Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa)

Photoacoustic processing of decellularized extracellular matrix for biofabricating living constructs

The diverse biomolecular landscape of tissue-specific decellularized extracellular matrix (dECM) biomaterials provides a multiplicity of bioinstructive cues to target cells, rendering them highly valuable for various biomedical applications. However, the isolation of dECM biomaterials entails cumbersome xenogeneic enzymatic digestions and also additional inactivation procedures. Such, increases processing time, increments costs and introduces residues of non-naturally present proteins in dECM formulations that remain present even after inactivation. To overcome these limitations, herein we report an innovative conjugation of light and ultrasound-mediated dECM biomaterial processing for fabricating dECM biomaterials. Such approach gathers on ultrasound waves to facilitate dECM-in-liquid processing and visible light photocrosslinking of tyrosine residues naturally present in dECM biomaterials. This dual step methodology unlocked the in-air production of cell laden dECM hydrogels or programmable dECM hydrogel spherical-like beads by using superhydrophobic surfaces. These in-air produced units do not require any additional solvents and successfully supported both fibroblasts and breast cancer cells viability upon encapsulation or surface seeding. In addition, the optimized photoacoustic methodology also enabled a rapid formulation of dECM biomaterial inks with suitable features for biofabricating volumetrically defined living constructs through embedded 3D bioprinting. The biofabricated dECM hydrogel constructs supported cell adhesion, spreading and viability for 7 days. Overall, the implemented photoacoustic processing methodology of dECM biomaterials offers a rapid and universal strategy for upgrading their processing from virtually any tissue. STATEMENT OF SIGNIFICANCE: Leveraging decellularized extracellular matrix (dECM) as cell instructive biomaterials has potential to open new avenues for tissue engineering and in vitro disease modelling. The processing of dECM remains however, lengthy, costly and introduces non-naturally present proteins in the final biomaterials formulations. In this regard, here we report an innovative light and ultrasound two-step methodology that enables rapid dECM-in-liquid processing and downstream photocrosslinking of dECM hydrogel beads and 3D bioprinted constructs. Such photoacoustic based processing constitutes a universally applicable method for processing any type of tissue-derived dECM biomaterials.

A chromosome-level genome of Chenghua pig provides new insights into the domestication and local adaptation of pigs

As a country with abundant genetic resources of pigs, the domestication history of pigs in China and the adaptive evolution of Chinese pig breeds at different latitudes have rarely been elucidated at the genome-wide level. To fill this gap, we first assembled a high-quality chromosome-level genome of the Chenghua pig and used it as a benchmark to analyse the genomes of 272 samples from three genera of three continents. The divergence of the three species belonging to three genera, Phacochoerus africanus, Potamochoerus porcus, and Sus scrofa, was assessed. The introgression of pig breeds redefined that the migration routes were basically from southern China to central and southwestern China, then spread to eastern China, arrived in northern China, and finally reached Europe. The domestication of pigs in China occurred ∼12,000 years ago, earlier than the available Chinese archaeological domestication evidence. In addition, FBN1 and NR6A1 were identified in our study as candidate genes related to extreme skin thickness differences in Eurasian pig breeds and adaptive evolution at different latitudes in Chinese pig breeds, respectively. Our study provides a new resource for the pig genomic pool and refines our understanding of pig genetic diversity, domestication, migration, and adaptive evolution at different latitudes.

Haplotype-resolved 3D chromatin architecture of the hybrid pig

In diploid mammals, allele-specific three-dimensional (3D) genome architecture may lead to imbalanced gene expression. Through ultradeep in situ Hi-C sequencing of three representative somatic tissues (liver, skeletal muscle, and brain) from hybrid pigs generated by reciprocal crosses of phenotypically and physiologically divergent Berkshire and Tibetan pigs, we uncover extensive chromatin reorganization between homologous chromosomes across multiple scales. Haplotype-based interrogation of multi-omic data revealed the tissue dependence of 3D chromatin conformation, suggesting that parent-of-origin-specific conformation may drive gene imprinting. We quantify the effects of genetic variations and histone modifications on allelic differences of long-range promoter-enhancer contacts, which likely contribute to the phenotypic differences between the parental pig breeds. We also observe the fine structure of somatically paired homologous chromosomes in the pig genome, which has a functional implication genome-wide. This work illustrates how allele-specific chromatin architecture facilitates concomitant shifts in allele-biased gene expression, as well as the possible consequential phenotypic changes in mammals.

