Molecular characterization of breeds and its use in conservation

Genome-wide detections for runs of homozygosity and selective signatures reveal novel candidate genes under domestication in chickens

BACKGROUND

Indigenous chickens were developed through a combination of natural and artificial selection; essentially, changes in genomes led to the formation of these modern breeds via admixture events. However, their confusing genetic backgrounds include a genomic footprint regulating complex traits, which is not conducive to modern animal breeding.

RESULTS

To better evaluate the candidate regions under domestication in indigenous chickens, we considered both runs of homozygosity (ROHs) and selective signatures in 13 indigenous chickens. The genomes of Silkie feather chickens presented the highest heterozygosity, whereas the highest inbreeding status and ROH number were found in Luhua chickens. Short ROH (< 1 Mb), were the principal type in all chickens. A total of 291 ROH islands were detected, and QTLdb mapping results indicated that body weight and carcass traits were the most important traits. An ROH on chromosome 2 covering VSTM2A gene was detected in 12 populations. Combined analysis with the Tajima's D index revealed that 18 genes (e.g., VSTM2A, BBOX1, and RYR2) were under selection and covered by ROH islands. Transcriptional analysis results showed that RYR2 and BBOX1 were specifically expressed in the heart and muscle tissue, respectively.

CONCLUSION

Based on genome-wide scanning for ROH and selective signatures, we evaluated the genomic characteristics and detected significant candidate genes covered by ROH islands and selective signatures. The findings in this study facilitated the understanding of genetic diversity and provided valuable insights for chicken breeding and conservation strategies.

Evaluation of the effect of the addition of an olive oil-derived antioxidant (Pectoliv-80A) in the extender for cryopreservation of rooster sperm through the use of a discriminant statistical tool

During the poultry sperm cryopreservation process, an excess of reactive oxygen species is generated resulting in oxidative stress which harms the quality of avian spermatozoa. To counteract this effect, the addition of exogenous antioxidants, such as Pectoliv-80A (a by-product of olive oil), to the cryopreservation diluent is interesting. For this purpose, 16 roosters belonging to the Utrerana avian breed were used. Six semen pools (from the 6 different replicates) were divided into 4 aliquots corresponding to different concentrations of Pectoliv-80A that were tested (0, 300, 400, and 500 μg/mL), and the cryopreservation process was carried out. To evaluate post-thawing semen quality, different parameters such as motility, membrane functionality, reactive oxygen species production, lipid peroxidation, and acrosome integrity were studied. A discriminant canonical analysis was used to determine both the differences between the Pectoliv-80A concentration groups and the discriminant power of the aforementioned parameter used for semen evaluation. Total motility and membrane functionality were reported to be the most discriminant variables for differentiating the different antioxidant enrichment groups and concluded that concentrations of 300 μg/mL showed the most desirable quality of post-thawing semen. The present study could lead to the optimization of both cryopreservation and quality evaluation techniques of the sperm of rooster species, that support the conservation program of endangered local breeds.

Structure and genetic variability of the Costa Rican Paso horse

The Costa Rican Paso Horse (CPC) is a breed developed in Costa Rica. The objectives were to estimate the genetic structure and evaluate the levels of genetic variability of the population. The genotypes of 14 microsatellites in 3654 records (2052 females and 1602 males) were analyzed. Expected (He) and observed (Ho) heterozygosity, polymorphic information content (CIP), fixation index (FIS), Shannon index, as well as Hardy-Weinberg disequilibrium (DHW) were evaluated. Kinship relationships (Rij) were estimated throughout the entire population. The effective population size (Ne) was calculated, alternating allele frequencies less than 0.05, 0.02 and 0.01. The Bayesian clustering study was carried out to infer how many lines are appropriate from the analysis of genotypes using multiple loci. The number of alleles per locus ranged from 7 to 17, with an average value of 9.6; nine loci presented DHW (P < 0.05); two loci presented negative FIS values, the same as Ho > He; the average of CIP, Ho and He was 0.254, 0.756 and 0.785, respectively. At the 12 loci where He > Ho, the differences ranged from 0.002 to 0.341 (0.036 on average). For Ne, the estimates were 201.9, 230.1, and 241.5. In the Rij, 54.86% of the estimates were in the interval of 0.01 to 77.7%. The number of lines that define the population corresponds to three, with an approximate composition of 33.1%, 32.4% and 34.5%, respectively. The CPC, as a subdivided population with DHW and a reduction in heterozygotes may be associated with possible Wahlund effects. Keywords: Wahlund effect, equines, genetic markers, synthetic breed, Hardy Weinberg.

Genomic insights into the conservation of wild and domestic animal diversity: A review

Due to environmental change and anthropogenic activities, global biodiversity has suffered an unprecedented loss, and the world is now heading toward the sixth mass extinction event. This urges the need to step up our efforts to promote the sustainable use of animal genetic resources and plan effective strategies for their conservation. Although habitat preservation and restoration are the primary means of conserving biodiversity, genomic technologies offer a variety of novel tools for identifying biodiversity hotspots and thus, support conservation efforts. Conservation genomics is a broad area of science that encompasses the application of genomic data from thousands or tens of thousands of genome-wide markers to address important conservation biology concerns. Genomic approaches have revolutionized the way we understand and manage animal populations, providing tools to identify and preserve unique genetic variants and alleles responsible for adaptive genetic variation, reducing the deleterious consequences of inbreeding, and increasing the adaptive potential of threatened species. The advancement of genomic technologies, particularly comparative genomic approaches, and the increased accessibility of genomic resources in the form of genome-enabled taxa for non-model organisms, provides a distinct advantage in defining conservation units over traditional genetics approaches. The objective of this review is to provide an exhaustive overview of the concept of conservation genomics, discuss the rationale behind the transition from conservation genetics to genomic approaches, and emphasize the potential applications of genomic techniques for conservation purposes. We also highlight interesting case studies in both livestock and wildlife species where genomic techniques have been used to accomplish conservation goals. Finally, we address some challenges and future perspectives in this field.

The Role of Reproduction and Genetic Variation in Polish White-Backed Cows in the Breed Restoration Process

Local breeds are the main reservoir of biodiversity of farm animals. According to FAO, they account for 87% of all described breeds in the world. To ensure that they are adequately protected, they should be continually monitored for genetic variation. Another crucial factor is reproduction, which is the most important guarantee of population growth. In the present study, genetic variation in 372 Polish White-Backed cows was determined using DNA microsatellite sequences, taking into account their parentage. Reproductive parameters were analysed as well, based on data from 3658 lactations of 1128 Polish White-Backed cows. The results indicate that despite the small initial population and the implementation of a moderate selection of animals, the existing population of Polish White-Backed cattle has a high level of genetic variation, reflected in the degree of heterozygosity (0.761). Regarding reproductive traits, despite their late age at first calving, Polish White-Backed cows were shown to be distinguished by very good fertility parameters in comparison to other breeds raised in Poland. These findings not only confirm the value of protecting local cattle breeds around the world but may also be of importance in developing selection indices for highly productive breeds, in which reproductive functioning should be one of the most important factors considered.

Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breeds

Knowledge of linkage disequilibrium (LD), genetic structure and genetic diversity are some key parameters to study the breeding history of indigenous small ruminants. In this study, the OvineSNP50 Bead Chip array was used to estimate and compare LD, genetic diversity, effective population size (Ne) and genomic inbreeding in 186 individuals, from three Iranian indigenous sheep breeds consisting of Baluchi (n = 96), Lori-Bakhtiari (n = 47) and Zel (n = 47). The results of principal component analysis (PCA) revealed that all animals were allocated to the groups that they sampled and the admixture analysis revealed that the structure within the populations is best explained when separated into three groups (K  =  3). The average r2 values estimated between adjacent single nucleotide polymorphisms (SNPs) at distances up to 10Kb, were 0.388±0.324, 0.353±0.311, and 0.333±0.309 for Baluchi, Lori-Bakhtiari and Zel, respectively. Estimation of genetic diversity and effective population size (Ne) showed that the Zel breed had the highest heterozygosity and Ne, whereas the lowest value was found in Baluchi breed. Estimation of genomic inbreeding using FROH (based on the long stretches of consecutive homozygous genotypes) showed the highest inbreeding coefficient in Baluchi and the lowest in Zel breed that could be due to higher pressure of artificial selection on Baluchi breed. The results of genomic inbreeding and Ne showed an increase in sharing haplotypes in Baluchi, leading to the enlargement of LD and the consequences of linkage disequilibrium and haplotype blocks confirmed this point. Also, the persistence of the LD phase between Zel and Lori-Bakhtiari was highest indicating that these two breeds would be combined in a multi-breed training population in genomic selection studies.

Hotspot analysis for organic laying hen husbandry—identification of sustainability problems as potential risk points to lose consumers’ trust

Over the last decade, there has been growing societal concern about the welfare of farmed animals. Although organic agriculture provides higher living standards, there are still critical points which can damage consumers’ trust in organic livestock farming. That is a risk, as especially organic farming relies on consumer trust. A hotspot analysis was conducted to identify critical points within the organic laying hen husbandry in Germany. This methodology aims to examine the sustainability of a product along its whole life cycle. Based on literature reviews, the life phases breeding, keeping, feeding, animal health, transport, and slaughter were assessed with ecological, social, and animal welfare criteria. Finally, the results were triangulated with various experts, and the critical points were classified in terms of their potential to diverge from consumers’ expectations. Our results show a high dependency of the organic sector on the conventional breeding process and its specialized breeds. This fact involves critical points which contradict the ideology of organic farming. The loopholes in the organic EU regulations in transport and slaughter were identified as additional threats to consumer trust in the organic system. The overall not better animal health compared to the conventional poultry system and the high numbers of poultry kept on some organic farms are also possible causes of disappointment in consumers’ vision of organic livestock farming. Therefore, we recommend an adjustment of some organic EU regulations regarding these points. Further, a linkage of the organic certification of a slaughterhouse to higher animal welfare standards during slaughter should be considered.

Maintenance of genetic diversity in subdivided populations using genomic coancestry matrices

For both undivided and subdivided populations, the consensus method to maintain genetic diversity is the Optimal Contribution (OC) method. For subdivided populations, this method determines the optimal contribution of each candidate to each subpopulation to maximize global genetic diversity (which implicitly optimizes migration between subpopulations) while balancing the relative levels of coancestry between and within subpopulations. Inbreeding can be controlled by increasing the weight given to within-subpopulation coancestry (λ). Here we extend the original OC method for subdivided populations that used pedigree-based coancestry matrices, to the use of more accurate genomic matrices. Global levels of genetic diversity, measured as expected heterozygosity and allelic diversity, their distributions within and between subpopulations, and the migration pattern between subpopulations, were evaluated via stochastic simulations. The temporal trajectory of allele frequencies was also investigated. The genomic matrices investigated were (i) the matrix based on deviations of the observed number of alleles shared by two individuals from the expected number under Hardy-Weinberg equilibrium; and (ii) a matrix based on a genomic relationship matrix. The matrix based on deviations led to higher global and within-subpopulation expected heterozygosities, lower inbreeding and similar allelic diversity than the second genomic and pedigree-based matrices when a relatively high weight was given to the within-subpopulation coancestries (λ ≥ 5). Under this scenario, allele frequencies moved only slightly away from the initial frequencies. Therefore, the recommended strategy is to use the former matrix in the OC methodology giving a high weight to the within-subpopulation coancestry.

The study of selection signature and its applications on identification of candidate genes using whole genome sequencing data in chicken - a review

Chicken is a major source of protein for the increasing human population and is useful for research purposes. There are almost 1,600 distinct regional breeds of chicken across the globe, among which a large body of genetic and phenotypic variations has been accumulated due to extensive natural and artificial selection. Moreover, natural selection is a crucial force for animal domestication. Several approaches have been adopted to detect selection signatures in different breeds of chicken using whole genome sequencing (WGS) data including integrated haplotype score (iHS), cross-populated extend haplotype homozygosity test (XP-EHH), fixation index (F_ST), cross-population composite likelihood ratio (XP-CLR), nucleotide diversity (Pi), and others. In addition, gene enrichment analyses are utilized to determine KEGG pathways and gene ontology (GO) terms related to traits of interest in chicken. Herein, we review different studies that have adopted diverse approaches to detect selection signatures in different breeds of chicken. This review systematically summarizes different findings on selection signatures and related candidate genes in chickens. Future studies could combine different selection signatures approaches to strengthen the quality of the results thereby providing more affirmative inference. This would further aid in deciphering the importance of selection in chicken conservation for the increasing human population.

Assessment of Genetic Diversity and Conservation in South African Indigenous Goat Ecotypes: A Review

Goats were amongst the first livestock to be domesticated more than 10,000 years ago for their meat, milk, skin, and fiber. They were introduced to Southern Africa by migrating nations from Central Africa to the south. Due to local adaptation to the different agro-ecological zones and selection, indigenous goats are identified as ecotypes within the indigenous veld goat breed. Their ability to thrive in a resource-limited production system and in challenging environmental conditions makes them valuable animal resources for small-scale and emerging farmers. They play important roles in household agriculture and cultural activities as well as in poverty alleviation. Studies have described the phenotypic and genetic variations in indigenous goats, targeting the major goat-producing regions and the breeds of South Africa. In turn, information is restricted to certain breeds and regions, and the experimental design is often not adequate to inform the conservation status and priorities in changing environments. Advances in genomics technologies have availed more opportunities for the assessment of the biodiversity, demographic histories, and detection regions associated with local adaptation. These technologies are essential for breeding and conservation strategies for sustainable production for food security. This review focuses on the status of indigenous goats in South Africa and the application of genomics technologies for characterization, with emphasis on prioritization for conservation and sustainable utilization.

Unveiling new perspective of phylogeography, genetic diversity, and population dynamics of Southeast Asian and Pacific chickens

The complex geographic and temporal origins of chicken domestication have attracted wide interest in molecular phylogeny and phylogeographic studies as they continue to be debated up to this day. In particular, the population dynamics and lineage-specific divergence time estimates of chickens in Southeast Asia (SEA) and the Pacific region are not well studied. Here, we analyzed 519 complete mitochondrial DNA control region sequences and identified 133 haplotypes with 70 variable sites. We documented 82.7% geographically unique haplotypes distributed across major haplogroups except for haplogroup C, suggesting high polymorphism among studied individuals. Mainland SEA (MSEA) chickens have higher overall genetic diversity than island SEA (ISEA) chickens. Phylogenetic trees and median-joining network revealed evidence of a new divergent matrilineage (i.e., haplogroup V) as a sister-clade of haplogroup C. The maximum clade credibility tree estimated the earlier coalescence age of ancestral D-lineage (i.e., sub-haplogroup D2) of continental chickens (3.7 kya; 95% HPD 1985-4835 years) while island populations diverged later at 2.1 kya (95% HPD 1467-2815 years). This evidence of earlier coalescence age of haplogroup D ancestral matriline exemplified dispersal patterns to the ISEA, and thereafter the island clade diversified as a distinct group.

