Farm-by-farm analysis of microsatellite, mtDNA and SNP genotype data reveals inbreeding and crossbreeding as threats to the survival of a native Spanish pig breed

Population genetics reveals new introgression in the nucleus herd of min pigs

OBJECTIVE

Min pigs are a unique genetic resource among local pig breeds in China. They have more excellent characteristics in cold and stress resistance, good meat quality, and a high reproductive rate. However, the genetic structure and driving factors remain unclear in the nucleus herd. In this study, the genetic diversity of Min pigs was studied to reveal the formation mechanism of its unique genetic structure. We hope to protect and develop the genetic resources of Min pigs.

METHODS

We analyzed different types of genes to identify the genetic structure and gene introgression pattern of Min pigs. The nuclear DNA dataset includes information on 21 microsatellite loci and 6 Y-chromosome genes, and the mitochondrial D-loop gene is selected to represent maternal lineages. The above genes are all from the nucleus herd of Min pigs.

RESULTS

The results of genetic structure identification and analysis of potential exogenous gene introgression patterns indicate that the nucleus herd of Min pigs maintains a high level of genetic diversity (polymorphism information content = 0.713, expected heterozygosity = 0.662, observed heterozygosity = 0.612). Compared with other Asian pig breeds, the formation of Min pig breeds is more special. Gene introgression from European pig breeds to Min pigs has occurred, which is characterized by complete introgression of paternal genes and incomplete introgression of maternal genes.

CONCLUSION

Gene introgression caused by cross-breeding is not the main factor leading to the formation of the current genetic structure of Min pigs, but this process has increased the level of genetic diversity in the nucleus herd. Compared with the influence of gene introgression, our research suggest that artificial selection and environmental adaptive evolution make Min pigs form unique genetic characteristics.

Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer

Deer genera around the globe are threatened by anthropogenic interference. The translocation of alien species and their subsequent genetic introgression into indigenous deer populations is particularly harmful to the species of greatest conservation concern. Products derived from deer, including venison and antler velvet, are also at risk of fraudulent labeling. The current molecular markers used to genetically identify deer species were developed from genome sequences and have limited applicability for cross-species amplification. The absence of efficacious diagnostic techniques for identifying deer species has hampered conservation and wildlife crime investigation efforts. Expressed sequence tag-simple sequence repeat (EST-SSR) markers are reliable tools for individual and species identification, especially in terms of cross-species genotyping. We conducted transcriptome sequencing of sambar (Rusa unicolor) antler velvet and acquired 11,190 EST-SSRs from 65,074 newly assembled unigenes. We identified a total of 55 unambiguous amplicons in sambar (n = 45), which were selected as markers to evaluate cross-species genotyping in sika deer (Cervus nippon, n = 30) and red deer (Cervus elaphus, n = 46), resulting in cross-species amplification rates of 94.5% and 89.1%, respectively. Based on polymorphic information content (>0.25) and genotyping fidelity, we selected 16 of these EST-SSRs for species identification. This marker set revealed significant genetic differentiation based on the fixation index and genetic distance values. Principal coordinate analysis and STRUCTURE analysis revealed distinct clusters of species and clearly identified red-sika hybrids. These markers showed applicability across different genera and proved suitable for identification and phylogenetic analyses across deer species.

Evaluation of genetic richness among Vietnamese native pig breeds using microsatellite markers

We have elucidated genetic relationships of Vietnamese native pigs (VNP) using preliminarily collected samples by a single-nucleotide polymorphism (SNP) array. In order to confirm our previous results and compare with the results of a previous study using microsatellite (MS) markers, we aimed to characterize genetic diversity and population structure in wider varieties (24 breeds from 21 Provinces) of VNP across the country using 20 polymorphic MS markers recommended by ISAG/FAO (International Society for Animal Genetics/Food and Agriculture Organization) for diversity study. In this study, we collected 1,136 DNA samples of the VNPs and three exotic breeds. Our results revealed that the average number of alleles and allelic richness across the loci in VNPs were 10.0 and 7.6, which were higher than those of exotic breeds. Genomic components among VNPs were subjected to the sampling locations. Interestingly, Co Binh Thuan showed remarkable genetic feature compared to the other VNPs, because the habitation of Co Binh Thuan was relatively far from the other breeds. The results of this study provided useful information for exploitation, conservation, and development trends of the VNP breeds. More recently, African swine fever caused significant damage to most of the VNP populations. Therefore, our findings will help a reconstruction scheme of the VNP genetic resources.

