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

Integrated analysis strategy of genome-wide functional gene mining reveals DKK2 gene underlying meat quality in Shaziling synthesized pigs

BACKGROUND

Shaziling pig is a well-known indigenous breed in China who has superior meat quality traits. However, the genetic mechanism and genomic evidence underlying meat quality characteristics of Shaziling pigs are still unclear. To explore and investigate the germplasm characteristics of Shaziling pigs, we totally analyzed 67 individual's whole genome sequencing data for the first time (20 Shaziling pigs [S], 20 Dabasha pigs [DBS], 11 Yorkshire pigs [Y], 10 Berkshire pigs [BKX], 5 Basha pigs [BS] and 1 Warthog).

RESULTS

A total of 2,538,577 SNPs with high quality were detected and 9 candidate genes which was specifically selected in S and shared in S to DBS were precisely mined and screened using an integrated analysis strategy of identity-by-descent (IBD) and selective sweep. Of them, dickkopf WNT signaling pathway inhibitor 2 (DKK2), the antagonist of Wnt signaling pathway, was the most promising candidate gene which was not only identified an association of palmitic acid and palmitoleic acid quantitative trait locus in PigQTLdb, but also specifically selected in S compared to other 48 Chinese local pigs of 12 populations and 39 foreign pigs of 4 populations. Subsequently, a mutation at 12,726-bp of DKK2 intron 1 (g.114874954 A > C) was identified associated with intramuscular fat content using method of PCR-RFLP in 21 different pig populations. We observed DKK2 specifically expressed in adipose tissues. Overexpression of DKK2 decreased the content of triglyceride, fatty acid synthase and expression of relevant genes of adipogenic and Wnt signaling pathway, while interference of DKK2 got contrary effect during adipogenesis differentiation of porcine preadipocytes and 3T3-L1 cells.

CONCLUSIONS

Our findings provide an analysis strategy for mining functional genes of important economic traits and provide fundamental data and molecular evidence for improving pig meat quality traits and molecular breeding.

The computational implementation of a platform of relative identity-by-descent scores algorithm for introgressive mapping

With the development of genotyping and sequencing technology, researchers working in the area of conservation genetics are able to obtain the genotypes or even the sequences of a representative sample of individuals from the population. It is of great importance to examine the genomic variants and genes that are highly preferred or pruned during the process of adaptive introgression or long-term hybridization. To the best of our knowledge, we are the first to develop a platform with computational integration of a relative identity-by-descent (rIBD) scores algorithm for introgressive mapping. The rIBD algorithm is designed for mapping the fine-scaled genomic regions under adaptive introgression between the source breeds and the admixed breed. Our rIBD calculation platform provides compact functions including reading input information and uploading of files, rIBD calculation, and presentation of the rIBD scores. We analyzed the simulated data using the rIBD calculation platform and calculated the average IBD score of 0.061 with a standard deviation of 0.124. The rIBD scores generally follow a normal distribution, and a cut-off of 0.432 and -0.310 for both positive and negative rIBD scores is derived to enable the identification of genomic regions showing significant introgression signals from the source breed to the admixed breed. A list of genomic regions with detailed calculated rIBD scores is reported, and all the rIBD scores for each of the considered windows are presented in plots on the rIBD calculation platform. Our rIBD calculation platform provides a user-friendly tool for the calculation of fine-scaled rIBD scores for each of the genomic regions to map possible functional genomic variants due to adaptive introgression or long-term hybridization.

Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree

The mutation rate used in the previous analyses of pig evolution and demographics was cursory and hence invited potential bias in inferring evolutionary history. Herein, we estimated the de novo mutation rate of pigs as 3.6 × 10^-9 per base per generation using high-quality whole-genome sequencing data from nine individuals in a three-generation pedigree through stringent filtering and validation. Using this mutation rate, we re-investigated the evolutionary history of pigs. The estimated divergence time of ∼ 10 kiloyears ago (KYA) between European wild and domesticated pigs was consistent with the domestication time of European pigs based on archaeological evidence. However, other divergence events inferred here were not as ancient as previously described. Our estimates suggested that Sus speciation occurred ∼ 1.36 million years ago (MYA); European wild pigs split from Asian wild pigs only ∼ 219 KYA; and south and north Chinese wild pigs split ∼ 25 KYA. Meanwhile, our results showed that the most recent divergence event between Chinese wild and domesticated pigs occurred in the Hetao plain, North China, approximately 20 KYA, supporting the possibly independent domestication in North China along the middle Yellow River. We also found that the maximum effective population size of pigs was ∼ 6 times larger than the previous estimate. An archaic migration from other Sus species originating ∼ 2 MYA to European pigs was detected during western colonization of pigs; this interfered with the previous demographic inference. Our de novo mutation rate estimation and its consequences for demographic history inference reasonably provide a new vision regarding the evolutionary history of pigs.

Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes

Throughout its distribution across Eurasia, domestic pig (Sus scrofa) populations have acquired differences through natural and artificial selection, and have often interbred. We resequenced 80 Eurasian pigs from nine different Asian and European breeds; we identify 42,288 reliable SNPs on the Y chromosome in a panel of 103 males, among which 96.1% are newly detected. Based on these new data, we elucidate the evolutionary history of pigs through the lens of the Y chromosome. We identify two highly divergent haplogroups: one present only in Asia and one fixed in Europe but present in some Asian populations. Analyzing the European haplotypes present in Asian populations, we find evidence of three independent waves of introgression from Europe to Asia in last 200 years, agreeing well with the literature and historical records. The diverse European lineages were brought in China by humans and left significant imprints not only on the autosomes but also on the Y chromosome of geographically and genetically distinct Chinese pig breeds. We also find a general excess of European ancestry on Y chromosomes relative to autosomes in Chinese pigs, an observation that cannot be explained solely by sex-biased migration and genetic drift. The European Y haplotype is associated with leaner meat production, and we hypothesize that the European Y chromosome increased in frequency in Chinese populations due to artificial selection. We find evidence of Y chromosomal gene flow between Sumatran wild boar and Chinese pigs. Our results demonstrate how human-mediated admixture and selection shaped the distribution of modern swine Y chromosomes.

Large-scale genomic analysis reveals the genetic cost of chicken domestication

BACKGROUND

Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication.

RESULTS

We analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the "cost of domestication" hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes.

CONCLUSION

This study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection.

Genomics of Adaptations in Ungulates

Ungulates are a group of hoofed animals that have long interacted with humans as essential sources of food, labor, clothing, and transportation. These consist of domesticated, feral, and wild species raised in a wide range of habitats and biomes. Given the diverse and extreme environments inhabited by ungulates, unique adaptive traits are fundamental for fitness. The documentation of genes that underlie their genomic signatures of selection is crucial in this regard. The increasing availability of advanced sequencing technologies has seen the rapid growth of ungulate genomic resources, which offers an exceptional opportunity to understand their adaptive evolution. Here, we summarize the current knowledge on evolutionary genetic signatures underlying the adaptations of ungulates to different habitats.

Animal domestication in the era of ancient genomics

The domestication of animals led to a major shift in human subsistence patterns, from a hunter-gatherer to a sedentary agricultural lifestyle, which ultimately resulted in the development of complex societies. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have been substantially altered during their adaptation to the human niche. Recent methodological innovations, such as improved ancient DNA extraction methods and next-generation sequencing, have enabled the sequencing of whole ancient genomes. These genomes have helped reconstruct the process by which animals entered into domestic relationships with humans and were subjected to novel selection pressures. Here, we discuss and update key concepts in animal domestication in light of recent contributions from ancient genomics.

Matching STR and SNP genotyping to discriminate between wild boar, domestic pigs and their recent hybrids for forensic purposes

The genetic discrimination between phylogenetically close taxa can be challenging if their gene pools are not differentiated and there are many shared polymorphisms. The gene flow between wild boar (Sus scrofa) and domestic pig (S. s. domesticus) has never been interrupted from domestication onwards, due to non-stop natural and human-mediated crossbreeding. To date there are no individual genetic markers that are able to distinguish between the two forms, nor even to identify effectively their hybrids. We developed a combined molecular protocol based on multiplex porcine-specific STR-profiling system and new real time PCR-based assays of single polymorphisms in the NR6A1 and MC1R genes to gain high diagnostic power in the differentiation of wild boar, pig and hybrids for forensic purposes. The combined approach correctly assigned individuals to one or the other parental gene pool and identified admixed genotypes. Evidence was found for substantial reduction of false negative results by using multiple marker systems jointly, compared to their use individually. Our protocol is a powerful and cost-effective diagnostic tool that can easily be adopted by most forensic laboratories to assist authorities contrast food adulteration, assure veterinary public health and fight against wildlife crimes, like poaching and illegal detention of wild animals.

Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics

Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed new light on the genetic origins of domesticates, and on the process of domestication itself. High-resolution paleogenomic data sets now provide unprecedented opportunities to explore the development of animal agriculture across the world. In addition, functional population genomics studies of domestic and wild animals can deliver comparative information useful for understanding recent human evolution.

A functional regulatory variant of MYH3 influences muscle fiber-type composition and intramuscular fat content in pigs

Muscle development and lipid accumulation in muscle critically affect meat quality of livestock. However, the genetic factors underlying myofiber-type specification and intramuscular fat (IMF) accumulation remain to be elucidated. Using two independent intercrosses between Western commercial breeds and Korean native pigs (KNPs) and a joint linkage-linkage disequilibrium analysis, we identified a 488.1-kb region on porcine chromosome 12 that affects both reddish meat color (a*) and IMF. In this critical region, only the MYH3 gene, encoding myosin heavy chain 3, was found to be preferentially overexpressed in the skeletal muscle of KNPs. Subsequently, MYH3-transgenic mice demonstrated that this gene controls both myofiber-type specification and adipogenesis in skeletal muscle. We discovered a structural variant in the promotor/regulatory region of MYH3 for which Q allele carriers exhibited significantly higher values of a* and IMF than q allele carriers. Furthermore, chromatin immunoprecipitation and cotransfection assays showed that the structural variant in the 5'-flanking region of MYH3 abrogated the binding of the myogenic regulatory factors (MYF5, MYOD, MYOG, and MRF4). The allele distribution of MYH3 among pig populations worldwide indicated that the MYH3 Q allele is of Asian origin and likely predates domestication. In conclusion, we identified a functional regulatory sequence variant in porcine MYH3 that provides novel insights into the genetic basis of the regulation of myofiber type ratios and associated changes in IMF in pigs. The MYH3 variant can play an important role in improving pork quality in current breeding programs.

Deleterious alleles in the context of domestication, inbreeding, and selection

Each individual has a certain number of harmful mutations in its genome. These mutations can lower the fitness of the individual carrying them, dependent on their dominance and selection coefficient. Effective population size, selection, and admixture are known to affect the occurrence of such mutations in a population. The relative roles of demography and selection are a key in understanding the process of adaptation. These are factors that are potentially influenced and confounded in domestic animals. Here, we hypothesize that the series of events of bottlenecks, introgression, and strong artificial selection associated with domestication increased mutational load in domestic species. Yet, mutational load is hard to quantify, so there are very few studies available revealing the relevance of evolutionary processes. The precise role of artificial selection, bottlenecks, and introgression in further increasing the load of deleterious variants in animals in breeding and conservation programmes remains unclear. In this paper, we review the effects of domestication and selection on mutational load in domestic species. Moreover, we test some hypotheses on higher mutational load due to domestication and selective sweeps using sequence data from commercial pig and chicken lines. Overall, we argue that domestication by itself is not a prerequisite for genetic erosion, indicating that fitness potential does not need to decline. Rather, mutational load in domestic species can be influenced by many factors, but consistent or strong trends are not yet clear. However, methods emerging from molecular genetics allow discrimination of hypotheses about the determinants of mutational load, such as effective population size, inbreeding, and selection, in domestic systems. These findings make us rethink the effect of our current breeding schemes on fitness of populations.

Using Genomic Data to Infer Historic Population Dynamics of Nonmodel Organisms

Genome sequence data are now being routinely obtained from many nonmodel organisms. These data contain a wealth of information about the demographic history of the populations from which they originate. Many sophisticated statistical inference procedures have been developed to infer the demographic history of populations from this type of genomic data. In this review, we discuss the different statistical methods available for inference of demography, providing an overview of the underlying theory and logic behind each approach. We also discuss the types of data required and the pros and cons of each method. We then discuss how these methods have been applied to a variety of nonmodel organisms. We conclude by presenting some recommendations for researchers looking to use genomic data to infer demographic history.

