Signatures of diversifying selection in European pig breeds

Automated landmark-based cat facial analysis and its applications

Facial landmarks, widely studied in human affective computing, are beginning to gain interest in the animal domain. Specifically, landmark-based geometric morphometric methods have been used to objectively assess facial expressions in cats, focusing on pain recognition and the impact of breed-specific morphology on facial signaling. These methods employed a 48-landmark scheme grounded in cat facial anatomy. Manually annotating these landmarks, however, is a labor-intensive process, deeming it impractical for generating sufficiently large amounts of data for machine learning purposes and for use in applied real-time contexts with cats. Our previous work introduced an AI pipeline for automated landmark detection, which showed good performance in standard machine learning metrics. Nonetheless, the effectiveness of fully automated, end-to-end landmark-based systems for practical cat facial analysis tasks remained underexplored. In this paper we develop AI pipelines for three benchmark tasks using two previously collected datasets of cat faces. The tasks include automated cat breed recognition, cephalic type recognition and pain recognition. Our fully automated end-to-end pipelines reached accuracy of 75% and 66% in cephalic type and pain recognition respectively, suggesting that landmark-based approaches hold promise for automated pain assessment and morphological explorations.

High-throughput untargeted metabolomics reveals metabolites and metabolic pathways that differentiate two divergent pig breeds

Metabolomics can describe the molecular phenome and may contribute to dissecting the biological processes linked to economically relevant traits in livestock species. Comparative analyses of metabolomic profiles in purebred pigs can provide insights into the basic biological mechanisms that may explain differences in production performances. Following this concept, this study was designed to compare, on a large scale, the plasma metabolomic profiles of two Italian heavy pig breeds (Italian Duroc and Italian Large White) to indirectly evaluate the impact of their different genetic backgrounds on the breed metabolomes. We utilised a high-throughput untargeted metabolomics approach in a total of 962 pigs that allowed us to detect and relatively quantify 722 metabolites from various biological classes. The molecular data were analysed using a bioinformatics pipeline specifically designed for identifying differentially abundant metabolites between the two breeds in a robust and statistically significant manner, including the Boruta algorithm, which is a Random Forest wrapper, and sparse Partial Least Squares Discriminant Analysis (sPLS-DA) for feature selection. After thoroughly evaluating the impact of random components on missing value imputation, 100 discriminant metabolites were selected by Boruta and 17 discriminant metabolites (all included within the previous list) were identified with sPLS-DA. About half of the 100 discriminant metabolites had a higher concentration in one or the other breed (48 in Italian Large White pigs, with a prevalence of amino acids and peptides; 52 in Italian Duroc pigs, with a prevalence of lipids). These metabolites were from seven distinct super pathways and had an absolute mean value of percentage difference between the two breeds (|Δ|%) of 39.2 ± 32.4. Six of these metabolites had |Δ|%> 100. A general correlation network analysis based on Boruta-identified metabolites consisted of 31 singletons and 69 metabolites connected by 141 edges, with two large clusters (> 15 nodes), three medium clusters (3-6 nodes) and eight additional pairs, with most metabolites belonging to the same super pathway. The major cluster representing the lipids super-pathway included 24 metabolites, primarily sphingomyelins. Overall, this study identified metabolomic differences between Italian Duroc and Italian Large White pigs explained by the specific genetic background of the two breeds. These biomarkers can explain the biological differences between these two breeds and can have potential practical applications in pig breeding and husbandry.

Computational investigation of the social function of domestic cat facial signals

There is growing interest in the facial signals of domestic cats. Domestication may have shifted feline social dynamics towards a greater emphasis on facial signals that promote affiliative bonding. Most studies have focused on cat facial signals during human interactions or in response to pain. Research on intraspecific facial communication in cats has predominantly examined non-affiliative social interactions. A recent study by Scott and Florkiewicz1 demonstrated significant differences between cats' facial signals during affiliative and non-affiliative intraspecific interactions. This follow-up study applies computational approaches to make two main contributions. First, we develop a machine learning classifier for affiliative/non-affiliative interactions based on manual CatFACS codings and automatically detected facial landmarks, reaching above 77% in CatFACS codings and 68% in landmarks by integrating a temporal dimension. Secondly, we introduce novel measures for rapid facial mimicry based on CatFACS coding. Our analysis suggests that domestic cats exhibit more rapid facial mimicry in affiliative contexts than non-affiliative ones, which is consistent with the proposed function of mimicry. Moreover, we found that ear movements (such as EAD103 and EAD104) are highly prone to rapid facial mimicry. Our research introduces new possibilities for analyzing cat facial signals and exploring shared moods with innovative AI-based approaches.

Signatures of selection analyses reveal genomic differences among three heavy pig breeds that constitute the genetic backbone of a dry-cured ham production system

The Italian pig farming industry is unique in its focus on raising heavy pigs primarily for the production of high-quality dry-cured hams. These products require pigs to be slaughtered at a live weight of around 170 kg at 9 months of age. The primary breeds used in this system are Italian Duroc, Italian Landrace, and Italian Large White which are crossed to produce lines that meet standard requirements. Over the past four decades, selection and breeding programmes for these breeds have been subjected to distinct selective pressures to highlight the characteristics of each breed. In this study, we investigated the genome of these breeds by analysing high-density single nucleotide polymorphism data from over 9 000 pigs to scan for signatures of selection using four different methods, two within breeds and two across breeds. This allowed to identify the genomic regions that differentiate these breeds as well as any relevant genes and biological terms. On a global scale, we found that the Italian Duroc breed exhibited a higher genetic differentiation from the Italian Landrace and Italian Large White breeds, with a pairwise FST value of 0.20 compared with the 0.13 between Italian Landrace and Italian Large White. This may reflect either their different origins or the different breeding goals, which are more similar for the Italian Landrace and Italian Large White breeds. Despite these genetic differences at a global level, few signatures of selection regions reached complete fixation, possibly due to challenges in detecting selection linked to quantitative polygenic traits. The differences among the three breeds are confirmed by the low level of overlap in the regions detected. Genetic enrichment analyses of the three breeds revealed pathways and genes related to various productive traits associated with growth and fat deposition. This may indicate a common selection direction aimed at enhancing specific production traits, though different biological mechanisms are likely targeted by the same directional selection in these three breeds. Therefore, these genes may play a critical role in determining the distinctive characteristics of Italian Duroc, Italian Landrace, and Italian Large White, and potentially influence the traits in crossbred pigs derived from them. Overall, the insights gained from this study will contribute to understanding how directional selection has shaped the genome of these heavy pig breeds and to better address selection strategies aimed at enhancing the meat processing industry linked with dry-cured ham production chains.

Elucidation of population stratifying markers and selective sweeps in crossbred Landlly pig population using genome-wide SNP data

The present study was aimed at the identification of population stratifying markers from the commercial porcine SNP 60K array and elucidate the genome-wide selective sweeps in the crossbred Landlly pig population. Original genotyping data, generated on Landlly pigs, was merged in various combinations with global suid breeds that were grouped as exotic (global pig breeds excluding Indian and Chinese), Chinese (Chinese pig breeds only), and outgroup pig populations. Post quality control, the genome-wide SNPs were ranked for their stratifying power within each dataset in TRES (using three different criteria) and FIFS programs and top-ranked SNPs (0.5K, 1K, 2K, 3K, and 4K densities) were selected. PCA plots were used to assess the stratification power of low-density panels. Selective sweeps were elucidated in the Landlly population using intra- and inter-population haplotype statistics. Additionally, Tajima's D-statistics were calculated to determine the status of balancing selection in the Landlly population. PCA plots showed 0.5K marker density to effectively stratify Landlly from other pig populations. The A-score in DAPC program revealed the Delta statistic of marker selection to outperform other methods (informativeness and FST methods) and that 3000-marker density was suitable for stratification of Landlly animals from exotic pig populations. The results from selective sweep analysis revealed the Landlly population to be under selection for mammary (NAV2), reproductive efficiency (JMY, SERGEF, and MAP3K20), body conformation (FHIT, WNT2, ASRB, DMGDH, and BHMT), feed efficiency (CSRNP1 and ADRA1A), and immunity (U6, MYO3B, RBMS3, and FAM78B) traits. More than two methods suggested sweeps for immunity and feed efficiency traits, thus giving a strong indication for selection in this direction. The study is the first of its kind in Indian pig breeds with a comparison against global breeds. In conclusion, 500 markers were able to effectively stratify the breeds. Different traits under selective sweeps (natural or artificial selection) can be exploited for further improvement.