Crossbreeding and consanguinity management in pig farms in the departments of Ouémé and Plateau in Benin

Background:

The improvement in pig zootechnical performances is a common practice in Benin. This improvement of the performances is made by the choice of the best reproducers in farms and the crossbreeding between the different breeds.

Aim:

This study aims to characterize practices related to consanguinity management in pigs reared in Ouémé and Plateau.

Materials and Methods:

Crossbreeding and consanguinity data were collected from 60 farms in these two departments. Frequencies and averages were calculated and compared between departments, genetic types, and origin of progenitors.

Results:

The majority of the investigated pig farmers in both departments were married men of primary or secondary education level. Most of them cross animals without a specific crossbreeding scheme. These crossings were performed to a greater extent (p<0.05) in Ouémé (94.28%) than in Plateau (52%). In general, farmers cross improved animals of high breeding values with the crossbred ones. These crossings were mainly performed to improve zootechnical performances. Renewing animals were commonly chosen from the farm or were provided from nearby farms. The majority of pig breeders in Ouémé (100%) and Plateau (86.67%) obtained reproductive animals from nearby farms. Males and females were sometimes bought from the same farm or from farms that pig breeders have sold reproductive animals in the previous years. In the case of selection within their own farm, male and female progenitors are separated at puberty by the majority of the breeders of Plateau (42.11%) and Ouéme (50%). Inbred mating was reported by breeders. More than half of breeders mate animals having a parental link in both departments. The mating was performed between animals of the same mother in 37.93% of farms in Ouémé and in 45.46% in Plateau. The main consanguinity consequences mentioned by the breeders were the high mortality at birth and weaning, piglets’ weakness at the birth, the slow growth, and the decrease in litter size. Sows with at least one parent from external farm had a litter size at birth and weaning and a live-born piglets’ number significantly higher than sows with both parents from the same farm.

Conclusion:

Rigorous monitoring of crossing and the filial links are necessary for pig farms for ensuring the improvement of zootechnical performances.

Whole genome SNPs discovery in Nero Siciliano pig

Autochthonous pig breeds represent an important genetic reserve to be utilized mainly for the production of typical products. To explore its genetic variability, here we present for the first time whole genome sequencing data and SNPs discovered in a male domestic Nero Siciliano pig compared to the last pig reference genome Sus scrofa11.1.A total of 346.8 million paired reads were generated by sequencing. After quality control, 99.03% of the reads were mapped to the reference genome, and over 11 million variants were detected.Additionally, we evaluated sequence diversity in 21 fitness-related loci selected based on their biological function and/or their proximity to relevant QTLs. We focused on genes that have been related to environmental adaptation and reproductive traits in previous studies regarding local breeds. A total of 6,747 variants were identified resulting in a rate of 1 variant every ~276 bases. Among these variants 1,132 were novel to the dbSNP151 database. This study represents a first step in the genetic characterization of Nero Siciliano pig and also provides a platform for future comparative studies between this and other swine breeds.

Genome-wide SNP data unveils the globalization of domesticated pigs

BACKGROUND

Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection.

RESULTS

A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection.

CONCLUSIONS

Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation.

Association of BF, RBP4, and ESR2 Genotypes with Litter Size in an Autochthonous Pig Population

The aim of the present study was to determine any potential association of the BF, RBP4, and ESR2 genes with reproduction traits in an autochthonous Greek pig population. The PCR-RFLP methodology was implemented for genotyping purposes of the examined genes. No deviation from the Hardy-Weinberg equilibrium was observed for the examined loci, while the B allele noted to be the more frequent in all analyzed genes. In addition, sows with the AA genotype of BF gene found to produce significantly lower numbers of the total born piglets (TNB) and number of piglets born alive (TNA), while the respective BB genotype significantly exceeded in TNB and NBA traits compared to the other two genotypes (P < 0.001). In the case of RBP4 gene, sows with the AB genotype noted to have significant higher values of TNB and NBA in regard to the respective homozygous genotypes (AA or BB), while the BB genotype showed intermediate results (P < 0.001). There were no statistical differences between the BB genotype and the AB genotype of ESR2 locus in regard to the examined traits. However, a noticeable superiority (P < 0.01) of the BB genotype compared to the homozygous AA genotype, adding almost 2 piglets/litter in TNB and NBA trait, was found.