Human-Mediated Introgression of Haplotypes in a Modern Dairy Cattle Breed

Domestic animals can serve as model systems of adaptive introgression and their genomic signatures. In part, their usefulness as model systems is due to their well-known histories. Different breeding strategies such as introgression and artificial selection have generated numerous desirable phenotypes and superior performance in domestic animals. The modern Danish Red Dairy Cattle is studied as an example of an introgressed population. It originates from crossing the traditional Danish Red Dairy Cattle with the Holstein and Brown Swiss breeds, both known for high milk production. This crossing happened, among other things due to changes in the production system, to raise milk production and overall performance. The genomes of modern Danish Red Dairy Cattle are heavily influenced by regions introgressed from the Holstein and Brown Swiss breeds and under subsequent selection in the admixed population. The introgressed proportion of the genome was found to be highly variable across the genome. Haplotypes introgressed from Holstein and Brown Swiss contained or overlapped known genes affecting milk production, as well as protein and fat content (CD14, ZNF215, BCL2L12, and THRSP for Holstein origin and ITPR2, BCAT1, LAP3, and MED28 for Brown Swiss origin). Genomic regions with high introgression signals also contained genes and enriched QTL associated with calving traits, body confirmation, feed efficiency, carcass, and fertility traits. These introgressed signals with relative identity-by-descent scores larger than the median showing Holstein or Brown Swiss introgression are mostly significantly correlated with the corresponding test statistics from signatures of selection analyses in modern Danish Red Dairy Cattle. Meanwhile, the putative significant introgressed signals have a significant dependency with the putative significant signals from signatures of selection analyses. Artificial selection has played an important role in the genomic footprints of introgression in the genome of modern Danish Red Dairy Cattle. Our study on a modern cattle breed contributes to an understanding of genomic consequences of selective introgression by demonstrating the extent to which adaptive effects contribute to shape the specific genomic consequences of introgression.

Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

Background

Currently, genome-wide scans for positive selection signatures in commercial breed have been investigated. However, few studies have focused on selection footprints of indigenous breeds. Laiwu pig is an invaluable Chinese indigenous pig breed with extremely high proportion of intramuscular fat (IMF), and an excellent model to detect footprint as the result of natural and artificial selection for fat deposition in muscle.

Result

In this study, based on GeneSeek Genomic profiler Porcine HD data, three complementary methods, F_ST, iHS (integrated haplotype homozygosity score) and CLR (composite likelihood ratio), were implemented to detect selection signatures in the whole genome of Laiwu pigs. Totally, 175 candidate selected regions were obtained by at least two of the three methods, which covered 43.75 Mb genomic regions and corresponded to 1.79% of the genome sequence. Gene annotation of the selected regions revealed a list of functionally important genes for feed intake and fat deposition, reproduction, and immune response. Especially, in accordance to the phenotypic features of Laiwu pigs, among the candidate genes, we identified several genes, NPY1R, NPY5R, PIK3R1 and JAKMIP1, involved in the actions of two sets of neurons, which are central regulators in maintaining the balance between food intake and energy expenditure.

Conclusions

Our results identified a number of regions showing signatures of selection, as well as a list of functionally candidate genes with potential effect on phenotypic traits, especially fat deposition in muscle. Our findings provide insights into the mechanisms of artificial selection of fat deposition and further facilitate follow-up functional studies.

Electronic supplementary material

The online version of this article (10.1186/s12863-018-0622-y) contains supplementary material, which is available to authorized users.

Insights into Platypus Population Structure and History from Whole-Genome Sequencing

The platypus is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian phylogenetic tree. Despite widespread interest in its unusual biology, little is known about its population structure or recent evolutionary history. To provide new insights into the dispersal and demographic history of this iconic species, we sequenced the genomes of 57 platypuses from across the whole species range in eastern mainland Australia and Tasmania. Using a highly improved reference genome, we called over 6.7 M SNPs, providing an informative genetic data set for population analyses. Our results show very strong population structure in the platypus, with our sampling locations corresponding to discrete groupings between which there is no evidence for recent gene flow. Genome-wide data allowed us to establish that 28 of the 57 sampled individuals had at least a third-degree relative among other samples from the same river, often taken at different times. Taking advantage of a sampled family quartet, we estimated the de novo mutation rate in the platypus at 7.0 × 10-9/bp/generation (95% CI 4.1 × 10-9-1.2 × 10-8/bp/generation). We estimated effective population sizes of ancestral populations and haplotype sharing between current groupings, and found evidence for bottlenecks and long-term population decline in multiple regions, and early divergence between populations in different regions. This study demonstrates the power of whole-genome sequencing for studying natural populations of an evolutionarily important species.

Population size may shape the accumulation of functional mutations following domestication

BACKGROUND

Population genetics theory predicts an important role of differences in the effective population size (N e ) among species on shaping the accumulation of functional mutations by regulating the selection efficiency. However, this correlation has never been tested in domesticated animals.