Genomic evidence for human-mediated introgressive hybridization and selection in the developed breed

BACKGROUND

The pig (Sus Scrofa) is one of the oldest domesticated livestock species that has undergone extensive improvement through modern breeding. European breeds have advantages in lean meat development and highly-productive body type, whereas Asian breeds possess extraordinary fat deposition and reproductive performance. Consequently, Eurasian breeds have been extensively used to develop modern commercial breeds for fast-growing and high prolificacy. However, limited by the sequencing technology, the genome architecture of some nascent developed breeds and the human-mediated impact on their genomes are still unknown.

RESULTS

Through whole-genome analysis of 178 individuals from an Asian locally developed pig breed, Beijing Black pig, and its two ancestors from two different continents, we found the pervasive inconsistent gene trees and species trees across the genome of Beijing Black pig, which suggests its introgressive hybrid origin. Interestingly, we discovered that this developed breed has more genetic relationships with European pigs and an unexpected introgression from Asian pigs to this breed, which indicated that human-mediated introgression could form the porcine genome architecture in a completely different type compared to native introgression. We identified 554 genomic regions occupied 63.30 Mb with signals of introgression from the Asian ancestry to Beijing Black pig, and the genes in these regions enriched in pathways associated with meat quality, fertility, and disease-resistant. Additionally, a proportion of 7.77% of genomic regions were recognized as regions that have been under selection. Moreover, combined with the results of a genome-wide association study for meat quality traits in the 1537 Beijing Black pig population, two important candidate genes related to meat quality traits were identified. DNAJC6 is related to intramuscular fat content and fat deposition, and RUFY4 is related to meat pH and tenderness.

CONCLUSIONS

Our research provides insight for analyzing the origins of nascent developed breeds and genome-wide selection remaining in the developed breeds mediated by humans during modern breeding.

Genetic introgression from commercial European pigs to the indigenous Chinese Lijiang breed and associated changes in phenotypes

BACKGROUND

Gene flow is crucial for enhancing economic traits of livestock. In China, breeders have used hybridization strategies for decades to improve livestock performance. Here, we performed whole-genome sequencing of a native Chinese Lijiang pig (LJP) breed. By integrating previously published data, we explored the genetic structure and introgression of genetic components from commercial European pigs (EP) into the LJP, and examined the impact of this introgression on phenotypic traits.

RESULTS

Our analysis revealed significant introgression of EP breeds into the LJP and other domestic pig breeds in China. Using a haplotype-based approach, we quantified introgression levels and compared EP to LJP and other Chinese domestic pigs. The results show that EP introgression is widely prevalent in Chinese domestic pigs, although there are significant differences between breeds. We propose that LJP could potentially act as a mediator for the transmission of EP haplotypes. We also examined the correlation between EP introgression and the number of thoracic vertebrae in LJP and identified VRTN and STUM as candidate genes for this trait.

CONCLUSIONS

Our study provides evidence of introgressed European haplotypes in the LJP breed and describes the potential role of EP introgression on phenotypic changes of this indigenous breed.

Copy number variants selected during pig domestication inferred from whole genome resequencing

Over extended periods of natural and artificial selection, China has developed numerous exceptional pig breeds. Deciphering the germplasm characteristics of these breeds is crucial for their preservation and utilization. While many studies have employed single nucleotide polymorphism (SNP) analysis to investigate the local pig germplasm characteristics, copy number variation (CNV), another significant type of genetic variation, has been less explored in understanding pig resources. In this study, we examined the CNVs of 18 Wanbei pigs (WBP) using whole genome resequencing data with an average depth of 12.61. We identified a total of 8,783 CNVs (~30.07 Mb, 1.20% of the pig genome) in WBP, including 8,427 deletions and 356 duplications. Utilizing fixation index (Fst), we determined that 164 CNVs were within the top 1% of the Fst value and defined as under selection. Functional enrichment analyses of the genes associated with these selected CNVs revealed genes linked to reproduction (SPATA6, CFAP43, CFTR, BPTF), growth and development (NR6A1, SMYD3, VIPR2), and immunity (PARD3, FYB2). This study enhances our understanding of the genomic characteristics of the Wanbei pig and offers a theoretical foundation for the future breeding of this breed.

Ascertaining the genetic background of the Celtic-Iberian pig strain: A signatures of selection approach

Celtic-Iberian pig breeds were majority in Spain and Portugal until the first half of the 20th century. In the 1990s, they were nearly extinct as a result of the introduction of foreign improved pig breeds. Despite its historical importance, the genetic background of the Celtic-Iberian pig strain is poorly documented. In this study, we have identified genomic regions that might contain signatures of selection peculiar of the Celtic-Iberian genetic lineage. A total of 153 DNA samples of Celtic-Iberian pigs (Spanish Gochu Asturcelta and Portuguese Bísara breeds), Iberian pigs (Spanish Iberian and Portuguese Alentejano breeds), Cinta Senese pig, Korean local pig and Cosmopolitan pig (Hampshire, Landrace and Large White individuals) were analysed. A pairwise-comparison approach was applied: the Gochu Asturcelta and the Bísara samples as test populations and the five other pig populations as reference populations. Three different statistics (XP-EHH, FST and ΔDAF) were computed on each comparison. Strict criteria were used to identify selection sweeps in order to reduce the noise brought on by the Gochu Asturcelta and Bísara breeds' severe population bottlenecks. Within test population, SNPs used to construct potential candidate genomic areas under selection were only considered if they were identified in four of ten two-by-two pairwise comparisons and in at least two of three statistics. Genomic regions under selection constructed within test population were subsequently overlapped to construct candidate regions under selection putatively unique to the Celtic-Iberian pig strain. These genomic regions were finally used for enrichment analyses. A total of 39 candidate regions, mainly located on SSC5 and SSC9 and covering 3130.5 kb, were identified and could be considered representative of the ancient genomic background of the Celtic-Iberian strain. Enrichment analysis allowed to identify a total of seven candidate genes (NOL12, LGALS1, PDXP, SH3BP1, GGA1, WIF1, and LYPD6). Other studies reported that the WIF1 gene is associated with ear size, one of the characteristic traits of the Celtic-Iberian pig strain. The function of the other candidate genes could be related to reproduction, adaptation and immunity traits, indirectly fitting with the rusticity of a non-improved pig strain traditionally exploited under semi-extensive conditions.

Ambivalence towards pork belly: exploring its significance and contradictions from the perspectives of the food industry and nutritional science

Pork is the most consumed meat in South Korea, and pork belly is the preferred cut. However, pork production cannot meet the demand, leading to a heavy reliance on imports, particularly for pork bellies. In contrast, low-fat cuts face oversupply problems owing to low demand and export challenges. Pork belly fat content varies with breed, sex, growth rate, and fatty acid composition. Western countries favor higher fat saturation for processed products, whereas South Koreans prefer grilled or roasted bellies. Excessive consumption of high-fat pork cuts like pork belly, which is rich in saturated fatty acids, can increase the risk of severe diseases, highlighting the importance of reducing saturated fat intake and increasing the consumption of monounsaturated fatty acids and polyunsaturated fatty acids to mitigate these risks. The pork industry and public health sector should diversify production, promote leaner pork, and raise awareness about the implications of excessive pork consumption.