Comprehensive Atlas of Alternative Splicing Reveals NSRP1 Promoting Adipogenesis through CCDC18

Alternative splicing (AS) plays a crucial role in regulating gene expression, function, and diversity. However, limited reports exist on the identification and comparison of AS in Eastern and Western pigs. Here, we analyzed 243 transcriptome data from eight tissues, integrating information on transcription factors (TFs), selection signals, splicing factors (SFs), and quantitative trait loci (QTL) to comprehensively study alternative splicing events (ASEs) in pigs. Five ASE types were identified, with Mutually Exclusive Exon (MXE) and Skipped Exon (SE) ASEs being the most prevalent. A significant portion of genes with ASEs (ASGs) showed conservation across all eight tissues (63.21-76.13% per tissue). Differentially alternative splicing genes (DASGs) and differentially expressed genes (DEGs) exhibited tissue specificity, with blood and adipose tissues having more DASGs. Functional enrichment analysis revealed coDASG_DEGs in adipose were enriched in pathways associated with adipose deposition and immune inflammation, while coDASG_DEGs in blood were enriched in pathways related to immune inflammation and metabolism. Adipose deposition in Eastern pigs might be linked to the down-regulation of immune-inflammation-related pathways and reduced insulin resistance. The TFs, selection signals, and SFs appeared to regulate ASEs. Notably, ARID4A (TF), NSRP1 (SF), ANKRD12, IFT74, KIAA2026, CCDC18, NEXN, PPIG, and ROCK1 genes in adipose tissue showed potential regulatory effects on adipose-deposition traits. NSRP1 could promote adipogenesis by regulating alternative splicing and expression of CCDC18. Conducting an in-depth investigation into AS, this study has successfully identified key marker genes essential for pig genetic breeding and the enhancement of meat quality, which will play important roles in promoting the diversity of pork quality and meeting market demand.

Pig pangenome graph reveals functional features of non-reference sequences

BACKGROUND

The reliance on a solitary linear reference genome has imposed a significant constraint on our comprehensive understanding of genetic variation in animals. This constraint is particularly pronounced for non-reference sequences (NRSs), which have not been extensively studied.

RESULTS

In this study, we constructed a pig pangenome graph using 21 pig assemblies and identified 23,831 NRSs with a total length of 105 Mb. Our findings revealed that NRSs were more prevalent in breeds exhibiting greater genetic divergence from the reference genome. Furthermore, we observed that NRSs were rarely found within coding sequences, while NRS insertions were enriched in immune-related Gene Ontology terms. Notably, our investigation also unveiled a close association between novel genes and the immune capacity of pigs. We observed substantial differences in terms of frequencies of NRSs between Eastern and Western pigs, and the heat-resistant pigs exhibited a substantial number of NRS insertions in an 11.6 Mb interval on chromosome X. Additionally, we discovered a 665 bp insertion in the fourth intron of the TNFRSF19 gene that may be associated with the ability of heat tolerance in Southern Chinese pigs.

CONCLUSIONS

Our findings demonstrate the potential of a graph genome approach to reveal important functional features of NRSs in pig populations.