RESULTS

Here, we synthesized 62 whole genome data in eight domesticated species (cat, dog, pig, goat, sheep, chicken, cattle and horse) and compared domesticates with their wild (or ancient) relatives. Genes with significantly different selection pressures (revealed by nonsynonymous/synonymous substitution rate ratios, Ka/Ks or ω) between domesticated (Dω) and wild animals (Wω) were determined by likelihood-ratio tests. Species-level effective population sizes (N e ) were evaluated by the pairwise sequentially Markovian coalescent (PSMC) model, and Dω/Wω were calculated for each species to evaluate the changes in accumulation of functional mutations after domestication relative to pre-domestication period. Correlation analysis revealed that the most recent (~ 10.000 years ago) N e (s) are positively correlated with Dω/Wω. This result is consistent with the corollary of the nearly neutral theory, that higher N e could boost the efficiency of positive selection, which might facilitate the overall accumulation of functional mutations. In addition, we also evaluated the accumulation of radical and conservative mutations during the domestication transition as: Dradical/Wradical and Dconservative/Wconservative, respectively. Surprisingly, only Dradical/Wradical ratio exhibited a positive correlation with N e (p < 0.05), suggesting that domestication process might magnify the accumulation of radical mutations in species with larger N e .

CONCLUSIONS

Our results confirm the classical population genetics theory prediction and highlight the important role of species' N e in shaping the patterns of accumulation of functional mutations, especially radical mutations, in domesticated animals. The results aid our understanding of the mechanisms underlying the accumulation of functional mutations after domestication, which is critical for understanding the phenotypic diversification associated with this process.

A systematic survey to identify lethal recessive variation in highly managed pig populations

BACKGROUND

Lethal recessive variation can cause prenatal death of homozygous offspring. Although usually present at low-frequency in populations, the impact on individual fitness can be substantial. Until recently, the presence of recessive embryonic lethal variation could only be measured indirectly through reduced fertility. In this study, we estimate the presence of genetic loci associated with both early and late termination of development during gestation in pigs from the wealth of genome data routinely generated by a commercial breeding company.

RESULTS

We examined three commercial pig (Sus scrofa) populations for potentially deleterious genetic variation based on 80 K SNP-chip genotypes, and estimate the effects on reproductive traits. 24,000 pigs from three populations were analyzed for missing or depletion of homozygous haplotypes. We identified 145 haplotypes (ranging from 0.5-4 Mb in size) in the genome with complete absence or depletion of homozygous animals. Thirty-five haplotypes show a negative effect on at least one of the analysed reproductive traits (total number born, number of stillborn, and number of mummified piglets). One variant in particular appeared to result in relative late termination of development of fetuses, responsible for a significant fraction of observed stillborn piglets ('mummies'), as they die mid-gestation. Moreover, we identified the BMPER gene as a likely candidate underlying this phenomenon.

CONCLUSIONS

Our study shows that although lethal recessive variation is present, the frequency of these alleles is invariably low in these highly managed populations. Nevertheless, due to cumulative effects of deleterious variants, large numbers of affected offspring are produced. Furthermore, our study demonstrates the use of a large-scale commercial genetic experiment to systematically screen for 'natural knockouts' that can increase understanding of gene function.

Comparison of Single Genome and Allele Frequency Data Reveals Discordant Demographic Histories

Inference of demographic history from genetic data is a primary goal of population genetics of model and nonmodel organisms. Whole genome-based approaches such as the pairwise/multiple sequentially Markovian coalescent methods use genomic data from one to four individuals to infer the demographic history of an entire population, while site frequency spectrum (SFS)-based methods use the distribution of allele frequencies in a sample to reconstruct the same historical events. Although both methods are extensively used in empirical studies and perform well on data simulated under simple models, there have been only limited comparisons of them in more complex and realistic settings. Here we use published demographic models based on data from three human populations (Yoruba, descendants of northwest-Europeans, and Han Chinese) as an empirical test case to study the behavior of both inference procedures. We find that several of the demographic histories inferred by the whole genome-based methods do not predict the genome-wide distribution of heterozygosity, nor do they predict the empirical SFS. However, using simulated data, we also find that the whole genome methods can reconstruct the complex demographic models inferred by SFS-based methods, suggesting that the discordant patterns of genetic variation are not attributable to a lack of statistical power, but may reflect unmodeled complexities in the underlying demography. More generally, our findings indicate that demographic inference from a small number of genomes, routine in genomic studies of nonmodel organisms, should be interpreted cautiously, as these models cannot recapitulate other summaries of the data.