Intrauterine growth restriction defined by increased brain-to-liver weight ratio affects postnatal growth and protein efficiency in pigs

Intrauterine growth restriction (IUGR) refers to impaired foetal growth during gestation, resulting in permanent stunting effects on the offspring. This study aimed to investigate the effects of IUGR on growth performance, body composition, blood metabolites, and meat quality of pigs from birth (n = 268) to slaughter (n = 93). IUGR piglets have prioritised brain development as a foetal adaptive reaction to placental insufficiency. This survival mechanism results in a higher brain-to-liver weight ratio (BrW/LW). One day (±1) after birth, computed tomography (CT) was performed on each piglet to assess their brain and liver weights. A threshold value of 0.78 (mean + SD) was chosen to divide the piglets into two categories - NORM (BrW/LW < 0.78) and IUGR (BrW/LW > 0.78). Moreover, each piglet was classified as either normal (score 1), mild IUGR (score 2), or severe IUGR (score 3) based on the head morphology. BW was recorded weekly, and average daily gain (ADG) was calculated for lactation, starter, grower, and finisher periods. Body composition was assessed after weaning (29.6 ± 0.7 d), at 20 kg (64 ± 7.2 d), 100 kg (165 ± 12.3 d), and on the carcasses using Dual-energy X-ray absorptiometry (DXA). Content and deposition rates of single nutrients, as well as energy and CP efficiency, were measured at 20 and 100 kg. Feed intake was recorded from 20 kg to slaughter. Meat quality was assessed on the carcasses. A total of 70% of the piglets assigned a score of 3 were NORM according to their BrW/LW. The IUGR category showed a lower ADG in the lactation (P < 0.01), starter (P = 0.07), and grower phases (P < 0.05) and a reduced CP efficiency in the grower-finisher period (P < 0.01) compared to the NORM group. IUGR pigs had a lower gain-to-feed ratio in the finisher period (P = 0.01) despite similar average daily feed intake, and they required more days (P < 0.01) to reach the slaughter weight. Additionally, their meat was darker (P = 0.01) than that of NORM pigs. The BrW/LW was inversely proportional to the ADG from birth to slaughter and negatively correlated with the CP deposition rate and efficiency in the grower-finisher period (P < 0.01). Furthermore, the higher the BrW/LW, the longer it took the pigs to reach the slaughter weight (P < 0.01). In conclusion, the identification of IUGR piglets based on the head morphology does not always agree with an increased BrW/LW. IUGR affects growth performance from birth to slaughter, CP efficiency in the grower-finisher period and meat quality.

A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits

BACKGROUND

Intense selection of modern pig breeds has resulted in genetic improvement of production traits while the performance of local pig breeds has remained lower. As local pig breeds have been bred in extensive systems, they have adapted to specific environmental conditions, resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds that have been genetically characterized using DNA-pool sequencing data and phenotypically characterized using breed level phenotypes related to stature, fatness, growth, and reproductive performance traits. These data were analyzed using a dedicated approach to detect signatures of selection linked to phenotypic traits in order to uncover potential candidate genes that may underlie adaptation to specific environments.

RESULTS

Analysis of the genetic data of European pig breeds revealed four main axes of genetic variation represented by the Iberian and three modern breeds (i.e. Large White, Landrace, and Duroc). In addition, breeds clustered according to their geographical origin, for example French Gascon and Basque breeds, Italian Apulo Calabrese and Casertana breeds, Spanish Iberian, and Portuguese Alentejano breeds. Principal component analysis of the phenotypic data distinguished the larger and leaner breeds with better growth potential and reproductive performance from the smaller and fatter breeds with low growth and reproductive efficiency. Linking the signatures of selection with phenotype identified 16 significant genomic regions associated with stature, 24 with fatness, 2 with growth, and 192 with reproduction. Among them, several regions contained candidate genes with possible biological effects on stature, fatness, growth, and reproductive performance traits. For example, strong associations were found for stature in two regions containing, respectively, the ANXA4 and ANTXR1 genes, for fatness in a region containing the DNMT3A and POMC genes and for reproductive performance in a region containing the HSD17B7 gene.

CONCLUSIONS

In this study on European local pig breeds, we used a dedicated approach for detecting signatures of selection that were supported by phenotypic data at the breed level to identify potential candidate genes that may have adapted to different living environments and production systems.

The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation

Structural variations have emerged as an important driving force for genome evolution and phenotypic variation in various organisms, yet their contributions to genetic diversity and adaptation in domesticated animals remain largely unknown. Here we constructed a pangenome based on 250 sequenced individuals from 32 pig breeds in Eurasia and systematically characterized coding sequence presence/absence variations (PAVs) within pigs. We identified 308.3-Mb nonreference sequences and 3438 novel genes absent from the current reference genome. Gene PAV analysis showed that 16.8% of the genes in the pangene catalog undergo PAV. A number of newly identified dispensable genes showed close associations with adaptation. For instance, several novel swine leukocyte antigen (SLA) genes discovered in nonreference sequences potentially participate in immune responses to productive and respiratory syndrome virus (PRRSV) infection. We delineated previously unidentified features of the pig mobilome that contained 490,480 transposable element insertion polymorphisms (TIPs) resulting from recent mobilization of 970 TE families, and investigated their population dynamics along with influences on population differentiation and gene expression. In addition, several candidate adaptive TE insertions were detected to be co-opted into genes responsible for responses to hypoxia, skeletal development, regulation of heart contraction, and neuronal cell development, likely contributing to local adaptation of Tibetan wild boars. These findings enhance our understanding on hidden layers of the genetic diversity in pigs and provide novel insights into the role of SVs in the evolutionary adaptation of mammals.

Genetic and Phenotypic Characteristics of Belted Pig Breeds: A Review

Belted pig breeds have unique, distinguishing phenotypic characteristics. This review summarises the current knowledge on pig breeds displaying a belted coat pattern. Belts of different widths and positions around the animal's trunk characterise specific pig breeds from all around the world. All the breeds included in the present paper have been searched through the FAO domestic animal diversity information system (DAD-IS), Every country was checked to identify all breeds described as having black or red piebald coat pattern variations. Advances in genomic technologies have made it possible to identify the specific genes and genetic markers associated with the belted phenotype and explore the genetic relationships between different local breeds. Thus, the origin, history, and production traits of these breeds, together with all the genomic information related to the mechanism of skin pigmentation, are discussed. By increasing our understanding of these breeds, we can appreciate the richness of our biological and cultural heritage and work to preserve the biodiversity of the world's animals.

Analysis of polygenic selection in purebred and crossbred pig genomes using generation proxy selection mapping

BACKGROUND

Artificial selection on quantitative traits using breeding values and selection indices in commercial livestock breeding populations causes changes in allele frequency over time at hundreds or thousands of causal loci and the surrounding genomic regions. In population genetics, this type of selection is called polygenic selection. Researchers and managers of pig breeding programs are motivated to understand the genetic basis of phenotypic diversity across genetic lines, breeds, and populations using selection mapping analyses. Here, we applied generation proxy selection mapping (GPSM), a genome-wide association analysis of single nucleotide polymorphism (SNP) genotypes (38,294-46,458 markers) of birth date, in four pig populations (15,457, 15,772, 16,595 and 8447 pigs per population) to identify loci responding to artificial selection over a period of five to ten years. Gene-drop simulation analyses were conducted to provide context for the GPSM results. Selected loci within and across each population of pigs were compared in the context of swine breeding objectives.

RESULTS

The GPSM identified 49 to 854 loci as under selection (Q-values less than 0.10) across 15 subsets of pigs based on combinations of populations. The number of significant associations increased when data were pooled across populations. In addition, several significant associations were identified in more than one population. These results indicate concurrent selection objectives, similar genetic architectures, and shared causal variants responding to selection across these pig populations. Negligible error rates (less than or equal to 0.02%) of false-positive associations were found when testing GPSM on gene-drop simulated genotypes, suggesting that GPSM distinguishes selection from random genetic drift in actual pig populations.

CONCLUSIONS

This work confirms the efficacy and the negligible error rates of the GPSM method in detecting selected loci in commercial pig populations. Our results suggest shared selection objectives and genetic architectures across swine populations. The identified polygenic selection highlights loci that are important to swine production.