Mitochondrial Whole D-Loop Variability in Polish Draft Horses of Sztumski Subtype

The Polish draft horse (PDH) breed is a result of crossing local mares with imported cold-blooded stallions, such as Belgians, Ardennes, Fjords, and others. A part of the broodmare stock investigated in this study was also imported from various countries, such as Denmark. In this study, we investigate the genetic composition of the PDH by analyzing the whole mitochondrial d-loop variability and comparing it to previously demonstrated whole d-loop sequences of other cold-blooded breeds: Ardennais, Belgian, Breton, Clydesdale, Noriker, Norwegian Fjord, Percheron, and Suffolk. Our results show high nucleotide diversity within the PDH population (π = 0.011), and the existence of two main haplogroups: one of relatively concise origin, with strong kinship to the Belgian breed, and the second showing close relation to the majority of other analyzed cold-blooded breeds. Some of the PDH maternal strains clustered separately, which can be a result of the influence of other unidentified breeds that served as a foundation stock for the present population. This present study explains the genetic relationship of the PDH to other cold-blooded breeds and indicates the high genetic diversity of the breed.

Genome-wide run of homozygosity analysis reveals candidate genomic regions associated with environmental adaptations of Tibetan native chickens

Background

In Tibet, the two most important breeds are Tibetan chicken and Lhasa white chicken, and the duo exhibit specific adaptations to the high altitude thereby supplying proteins for humans living in the plateau. These breeds are partly included in the conservation plans because they represent important chicken genetic resources. However, the genetic diversity of these chickens is rarely investigated. Based on whole-genome sequencing data of 113 chickens from 4 populations of Tibetan chicken including Shigatse (SH), Nyemo (NM), Dagze (DZ) and Nyingchi (LZ), as well as Lhasa white (LW) chicken breed, we investigated the genetic diversity of these chicken breeds by genetic differentiation, run of homozygosity (ROH), genomic inbreeding and selection signature analyses.

Results

Our results revealed high genetic diversity across the five chicken populations. The linkage disequilibrium decay was highest in LZ, while subtle genetic differentiation was found between LZ and other populations (Fst ranging from 0.05 to 0.10). Furthermore, the highest ROH-based inbreeding estimate (F_ROH) of 0.11 was observed in LZ. In other populations, the F_ROH ranged from 0.04 to 0.06. In total, 74, 111, 62, 42 and 54 ROH islands containing SNPs ranked top 1% for concurrency were identified in SH, NM, DZ, LZ and LW, respectively. Genes common to the ROH islands in the five populations included BDNF, CCDC34, LGR4, LIN7C, GLS, LOC101747789, MYO1B, STAT1 and STAT4. This suggested their essential roles in adaptation of the chickens. We also identified a common candidate genomic region harboring AMY2A, NTNG1 and VAV3 genes in all populations. These genes had been implicated in digestion, neurite growth and high-altitude adaptation.

Conclusions

High genetic diversity is observed in Tibetan native chickens. Inbreeding is more intense in the Nyingchi population which is also genetically distant from other chicken populations. Candidate genes in ROH islands are likely to be the drivers of adaptation to high altitude exhibited by the five Tibetan native chicken populations. Our findings contribute to the understanding of genetic diversity offer valuable insights for the genetic mechanism of adaptation, and provide veritable tools that can help in the design and implementation of breeding and conservation strategies for Tibetan native chickens.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08280-z.

Morphometric and microsatellite-based comparative genetic diversity analysis in Bubalus bubalis from North India

To understand the similarities and dissimilarities of a breed structure among different buffalo breeds of North India, it is essential to capture their morphometric variation, genetic diversity, and effective population size. In the present study, diversity among three important breeds, namely, Murrah, Nili-Ravi and Gojri were studied using a parallel approach of morphometric characterization and molecular diversity. Morphology was characterized using 13 biometric traits, and molecular diversity through a panel of 22 microsatellite DNA markers recommended by FAO, Advisory Group on Animal Genetic Diversity, for diversity studies in buffaloes. Canonical discriminate analysis of biometric traits revealed different clusters suggesting distinct genetic entities among the three studied populations. Analysis of molecular variance revealed 81.8% of genetic variance was found within breeds, while 18.2% of the genetic variation was found between breeds. Effective population sizes estimated based on linkage disequilibrium were 142, 75 and 556 in Gojri, Nili-Ravi and Murrah populations, respectively, indicated the presence of sufficient genetic variation and absence of intense selection among three breeds. The Bayesian approach of STRUCTURE analysis (at K = 3) assigned all populations into three clusters with a degree of genetic admixture in the Murrah and Nili-Ravi buffalo populations. Admixture analysis reveals introgression among Murrah and Nili-Ravi breeds while identified the Gojri as unique buffalo germplasm, indicating that there might be a common origin of Murrah and Nili-Ravi buffaloes. The study provides important insights on buffalo breeds of North India that could be utilized in designing an effective breeding strategy, with an appropriate choice of breeds for upgrading local non-descript buffaloes along with conservation of unique germplasm.

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.

On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Background

During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach.

Results

Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools.

Conclusions

This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00639-w.

Genetic Diversity and Population Structure of Dromedary Camel-Types

The dromedary camel is a unique livestock for its adaptations to arid-hot environments and its ability to provide goods under extreme conditions. There are no registries or breed standards for camels. Thus, named camel populations (i.e., camel-types) were examined for genetic uniqueness and breed status. Camel populations are generally named based on shared phenotype, country or region of origin, tribal ownership, or the ecology of their habitat. A dataset of 10 Short-Tandem Repeat markers genotyped for 701 individual camels from 27 camel-types was used to quantify genetic diversity within camel-types, compare genetic diversity across camel-types, determine the population genetic structure of camel-types, and identify camel-types that may represent true breeds. Summary statistics (genotyping call rate, heterozygosity, inbreeding coefficient FIS, and allelic frequencies) were calculated and population-specific analyses (pairwise FST, neighbor-joining tree, relatedness, Nei's genetic distance, principal coordinate analysis [PCoA], and STRUCTURE) were performed. The most notable findings were 1) little variation in genetic diversity was found across the camel-types, 2) the highest genetic diversity measure was detected in Targui and the lowest was in Awarik, 3) camel-types from Asia (especially the Arabian Peninsula) exhibited higher genetic diversity than their counterparts in Africa, 4) the highest DeltaK value of population structure separated camel-types based on geography (Asia vs. Africa), 5) the most distinct camel-types were the Omani, Awarik, and the Gabbra, 6) camel-types originating from the same country did not necessarily share high genetic similarity (e.g., camel-types from Oman), and 7) camel-type names were not consistently indicative of breed status.