Landscape genomic approach to detect selection signatures in locally adapted Brazilian swine genetic groups

Samples of 191 animals from 18 different Brazilian locally adapted swine genetic groups were genotyped using Illumina Porcine SNP60 BeadChip in order to identify selection signatures related to the monthly variation of Brazilian environmental variables. Using BayeScan software, 71 SNP markers were identified as FST outliers and 60 genotypes (58 markers) were found by Samβada software in 371 logistic models correlated with 112 environmental variables. Five markers were identified in both methods, with a Kappa value of 0.073 (95% CI: 0.011-0.134). The frequency of these markers indicated a clear north-south country division that reflects Brazilian environmental differences in temperature, solar radiation, and precipitation. Global spatial territory correlation for environmental variables corroborates this finding (average Moran's I = 0.89, range from 0.55 to 0.97). The distribution of alleles over the territory was not strongly correlated with the breed/genetic groups. These results are congruent with previous mtDNA studies and should be used to direct germplasm collection for the National gene bank.

Population admixture in Chinese and European Sus scrofa

Relationships between different populations were investigated using Porcine 60 K data from 1,135 domestic pigs and wild boars across Europe and China. The results indicate that most European breeds have been introgressed with Chinese ancestry, but the extent of introgression varies considerably among breeds. Moreover, the main source of this introgression is pigs from South China, closely related to Bamaxiang and Dongshan pigs. Contributions from East and Central Chinese pig breeds are also detectable. Phylogeny reconstruction places European wild boars among European domestic breeds. Coalescent simulations indicate that this may be the result of gene flow from European wild boars to European domestic pigs. These results will facilitate further genomic studies such as genome-wide association studies, selection signature detection and genomic prediction.

A Pathway-Centered Analysis of Pig Domestication and Breeding in Eurasia

Ascertaining the molecular and physiological basis of domestication and breeding is an active area of research. Due to the current wide distribution of its wild ancestor, the wild boar, the pig (Sus scrofa) is an excellent model to study these processes, which occurred independently in East Asia and Europe ca. 9000 yr ago. Analyzing genome variability patterns in terms of metabolic pathways is attractive since it considers the impact of interrelated functions of genes, in contrast to genome-wide scans that treat genes or genome windows in isolation. To that end, we studied 40 wild boars and 123 domestic pig genomes from Asia and Europe when metabolic pathway was the unit of analysis. We computed statistical significance for differentiation (Fst) and linkage disequilibrium (nSL) statistics at the pathway level. In terms of Fst, we found 21 and 12 pathways significantly differentiated at a q-value < 0.05 in Asia and Europe, respectively; five were shared across continents. In Asia, we found six significant pathways related to behavior, which involved essential neurotransmitters like dopamine and serotonin. Several significant pathways were interrelated and shared a variable percentage of genes. There were 12 genes present in >10 significant pathways (in terms of Fst), comprising genes involved in the transduction of a large number of signals, like phospholipase PCLB1, which is expressed in the brain, or ITPR3, which has an important role in taste transduction. In terms of nSL, significant pathways were mainly related to reproductive performance (ovarian steroidogenesis), a similarly important target trait during domestication and modern animal breeding. Different levels of recombination cannot explain these results, since we found no correlation between Fst and recombination rate. However, we did find an increased ratio of deleterious mutations in domestic vs. wild populations, suggesting a relaxed functional constraint associated with the domestication and breeding processes. Purifying selection was, nevertheless, stronger in significantly differentiated pathways than in random pathways, mainly in Europe. We conclude that pathway analysis facilitates the biological interpretation of genome-wide studies. Notably, in the case of pig, behavior played an important role, among other physiological and developmental processes.

Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs

Early pig farmers in Europe imported Asian pigs to cross with their local breeds in order to improve traits of commercial interest. Current genomics techniques enabled genome-wide identification of these Asian introgressed haplotypes in modern European pig breeds. We propose that the Asian variants are still present because they affect phenotypes that were important for ancient traditional, as well as recent, commercial pig breeding. Genome-wide introgression levels were only weakly correlated with gene content and recombination frequency. However, regions with an excess or absence of Asian haplotypes (AS) contained genes that were previously identified as phenotypically important such as FASN, ME1, and KIT. Therefore, the Asian alleles are thought to have an effect on phenotypes that were historically under selection. We aimed to estimate the effect of AS in introgressed regions in Large White pigs on the traits of backfat (BF) and litter size. The majority of regions we tested that retained Asian deoxyribonucleic acid (DNA) showed significantly increased BF from the Asian alleles. Our results suggest that the introgression in Large White pigs has been strongly determined by the selective pressure acting upon the introgressed AS. We therefore conclude that human-driven hybridization and selection contributed to the genomic architecture of these commercial pigs.