Permanent Tooth Eruption Patterns in Nigerian Local Pigs

Pigs are diphyodonts with heterodont dentition and have been used in studies involving teeth and jawbone regeneration, and dental implants. Patterns of tooth eruption are used to age animals and determine the effects of environmental and genetic influences on occurrence of variations. As with other species, variations exist in the tooth eruption pattern in pigs. The aim of this study was to determine the permanent teeth eruption patterns of Nigerian local pigs. Twenty-six healthy pigs were observed throughout the study period. Pigs were firmly held in dorsal or lateral recumbency and their mouths gently held open to visually examine all quadrants of the dental arches (right and left maxillary, right and left mandibular). Observations were recorded from 16 weeks of age, until the last permanent tooth erupted. Results obtained from the study showed that males had lower mean values for eruption time (54%) of examined teeth in comparison to females. The mean values of eruption time for the maxillary third incisor, the mandibular and maxillary canines, and the mandibular fourth premolar teeth were statistically significant in the males (P = .0017, P = .0088, P = .0002 and P = .0244, respectively). Sixty-nine percent of the adult pigs did not have eruption of the mandibular first premolar, while polydontia was observed in the maxillary and mandibular incisors. These results show that intra-breed and inter-breed variations exist in the dental eruption pattern in pigs. The data obtained from this study can be used for comparative dental studies and can aid further research on the developmental anatomy of Nigerian local pigs.

Genetic differentiation following recent domestication events: A study of farmed Nile tilapia (Oreochromis niloticus) populations

Nile tilapia (Oreochromis niloticus) is among the most farmed finfish worldwide, distributed across different environmental conditions. Its wide distribution has mainly been facilitated by several breeding programs and widespread dissemination of genetically improved strains. In the first Nile tilapia study exploiting a whole-genome pooled sequencing (Poolseq) approach, we identified the genetic structure and signatures of selection in diverse, farmed Nile tilapia populations, with a particular focus on the GIFT strain, developed in the 1980s, and currently managed by WorldFish (GIFTw). We also investigated important farmed strains from The Philippines and Africa. Using both SNP array data and Poolseq SNPs, we characterized the population structure of these samples. We observed the greatest separation between the Asian and African populations and greater admixture in the Asian populations than in the African ones. We also established that the SNP array data were able to successfully resolve relationships between these diverse Nile tilapia populations. The Poolseq data identified genomic regions with high levels of differentiation (F ST) between GIFTw and the other populations. Gene ontology terms associated with mesoderm development were significantly enriched in the genes located in these regions. A region on chromosome Oni06 was genetically differentiated in pairwise comparisons between GIFTw and all other populations. This region contains genes associated with muscle-related traits and overlaps with a previously published QTL for fillet yield, suggesting that these traits may have been direct targets for selection on GIFT. A nearby region was also identified using XP-EHH to detect genomic differentiation using the SNP array data. Genomic regions with high or extended homozygosity within each population were also identified. This study provides putative genomic landmarks associated with the recent domestication process in several Nile tilapia populations, which could help to inform their genetic management and improvement.

Genome-wide association study reveals that the IBSP locus affects ear size in cattle

Ear size is a classical model for hot climate adaptation following the evolution, but the genetic basis of the traits associated with ear size remains to be elucidated. Here, we performed a genome-wide association study on 158 cattle to explain the genetic mechanism of ear size. One region on BTA6 between 36.79 and 38.80 Mb included 50 suggestive SNPs and 4 significant SNPs that were significantly associated with ear size. The most significant locus (P = 1.30 × 10-8) was a missense mutation (T250I) on the seventh exon of integrin-binding sialoprotein (IBSP), which had an allele substitution effect of 23.46 cm2 for ear size. Furthermore, this mutation will cause changes in the three-dimensional structure of the protein. To further identify genes underlying this typical feature, we performed a genome scan among nine cattle breeds with different ear sizes by using SweeD. Results suggested that IBSP was under positive selection among four breeds with relatively large ear sizes. The expression levels of IBSP in ear tissues of large- and small-ear cattle were significantly different. A haplotype diversity survey of this missense mutation in worldwide cattle breeds strongly implied that the origin of this missense mutation event was Bos taurus. These findings have important theoretical importance for the exploration of major genes associated with ear size and provide important molecular markers for the identification of cattle germplasm resources.

Screening of candidate genes related to differences in growth and development between Chinese indigenous and Western pig breeds

Neijiang (NJ) and Yacha (YC) are two indigenous pig breeds in the Sichuan basin of China, displaying higher resistance to diseases, lower lean ratio, and slower growth rate than the commercial Western pig breed Yorkshire (YS). The molecular mechanisms underlying the differences in growth and development between these pig breeds are still unknown. In the present study, five pigs from NJ, YC, and YS breeds were subjected to the whole genome resequencing, and then the differential single-nucleotide polymorphisms (SNPs) were screened using a 10-kb window sliding in 1-kb step using the F_st method. Finally, 48,924, 48,543, and 46,228 nonsynonymous single-nucleotide polymorphism loci (nsSNPs) were identified between NJ and YS, NJ and YC, and YC and YS, which highly or moderately affected 2,490, 800, and 444 genes, respectively. Moreover, three nsSNPs were detected in the genes of acetyl-CoA acetyltransferase 1 (ACAT1) insulin-like growth factor 2 receptor (IGF2R), insulin-like growth factor 2 and mRNA-binding protein 3 (IGF2BP3), which potentially affected the transformation of acetyl-CoA to acetoacetyl-CoA and the normal functions of the insulin signaling pathways. Moreover, serous determinations revealed significantly lower acetyl-CoA content in YC than in YS, supporting that ACAT1 might be a reason explaining the differences in growth and development between YC and YS breeds. Contents of phosphatidylcholine (PC) and phosphatidic acid (PA) significantly differed between the pig breeds, suggesting that glycerophospholipid metabolism might be another reason for the differences between Chinese and Western pig breeds. Overall, these results might contribute basic information to understand the genetic differences determining the phenotypical traits in pigs.

Reprogramming of the gut microbiota following feralization in Sus scrofa

BACKGROUND

Wild boar has experienced several evolutionary trajectories from which domestic (under artificial selection) and the feral pig (under natural selection) originated. Strong adaptation deeply affects feral population's morphology and physiology, including the microbiota community. The gut microbiota is generally recognized to play a crucial role in maintaining host health and metabolism. To date, it is unclear whether feral populations' phylogeny, development stages or lifestyle have the greatest impact in shaping the gut microbiota, as well as how this can confer adaptability to new environments. Here, in order to deepen this point, we characterized the gut microbiota of feral population discriminating between juvenile and adult samples, and we compared it to the microbiota structure of wild boar and domestic pig as the references. Gut microbiota composition was estimated through the sequencing of the partial 16S rRNA gene by DNA metabarcoding and High Throughput Sequencing on DNA extracted from fecal samples.

RESULTS

The comparison of microbiota communities among the three forms showed significant differences. The feral form seems to carry some bacteria of both domestic pigs, derived from its ancestral condition, and wild boars, probably as a sign of a recent re-adaptation strategy to the natural environment. In addition, interestingly, feral pigs show some exclusive bacterial taxa, also suggesting an innovative nature of the evolutionary trajectories and an ecological segregation in feral populations, as already observed for other traits.

CONCLUSIONS

The feral pig showed a significant change between juvenile and adult microbiota suggesting an influence of the wild environment in which these populations segregate. However, it is important to underline that we certainly cannot overlook that these variations in the structure of the microbiota also depended on the different development stages of the animal, which in fact influence the composition of the intestinal microbiota. Concluding, the feral pigs represent a new actor living in the same geographical space as the wild boars, in which its gut microbial structure suggests that it is mainly the result of environmental segregation, most different from its closest relative. This gives rise to interesting fields of exploration regarding the changed ecological complexity and the consequent evolutionary destiny of the animal communities involved in this phenomenon.

Selection signatures for fiber production in commercial species: A review

Natural fibers derived from diverse animal species have gained increased attention in recent years due to their favorable environmental effects, long-term sustainability benefits, and remarkable physical and mechanical properties that make them valuable raw materials used for textile and non-textile production. Domestication and selective breeding for the economically significant fiber traits play an imperative role in shaping the genomes and, thus, positively impact the overall productivity of the various fiber-producing species. These selection pressures leave unique footprints on the genome due to alteration in the allelic frequencies at specific loci, characterizing selective sweeps. Recent advances in genomics have enabled the discovery of selection signatures across the genome using a variety of methods. The increased demand for 'green products' manufactured from natural fibers necessitates a detailed investigation of the genomes of the various fiber-producing plant and animal species to identify the candidate genes associated with important fiber attributes such as fiber diameter/fineness, color, length, and strength, among others. The objective of this review is to present a comprehensive overview of the concept of selection signature and selective sweeps, discuss the main methods used for its detection, and address the selection signature studies conducted so far in the diverse fiber-producing animal species.