Genetic Diversity and Population Genetic Structure of a Guzerá (Bos indicus) Meta-Population

The Brazilian Guzerá population originated from a few founders introduced from India. These animals adapted well to the harsh environments in Brazil, were selected for beef, milk, or dual-purpose (beef and milk), and were extensively used to produce crossbred animals. Here, the impact of these historical events with regard to the population structure and genetic diversity in a Guzerá meta-population was evaluated. DNA samples of 744 animals (one dairy, nine dual-purpose, and five beef herds) were genotyped for 21 microsatellite loci. Ho, He, PIC, Fis, Fit, and Fst estimates were obtained considering either farms or lineages as subpopulations. Mean Ho (0.73) and PIC (0.75) suggest that genetic diversity was efficiently conserved. Fit, Fis and Fst values (95% CI) pointed to a low fixation index, and large genetic diversity: Fit (Farms = 0.021-0.100; lineages = 0.021-0.100), Fis (Farms = -0.007-0.076; lineages = -0.014-0.070), and Fst (Farms = 0.0237-0.032; lineages = 0.029-0.038). The dual-purpose herds/selection lines are the most uniform subpopulation, while the beef one preserved larger amounts of genetic diversity among herds. In addition, the dairy herd showed to be genetically distant from other herds. Taken together, these results suggest that this Guzerá meta-population has high genetic diversity, a low degree of population subdivision, and a low inbreeding level.

Genetic characterisation of non-descript cattle populations in communal areas of South Africa

Context Indigenous cattle breeds represent an important genetic resource for livelihood of communal-area inhabitants. Indigenous breeds have the ability to withstand harsh climatic conditions, can adapt genetically to poor-quality forages and are resistant to parasites and diseases. These unique traits possessed by indigenous breeds are under threat because of unrestrained crossing with exotic commercial breeds, and this can lead to total loss of a breed. Aims The study was conducted to assess the genetic diversity and population structure of South African non-descript communal beef cattle populations by using 25 microsatellite markers. Methods Unrelated and non-descript animals (n = 150) were sampled from communal areas from five (5) provinces of South Africa, namely, Eastern Cape, KwaZulu–Natal, Limpopo, Mpumalanga and the North West, with 30 samples per breed taken. Six (6) known cattle breeds (n = 180) were used as a reference population. This included Angus, Afrikaner, Bonsmara, Brahman, Drakensberger and the Nguni, with 30 samples per breed. Key results High level of genetic diversity was found across the five non-descript populations, with an average heterozygosity of 75%. The Limpopo population was found to be the most diverse population, with the highest average number of alleles (8.5) and heterozygosity (ranging between observed heterozygosity of 70% and expected heterozygosity of 79%). STRUCTURE software assigned populations (2 ≤ K ≤ 20), with the most probable cluster being at K = 7. The Eastern Cape, KwaZulu–Natal and Limpopo populations had genetic material similar to those possessed by the Nguni and Bonsmara reference populations. Conclusions Results from the study showed that most genetic differentiation occurred within populations rather than among populations, and this might be due to the fact that there is no selection for or against any specific production trait expressed in the populations. Implications The obtained information will serve as a baseline for the development and implementation of sound breeding programs that will assist in controlling the gene flow, so as to lower the possible genetic dilution of the currently available genetic material.

Examination of the efficacy of small genetic panels in genomic conservation of companion animal populations

In many ways, dogs are an ideal model for the study of genetic erosion and population recovery, problems of major concern in the field of conservation genetics. Genetic diversity in many dog breeds has been declining systematically since the beginning of the 1800s, when modern breeding practices came into fashion. As such, inbreeding in domestic dog breeds is substantial and widespread and has led to an increase in recessive deleterious mutations of high effect as well as general inbreeding depression. Pedigrees can in theory be used to guide breeding decisions, though are often incomplete and do not reflect the full history of inbreeding. Small microsatellite panels are also used in some cases to choose mating pairs to produce litters with low levels of inbreeding. However, the long-term impact of such practices has not been thoroughly evaluated. Here, we use forward simulation on a model of the dog genome to examine the impact of using limited marker panels to guide pairwise mating decisions on genome-wide population-level genetic diversity. Our results suggest that in unmanaged populations, where breeding decisions are made at the pairwise-rather than population-level, such panels can lead to accelerated loss of genetic diversity at genome regions unlinked to panel markers, compared to random mating. These results demonstrate the importance of genome-wide genetic panels for managing and conserving genetic diversity in dogs and other companion animals.

Genetic Characterization of Mangalarga Marchador Breed Horses Based on Microsatellite Molecular Markers

The Mangalarga Marchador (MM) horse breed has expressive importance in the Brazilian economy. Thus, the aim of this study was to investigate diversity in the MM breed. A database with a total of 3,193 genotyped horses was used (MM, n = 2,829; Andalusian - AND, n = 67; Pure Blood Lusitano - LUS, n = 43; English Thoroughbred - THO, n = 54; Arabian - ARA, n = 99; Campolina - CAM, n = 61; and Mangalarga - MAN, n = 40) for 13 microsatellite. Diversity parameters were estimates, such as mean number of alleles (Nm_a) and the number of rare alleles (AR), expected heterozygosity (He), F statistics, genetic distances, Hardy-Weinberg equilibrium test (HWE), population structure, and others. The Nm_a was 10.85, the AR was prevalent in the MM, and the He was 0.7402. In MM, the values of Fis (-0.0195), Fit (0.0566), Fst (0.0748), and deviations of HWE were observed. The genetic distances of the ARA and THO breeds with the other breeds were greater than the distances between the Brazilian breeds and between these and the breeds in the Iberian Peninsula. The population structure indicated that MM was substructured, yet there were some more genetically defined breeding farms. The genetic diversity is satisfactory for MM conservation, but the population is substructure, and parameters indicate moderate gene flow and the existence, though few, of crosses with other horse breeds. Immediate implementation of a genetic breeding program is required, especially seeking to conserve the structure of the MM breed as a well-defined genetic entity.

Monitoring of genetically close Tsaiya duck populations using novel microsatellite markers with high polymorphism

OBJECTIVE

A set of microsatellite markers with high polymorphism from Tsaiya duck were used for the genetic monitoring and genetic structure analysis of Brown and White Tsaiya duck populations in Taiwan.

METHODS

The synthetic short tandem repeated probes were used to isolate new microsatellite markers from the genomic DNA of Tsaiya ducks. Eight populations, a total of 566 samples, sourced from Ilan Branch, Livestock Research Institute were genotyped through novel and known markers. The population genetic variables were calculated using optional programs in order to describe and monitor the genetic variability and the genetic structures of these Tsaiya duck populations.

RESULTS

In total 24 primer pairs, including 17 novel microsatellite loci from this study and seven previously known loci, were constructed for the detection of genetic variations in duck populations. The average values for the allele number, the effective number of alleles, the observed heterozygosity, the expected heterozygosity, and the polymorphism information content were 11.29, 5.370, 0.591, 0.746, and 0.708, respectively. The results of analysis of molecular variance and principal component analysis indicated a contracting Brown Tsaiya duck cluster and a spreading White Tsaiya duck cluster. The Brown Tsaiya ducks and the White Tsaiya ducks with Pekin ducks were just split to six clusters and three clusters when K was set equal to 6 and 3 in the Bayesian cluster analysis. The individual phylogenetic tree revealed eight taxa, and each individual was assigned to its own population.

CONCLUSION

According to our study, the 24 novel microsatellite markers exhibited a high capacity to analyze relationships of inter- and intra-population in those populations with a relatively limited degree of genetic diversity. We suggest that duck farms in Taiwan could use the new (novel) microsatellite set to monitor the genetic characteristics and structures of their Tsaiya duck populations at various intervals in order to ensure quality breeding and conservation strategies.