Uncovering Evolutionary Adaptations in Common Warthogs through Genomic Analyses

In the Suidae family, warthogs show significant survival adaptability and trait specificity. This study offers a comparative genomic analysis between the warthog and other Suidae species, including the Luchuan pig, Duroc pig, and Red River hog. By integrating the four genomes with sequences from the other four species, we identified 8868 single-copy orthologous genes. Based on 8868 orthologous protein sequences, phylogenetic assessments highlighted divergence timelines and unique evolutionary branches within suid species. Warthogs exist on different evolutionary branches compared to DRCs and LCs, with a divergence time preceding that of DRC and LC. Contraction and expansion analyses of warthog gene families have been conducted to elucidate the mechanisms of their evolutionary adaptations. Using GO, KEGG, and MGI databases, warthogs showed a preference for expansion in sensory genes and contraction in metabolic genes, underscoring phenotypic diversity and adaptive evolution direction. Associating genes with the QTLdb-pigSS11 database revealed links between gene families and immunity traits. The overlap of olfactory genes in immune-related QTL regions highlighted their importance in evolutionary adaptations. This work highlights the unique evolutionary strategies and adaptive mechanisms of warthogs, guiding future research into the distinct adaptability and disease resistance in pigs, particularly focusing on traits such as resistance to African Swine Fever Virus.

Thermoregulation in the wild boar (Sus scrofa)

The wild boar (Sus scrofa) originates from warm islands but now inhabits large areas of the world, with Antarctica as the only continent not inhabited by this species. One might be tempted to think that its wide distribution results from increasing environmental temperatures. However, any effect of temperature is only indirect: Abundant availability of critical food resources can fully compensate the negative effects of cold winters on population growth. Here, we asked if temperature as a habitat factor is unimportant compared with other habitat indices, simply because wild boars are excellent thermoregulators. We found that the thermoneutral zone in summer was approximately 6-24 °C. In winter, the thermoneutral zone was lowered to 0-7 °C. The estimated increase in the heart rate and energy expenditure in the cold was less than 30% per 10 °C temperature decline. This relatively small increase of energy expenditure during cold exposure places the wild boar in the realm of arctic animals, such as the polar bear, whereas tropical mammals raise their energy expenditure several fold. The response of wild boars to high Ta was weak across all seasons. In the heat, wild boars avoid close contact to conspecifics and particularly use wallowing in mud or other wet substrates to cool and prevent hyperthermia. Wild boars also rely on daily cycles, especially of rhythms in subcutaneous temperature that enables them to cheaply build large core-shell gradients, which serve to lower heat loss. We argue it is predominantly this ability which allowed wild boars to inhabit most climatically diverse areas in the world.

Comprehensive Analysis of CircRNA Expression Profiles in Multiple Tissues of Pigs

Circular RNAs (circRNAs) are a class of non-coding RNAs with diverse functions, and previous studies have reported that circRNAs are involved in the growth and development of pigs. However, studies about porcine circRNAs over the past few years have focused on a limited number of tissues. Based on 215 publicly available RNA sequencing (RNA-seq) samples, we conducted a comprehensive analysis of circRNAs in nine pig tissues, namely, the gallbladder, heart, liver, longissimus dorsi, lung, ovary, pituitary, skeletal muscle, and spleen. Here, we identified a total of 82,528 circRNAs and discovered 3818 novel circRNAs that were not reported in the CircAtlas database. Moreover, we obtained 492 housekeeping circRNAs and 3489 tissue-specific circRNAs. The housekeeping circRNAs were enriched in signaling pathways regulating basic biological tissue activities, such as chromatin remodeling, nuclear-transcribed mRNA catabolic process, and protein methylation. The tissue-specific circRNAs were enriched in signaling pathways related to tissue-specific functions, such as muscle system process in skeletal muscle, cilium organization in pituitary, and cortical cytoskeleton in ovary. Through weighted gene co-expression network analysis, we identified 14 modules comprising 1377 hub circRNAs. Additionally, we explored circRNA-miRNA-mRNA networks to elucidate the interaction relationships between tissue-specific circRNAs and tissue-specific genes. Furthermore, our conservation analysis revealed that 19.29% of circRNAs in pigs shared homologous positions with their counterparts in humans. In summary, this extensive profiling of housekeeping, tissue-specific, and co-expressed circRNAs provides valuable insights into understanding the molecular mechanisms of pig transcriptional expression, ultimately deepening our understanding of genetic and biological processes.

Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences

High-quality whole-genome resequencing in large-scale pig populations with pedigree structure and multiple breeds would enable accurate construction of haplotype and robust selection-signature detection. Here, we sequence 740 pigs, combine with 149 of our previously published resequencing data, retrieve 207 resequencing datasets, and form a panel of worldwide distributed wild boars, aboriginal and highly selected pigs with pedigree structures, amounting to 1096 genomes from 43 breeds. Combining with their haplotype-informative reads and pedigree structure, we accurately construct a panel of 1874 haploid genomes with 41,964,356 genetic variants. We further demonstrate its valuable applications in GWAS by identifying five novel loci for intramuscular fat content, and in genomic selection by increasing the accuracy of estimated breeding value by 36.7%. In evolutionary selection, we detect MUC13 gene under a long-term balancing selection, as well as NPR3 gene under positive selection for pig stature. Our study provides abundant genomic variations for robust selection-signature detection and accurate haplotypes for deciphering complex traits in pigs.

The Landscape of Accessible Chromatin and Developmental Transcriptome Maps Reveal a Genetic Mechanism of Skeletal Muscle Development in Pigs

The epigenetic regulation mechanism of porcine skeletal muscle development relies on the openness of chromatin and is also precisely regulated by transcriptional machinery. However, fewer studies have exploited the temporal changes in gene expression and the landscape of accessible chromatin to reveal the underlying molecular mechanisms controlling muscle development. To address this, skeletal muscle biopsy samples were taken from Landrace pigs at days 0 (D0), 60 (D60), 120 (D120), and 180 (D180) after birth and were then analyzed using RNA-seq and ATAC-seq. The RNA-seq analysis identified 8554 effective differential genes, among which ACBD7, TMEM220, and ATP1A2 were identified as key genes related to the development of porcine skeletal muscle. Some potential cis-regulatory elements identified by ATAC-seq analysis contain binding sites for many transcription factors, including SP1 and EGR1, which are also the predicted transcription factors regulating the expression of ACBD7 genes. Moreover, the omics analyses revealed regulatory regions that become ectopically active after birth during porcine skeletal muscle development after birth and identified 151,245, 53,435, 30,494, and 40,911 peaks. The enriched functional elements are related to the cell cycle, muscle development, and lipid metabolism. In summary, comprehensive high-resolution gene expression maps were developed for the transcriptome and accessible chromatin during postnatal skeletal muscle development in pigs.

A web tool for the global identification of pig breeds

BACKGROUND

Natural and artificial selection for more than 9000 years have led to a variety of domestic pig breeds. Accurate identification of pig breeds is important for breed conservation, sustainable breeding, pork traceability, and local resource registration.

RESULTS

We evaluated the performance of four selectors and six classifiers for breed identification using a wide range of pig breeds (N = 91). The internal cross-validation and external independent testing showed that partial least squares regression (PLSR) was the most effective selector and partial least squares-discriminant analysis (PLS-DA) was the most powerful classifier for breed identification among many breeds. Five-fold cross-validation indicated that using PLSR as the selector and PLS-DA as the classifier to discriminate 91 pig breeds yielded 98.4% accuracy with only 3K single nucleotide polymorphisms (SNPs). We also constructed a reference dataset with 124 pig breeds and used it to develop the web tool iDIGs ( http://alphaindex.zju.edu.cn/iDIGs_en/ ) as a comprehensive application for global pig breed identification. iDIGs allows users to (1) identify pig breeds without a reference population and (2) design small panels to discriminate several specific pig breeds.

CONCLUSIONS

In this study, we proved that breed identification among a wide range of pig breeds is feasible and we developed a web tool for such pig breed identification.