ABBREVIATIONS

TNB: Total number of born piglets; NBA: Number of piglets born alive.

Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances

Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.

Relationships among and variation within rare breeds of swine

Extinction of rare breeds of livestock threatens to reduce the total genetic variation available for selection in the face of the changing environment and new diseases. Swine breeds facing extinction typically share characteristics such as small size, slow growth rate, and high fat percentage, which limit them from contributing to commercial production. Compounding the risk of loss of variation is the lack of pedigree information for many rare breeds due to inadequate herd books, which increases the chance that producers are breeding closely related individuals. By making genetic data available, producers can make more educated breeding decisions to preserve genetic diversity in future generations, and conservation organizations can prioritize investments in breed preservation. The objective of this study was to characterize genetic variation within and among breeds of swine and prioritize heritage breeds for preservation. Genotypes from the Illumina PorcineSNP60 BeadChip (GeneSeek, Lincoln, NE) were obtained for Guinea, Ossabaw Island, Red Wattle, American Saddleback, Mulefoot, British Saddleback, Duroc, Landrace, Large White, Pietrain, and Tamworth pigs. A whole-genome analysis toolset was used to construct a genomic relationship matrix and to calculate inbreeding coefficients for the animals within each breed. Relatedness and average inbreeding coefficient differed among breeds, and pigs from rare breeds were generally more closely related and more inbred ( < 0.05). A multidimensional scaling diagram was constructed based on the SNP genotypes. Animals within breeds clustered tightly together except for 2 Guinea pigs. Tamworth, Duroc, and Mulefoot tended to not cluster with the other 7 breeds.

Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025

Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that “…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity.” However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societal in origin and are predicated on the value (e.g., socio-economic and cultural) of these resources to farmers, rural communities and society as a whole. The overall conclusion is that despite the fact that the livestock sector has been relatively well-organized in the application of genetic methodologies to date, there is still a large gap between the current state-of-the-art in the use of tools to characterize genomic resources and its application to many non-commercial and local breeds, hampering the consistent utilization of genetic and genomic data as indicators of genetic erosion and diversity. The livestock genomic sector therefore needs to make a concerted effort in the coming decade to enable to the democratization of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development.

Genetic admixture analysis in Prestice Black-Pied pigs

Abstract. The Prestice Black-Pied pig (PC) is a genetic resource of the Czech Republic. Information about boar variability has been provided in preceding papers. The objective of this work was to compare genetic variability of boars and sows. A total of 21 microsatellite markers were used to study genetic diversity and population structure of 149 PC breeding animals. In this paper, current parameters of assessments of diversity in PC are listed. All loci were polymorphic, and a total of 167 alleles were observed across the studied loci. The range of alleles was found to be 4 to 15 with a mean of 7.95. Overall allele frequency ranged from 0.07 to 0.25. The calculated observed and expected heterozygosity values were 0.70 and 0.73, respectively. The polymorphism information content (PIC) was 0.69 and the overall within-population inbreeding estimate (FIS) was 0.04. Genetic differentiation and population subdivision were tested. The level of admixture of breeds used for improvement of the PC breed was evaluated (Landrace, Large White and Pietrain). Five percent of analysed PC breeding boars had more than 20% admixture of other monitored breeds. The obtained results are important for the future sustainability of this local breed.

Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds

BACKGROUND

A major concern in conservation genetics is to maintain the genetic diversity of populations. Genetic variation in livestock species is threatened by the progressive marginalisation of local breeds in benefit of high-output pigs worldwide. We used high-density SNP and re-sequencing data to assess genetic diversity of local pig breeds from Europe. In addition, we re-sequenced pigs from commercial breeds to identify potential candidate mutations responsible for phenotypic divergence among these groups of breeds.