Optimal Management of Genetic Diversity in Subdivided Populations

One of the main objectives of conservation programs is the maintenance of genetic diversity because this provides the adaptive potential of populations to face new environmental challenges. Genetic diversity is generally assessed by means of neutral molecular markers, and it is usually quantified by the expected heterozygosity under Hardy-Weinberg equilibrium and the number of alleles per locus or allelic diversity. These two measures of genetic diversity are complementary because whereas the former is directly related to genetic variance for quantitative traits and, therefore, to the short-term response to selection and adaptation, the latter is more sensitive to population bottlenecks and relates more strongly to the long-term capacity of adaptation of populations. In the context of structured populations undergoing conservation programs, it is important to decide the optimum management strategy to preserve as much genetic diversity as possible while avoiding inbreeding. Here we examine, through computer simulations, the consequences of choosing a conservation strategy based on maximizing either heterozygosity or allelic diversity of single-nucleotide polymorphism haplotypes in a subdivided population. Our results suggest that maximization of allelic diversity can be more efficient in maintaining the genetic diversity of subdivided populations than maximization of expected heterozygosity because the former maintains a larger number of alleles while making a better control of inbreeding. Thus, maximization of allelic diversity should be a recommended strategy in conservation programs for structured populations.

Identification of novel single nucleotide polymorphisms in the PRKAG3 gene of Pakistani river buffalo

Pakistani river buffalo is classified in five breeds out of which Kundi buffalo has been least documented. This study is designed to find single nucleotide polymorphisms (SNPs) in exonic and in-tronic regions of PRKAG3 (AMP-activated, Gamma3 non-catalytic subunit) gene in the Kundi buf-falo. The PRKAG3 gene of 95 animals each from Kundi and Nili-Ravi were sequenced for identifica-tion of novel SNPs. Comparing with the Nili Ravi breed of buffalo PRKAG3 gene, six SNP sites were identified in the Kundi buffalo. The novel SNPs found in this work can function as a genomic indicator for genetic-phenotypic relationship of PRKAG3 gene with milk and meat production in buffalo. This is the first report of SNPs in PRKAG3 gene of Kundi Buffalo.

Key Genetic Parameters for Population Management

Population management has the primary task of maximizing the long-term competitiveness of a breed. Breeds compete with each other for being able to supply consumer demands at low costs and also for funds from conservation programs. The competition for consumer preference is won by breeds with high genetic gain for total merit who maintained a sufficiently high genetic diversity, whereas the competition for funds is won by breeds with high conservation value. The conservation value of a breed could be improved by increasing its contribution to the gene pool of the species. This may include the recovery of its original genetic background and the maintenance of a high genetic diversity at native haplotype segments. The primary objective of a breeding program depends on the genetic state of the population and its intended usage. In this paper, we review the key genetic parameters that are relevant for population management, compare the methods for estimating them, derive the formulas for predicting their value at a future time, and clarify their usage in various types of breeding programs that differ in their main objectives. These key parameters are kinships, native kinships, breeding values, Mendelian sampling variances, native contributions, and mutational effects. Population management currently experiences a transition from using pedigree-based estimates to marker-based estimates, which improves the accuracies of these estimates and thereby increases response to selection. In addition, improved measures of the factors that determine the competitiveness of a breed and utilize auxiliary parameters, such as Mendelian sampling variances, mutational effects, and native kinships, enable to improve further upon historic recommendations for genetic population management.

Insights into the genetic diversity of indigenous goats and their conservation priorities

Objective

An experiment was conducted to evaluate genetic diversity of 26 Chinese indigenous goats by 30 microsatellite markers, and then to define conservation priorities to set up the protection programs according to the weight given to within- and between-breed genetic diversity.

Methods

Twenty-six representative populations of Chinese indigenous goats, 1,351 total, were sampled from different geographic regions of China. Within-breed genetic diversity and marker polymorphism were estimated calculating the mean number of alleles, observed heterozygosities, expected heterozygosities, fixation index, effective number of alleles and allelic richness. Conservation priorities were analyzed by statistical methods.

Results

A relatively high level of genetic diversity was found in twenty-four population; the exceptions were in the Daiyun and Fuqing goat populations. Within-breed kinship coefficient matrices identified seven highly inbred breeds which should be of concern. Of these, six breeds receive a negative contribution to heterozygosity when the method was based on proportional contribution to heterozygosity. Based on Weitzman or Piyasatian and Kinghorn methods, the breeds distant from others i.e. Inner Mongolia Cashmere goat, Chengdu Brown goat and Leizhou goat obtain a high ranking. Evidence from Caballero and Toro and Fabuel et al method prioritized Jining Gray goat, Liaoning Cashmere goat, and Inner Mongolia Cashmere goat, which agree with results from Kinship-based methods.

Conclusion

Conservation priorities were determined according to multiple methods. Our results suggest Inner Mongolia Cashmere goat (most methods), Jining Gray goat and Liaoning Cashmere goat (high contribution to heterozygosity and total diversity) should be prioritized based on most methods. Furthermore, Daiyun goat and Shannan White goat also should be prioritized based on consideration of effective population size. However, if one breed can continually survive under changing conditions, the straightforward approach would be to increase its utilization and attraction for production via mining breed germplasm characteristics.

Genetic Polymorphism and Bottleneck Analysis of Balkhi, Hashtnagri, and Michni Sheep Populations Using Microsatellite Markers

Pakistan is rich in sheep genetic resources. Balkhi, Hashtnagri, and Michni are neighboring sheep populations found in Khyber Pakhtunkhwa province of Pakistan. In this study, we analyzed the genetic structures and bottleneck incidents within these sheep populations using 31 microsatellite DNA markers. Total numbers of 116, 100, and 95 alleles, with average numbers of 3.20, 3.26, and 3.74 alleles per locus were observed, respectively, in Balkhi, Hashtnagri, and Michni population. Mean observed heterozygosity was 0.402 in Balkhi, 0.416 in Hashtnagri, and 0.522 in Michni population. All the three sheep populations showed significantly high inbreeding. Michni population was found to be in mutation drift equilibrium, showing the absence of genetic bottleneck. The data of Balkhi and Hashtnagri indicated the presence of genetic bottleneck in these populations. These results suggest a moderate level of genetic diversity within Michni population that may be useful for breed improvement programs. Hashtnagri and Balkhi populations having low within breed genetic variability may contain some valuable characteristics that need to be conserved.

The impact of using old germplasm on genetic merit and diversity-A cattle breed case study

Artificial selection and high genetic gains in livestock breeds led to a loss of genetic diversity. Current genetic diversity conservation actions focus on long-term maintenance of breeds under selection. Gene banks play a role in such actions by storing genetic materials for future use and the recent development of genomic information is facilitating characterization of gene bank material for better use. Using the Meuse-Rhine-Issel Dutch cattle breed as a case study, we inferred the potential role of germplasm of old individuals for genetic diversity conservation of the current population. First, we described the evolution of genetic merit and diversity over time and then we applied the optimal contribution (OC) strategy to select individuals for maximizing genetic diversity, or maximizing genetic merit while constraining loss of genetic diversity. In the past decades, genetic merit increased while genetic diversity decreased. Genetic merit and diversity were both higher in an OC scenario restricting the rate of inbreeding when old individuals were considered for selection, compared to considering only animals from the current population. Thus, our study shows that gene bank material, in the form of old individuals, has the potential to support long-term maintenance and selection of breeds.