Intravenous AAV9 administration results in safe and widespread distribution of transgene in the brain of mini-pig

Animal models are important for understanding the pathogenesis of human diseases and for developing and testing new drugs. Pigs have been widely used in the research on the cardiovascular, skin barrier, gastrointestinal, and central nervous systems as well as organ transplantation. Recently, pigs also become an attractive large animal model for the study of neurodegenerative diseases because their brains are very similar to human brains in terms of mass, gully pattern, vascularization, and the proportions of the gray and white matters. Although adeno-associated virus type 9 (AAV9) has been widely used to deliver transgenes in the brain, its utilization in large animal models remains to be fully characterized. Here, we report that intravenous injection of AAV9-GFP can lead to widespread expression of transgene in various organs in the pig. Importantly, GFP was highly expressed in various brain regions, especially the striatum, cortex, cerebellum, hippocampus, without detectable inflammatory responses. These results suggest that intravenous AAV9 administration can be used to establish large animal models of neurodegenerative diseases caused by gene mutations and to treat these animal models as well.

The Innovative Informatics Approaches of High-Throughput Technologies in Livestock: Spearheading the Sustainability and Resiliency of Agrigenomics Research

For more than a decade, next-generation sequencing (NGS) has been emerging as the mainstay of agrigenomics research. High-throughput technologies have made it feasible to facilitate research at the scale and cost required for using this data in livestock research. Scale frameworks of sequencing for agricultural and livestock improvement, management, and conservation are partly attributable to innovative informatics methodologies and advancements in sequencing practices. Genome-wide sequence-based investigations are often conducted worldwide, and several databases have been created to discover the connections between worldwide scientific accomplishments. Such studies are beginning to provide revolutionary insights into a new era of genomic prediction and selection capabilities of various domesticated livestock species. In this concise review, we provide selected examples of the current state of sequencing methods, many of which are already being used in animal genomic studies, and summarize the state of the positive attributes of genome-based research for cattle (Bos taurus), sheep (Ovis aries), pigs (Sus scrofa domesticus), horses (Equus caballus), chickens (Gallus gallus domesticus), and ducks (Anas platyrhyncos). This review also emphasizes the advantageous features of sequencing technologies in monitoring and detecting infectious zoonotic diseases. In the coming years, the continued advancement of sequencing technologies in livestock agrigenomics will significantly influence the sustained momentum toward regulatory approaches that encourage innovation to ensure continued access to a safe, abundant, and affordable food supplies for future generations.

Trajectory of livestock genomics in South Asia: A comprehensive review

Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements.

Whole-genome sequence analysis reveals selection signatures for important economic traits in Xiang pigs

Xiang pig (XP) is one of the best-known indigenous pig breeds in China, which is characterized by its small body size, strong disease resistance, high adaptability, favorite meat quality, small litter sizes, and early sexual maturity. However, the genomic evidence that links these unique traits of XP is still poorly understood. To identify the genomic signatures of selection in XP, we performed whole-genome resequencing on 25 unrelated individual XPs. We obtained 876.70 Gb of raw data from the genomic libraries. The LD analysis showed that the lowest level of linkage disequilibrium was observed in Xiang pig. Comparative genomic analysis between XPs and other breeds including Tibetan, Meishan, Duroc and Landrace revealed 3062, 1228, 907 and 1519 selected regions, respectively. The genes identified in selected regions of XPs were associated with growth and development processes (IGF1R, PROP1, TBX19, STAC3, RLF, SELENOM, MSTN), immunity and disease resistance (ZCCHC2, SERPINB2, ADGRE5, CYP7B1, STAT6, IL2, CD80, RHBDD3, PIK3IP1), environmental adaptation (NR2E1, SERPINB8, SERPINB10, SLC26A7, MYO1A, SDR9C7, UVSSA, EXPH5, VEGFC, PDE1A), reproduction (CCNB2, TRPM6, EYA3, CYP7B1, LIMK2, RSPO1, ADAM32, SPAG16), meat quality traits (DECR1, EWSR1), and early sexual maturity (TAC3). Through the absolute allele frequency difference (ΔAF) analysis, we explored two population-specific missense mutations occurred in NR6A1 and LTBP2 genes, which well explained that the vertebrae numbers of Xiang pigs were less than that of the European pig breeds. Our results indicated that Xiang pigs were less affected by artificial selection than the European and Meishan pig breeds. The selected candidate genes were mainly involved in growth and development, disease resistance, reproduction, meat quality, and early sexual maturity. This study provided a list of functional candidate genes, as well as a number of genetic variants, which would provide insight into the molecular basis for the unique traits of Xiang pig.