Population differentiated copy number variation between Eurasian wild boar and domesticated pig populations

Sus scrofa is a globally distributed livestock species that still maintains two different ways of life: wild and domesticated. Herein, we detected copy number variation (CNV) of 328 animals using short read alignment on Sscrofa11.1. We compared CNV among five groups of porcine populations: Asian domesticated (AD), European domesticated (ED), Asian wild (AW), European wild (EW), and Near Eastern wild (NEW). In total, 21,673 genes were identified on 154,872 copy number variation region (CNVR). Differences in gene copy numbers between populations were measured by considering the variance-based value [Formula: see text] and the one-way ANOVA test followed by Scheffe test. As a result, 111 genes were suggested as copy number variable genes. Abnormally gained copy number on EEA1 in all populations was suggested the presence of minor CNV in the reference genome assembly, Sscrofa11.1. Copy number variable genes were related to meat quality, immune response, and reproduction traits. Hierarchical clustering of all individuals and mean pairwise [Formula: see text] in breed level were visualized genetic relationship of 328 individuals and 56 populations separately. Our findings have shown how the complex history of pig evolution appears in genome-wide CNV of various populations with different regions and lifestyles.

Lymphoid enhancer binding factor 1 is associated with nose color in Yunong black pigs

Yunong black pig is an indigenous black pig breed being cultivated that has a pure black whole body. However, some individuals appear with a white spot on the nose. We performed case-control association studies and F_ST approaches in 76 animals with nose color records (26 white-nosed pigs vs. 50 black-nosed pigs) by Illumina Porcine SNP50 BeadChip data. In total, 76 SNPs, which included 2 genome-wide significant SNPs and 18 chromosome-wide suggestive SNPs, were identified by association study. The top-ranked 0.1% windows of F_ST results as signals under selection and 24 windows were selected. The lymphoid enhancer binding factor 1 was identified as candidate gene with strong signal in analyses of genome-wide association study and F_ST in black- and white-nosed pigs. Overall, our findings provide evidence that nose color is a heritable trait influenced by many loci. The results contribute to expand our understanding of pigmentation in pigs and provide SNP markers for skin color and related traits selection in Yunong black pigs. Additional research on the genetic link between nose pigmentation is needed.

Genome-Wide Association Analysis Reveals Novel Loci Related with Visual Score Traits in Nellore Cattle Raised in Pasture-Based Systems

Body conformation traits assessed based on visual scores are widely used in Zebu cattle breeding programs. The aim of this study was to identify genomic regions and biological pathways associated with body conformation (CONF), finishing precocity (PREC), and muscling (MUSC) in Nellore cattle. The measurements based on visual scores were collected in 20,807 animals raised in pasture-based systems in Brazil. In addition, 2775 animals were genotyped using a 35 K SNP chip, which contained 31,737 single nucleotide polymorphisms after quality control. Single-step GWAS was performed using the BLUPF90 software while candidate genes were identified based on the Ensembl Genes 69. PANTHER and REVIGO platforms were used to identify key biological pathways and STRING to create gene networks. Novel candidate genes were revealed associated with CONF, including ALDH9A1, RXRG, RAB2A, and CYP7A1, involved in lipid metabolism. The genes associated with PREC were ELOVL5, PID1, DNER, TRIP12, and PLCB4, which are related to the synthesis of long-chain fatty acids, lipid metabolism, and muscle differentiation. For MUSC, the most important genes associated with muscle development were SEMA6A, TIAM2, UNC5A, and UIMC1. The polymorphisms identified in this study can be incorporated in commercial genotyping panels to improve the accuracy of genomic evaluations for visual scores in beef cattle.

Common protein-coding variants influence the racing phenotype in galloping racehorse breeds

Selection for system-wide morphological, physiological, and metabolic adaptations has led to extreme athletic phenotypes among geographically diverse horse breeds. Here, we identify genes contributing to exercise adaptation in racehorses by applying genomics approaches for racing performance, an end-point athletic phenotype. Using an integrative genomics strategy to first combine population genomics results with skeletal muscle exercise and training transcriptomic data, followed by whole-genome resequencing of Asian horses, we identify protein-coding variants in genes of interest in galloping racehorse breeds (Arabian, Mongolian and Thoroughbred). A core set of genes, G6PC2, HDAC9, KTN1, MYLK2, NTM, SLC16A1 and SYNDIG1, with central roles in muscle, metabolism, and neurobiology, are key drivers of the racing phenotype. Although racing potential is a multifactorial trait, the genomic architecture shaping the common athletic phenotype in horse populations bred for racing provides evidence for the influence of protein-coding variants in fundamental exercise-relevant genes. Variation in these genes may therefore be exploited for genetic improvement of horse populations towards specific types of racing.

An insight into the runs of homozygosity distribution and breed differentiation in Mangalitsa pigs

Mangalitsa pigs exhibit three distinct coat color patterns based on which they are described as Red, Blond, and Swallow-bellied. The current study investigated genome-wide diversity and selection signatures in the three breeds using fixation index, runs of homozygosity and population structure analyses. The analyses were originally based on quality-controlled data on 77 Mangalitsa animals from Germany, including 23 Blond, 30 Swallow-bellied and 24 Red Mangalitsa genotyped with a customized version of the ProcineSNP60 v2 Genotyping Bead Chip. Also, 20 Hungarian Mangalitsa genotypes were included as outgroup data for comparison. Estimates of observed heterozygosity were 0.27, 0.28, and 0.29, and inbreeding coefficients estimated based on runs of homozygosity were 24.11%, 20.82%, and 16.34% for Blond, Swallow-bellied and Red Mangalitsa, respectively. ROH islands were detected in all breeds, however, none of these were shared amongst them. The KIF16B gene previously reported to play a role in synaptic signaling was found in a ROH island (SSC17: 16–26) in Swallow-bellied Mangalitsa. The same gene was found to harbor a significantly differentiated SNP (MARC0032380) while contrasting either Blond or Red to Swallow-belied Mangalitsa. In the Red Mangalitsa, some ROH islands were associated with genes that play a role in meat quality traits, i.e., ABCA12, VIL1, PLSCR5, and USP37. Our population structure analysis highlighted a separation of the three breeds, but also showed the closest relatedness between Red and Blond Mangalitsa pigs. Findings of this study improve our understanding of the diversity in the three breeds of Mangalitsa pigs.

Assessing Genetic Diversity and Searching for Selection Signatures by Comparison between the Indigenous Livni and Duroc Breeds in Local Livestock of the Central Region of Russia

Indigenous pig breeds are mainly associated with the adaptive capacity that is necessary to respond adequately to climate change, food security, and livelihood needs, and natural resources conservation. Livni pigs are an indigenous fat-type breed farmed in a single farm in the Orel region and located in the Central European part of the Russian Federation. To determine the genomic regions and genes that are affected by artificial selection, we conducted the comparative study of two pig breeds with different breeding histories and breeding objectives, i.e., the native fat-type Livni and meat-type Duroc breeds using the Porcine GGP HD BeadChip, which contains ~80,000 SNPs. To check the Livni pigs for possible admixture, the Landrace and the Large White breeds were included into the study of genetic diversity as these breeds participated in the formation of the Livni pigs. We observed the highest level of genetic diversity in Livni pigs compared to commercial breeds (UHE = 0.409 vs. 0.319–0.359, p < 0.001; AR = 1.995 vs. 1.894–1.964, p < 0.001). A slight excess of heterozygotes was found in all of the breeds. We identified 291 candidate genes, which were localized within the regions under putative selection, including 22 and 228 genes, which were specific for Livni and Duroc breeds, respectively, and 41 genes common for both breeds. A detailed analysis of the molecular functions identified the genes, which were related to the formation of meat and fat traits, and adaptation to environmental stress, including extreme temperatures, which were different between breeds. Our research results are useful for conservation and sustainable breeding of Livni breed, which shows a high level of genetic diversity. This makes Livni one of the valuable national pig genetic resources.