RESULTS

Our results point out some local breeds with low genetic diversity, whose genome shows a high proportion of regions of homozygosis (>50%) and that harbour a large number of potentially damaging mutations. We also observed a high correlation between genetic diversity estimates using high-density SNP data and Next Generation Sequencing data (r = 0.96 at individual level). The study of non-synonymous SNPs that were fixed in commercial breeds and also in any local breed, but with different allele, revealed 99 non-synonymous SNPs affecting 65 genes. Candidate mutations that may underlie differences in the adaptation to the environment were exemplified by the genes AZGP1 and TAS2R40. We also observed that highly productive breeds may have lost advantageous genotypes within genes involve in immune response--e.g. IL12RB2 and STAB1-, probably as a result of strong artificial in the intensive production systems in pig.

CONCLUSIONS

The high correlation between genetic diversity computed with the 60K SNP and whole genome re-sequence data indicates that the Porcine 60K SNP Beadchip provides reliable estimates of genomic diversity in European pig populations despite the expected bias. Moreover, this analysis gave insights for strategies to the genetic characterization of local breeds. The comparison between re-sequenced local pigs and re-sequenced commercial pigs made it possible to report candidate mutations to be responsible for phenotypic divergence among those groups of breeds. This study highlights the importance of low input breeds as a valuable genetic reservoir for the pig production industry. However, the high levels of ROHs, inbreeding and potentially damaging mutations emphasize the importance of the genetic characterization of local breeds to preserve their genomic variability.

Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations

The merging of populations after an extended period of isolation and divergence is a common phenomenon, in natural settings as well as due to human interference. Individuals with such hybrid origins contain genomes that essentially form a mosaic of different histories and demographies. Pigs are an excellent model species to study hybridization because European and Asian wild boars diverged ~1.2 Mya, and pigs were domesticated independently in Europe and Asia. During the Industrial Revolution in England, pigs were imported from China to improve the local pigs. This study utilizes the latest genomics tools to identify the origin of haplotypes in European domesticated pigs that are descendant from Asian and European populations. Our results reveal fine-scale haplotype structure representing different ancient demographic events, as well as a mosaic composition of those distinct histories due to recently introgressed haplotypes in the pig genome. As a consequence, nucleotide diversity in the genome of European domesticated pigs is higher when at least one haplotype of Asian origin is present, and haplotype length correlates negatively with recombination frequency and nucleotide diversity. Another consequence is that the inference of past effective population size is influenced by the background of the haplotypes in an individual, but we demonstrate that by careful sorting based on the origin of haplotypes, both distinct demographic histories can be reconstructed. Future detailed mapping of the genomic distribution of variation will enable a targeted approach to increase genetic diversity of captive and wild populations, thus facilitating conservation efforts in the near future.

Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula

BACKGROUND

Inbreeding is among the major concerns in management of local livestock populations. The effective population size of these populations tends to be small, which enhances the risk of fitness reduction and extinction. High-density SNP data make it possible to undertake novel approaches in conservation genetics of endangered breeds and wild populations.A total of 97 representative samples of domestic and wild pig populations from the Iberian Peninsula, subjected to different levels of threat with extinction, were genotyped with a 60 K SNP panel. Data analyses based on: (i) allele frequency differences; (ii) linkage disequilibrium and (iii) runs of homozygosity were integrated to study population relationships, inbreeding and demographic history.

RESULTS

The domestic pigs analyzed belonged to local Spanish and Portuguese breeds: Iberian ─ including the variants Retinto Iberian, Negro Iberian and Manchado de Jabugo ─, Bisaro and Chato Murciano. The population structure and persistence of phase analysis suggested high genetic relations between Iberian variants, with recent crossbreeding of Manchado de Jabugo with other pig populations. Chato Murciano showed a high frequency of long runs of homozygosity indicating recent inbreeding and reflecting the recent bottleneck reported by historical records. The Chato Murciano and the Manchado de Jabugo breeds presented the lowest effective population sizes in accordance with their status of highly inbred breeds. The Iberian wild boar presented a high frequency of short runs of homozygosity indicating past small population size but no signs of recent inbreeding. The Iberian breed showed higher genetic similarities with Iberian wild boar than the other domestic breeds.