Interpretation of Manhattan Plots and Other Outputs of Genome-Wide Association Studies

With increasing marker density, estimation of recombination rate between a marker and a causal mutation using linkage analysis becomes less important. Instead, linkage disequilibrium (LD) becomes the major indicator for gene mapping through genome-wide association studies (GWAS). In addition to the linkage between the marker and the causal mutation, many other factors may contribute to the LD, including population structure and cryptic relationships among individuals. As statistical methods and software evolve to improve statistical power and computing speed in GWAS, the corresponding outputs must also evolve to facilitate the interpretation of input data, the analytical process, and final association results. In this chapter, our descriptions focus on (1) considerations in creating a Manhattan plot displaying the strength of LD and locations of markers across a genome; (2) criteria for genome-wide significance threshold and the different appearance of Manhattan plots in single-locus and multiple-locus models; (3) exploration of population structure and kinship among individuals; (4) quantile-quantile (QQ) plot; (5) LD decay across the genome and LD between the associated markers and their neighbors; (6) exploration of individual and marker information on Manhattan and QQ plots via interactive visualization using HTML. The ultimate objective of this chapter is to help users to connect input data to GWAS outputs to balance power and false positives, and connect GWAS outputs to the selection of candidate genes using LD extent.

Long-read assembly of the Chinese indigenous Ningxiang pig genome and identification of genetic variations in fat metabolism among different breeds

Advances in long-read sequencing technology and genome assembly provide an opportunity to improve the pig genome and reveal the full range of structural variations (SVs) between local Chinese and European pigs. To date, little is known about the genomes of some unique Chinese indigenous breeds, such as the Ningxiang pig. Here, we report the sequencing and assembly of a highly contiguous Ningxiang pig genome (NX) via an integration of PacBio single-molecule real-time sequencing, Illumina next-generation sequencing, BioNano optical mapping and Hi-C (chromosome conformation capture) approaches. The assembled genome comprises 2.44 Gb with a contig N50 of 26.1 Mb and 418 contigs in total. These contigs are organized into 121 scaffolds with a scaffold N50 of 139.0 Mb. More than 99.1% of the assembled sequence could be localized to 19 pseudochromosomes and is annotated with 20,914 protein-coding genes and 34.04% repetitive sequences. Comparisons between the NX and European Duroc assemblies revealed many SVs in genes involved in the immune system, nervous system, lipid metabolism and environmental adaptation. The genetic variants include 47 Chinese domestic pig-specific SVs and the associated 74 genes may contribute to the differences in domestic traits compared to European pigs. Moreover, single nucleotide polymorphisms (SNPs) identified from whole genome resequencing data of 73 Chinese pigs, representing 17 geographically isolated breeds, showed their specific genetic variations, population structure and evolutionary patterns. Finally, we explore transcriptional regulation in the first intron of the MYL4 gene, as the genomic SV (281-bp deletion) in Ningxiang pig promotes its subcutaneous fat compared to European pig breeds. This work identifies a set of Asian-specific SVs and SNPs, which will be important resources for modern pig breeding and genetic conservation.

Atypical for northern ungulates, energy metabolism is lowest during summer in female wild boars (Sus scrofa)

Typically, large ungulates show a single seasonal peak of heart rate, a proxy of energy expenditure, in early summer. Different to other large ungulates, wild boar females had peak heart rates early in the year (at ~ April, 1), which likely indicates high costs of reproduction. This peak was followed by a trough over summer and a secondary summit in autumn/early winter, which coincided with the mast seeding of oak trees and the mating season. Wild boars counteracted the effects of cold temperatures by decreasing subcutaneous body temperature by peripheral vasoconstriction. They also passively gained solar radiation energy by basking in the sun. However, the shape of the seasonal rhythm in HR indicates that it was apparently not primarily caused by thermoregulatory costs but by the costs of reproduction. Wild boar farrow early in the year, visible in high HRs and sudden changes in intraperitoneal body temperature of females. Arguably, a prerequisite for this early reproduction as well as for high energy metabolism over winter is the broad variety of food consumed by this species, i.e., the omnivorous lifestyle. Extremely warm and dry summers, as experienced during the study years (2017, 2018), may increasingly become a bottleneck for food intake of wild boar.