The effects of recent changes in breeding preferences on maintaining traditional Dutch chicken genomic diversity

Traditional Dutch chicken breeds are marginalised breeds of ornamental and cultural-historical importance. In the last decades, miniaturising of existing breeds (so called neo-bantam) has become popular and resulted in alternatives to original large breeds. However, while backcrossing is increasing the neo-bantams homozygosity, genetic exchange between breeders may increase their genetic diversity. We use the 60 K SNP array to characterise the genetic diversity, demographic history, and level of inbreeding of Dutch heritage breeds, and particularly of neo-bantams. Commercial white layers are used to contrast the impact of management strategy on genetic diversity and demography. A high proportion of alleles was found to be shared between large fowls and neo-bantams, suggesting gene flow during neo-bantams development. Population admixture analysis supports these findings, in addition to revealing introgression from neo-bantams of the same breed and of phenotypically similar breeds. The prevalence of long runs of homozygosity (ROH) confirms the importance of recent inbreeding. A high diversity in management, carried out in small breeding units explains the high heterogeneity in diversity and ROH profile displayed by traditional breeds compared to commercial lines. Population bottlenecks may explain the long ROHs in large fowls, while repetitive backcrossing for phenotype selection may account for them in neo-bantams. Our results highlight the importance of using markers to inform breeding programmes on potentially harmful homozygosity to prevent loss of genetic diversity. We conclude that bantamisation has generated unique and identifiable genetic diversity. However, this diversity can only be preserved in the near future through structured breeding programmes.

Population structure and phylogenetic analysis of laboratory rabbits in Taiwan based on microsatellite markers

Laboratory rabbits used in Taiwan are primarily supplied by the Livestock Research Institute (LRI) and the Animal Drugs Inspection Branch (ADIB) of the Animal Health Research Institute. An analysis of the genetic characteristics and structure of these populations would thus be a fundamental step in building a long-term management programme for maintaining stable animal quality and preserving the genetic variation among the populations. In this study, DNA samples were isolated from founders of 5 populations: New Zealand White rabbits (NZW) and Japanese White rabbits (JPN) from the ADIB, NZW and Rex rabbits (REX) from the LRI, and NZW from a private rabbit breeding farm in Ban Ciao (BC). A set of microsatellite markers, 18 in total, was designed for genetic analysis. The average values for the allele number (Na), effective number of alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (H_E), and Wright’s fixation index (F_IS) were 5.50, 2.437, 0.442, 0.568 and 0.232, respectively. These results revealed that this set of microsatellite markers has high diversity and that the major local populations have a tendency toward inbreeding. At the same time, analysis of molecular variance results showed that the laboratory rabbits used in Taiwan have maintained a high level of within-population genetic differentiation (83%). The genetic differentiation among clusters was moderate (F_ST=0.18), and Bayesian cluster analysis showed that the most likely number of groups was 4 (K=4). Principal component analysis (PCA) also showed 4 divergent clusters. The LRI and BC NZW populations were not separated when K=4 was used in a Structure software analysis and were also hard to split until principal component 3 in PCA. The individual unrooted phylogenetic tree showed that the 5 populations were separated, except that some individuals from the LRI NZW population overlapped with the ADIB NZW and BC NZW populations. As such, in order to counteract the reduced F_IS (0.232) and maximise heterozygosity, the 3 NZW populations could be interbred or have new genes introduced into them. The set of microsatellite markers used herein was useful for studying the relationships and genetic diversities among these rabbit populations of Taiwan. Based on the resulting data, rabbit farms in Taiwan could select parental stocks for planned mating in the future as part of strategies to preserve and restore the rational breeding of laboratory rabbits.

Genetic analysis of the Hungarian draft horse population using partial mitochondrial DNA D-loop sequencing

Background

The Hungarian draft is a horse breed with a recent mixed ancestry created in the 1920s by crossing local mares with draught horses imported from France and Belgium. The interest in its conservation and characterization has increased over the last few years. The aim of this work is to contribute to the characterization of the endangered Hungarian heavy draft horse populations in order to obtain useful information to implement conservation strategies for these genetic stocks.

Methods

To genetically characterize the breed and to set up the basis for a conservation program, in the present study a hypervariable region of the mitochrondial DNA (D-loop) was used to assess genetic diversity in Hungarian draft horses. Two hundred and eighty five sequences obtained in our laboratory and 419 downloaded sequences available from Genbank were analyzed.

Results

One hundred and sixty-four haplotypes and thirty-six polymorphic sites were observed. High haplotype and nucleotide diversity values (H_d = 0.954 ± 0.004; π = 0.028 ± 0.0004) were identified in Hungarian population, although they were higher within than among the different populations (H_d = 0.972 ± 0.002; π = 0.03097 ± 0.002). Fourteen of the previously observed seventeen haplogroups were detected.

Discussion

Our samples showed a large intra- and interbreed variation. There was no clear clustering on the median joining network figure. The overall information collected in this work led us to consider that the genetic scenario observed for Hungarian draft breed is more likely the result of contributions from ‘ancestrally’ different genetic backgrounds. This study could contribute to the development of a breeding plan for Hungarian draft horses and help to formulate a genetic conservation plan, avoiding inbreeding while.

Which Individuals To Choose To Update the Reference Population? Minimizing the Loss of Genetic Diversity in Animal Genomic Selection Programs

Genomic selection (GS) is commonly used in livestock and increasingly in plant breeding. Relying on phenotypes and genotypes of a reference population, GS allows performance prediction for young individuals having only genotypes. This is expected to achieve fast high genetic gain but with a potential loss of genetic diversity. Existing methods to conserve genetic diversity depend mostly on the choice of the breeding individuals. In this study, we propose a modification of the reference population composition to mitigate diversity loss. Since the high cost of phenotyping is the limiting factor for GS, our findings are of major economic interest. This study aims to answer the following questions: how would decisions on the reference population affect the breeding population, and how to best select individuals to update the reference population and balance maximizing genetic gain and minimizing loss of genetic diversity? We investigated three updating strategies for the reference population: random, truncation, and optimal contribution (OC) strategies. OC maximizes genetic merit for a fixed loss of genetic diversity. A French Montbéliarde dairy cattle population with 50K SNP chip genotypes and simulations over 10 generations were used to compare these different strategies using milk production as the trait of interest. Candidates were selected to update the reference population. Prediction bias and both genetic merit and diversity were measured. Changes in the reference population composition slightly affected the breeding population. Optimal contribution strategy appeared to be an acceptable compromise to maintain both genetic gain and diversity in the reference and the breeding populations.

Genomic Regions in Local Endangered Sheep Encode Potentially Favorable Genes

The economic evaluation of farm animal genetic resources plays a key role in developing conservation programs. However, to date, the link between diversity as assessed by neutral genetic markers and the functional diversity is not yet understood. Two genome-wide comparisons, using over 44,000 Single Nucleotide Polymorphisms, identified the markers with the highest difference in allele frequency between the Alpago endangered breed and two clusters, composed of four specialized dairy sheep, and four meat breeds respectively. The genes in proximity of these markers were mapped to known pathways of the Gene Ontology to determine which ones were most represented. Our results indicated that the differences of the Alpago breed from the more productive sheep rely upon genes involved in cellular defense and repair mechanisms. A higher number of different markers and genes were detected in the comparison with the specialized dairy sheep. These genes play a role in complex biological processes: metabolic, homeostatic, neurological system, and macromolecular organization; such processes may possibly explain the evolution of gene function as a result of selection to improve milk yield.