The 'heritability' of domestication and its functional partitioning in the pig

We propose to estimate the proportion of variance explained by regression on genome-wide markers (or genomic heritability) when wild/domestic status is considered the phenotype of interest. This approach differs from the standard Fst in that it can accommodate genetic similarity between individuals in a general form. We apply this strategy to complete genome data from 47 wild and domestic pigs from Asia and Europe. When we partitioned the total genomic variance into components associated to subsets of single nucleotide polymorphisms (SNPs) defined in terms of their annotation, we found that potentially deleterious non-synonymous mutations (9566 SNPs) explained as much genetic variance as the whole set of 25 million SNPs. This suggests that domestication may have affected protein sequence to a larger extent than regulatory or other kinds of mutations. A pathway-guided analysis revealed ovarian steroidogenesis and leptin signaling as highly relevant in domestication. The genomic regression approach proposed in this study revealed molecular processes not apparent through typical differentiation statistics. We propose that at least some of these processes are likely new discoveries because domestication is a dynamic process of genetic selection, which may not be completely characterized by a static metric like Fst. Nevertheless, and despite some particularly influential mutation types or pathways, our analyses tend to rule out a simplistic genetic basis for the domestication process: neither a single pathway nor a unique set of SNPs can explain the process as a whole.

A decade of pig genome sequencing: a window on pig domestication and evolution

Insight into how genomes change and adapt due to selection addresses key questions in evolutionary biology and in domestication of animals and plants by humans. In that regard, the pig and its close relatives found in Africa and Eurasia represent an excellent group of species that enables studies of the effect of both natural and human-mediated selection on the genome. The recent completion of the draft genome sequence of a domestic pig and the development of next-generation sequencing technology during the past decade have created unprecedented possibilities to address these questions in great detail. In this paper, I review recent whole-genome sequencing studies in the pig and closely-related species that provide insight into the demography, admixture and selection of these species and, in particular, how domestication and subsequent selection of Sus scrofa have shaped the genomes of these animals.

Genetic characterization of local Criollo pig breeds from the Americas using microsatellite markers

Little is known about local Criollo pig genetic resources and relationships among the various populations. In this paper, genetic diversity and relationships among 17 Criollo pig populations from 11 American countries were assessed with 24 microsatellite markers. Heterozygosities, F-statistics, and genetic distances were estimated, and multivariate, genetic structure and admixture analyses were performed. The overall means for genetic variability parameters based on the 24 microsatellite markers were the following: mean number of alleles per locus of 6.25 ± 2.3; effective number of alleles per locus of 3.33 ± 1.56; allelic richness per locus of 4.61 ± 1.37; expected and observed heterozygosity of 0.62 ± 0.04 and 0.57 ± 0.02, respectively; within-population inbreeding coefficient of 0.089; and proportion of genetic variability accounted for by differences among breeds of 0.11 ± 0.01. Genetic differences were not significantly associated with the geographical location to which breeds were assigned or their country of origin. Still, the NeighborNet dendrogram depicted the clustering by geographic origin of several South American breeds (Criollo Boliviano, Criollo of northeastern Argentina wet, and Criollo of northeastern Argentina dry), but some unexpected results were also observed, such as the grouping of breeds from countries as distant as El Salvador, Mexico, Ecuador, and Cuba. The results of genetic structure and admixture analyses indicated that the most likely number of ancestral populations was 11, and most breeds clustered separately when this was the number of predefined populations, with the exception of some closely related breeds that shared the same cluster and others that were admixed. These results indicate that Criollo pigs represent important reservoirs of pig genetic diversity useful for local development as well as for the pig industry.