Current Analytical Methods and Research Trends Are Used to Identify Domestic Pig and Wild Boar DNA in Meat and Meat Products

The pig, one of the most important livestock species, is a meaningful source of global meat production. It is necessary, however, to prove whether a food product that a discerning customer selects in a store is actually made from pork or venison, or does not contain it at all. The problem of food authenticity is widespread worldwide, and cases of meat adulteration have accelerated the development of food and the identification methods of feed species. It is worth noting that several different molecular biology techniques can identify a porcine component. However, the precise differentiation between wild boar and a domestic pig in meat products is still challenging. This paper presents the current state of knowledge concerning the species identification of the domestic pig and wild boar DNA in meat and its products.

Recovering High-Quality Host Genomes from Gut Metagenomic Data through Genotype Imputation

Metagenomic datasets of host-associated microbial communities often contain host DNA that is usually discarded because the amount of data is too low for accurate host genetic analyses. However, genotype imputation can be employed to reconstruct host genotypes if a reference panel is available. Here, the performance of a two-step strategy is tested to impute genotypes from four types of reference panels built using different strategies to low-depth host genome data (≈2× coverage) recovered from intestinal samples of two chicken genetic lines. First, imputation accuracy is evaluated in 12 samples for which both low- and high-depth sequencing data are available, obtaining high imputation accuracies for all tested panels (>0.90). Second, the impact of reference panel choice in population genetics statistics on 100 chickens is assessed, all four panels yielding comparable results. In light of the observations, the feasibility and application of the applied imputation strategy are discussed for different species with regard to the host DNA proportion, genomic diversity, and availability of a reference panel. This method enables leveraging insofar discarded host DNA to get insights into the genetic structure of host populations, and in doing so, facilitates the implementation of hologenomic approaches that jointly analyze host and microbial genomic data.

Genomic analysis of the rare British Lop pig and identification of distinctive genomic markers

Concentration of production on a few commercial pig breeds has led to the marginalization of many native, numerically small breeds, increasing their risk of endangerment. In the UK, one such rare breed is the British Lop, a lop-eared breed, of similar origin to the Welsh breed. The objective of the present study was to address the genomic status of the British Lop and its relationship with other breeds and identify a small set of genomic markers that uniquely characterize and distinguish British Lop animals. Results have shown that the British Lop is a relatively distinct population with reduced genomic diversity and effective size consistent with its status as a rare breed. Furthermore, we demonstrated the genetic closeness of the British Lop to phenotypically similar breeds such as Landrace and Welsh as well Large White, Middle White and Pietrain. Finally, a set of 75 Single Nucleotide Polymorphisms distributed across multiple chromosomes were identified and validated as markers that can consistently distinguish British Lops from other closely related breeds. Results may inform breeding and management strategies aiming to enhance diversity as well as the development of a breed purity test.

Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

BACKGROUND

Past selection events left footprints in the genome of domestic animals, which can be traced back by stretches of homozygous genotypes, designated as runs of homozygosity (ROHs). The analysis of common ROH regions within groups or populations displaying potential signatures of selection requires high-quality SNP data as well as carefully adjusted ROH-defining parameters. In this study, we used a simultaneous testing of rule- and model-based approaches to perform strategic ROH calling in genomic data from different pig populations to detect genomic regions under selection for specific phenotypes.

RESULTS

Our ROH analysis using a rule-based approach offered by PLINK, as well as a model-based approach run by RZooRoH demonstrated a high efficiency of both methods. It underlined the importance of providing a high-quality SNP set as input as well as adjusting parameters based on dataset and population for ROH calling. Particularly, ROHs ≤ 20 kb were called in a high frequency by both tools, but to some extent covered different gene sets in subsequent analysis of ROH regions common for investigated pig groups. Phenotype associated ROH analysis resulted in regions under potential selection characterizing heritage pig breeds, known to harbour a long-established breeding history. In particular, the selection focus on fitness-related traits was underlined by various ROHs harbouring disease resistance or tolerance-associated genes. Moreover, we identified potential selection signatures associated with ear morphology, which confirmed known candidate genes as well as uncovered a missense mutation in the ABCA6 gene potentially supporting ear cartilage formation.

CONCLUSIONS

The results of this study highlight the strengths and unique features of rule- and model-based approaches as well as demonstrate their potential for ROH analysis in animal populations. We provide a workflow for ROH detection, evaluating the major steps from filtering for high-quality SNP sets to intersecting ROH regions. Formula-based estimations defining ROHs for rule-based method show its limits, particularly for efficient detection of smaller ROHs. Moreover, we emphasize the role of ROH detection for the identification of potential footprints of selection in pigs, displaying their breed-specific characteristics or favourable phenotypes.

Population structure of 3907 worldwide pigs and the introgression of Chinese indigenous pigs by European pigs

With the improvement in sequencing technology and the decrease in sequencing cost, increasing amounts of genomic data for pigs have been uploaded to public databases. However, no researchers have to date integrated all currently available data to uncover the global genetic status of pigs. Meanwhile, little is known about the introgression from European to Chinese pigs and its underlying influences. Therefore, we integrated the effective genotype data of 3907 pigs from 193 populations worldwide using population genetic analysis, gene flow analysis and a sharing-IBD study. These findings illustrate not only the population structure of 59 Chinese native breeds and others but also the amounts of gene flow and introgression that have occurred between Western and Chinese pigs. In addition, we demonstrate the presence of introgressed European haplotypes in Chinese indigenous breeds and identify relevant introgressed regions that contain genes associated with growth and feed efficiency. Moreover, we compare the introgression patterns of Western and Chinese pigs and further discuss possible explanations for why the level of introgression differs between Chinese pig breeds and Western modern breeds. Collectively, this study provides a fine global population structure analysis of pigs and presents evidence of European pigs being interbred with local breeds in China.

Whole-genome sequencing reveals the artificial selection and local environmental adaptability of pigeons (Columba livia)

To meet human needs, domestic pigeons (Columba livia) with various phenotypes have been bred to provide genetic material for our research on artificial selection and local environmental adaptation. Seven pigeon breeds were resequenced and can be divided into commercial varieties (Euro-pigeon, Shiqi, Shen King, Taishen, and Silver King), ornamental varieties (High Fliers), and local varieties (Tarim pigeon). Phylogenetic analysis based on population resequencing showed that one group contained local breeds and ornamental pigeons from China, whereas all commercial varieties were clustered together. It is revealed that the traditional Chinese ornamental pigeon is a branch of Tarim pigeon. Runs of homozygosity (ROH) and linkage disequilibrium (LD) analyses revealed significant differences in the genetic diversity of the three types of pigeons. Genome sweep analysis revealed that the selected genes of commercial breeds were related to body size, reproduction, and plumage color. The genomic imprinting genes left by the ornamental pigeon breeds were mostly related to special human facial features and muscular dystrophy. The Tarim pigeon has evolved genes related to chemical ion transport, photoreceptors, oxidative stress, organ development, and olfaction in order to adapt to local environmental stress. This research provides a molecular basis for pigeon genetic resource evaluation and genetic improvement and suggests that the understanding of adaptive evolution should integrate the effects of various natural environmental characteristics.

Proteomic Exploration of Porcine Oocytes During Meiotic Maturation in vitro Using an Accurate TMT-Based Quantitative Approach

The dynamic changes in protein expression are well known to be required for oocyte meiotic maturation. Although proteomic analysis has been performed in porcine oocytes during in vitro maturation, there is still no full data because of the technical limitations at that time. Here, a novel tandem mass tag (TMT)-based quantitative approach was used to compare the proteomic profiles of porcine immature and in vitro mature oocytes. The results of our study showed that there were 763 proteins considered with significant difference−450 over-expressed and 313 under-expressed proteins. The GO and KEGG analyses revealed multiple regulatory mechanisms of oocyte nuclear and cytoplasmic maturation such as spindle and chromosome configurations, cytoskeletal reconstruction, epigenetic modifications, energy metabolism, signal transduction and others. In addition, 12 proteins identified with high-confidence peptide and related to oocyte maturation were quantified by a parallel reaction monitoring technique to validate the reliability of TMT results. In conclusion, we provided a detailed proteomics dataset to enrich the understanding of molecular characteristics underlying porcine oocyte maturation in vitro.