Microsatellite based Genetic Variation among the Buffalo Breed Populations in Pakistan

Introduction

Eight microsatellite loci were used to define genetic diversity among five native water buffalo breeds in Pakistan.

Material and Methods

Blood samples (10 mL) from 25 buffaloes of each of the Nili, Ravi, Nili-Ravi, Kundhi, and Azi-Kheli breeds were collected aseptically from the jugular vein into 50 ml Falcon tubes containing 200 µl of 0.5 M EDTA. The phenol-chloroform method was used to extract DNA and the regions were amplified for microsatellite analysis. The eight microsatellite markers ETH10, INRA005, ILSTS029, ILSTS033, ILSTS049, ILSTS052, ETH225, and CSSM66 were analysed.

Results

The effective number of alleles across all loci was as usual lower than the observed values with a mean value of 2.52 alleles per locus. The overall allele frequency varied from 0.0041 for alleles B, I, and J over respective loci ILSTS052, INRA005, and ILSTS029 to 0.80 for allele H over locus ILSTS029. The average observed and expected heterozygosity values across all polymorphic loci in all studied buffalo breeds were 0.43 and 0.53, respectively. The overall value for polymorphic information content of considered microsatellite markers was 0.53, suggesting their appropriateness for genetic diversity analysis in buffalo. The mean Fis value was 0.13 and all loci except ILSTS049 were found significantly deviated from HWE, most likely due to non-random breeding. The five buffalo populations were genetically less diverse as indicated by a small mean Fst value (0.07). The average gene flow (Nm) indicative for population migration was calculated as 3.31. Nei’s original measures of genetic distance (Ds) revealed ancient divergence of the Nili and Azi-Kheli breeds (Ds = 0.1747) and recent divergence of the Nili and Ravi breeds (Ds = 0.0374).

Conclusion

These estimates of genetic diversity were seen to coincide with phenotypic differentiation among the studied buffalo breeds. The present study reports the first microsatellite marker-based genetic diversity analysis in Pakistani buffalo breeds, and might facilitate similar studies in other livestock breeds of Pakistan.

Potential emigration of Siberian cattle germplasm on Chirikof Island, Alaska

Feral cattle residing in Chirikof Island, Alaska, are relatively distinct from breeds used in commercial production in North America. However, preliminary evidence suggested that they exhibit substantial genetic relationship with cattle from Yakutian region of Siberia. Thus, our objective was to further elucidate quantify the origins, admixture and divergence of the Chirikof Island cattle relative to cattle from Siberia and USA. Subject animals were genotyped at 15 microsatellite loci. Compared with Turano-Mongolian and North American cattle, Chirikof Island cattle had similar variation, with slightly less observed heterozygosity, fewer alleles per locus and a positive fixation index. Analysis of the genetic distances revealed two primary clusters; one that contained the North American breeds and the Kazakh White head, and a second that contained the Yakutian and Kalmyk breeds, and the Chirikof population. Thus, it is suggested that Chirikof Island cattle may be a composite of British breeds emanating from North America and Turano-Mongolian cattle. A potential founder effect, consistent with historical records of the Russian-American period, may contribute to the adaptation of the Chirikof Island cattle to their harsh high-latitude environment. Further study of adaptive mechanisms manifest by these cattle is warranted.

Inter- and intra-genetic diversity in the Polish Konik horse: implications for the conservation program

The main objective of the study was to determine the genetic diversity in the Polish Konik (PK) population in the context of a currently conducted conservation program. A total of 94 horses of 16 PK dam lines currently distinguished by breeders were considered. Pedigree analyses were carried out for the whole population of PK registered in the studbook. Basic molecular parameters were estimated. The average group linkage clustering method was used based on the Euclidean similarity measurements between the lines. The allele frequency of 17 microsatellites was used to determine Euclidean distances. Inbreeding coefficients were extracted from the additive relationship matrix. Moreover, some pedigree parameters were estimated. The observed heterozygosity ranged from 0.48 to 0.76. The expected heterozygosity estimated for the dam lines was higher. PIC values were higher than 0.6 in all the lines. Fis ranged from –0.19 to 0.28, whereas Fit and Fst varied between 0.12 and 0.41 and 0.12 and 0.29, respectively. Minor dissimilarity distances existed for some dam lines. The inbreeding level was 9.3%. The average number of discrete generation equivalents reached 6.85. The majority of the dam lines are not genetically differentiated. Hence, a revision of the breeding strategy seems to be necessary.

Whole-genome sequence data uncover loss of genetic diversity due to selection

BACKGROUND

Whole-genome sequence (WGS) data give access to more complete structural genetic information of individuals, including rare variants, not fully covered by single nucleotide polymorphism chips. We used WGS to investigate the amount of genetic diversity remaining after selection using optimal contribution (OC), considering different methods to estimate the relationships used in OC. OC was applied to minimise average relatedness of the selection candidates and thus miminise the loss of genetic diversity in a conservation strategy, e.g. for establishment of gene bank collections. Furthermore, OC was used to maximise average genetic merit of the selection candidates at a given level of relatedness, similar to a genetic improvement strategy. In this study, we used data from 277 bulls from the 1000 bull genomes project. We measured genetic diversity as the number of variants still segregating after selection using WGS data, and compared strategies that targeted conservation of rare (minor allele frequency <5 %) versus common variants.

RESULTS

When OC without restriction on the number of selected individuals was applied, loss of variants was minimal and most individuals were selected, which is often unfeasible in practice. When 20 individuals were selected, the number of segregating rare variants was reduced by 29 % for the conservation strategy, and by 34 % for the genetic improvement strategy. The overall number of segregating variants was reduced by 30 % when OC was restricted to selecting five individuals, for both conservation and genetic improvement strategies. For common variants, this loss was about 15 %, while it was much higher, 72 %, for rare variants. Fewer rare variants were conserved with the genetic improvement strategy compared to the conservation strategy.

CONCLUSIONS

The use of WGS for genetic diversity quantification revealed that selection results in considerable losses of genetic diversity for rare variants. Using WGS instead of SNP chip data to estimate relationships slightly reduced the loss of rare variants, while using 50 K SNP chip data was sufficient to conserve common variants. The loss of rare variants could be mitigated by a few percent (up to 8 %) depending on which method is chosen to estimate relationships from WGS data.

Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information

Criollo pig breeds are descendants from pigs brought to the American continent starting with Columbus second trip in 1493. Pigs currently play a key role in social economy and community cultural identity in Latin America. The aim of this study was to establish conservation priorities among a comprehensive group of Criollo pig breeds based on a set of 24 microsatellite markers and using different criteria. Spain and Portugal pig breeds, wild boar populations of different European geographic origins and commercial pig breeds were included in the analysis as potential genetic influences in the development of Criollo pig breeds. Different methods, differing in the weight given to within- and between-breed genetic variability, were used in order to estimate the contribution of each breed to global genetic diversity. As expected, the partial contribution to total heterozygosity gave high priority to Criollo pig breeds, whereas Weitzman procedures prioritized Iberian Peninsula breeds. With the combined within- and between-breed approaches, different conservation priorities were achieved. The Core Set methodologies highly prioritized Criollo pig breeds (Cr. Boliviano, Cr. Pacifico, Cr. Cubano and Cr. Guadalupe). However, weighing the between- and within-breed components with FST and 1-FST, respectively, resulted in higher contributions of Iberian breeds. In spite of the different conservation priorities according to the methodology used, other factors in addition to genetic information also need to be considered in conservation programmes, such as the economic, cultural or historical value of the breeds involved.

