reconstitution. The proportion of breeds with stored cryomaterial was greater than 20% for ruminants and pigs, between 10% and 20% for equids, and below 10% for rabbit and avian species. According to the results of two logistic regressions, countries show significant differences in the proportion of populations collected for cryostorage, while breeds not-at-risk are more likely to have cryomaterial preserved than are other breeds. Also, a relatively larger proportion of transboundary breeds have cryomaterial in gene banks than do local breeds, likely due in part to the fact that multiple countries have the opportunity to collect this material. These results highlight the need for increased efforts in material collection for at-risk local breeds and regional coordination on cryoconservation of material from transboundary breeds.

Genetic homogenization of indigenous sheep breeds in Northwest Africa

Northwest-African sheep represent an ideal case-study for assessing the potential impact of genetic homogenization as a threat to the future of traditional breeds that are adapted to local conditions. We studied ten Algerian and Moroccan breeds of sheep, including three transboundary breeds, distributed over a large part of the Maghreb region, which represents a geographically and historically coherent unit. Our analysis of the dataset that involved carrying out Genome-wide SNP genotyping, revealed a high level of homogenization (ADMIXTURE, NetView, fineSTRUCTURE and IBD segments analyses), in such a way that some breeds from different origins appeared genetically undistinguished: by grouping the eight most admixed populations, we obtained a mean global FST value of 0.0024. The sPCA analysis revealed that the major part of Morocco and the Northern part of Algeria were affected by the phenomenon, including most of the breeds considered. Unsupervised cross-breeding with the popular Ouled-Djellal breed was identified as a proximate cause of this homogenization. The issue of transboundary breeds was investigated, and the Hamra breed in particular was examined via ROH fragments analysis. Genetic diversity was considered in the light of historical archives and anthropological works. All of these elements taken together suggest that homogenization as a factor affecting the Maghrebin sheep stock, has been particularly significant over the last few decades, although this process probably started much earlier. In particular, we have identified the policies set by the French administration during the colonial period of the region’s history as a causal factor that probably contributed significantly to this process. The genetic homogenization that we have observed calls into question the integrity of the farm animal genomic resources represented by these local breeds, whose conservation is of critical importance to the future of the livestock sector.

Whole-genome SNP analysis elucidates the genetic structure of Russian cattle and its relationship with Eurasian taurine breeds

BackgroundThe origin of native and locally developed Russian cattle breeds is linked to the historical, social, cultural, and climatic features of the diverse geographical regions of Russia. In the present study, we investigated the population structure of nine Russian cattle breeds and their relations to the cattle breeds from around the world to elucidate their origin. Genotyping of single nucleotide polymorphisms (SNPs) in Bestuzhev (n = 26), Russian Black-and-White (n = 21), Kalmyk (n = 14), Kholmogor (n = 25), Kostromsky (n = 20), Red Gorbatov (n = 23), Suksun (n = 20), Yakut (n = 25), and Yaroslavl cattle breeds (n = 21) was done using the Bovine SNP50 BeadChip. SNP profiles from an additional 70 breeds were included in the analysis as references.ResultsThe observed heterozygosity levels were quite similar in eight of the nine studied breeds (HO = 0.337–0.363) except for Yakut (Ho = 0.279). The inbreeding coefficients FIS ranged from -0.028 for Kalmyk to 0.036 for Russian Black-and-White and were comparable to those of the European breeds. The nine studied Russian breeds exhibited taurine ancestry along the C1 axis of the multidimensional scaling (MDS)-plot, but Yakut was clearly separated from the European taurine breeds on the C2 axis. Neighbor-Net and admixture analyses, discriminated three groups among the studied Russian breeds. Yakut and Kalmyk were assigned to a separate group because of their Turano-Mongolian origin. Russian Black-and-White, Kostromsky and Suksun showed transboundary European ancestry, which originated from the Holstein, Brown Swiss, and Danish Red breeds, respectively. The lowest level of introgression of transboundary breeds was recorded for the Kholmogor, Yaroslavl, Red Gorbatov and Bestuzhev breeds, which can be considered as an authentic genetic resource.ConclusionsWhole-genome SNP analysis revealed that Russian native and locally developed breeds have conserved authentic genetic patterns in spite of the considerable influence of Eurasian taurine cattle. In this paper, we provide fundamental genomic information that will contribute to the development of more accurate breed conservation programs and genetic improvement strategies.

The comparison of the lactation and milk yield and composition of selected breeds of sheep and goats.