Mixed signals from hybrid genomes

Admixture results from interbreeding between individuals from different populations or species that were previously genetically isolated from each other (Fig. ). Identifying admixture events in the genome is not always a straightforward task, because the genetic signature left behind fades with time as recombination events fragment the genomic segments introduced during the interbreeding event. Additionally, when the genetic architecture of populations or species that admix is not very different (e.g. they coalesce to a common ancestor recently), admixture signatures may be difficult to detect. Ignoring the effects of admixture can, however, pose severe problems for population genetic analyses that rely on the distribution of polymorphic markers across the genome. In this issue of Molecular Ecology, Bosse et al. () analyse genomic data from modern pigs to understand hybridization processes that occurred between domestic pigs from European and Asiatic origin, and between pigs and wild boars. Their results are interesting regarding the fine-scale distribution of admixture across the pig genome, and the way in which this admixture biases estimates of the effective population size in European domestic pigs. The implications of these results are significant, as they serve as a cautionary note on genomic analyses that depend on the distribution of polymorphic variants in potentially admixed populations.

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.

Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes

Traditionally, the process of domestication is assumed to be initiated by humans, involve few individuals and rely on reproductive isolation between wild and domestic forms. We analyzed pig domestication using over 100 genome sequences and tested whether pig domestication followed a traditional linear model or a more complex, reticulate model. We found that the assumptions of traditional models, such as reproductive isolation and strong domestication bottlenecks, are incompatible with the genetic data. In addition, our results show that, despite gene flow, the genomes of domestic pigs have strong signatures of selection at loci that affect behavior and morphology. We argue that recurrent selection for domestic traits likely counteracted the homogenizing effect of gene flow from wild boars and created 'islands of domestication' in the genome. Our results have major ramifications for the understanding of animal domestication and suggest that future studies should employ models that do not assume reproductive isolation.

A deep catalog of autosomal single nucleotide variation in the pig

A comprehensive catalog of variability in a given species is useful for many important purposes, e.g., designing high density arrays or pinpointing potential mutations of economic or physiological interest. Here we provide a genomewide, worldwide catalog of single nucleotide variants by simultaneously analyzing the shotgun sequence of 128 pigs and five suid outgroups. Despite the high SNP missing rate of some individuals (up to 88%), we retrieved over 48 million high quality variants. Of them, we were able to assess the ancestral allele of more than 39M biallelic SNPs. We found SNPs in 21,455 out of the 25,322 annotated genes in pig assembly 10.2. The annotation showed that more than 40% of the variants were novel variants, not present in dbSNP. Surprisingly, we found a large variability in transition / transversion rate along the genome, which is very well explained (R²=0.79) primarily by genome differences in in CpG content and recombination rate. The number of SNPs per window also varied but was less dependent of known factors such as gene density, missing rate or recombination (R²=0.48). When we divided the samples in four groups, Asian wild boar (ASWB), Asian domestics (ASDM), European wild boar (EUWB) and European domestics (EUDM), we found a marked correlation in allele frequencies between domestics and wild boars within Asia and within Europe, but not across continents, due to the large evolutive distance between pigs of both continents (~1.2 MYA). In general, the porcine species showed a small percentage of SNPs exclusive of each population group. EUWB and EUDM were predicted to harbor a larger fraction of potentially deleterious mutations, according to the SIFT algorithm, than Asian samples, perhaps a result of background selection being less effective due to a lower effective population size in Europe.

Genome data from a sixteenth century pig illuminate modern breed relationships

Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds.

Hybrid origin of European commercial pigs examined by an in-depth haplotype analysis on chromosome 1

Although all farm animals have an original source of domestication, a large variety of modern breeds exist that are phenotypically highly distinct from the ancestral wild population. This phenomenon can be the result of artificial selection or gene flow from other sources into the domesticated population. The Eurasian wild boar (Sus scrofa) has been domesticated at least twice in two geographically distinct regions during the Neolithic revolution when hunting shifted to farming. Prior to the establishment of the commercial European pig breeds we know today, some 200 years ago Chinese pigs were imported into Europe to improve local European pigs. Commercial European domesticated pigs are genetically more diverse than European wild boars, although historically the latter represents the source population for domestication. In this study we examine the cause of the higher diversity within the genomes of European commercial pigs compared to their wild ancestors by testing two different hypotheses. In the first hypothesis we consider that European commercial pigs are a mix of different European wild populations as a result of movement throughout Europe, hereby acquiring haplotypes from all over the European continent. As an alternative hypothesis, we examine whether the introgression of Asian haplotypes into European breeds during the Industrial Revolution caused the observed increase in diversity. By using re-sequence data for chromosome 1 of 136 pigs and wild boars, we show that an Asian introgression of about 20% into the genome of European commercial pigs explains the majority of the increase in genetic diversity. These findings confirm that the Asian hybridization, that was used to improve production traits of local breeds, left its signature in the genome of the commercial pigs we know today.