Investigation of the Genetic Architecture of Pigs Subjected to Breeding Intensification

Pigs are strategically important animals for the agricultural industry. An assessment of genetic differentiation between pigs, undergone and not undergone to selection intensification, is of particular interest. Our research was conducted on two groups of Large White pigs grown on the same farm but in different years. A total of 165 samples were selected with 78 LW_А (n = 78, the Russian selection) and LW_B (n = 87, a commercial livestock). For genotyping, we used GeneSeek^® GGP Porcine HD Genomic Profiler v1 (Illumina Inc, San Diego, CA, USA). To define breeding characteristics of selection, we used smoothing FST and segment identification of HBD (Homozygous-by-Descent). The results of smoothing FST showed 20 areas of a genome with strong ejection regions of the genome located on all chromosomes except SSC2, SSC3, and SSC8. The average realized autozygosity in Large White pigs of native selection was in (LW_A)—0.21, in LW_В—0.29. LW_А showed 13,338 HBD segments, 171 per one animal, and LW_B—15,747 HBD segments, 181 per one animal. The ejections found by the smoothing FST method were partially localized in the HBD regions. In these areas, the genes ((NCBP1, PLPPR1, GRIN3A, NBEA, TRPC4, HS6ST3, NALCN, SMG6, TTC3, KCNJ6, IKZF2, OBSL1, CARD10, ETV6, VWF, CCND2, TSPAN9, CDH13, CEP128, SERPINA11, PIK3CG, COG5, BCAP29, SLC26A4) were defined. The revealed genes can be of special interest for further studying their influence on an organism of an animal since they can act as candidate genes for selection-significant traits.

Transcriptome Analysis of mRNAs and Long Non-Coding RNAs During Subsequent Embryo Development of Porcine Cloned Zygotes After Vitrification

Cryopreservation of porcine cloned zygotes has important implications for biotechnology and biomedicine research; however, lower embryo developmental potential remains an urgent problem to be resolved. For exploring the sublethal cryodamages during embryo development, this study was designed to acquire the mRNA and long non-coding RNA (lncRNA) profiles of 2-cells, 4-cells and blastocysts derived from vitrified porcine cloned zygotes using transcriptome sequencing. We identified 167 differentially expressed (DE) mRNAs and 516 DE lncRNAs in 2-cell stage, 469 DE mRNAs and 565 lncRNAs in 4-cell stage, and 389 DE mRNAs and 816 DE lncRNAs in blastocyst stage. Functional enrichment analysis revealed that the DE mRNAs during embryo development were involved in many regulatory mechanisms related to cell cycle, cell proliferation, apoptosis, metabolism and others. Moreover, the target genes of DE lncRNAs in the three embryonic stages were also enriched in many key GO terms or pathways such as “defense response”, “linoleic acid metabolic process”, “embryonic axis specification”, “negative regulation of protein neddylation”, etc., In conclusion, the present study provided comprehensive transcriptomic data about mRNAs and lncRNAs for the vitrified porcine cloned zygotes during different developmental stages, which contributed to further understand the potential cryodamage mechanisms responsible for impaired embryo development.

Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth's biodiversity.

Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth's biodiversity.

Detecting the differential genomic variants using cross-population phenotype-associated variant (XP-PAV) of the Landrace and Yorkshire pigs in Korea

Although there have been many genome-wide association studies (GWAS) and selective sweep analyses to understand pig genomic regions related to growth performance, these methods considered only the gene effect and selection signal, respectively. In this study, we suggest the cross-population phenotype associated variant (XP-PAV) analysis as a novel method to determine the genomic variants with different effects between the two populations. XP-PAV analysis could reveal the differential genetic variants between the two populations by considering the gene effect and selection signal simultaneously. In this study, we used daily weight gain (DWG) and back fat thickness (BF) as phenotypes and the Landrace and Yorkshire populations were used for XP-PAV analysis. The main aim was to reveal the differential selection by considering the gene effect between Landrace and Yorkshire pigs. In the gene ontology analysis of XP-PAV results, differential selective genes in DWG analysis were involved in the regulation of interleukin-2 production and cell cycle G2/M transition. The protein modification and glycerophospholipid biosynthetic processes were the most enriched terms in the BF analysis. Therefore, we could identify genetic differences for immune and several metabolic pathways between Landrace and Yorkshire breeds using the XP-PAV analysis. In this study, we expect that XP-PAV analysis will play a role in determining useful selective variants with gene effects and provide a new interpretation of the genetic differences between the two populations.

Detecting the selection signatures in Chinese Duroc,Landrace, Yorkshire, Liangshan, and Qingyu pigs

Here we used two kinds of chips data from 5 pig breeds, Chinese Duroc (DD), Landrace (LL), Yorkshire (YY), Liangshan (LS), and Qingyu pigs (QY) in China to identify genes which show evidence of selection during domestication. Four breed pairs, LS-YY, QY-YY, DD-YY, and LL-YY pair, were performed to detect selection signatures using the Fst method. Then we identified a list of genes that played key roles in domestication and artificial selection. For example, the PTPRM gene was shared in LS-YY, QY-YY, and DD-YY pairs and it regulates a variety of cellular processes including cell growth, differentiation as signaling molecules. The HACD3 gene was shared in QY-YY and DD-YY pairs, and the HACD3 protein is involved in the production of very long-chain fatty acids of different chain lengths. Besides, the MYH11 gene that related to muscle contraction was found in LS-YY and LL-YY pair. These results suggested that genes related to immunity, disease resistance, and metabolism were subjected to strong selection pressure in Chinese domestic pigs in the progress of domestication and evolution; however, genes related to appearance, production performance, and reproduction were undergone strong artificial selection in commercial pig breeds.

Combined approaches identify known and novel genes associated with sheep litter size and non-seasonal breeding

Improvement of ewe reproduction is considerable by appropriately increasing litter size and sustaining non-seasonal breeding. However, their genetic makeups have not been entirely elucidated. Genome-wide analyses of 821 individuals were performed by combining three genomic approaches (genome-wide association study, XP-nSL, and runs of homozygosity). Consequently, 35 candidate genes including three domestication genes (TSHR, GTF2A1, and KITLG) were identified. Other than the FecB mutation at BMPR1B, we described a significant association of a missense mutation rs406686139 at seasonal lambing-associated TSHR gene with litter size. Some promising novel genes may be relevant for sheep reproduction by multitude biological processes, such as FETUB functioning in fertilization, HNRNPA1 in oogenesis, DCUN1D1 in spermatogenesis, and HRG in fertility outcome. The present study suggests that improvement of ewe reproduction is attributed to selective breeding, and casts light on the genetic basis and improvement of sheep reproduction.

Analysis of Homozygous-by-Descent (HBD) Segments for Purebred and Crossbred Pigs in Russia

Intensive selection raises the efficiency of pig farming considerably, but it also promotes the accumulation of homozygosity, which can lead to an increase in inbreeding and the accumulation of deleterious variation. The analysis of segments homozygous-by-descent (HBD) and non-HBD segments in purebred and crossbred pigs is of great interest. Research was carried out on 657 pigs, of which there were Large White (LW, n = 280), Landrace (LR, n = 218) and F1 female (♂LR × ♀LW) (F1, n = 159). Genotyping was performed using the GeneSeek^® GGP Porcine HD Genomic Profiler v1 (Illumina Inc., USA). To identify HBD segments and estimate autozygosity (inbreeding coefficient), we used the multiple HBD classes model. LW pigs exhibited 50,420 HBD segments, an average of 180 per animal; LR pigs exhibited 33,586 HBD segments, an average of 154 per animal; F1 pigs exhibited 21,068 HBD segments, an average of 132 per animal. The longest HBD segments in LW were presented in SSC1, SSC13 and SSC15; in LR, in SSC1; and in F1, in SSC15. In these segments, 3898 SNPs localized in 1252 genes were identified. These areas overlap with 441 QTLs (SSC1—238 QTLs; SSC13—101 QTLs; and SSC15—102 QTLs), including 174 QTLs for meat and carcass traits (84 QTLs—fatness), 127 QTLs for reproduction traits (100 QTLs—litter traits), 101 for production traits (69 QTLs—growth and 30 QTLs—feed intake), 21 QTLs for exterior traits (9 QTLs—conformation) and 18 QTLs for health traits (13 QTLs—blood parameters). Thirty SNPs were missense variants. Whilst estimating the potential for deleterious variation, six SNPs localized in the NEDD4, SEC11C, DCP1A, CCT8, PKP4 and TENM3 genes were identified, which may show deleterious variation. A high frequency of potential deleterious variation was noted for LR in DCP1A, and for LW in TENM3 and PKP4. In all cases, the genotype frequencies in F1 were intermediate between LR and LW. The findings presented in our work show the promise of genome scanning for HBD as a strategy for studying population history, identifying genomic regions and genes associated with important economic traits, as well as deleterious variation.