The objective of this study was to characterize the milk yield (MY) and milk composition of relevant sheep and goat breeds raised around the world to be used with nutrition models for diet formulation and nutrient balancing. A 2-step approach was used. First, a database developed by the Food and Agriculture Organization was used to identify relevant breeds (i.e., frequently raised) by comparing the occurrence of transboundary breed names across countries. We selected transboundary breeds that occurred more than 3 times and other relevant breeds obtained from the specialized literature that had milk production information (e.g., MY, days in milk, and milk fat, protein, and lactose). The majority of sheep breeds were classified as nondairy (76%) because they lacked milk production information. Karakul and Merino accounted for up to 2.4% of sheep breeds raised around the world, whereas the other individual breeds accounted for less than 1%. In contrast, nondairy breeds of goats accounted for 46.3% and of the remaining 53.7%, Saanen, Boer, Anglo-Nubian, Toggenburg, and Alpine accounted for 6.5, 5, 4.4, 4, and 3%, respectively, of the transboundary breeds. Second, a database compiled from published studies for the selected sheep (n = 65) and goats (n = 78) breeds were analyzed using a random coefficients model (studies and treatments within studies as random effects). For sheep breeds, the average and SD were 1.1 ± 0.3 kg/d for MY, 6.9 ± 1% for milk fat, 5.4 ± 0.4% for milk protein, 5 ± 0.3% for milk lactose, 17.7 ± 1.4% for milk total solids, and 1,073 ± 91 kcal/kg of milk energy. Lacaune had the greatest MY compared to Comisana and Tsigai (1.65 versus 0.83 and 0.62 kg/d; respectively, P < 0.05), but milk components were not different among breeds. For goats breeds, the average and SD across breeds were 1.7 ± 0.6 kg/d for MY, 4.2 ± 0.9% for milk fat, 3.3 ± 0.4% for milk protein, 4.4 ± 0.4% for milk lactose, 12.7 ± 1.1% for milk total solids, and 750 ± 75 kcal/kg of milk energy. Alpine had similar MY to Saanen (2.66 versus 2.55 kg/d, respectively; P > 0.05), but greater (P < 0.05) than other breeds. The Boer breed had the greatest milk fat, protein, lactose, and total solids than several other breeds, leading to the greatest milk energy content (907 kcal/kg). Because there are many factors that can alter MY and milk composition, averages provided in this study serve as guidelines, and nutritionists must obtain observed values when using nutrition models.

THEORETICAL, METHODOLOGICAL, SCIENTIFIC AND INSTITUTIONAL BASICS OF FORMATION OF BANK OF FARM ANIMAL GENETICS RESOURCES OF INSTITUTE OF ANIMAL BREDDING AND GENETICS NAMED M.V.ZUBETS OF NAAS

The authors has demonstrated the global nature of the problem of domesticated animal gene pool preservation caused by intensive using some transboundary breeds and reduction in the number of aborigen and local ones. Ignoring this problem leads to loss of biodiversity, the restoration of which with traditional methods of breeding work is not possible. The main aim of the article to highlight the key milestones of forming of the theory and methodology of farm animal gene pool preservation, contribute of Ukrainian scientists to the development of the some specific approaches.&#x0D; The prerequisite of the development and the role of the Bank of farm animal genetic resources of IABG named M.V.Zubets of NAAS in the system of biodiversity preservation were highlighted. As its prototype we considered the Republican Sperm Repository of Central Experimental Station of Artificial Insemination (Brovary). The article shows that solving of problem of farm animal gene pool preservation should be based on a combination of the whole complex of factors: theoretical and methodical, organizational, economic and technological. In the last decades Ukrainian scientists have developed organizational foundations of farm animal gene pool preservation; its basic principle is breed adaptation to the certain climatic zones. They have introduced the seven main organizational forms of the domesticated animal preservation including gene pool population, gene pool herd, relicted animal farm, collections’ nursery, farm of gene pool reserve, gene pool reproductor, bank of animal gene pool resources and other banks. They have initiated the development of the concept of creation and placement gene pool objects, its main link is bank of animal gene pool resources.&#x0D; The article shown that twelve research institutes of National Academy of Agrarian Sciences of Ukraine carry out scientific program "Preservation of animal’s gene poll". The Institute of Animal Breeding and Genetics named M.V.Zubets of NAAS is main institution that coordinates its activities. Bank of Animal Gene Pool Resources of institute has been recognized as a national treasure in 1986. Since 2009 Ukraine is a member of the European Regional Focal Point for Animal Genetic Resources at FAO.&#x0D; The authors state that IABG nd. a. M.V.Zubets of NAAS has developed a methodology for integrated assessment, management and long-term storage of gene pool resources. The scientists of the institute have introduced methods of genetic and population monitoring of the gene pool herds and systems of regulation and optimization of the number of the gene pool populations through a combination of biotechnological and genetic technologies of cryopreservation of sperm, embryos, oocytes, primary germ cells and DNA, directed selection and creation of virtual cryopreserved gene pool herds. They have identified categories of the gene pool objects for storage and optimal size of deposit, developed requirements for genetic material of each gene pool object of the different species of farm animals, as well as standards of main parameters of the gene pool micropopulations for the some species.&#x0D; The contribution of scientists of IABG nd. a. M.V.Zubets of NAAS in the development of the conceptual foundations of preservation of animal genetic resources as a cultural and intellectual heritage of the nation was concretized.&#x0D; The authors used the special historical and scientific methods of research.