CONCLUSIONS

High-density SNP data provided a consistent overview of population structure, demographic history and inbreeding of minority breeds and wild pig populations from the Iberian Peninsula. Despite the very different background of the populations used, we found a good agreement between the different analyses. Our results are also in agreement with historical reports and provide insight in the events that shaped the current genetic variation of pig populations from the Iberian Peninsula. The results exposed will aid to design and implement strategies for the future management of endangered minority pig breeds and wild populations.

Genetic variation and relationships of seven sturgeon species and ten interspecific hybrids

Background

Sturgeon cultivation is important for both industry and aquaculture in China. To date, more than 17 species or strains have been farmed for fillets and caviar production. Crossbreeding among different sturgeon species is frequent and the F2 hybrids are fertile. However, large-scale farming can have negative impacts on wild populations i.e. escape of exotic sturgeons and must be taken into consideration. Escape of exotic sturgeons can cause severe ecological problems, including threatening native sturgeon species once the exotic varieties become established or hybridize with native individuals. However, little is known about their genetic resources and variation.

Methods

Genetic diversity and introgression of seven sturgeon species were analyzed using mitochondrial DNA cytochrome oxidase subunit I (COI) and nine microsatellite markers. This study included 189 individuals from seven sturgeon species and 277 individuals from ten lineages of F2 hybrid strains.

Results

MtDNA COI sequences (632 bp long) were generated from 91 individuals across the 17 sturgeon strains and produced 23 different haplotypes. Haplotype diversity was high (h = 0.915 ± 0.015) and nucleotide diversity was low (π = 0.03680 ± 0.00153) in the seven sturgeon species and ten interspecific hybrids. Phylogenetic analyses resulted in almost identical tree topologies, and different haplotype structures were mainly related with sturgeons of different female parents. Analysis of molecular variance revealed that 81.73% of the genetic variance was due to matrilineal differences, while 9.40% resulted from strain variation. Pairwise Fst values obtained with POLYSAT software, were high among strains and ranged from 0.031 to 0.164. Admixture analysis assigned seven distinct groups and ten genotypes of admixed clusters composed of hybrid strains using STRUCTURE when assuming K = 7.

Conclusions

The interspecific mtDNA gene tree corresponded to the expected taxonomic divisions. These relationships were also supported by the results from the microsatellite analysis and contributed to unambiguously identify seven sturgeon species and ten F2 hybrid strains from sturgeon farms in China. Moreover, we found that introgressive hybridization is pervasive, exists in both purebred and hybrid sturgeons, and may reflect widespread mismanagement in sturgeon breeding in China.

Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape

Inbreeding has long been recognized as a primary cause of fitness reduction in both wild and domesticated populations. Consanguineous matings cause inheritance of haplotypes that are identical by descent (IBD) and result in homozygous stretches along the genome of the offspring. Size and position of regions of homozygosity (ROHs) are expected to correlate with genomic features such as GC content and recombination rate, but also direction of selection. Thus, ROHs should be non-randomly distributed across the genome. Therefore, demographic history may not fully predict the effects of inbreeding. The porcine genome has a relatively heterogeneous distribution of recombination rate, making Sus scrofa an excellent model to study the influence of both recombination landscape and demography on genomic variation. This study utilizes next-generation sequencing data for the analysis of genomic ROH patterns, using a comparative sliding window approach. We present an in-depth study of genomic variation based on three different parameters: nucleotide diversity outside ROHs, the number of ROHs in the genome, and the average ROH size. We identified an abundance of ROHs in all genomes of multiple pigs from commercial breeds and wild populations from Eurasia. Size and number of ROHs are in agreement with known demography of the populations, with population bottlenecks highly increasing ROH occurrence. Nucleotide diversity outside ROHs is high in populations derived from a large ancient population, regardless of current population size. In addition, we show an unequal genomic ROH distribution, with strong correlations of ROH size and abundance with recombination rate and GC content. Global gene content does not correlate with ROH frequency, but some ROH hotspots do contain positive selected genes in commercial lines and wild populations. This study highlights the importance of the influence of demography and recombination on homozygosity in the genome to understand the effects of inbreeding.