Genomic inbreeding coefficients based on the distribution of the length of runs of homozygosity in a closed line of Iberian pigs

BACKGROUND

The increasing availability of DNA markers provides new metrics of inbreeding based on single nucleotide polymorphisms (SNPs), i.e. molecular inbreeding or the proportion of runs of homozygosity (ROH), as alternatives to traditional pedigree-based inbreeding coefficients. However, none of these metrics incorporate the length of ROH as an indicator of recent inbreeding. Novel inbreeding coefficients that incorporate length of ROH as a random variable with an associated density are investigated.

METHODS

New inbreeding metrics based on the distribution of the length of ROH are proposed: (1) the Kolmolgorov-Smirnov test, (2) a function of the quantiles of the cumulative distribution function of an individual versus the population, and (3) fitting of an exponential distribution to ROH lengths (mean, variance, and the probability of drawing at random a ROH larger than a given threshold). The new inbreeding and pedigree-based metrics were compared using 217 sows of an Iberian line that belong to three groups: C1 (conservation), C2 (conservation derived from C1), and S (selected and derived from C1), with complete pedigrees and genotyped for 35,023 SNPs.

RESULTS

Correlations between pedigree-based and the new genomic inbreeding coefficients ranged from 0.22 to 0.72 but most ranged from 0.60 to 0.70. The correlation between quantile chromosomal inbreeding coefficients (using molecular information of just one chromosome at the time) and chromosomal length was 0.84 (SE = 0.14), supporting the hypothesis that these coefficients incorporate information on ROH length as an indication of recent inbreeding. Kolmogorov-Smirnov and exponential chromosomal inbreeding coefficients were also correlated with chromosomal length (0.57). Chromosome 1 had the largest quantile ROH inbreeding coefficient (largest ROH sizes), whereas chromosome 10 had the lowest (shortest ROH sizes). Selection for lean growth increased ROH-based inbreeding coefficients for group S when compared to unselected groups C1 and C2. At the chromosomal level, this comparison showed that the level of autozygosity and the length of ROH for most of the autosomes increased in the selection line.

CONCLUSIONS

Quantile and exponential probability inbreeding coefficients using ROH length as a random variable provide additional information about recent inbreeding compared to existing inbreeding coefficients such as molecular, pedigree-based or total ROH content inbreeding coefficients.

Allelic diversity for neutral markers retains a higher adaptive potential for quantitative traits than expected heterozygosity

The adaptive potential of a population depends on the amount of additive genetic variance for quantitative traits of evolutionary importance. This variance is a direct function of the expected frequency of heterozygotes for the loci which affect the trait (QTL). It has been argued, but not demonstrated experimentally, that long-term response to selection is more dependent on QTL allelic diversity than on QTL heterozygosity. Conservation programmes, aimed at preserving this variation, usually rely on neutral markers rather than on quantitative traits for making decisions on management. Here, we address, both through simulation analyses and experimental studies with Drosophila melanogaster, the question of whether allelic diversity for neutral markers is a better indicator of a high adaptive potential than expected heterozygosity. In both experimental and simulation studies, we established synthetic populations for which either heterozygosity or allelic diversity was maximized using information from QTL (simulations) or unlinked neutral markers (simulations and experiment). The synthetic populations were selected for the quantitative trait to evaluate the evolutionary potential provided by the two optimization methods. Our results show that maximizing the number of alleles of a low number of markers implies higher responses to selection than maximizing their heterozygosity.

Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle

Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore, the routine collection of genomic information would be an invaluable resource for effective management of breeding programs in small, endangered populations. The objective of the paper was to demonstrate how genomic data could be used to analyse (1) linkage disequlibrium (LD), LD decay and the effective population size (Ne_LD); (2) Inbreeding level and effective population size (Ne_ROH) based on runs of homozygosity (ROH); (3) Prediction of genomic breeding values (GEBV) using small within-breed and genomic information from other breeds. The Tyrol Grey population was used as an example, with the goal to highlight the potential of genomic analyses for small breeds. In addition to our own results we discuss additional use of genomics to assess relatedness, admixture proportions, and inheritance of harmful variants. The example data set consisted of 218 Tyrol Grey bull genotypes, which were all available AI bulls in the population. After standard quality control restrictions 34,581 SNPs remained for the analysis. A separate quality control was applied to determine ROH levels based on Illumina GenCall and Illumina GenTrain scores, resulting into 211 bulls and 33,604 SNPs. LD was computed as the squared correlation coefficient between SNPs within a 10 mega base pair (Mb) region. ROHs were derived based on regions covering at least 4, 8, and 16 Mb, suggesting that animals had common ancestors approximately 12, 6, and 3 generations ago, respectively. The corresponding mean inbreeding coefficients (F_ROH) were 4.0% for 4 Mb, 2.9% for 8 Mb and 1.6% for 16 Mb runs. With an average generation interval of 5.66 years, estimated Ne_ROH was 125 (Ne_{ROH>16 Mb}), 186 (Ne_{ROH>8 Mb}) and 370 (Ne_{ROH>4 Mb}) indicating strict avoidance of close inbreeding in the population. The LD was used as an alternative method to infer the population history and the Ne. The results show a continuous decrease in Ne_LD, to 780, 120, and 80 for 100, 10, and 5 generations ago, respectively. Genomic selection was developed for and is working well in large breeds. The same methodology was applied in Tyrol Grey cattle, using different reference populations. Contrary to the expectations, the accuracy of GEBVs with very small within breed reference populations were very high, between 0.13–0.91 and 0.12–0.63, when estimated breeding values and deregressed breeding values were used as pseudo-phenotypes, respectively. Subsequent analyses confirmed the high accuracies being a consequence of low reliabilities of pseudo-phenotypes in the validation set, thus being heavily influenced by parent averages. Multi-breed and across breed reference sets gave inconsistent and lower accuracies. Genomic information may have a crucial role in management of small breeds, even if its primary usage differs from that of large breeds. It allows to assess relatedness between individuals, trends in inbreeding and to take decisions accordingly. These decisions would be based on the real genome architecture, rather than conventional pedigree information, which can be missing or incomplete. We strongly suggest the routine genotyping of all individuals that belong to a small breed in order to facilitate the effective management of endangered livestock populations.

Genetic diversity in Hucul and Polish primitive horse breeds

Abstract. Pedigree and molecular data were used to evaluate genetic diversity in the Polish populations of the Polish primitive horse (also known as Polish Konik) and Hucul breeds over the time period of 30 years (1980–2011). Based on genotypes in 12 microsatellite loci (for 3865 Polish primitive horses and 1627 Huculs), as well as on pedigree data derived from over 7000 individuals (both breeds), several indices describing structure of the analysed populations were estimated. For both analysed breeds, we observed an increasing trend of inbreeding since 1980 which seems to be much more stable (oscillating around 10 % in the Polish primitive horse and 5 % in Hucul) since the beginning of 2000s when they were included in conservation programs in Poland. We observed that generally, indices related to genetic diversity are higher in the Hucul breed. Our study indicated that genetic diversity in the Polish primitive horse and Hucul breeds in Poland is still relatively high and conservation programs should be continued to keep it on the "safe" level in the future.