Genetic diversity and patterns of population structure in Creole goats from the Americas.

Biodiversity studies are more efficient when large numbers of breeds belonging to several countries are involved, as they allow for an in-depth analysis of the within- and between-breed components of genetic diversity. A set of 21 microsatellites was used to investigate the genetic composition of 24 Creole goat breeds (910 animals) from 10 countries to estimate levels of genetic variability, infer population structure and understand genetic relationships among populations across the American continent. Three commercial transboundary breeds were included in the analyses to investigate admixture with Creole goats. Overall, the genetic diversity of Creole populations (mean number of alleles=5.82±1.14, observed heterozygosity=0.585±0.074) was moderate and slightly lower than what was detected in other studies with breeds from other regions. The Bayesian clustering analysis without prior information on source populations identified 22 breed clusters. Three groups comprised more than one population, namely from Brazil (Azul and Graúna; Moxotó and Repartida) and Argentina (Long and shorthair Chilluda, Pampeana Colorada and Angora-type goat). Substructure was found in Criolla Paraguaya. When prior information on sample origin was considered, 92% of the individuals were assigned to the source population (threshold q≥0.700). Creole breeds are well-differentiated entities (mean coefficient of genetic differentiation=0.111±0.048, with the exception of isolated island populations). Dilution from admixture with commercial transboundary breeds appears to be negligible. Significant levels of inbreeding were detected (inbreeding coefficient>0 in most Creole goat populations, P<0.05). Our results provide a broad perspective on the extant genetic diversity of Creole goats, however further studies are needed to understand whether the observed geographical patterns of population structure may reflect the mode of goat colonization in the Americas.

Challenges and opportunities in genetic improvement of local livestock breeds.

Sufficient genetic variation in livestock populations is necessary both for adaptation to future changes in climate and consumer demand, and for continual genetic improvement of economically important traits. Unfortunately, the current trend is for reduced genetic variation, both within and across breeds. The latter occurs primarily through the loss of small, local breeds. Inferior production is a key driver for loss of small breeds, as they are replaced by high-output international transboundary breeds. Selection to improve productivity of small local breeds is therefore critical for their long term survival. The objective of this paper is to review the technology options available for the genetic improvement of small local breeds and discuss their feasibility. Most technologies have been developed for the high-input breeds and consequently are more favorably applied in that context. Nevertheless, their application in local breeds is not precluded and can yield significant benefits, especially when multiple technologies are applied in close collaboration with farmers and breeders. Breeding strategies that require cooperation and centralized decision-making, such as optimal contribution selection, may in fact be more easily implemented in small breeds.

Medžimurje horse population in Slovenia

In the nineteenth and early twentieth century the Medžimurje horse played an important role as a draft and working horse in the river Mura region. Nowadays, this area is split between Hungary, Austria, Slovenia and Croatia. In the frame of the project "Management of traditional transboundary breeds on example of a nearly forgotten breed the Murinsulaner", we collected data for cold blooded horses similar to the Medžimurje horse. Horses of this type do not exist in Austria anymore, in Croatia they were registered as an authothonous breed »Medjimurje horse«, and in Slovenia and Hungary this horse has a special section in the stud book for cold blooded horses as a Medžimurje type of horse. The Slovenian part of the population of the Medžimurje horse is quite heterogeneous regarding body measures. With respect to the scoring system used in the above mentioned project, the majority of scored animals were classified as »desired« or »satisfactory«. In order to further develop or to preserve this type of horse or to form a consolidated breed we would have to make a breeding program which would prevent mating among related animals and to cooperate with neighbouring countries in the field of breeding and selection. The only hope to preserve this type of horse on the long term in the region is by using it as a tourist attraction for carriage riding and/or as a draft horse in agriculture in marginal regions.