Genome-wide analysis of genetic diversity and artificial selection in Large White pigs in Russia

Breeding practices adopted at different farms are aimed at maximizing the profitability of pig farming. In this work, we have analyzed the genetic diversity of Large White pigs in Russia. We compared genomes of historic and modern Large White Russian breeds using 271 pig samples. We have identified 120 candidate regions associated with the differentiation of modern and historic pigs and analyzed genomic differences between the modern farms. The identified genes were associated with height, fitness, conformation, reproductive performance, and meat quality.

The Application of Geometric Morphometrics to Explore Potential Impacts of Anthropocentric Selection on Animals' Ability to Communicate via the Face: The Domestic Cat as a Case Study

During their domestication via artificial selection, humans have substantially modified the morphology and thus visual appearance of non-human animals. While research highlights the negative impact of these modifications on physical functioning, little is known about their impact on behavior and signaling, either toward humans or conspecifics. Changes in the appearance of the face, such as those associated with, but not limited to, facial expressions, form an important part of non-verbal communication. In companion animals, the face is one of their most visually diverse features (due to human-driven selection), which may impact the visual clarity of expressions and other forms of signaling. Using the domestic cat as our model, we applied a new analytical technique in order to understand the impact of breed variation on relative positioning of facial landmarks, chosen specifically for their association with the production of various facial movements, and the expression of affect. We then assessed the extent to which facial appearances known to be associated with a specific underlying state (i.e., pain, assessed via a validated, facial pain score), could be reliably detected in a morphologically diverse population. Substantial baseline variation in landmarks was identified at both the cephalic (e.g., brachycephalic, dolichocephalic, mesocephalic) as well as breed levels. While differences in facial pain scores could successfully differentiate between "pain" and "no pain" in the facial appearance of domestic shorthaired cats (DSH), these differences were no longer detectable when assessed within a larger more morphologically diverse population, after corrections for multiple testing were applied. There was also considerable overlap between pain scores in the DSH "pain" population and the neutral faces of other breeds. Additionally, for several paedomorphic breeds, their neutral face shapes produced scores indicative of greater pain, compared to most other breeds, including the DSH cats actually in pain. Our findings highlight the degree to which anthropocentric selection might disrupt the communicative content of animals' faces, in this case the domestic cat. These results also suggest a potential human preference for features extending beyond the infantile, to include negatively-valenced facial forms such as pain.

Tracing selection signatures in the pig genome gives evidence for selective pressures on a unique curly hair phenotype in Mangalitza

Selection for desirable traits and breed-specific phenotypes has left distinctive footprints in the genome of pigs. As representative of a breed with strong selective traces aiming for robustness, health and performance, the Mangalitza pig, a native curly-haired pig breed from Hungary, was investigated in this study. Whole genome sequencing and SNP chip genotyping was performed to detect runs of homozygosity (ROH) in Mangalitza and Mangalitza-crossbreeds. We identified breed specific ROH regions harboring genes associated with the development of the curly hair type and further characteristics of this breed. Further analysis of two matings of Mangalitza with straight-coated pig breeds confirmed an autosomal dominant inheritance of curly hair. Subsequent scanning of the genome for variant effects on this trait revealed two variants potentially affecting hair follicle development and differentiation. Validation in a large sample set as well as in imputed SNP data confirmed these variants to be Mangalitza-specific. Herein, we demonstrated how strong artificial selection has shaped the genome in Mangalitza pigs and left traces in the form of selection signatures. This knowledge on genomic variation promoting unique phenotypes like curly hair provides an important resource for futures studies unraveling genetic effects for special characteristics in livestock.

Sicilian Black Pig: An Overview

Simple Summary

The conservation of the genetic variability of animals used for food production and non-food raw materials and services is a problem of primary importance at a global level. In recent years, conservation of biodiversity in livestock species has been favoring the need to preserve genetic variability of the autochthonous breeds, exploiting them in the context of production systems. In this context, a precious genetic reserve is represented by autochthonous breeds used for the production of typical products used in Italian gastronomic traditions, of which some organoleptic properties of their meats that could disappear due to severe selection programs are being recovered. Currently, the survival of autochthonous breeds is linked to various reasons such as their rusticity, i.e., the adaptability to difficult environmental conditions, and to the higher market value of their productions obtained according to traditional methods compared to the industrial production types. As information on autochthonous Italian pigs is limited, further research aims at making better use of these breeds and at increasing the knowledge of their genetic variability.

Abstract

The Sicilian black pig (SB) (Nero Siciliano), also known as the Nero dei Nebrodi, Nero delle Madonie, or Nero dell’Etna pig ecotype, is an autochthonous Italian breed. The origins of this breed date back to Greek and Carthaginian dominations. In ancient times, its breeding was fairly common throughout Sicily, registering only a temporary reduction during the Arab domination. This breed is known primarily for its distinctive black coat, although some individuals display wattles and a partially or wholly white face. The SB pig has a birth rate with an average per sow of 7.6 piglets, each of 1.4 kg live body weight, showing an average daily gain (ADG) of 346 g/day during the fattening period. Slaughter generally takes place at an average age of 390 days, with an average live weight of 95 kg. This breed also appears to withstand adverse climatic conditions and resist disease. The purpose of this manuscript is to offer a general overview regarding the Sicilian Black pig and to consider the recent findings related to genome investigation. The recent application of Next Generation Sequencing (NGS) technologies in the study of the genome of autochthonous breeds showed that polymorphisms of some candidate genes for production performance and phenotypic traits represent important information for selection processes. The protection of autochthonous breeds, intended as sources of genomic diversity for the further improvements of pigs for commercial use, constitutes a valuable opportunity to create new sustainable pig chains.

Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

Background

A large number of pig breeds are distributed around the world, their features and characteristics vary among breeds, and they are valuable resources. Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved pig breeds.

Results

In this study, we performed GWAS using a standard mixed linear model with three types of genome variants (SNP, InDel, and CNV) that were identified from public, whole-genome, sequencing data sets. We used 469 pigs of 57 breeds, and we identified and analyzed approximately 19 million SNPs, 1.8 million InDels, and 18,016 CNVs. We defined six biological phenotypes by the characteristics of breed features to identify the associated genome variants and candidate genes, which included coat color, ear shape, gradient zone, body weight, body length, and body height. A total of 37 candidate genes was identified, which included 27 that were reported previously (e.g., PLAG1 for body weight), but the other 10 were newly detected candidate genes (e.g., ADAMTS9 for coat color).

Conclusion

Our study indicated that using GWAS across a modest number of breeds with high density genome variants provided efficient mapping of complex traits.

Supplementary Information

Supplementary information accompanies this paper at 10.1186/s40104-020-00520-8.

Investigating the impact of captivity and domestication on limb bone cortical morphology: an experimental approach using a wild boar model

The lack of bone morphological markers associated with the human control of wild animals has prevented the documentation of incipient animal domestication in archaeology. Here, we assess whether direct environmental changes (i.e. mobility reduction) could immediately affect ontogenetic changes in long bone structure, providing a skeletal marker of early domestication. We relied on a wild boar experimental model, analysing 24 wild-born specimens raised in captivity from 6 months to 2 years old. The shaft cortical thickness of their humerus was measured using a 3D morphometric mapping approach and compared with 23 free-ranging wild boars and 22 pigs from different breeds, taking into account sex, mass and muscle force differences. In wild boars we found that captivity induced an increase in cortical bone volume and muscle force, and a topographic change of cortical thickness associated with muscular expression along a phenotypic trajectory that differed from the divergence induced by selective breeding. These results provide an experimental proof of concept that changes in locomotor behaviour and selective breeding might be inferred from long bones morphology in the fossil and archaeological record. These trends need to be explored in the archaeological record and further studies are required to explore the developmental changes behind these plastic responses.