Integrated Analysis of lncRNA and mRNA in Subcutaneous Adipose Tissue of Ningxiang Pig

Simple Summary

This study shows the transcription profiles and the functional network in lncRNA and mRNA in the subcutaneous adipose tissue of Ningxiang piglets in four stages of development (piglets, nursery pigs, early fattening, and late fattening). A total of 2872 novel lncRNAs have now been determined. A total of 10,084 DEmRNAs and 931 DElncRNAs were determined. Interestingly, most DEmRNAs were up-regulated in the piglet stage and, in contrast, DElncRNAs were up-regulated in the late fattening stage. A complicated interaction between mRNAs and lncRNAs was determined via STEM and WGCNA, demonstrating that lncRNAs are an essential regulatory component in mRNAs. Modules 2 and 5 shows a similar mode of transcriptions for both mRNA and lncRNA, which are mainly involved in steroid biosynthesis, glycosphingolipid biosynthesis, metabolic pathways, and glycerolipid metabolism. The transcription levels of mRNAs and lncRNAs for both modules were higher in the early and late fattening stage. This may be explained by the active fatty acids, sterols, steroids, and lipid-related metabolic activity in the subcutaneous adipose tissue during the early and late fattening stage.

Abstract

Ningxiang pigs, a Chinese bred pig known for its tender meat and high quality unsaturated fatty acids. This study discovers the transcription profiles and functional networks in long non-coding RNA (lncRNA) and messenger RNA (mRNA) in subcutaneous adipose tissue. Subcutaneous adipose tissue was collected from piglet, nursery pig, early fattening, and late fattening stage of Ningxiang piglets, and lncRNA and mRNA transcription of each stage was profiled. A total of 339,204,926 (piglet), 315,609,246 (nursery), 266,798,202 (early fattening), and 343,740,308 (late fattening) clean reads were generated, and 2872 novel lncRNAs were identified. Additionally, 10,084 differential mRNAs (DEmRNAs) and 931 differential lncRNAs were determined. Most DEmRNAs were up-regulated in the piglet stage, while they were down-regulated in late fattening stage. A complicated interaction between mRNAs and lncRNAs was identified via STEM and WGCNA, demonstrated that lncRNAs are a significant regulatory component in mRNAs. The findings showed that modules 2 and 5 have a similar mode of transcription for both mRNA and lncRNA, and were mainly participated in steroid biosynthesis, glycosphingolipid biosynthesis, metabolic pathways, and glycerolipid metabolism. The mRNAs and lncRNAs transcription levels of both modules was higher in the early and late fattening stage, which may be due to the active activity of the metabolism in relation to fatty acids, sterols, steroids, and lipids in the subcutaneous adipose tissue during the early and late fattening stage. These findings could be expected to result in further research of the functional properties of lncRNA from subcutaneous adipose tissue at different stages of development in Ningxiang pigs.

The Meishan pig genome reveals structural variation-mediated gene expression and phenotypic divergence underlying Asian pig domestication

There are wide genomic and phenotypic differences between Asian and European pig breeds, yet the current reference genome is the European Duroc pig genome. A high-quality pig genome is lacking for genetic analysis of agricultural traits in Asian pigs. Here, using a hybrid approach, a high-quality reference genome (MSCAAS v1) for the Asian Meishan breed is assembled with a contig N50 size of 48.05 Mb. MSCAAS v1 outperforms the Duroc genome as a reference genome for Asian breeds. Genomic comparison reveals 49,103 structural variations (SVs) between Meishan and Duroc, 4.02% of which are Asian-specific SVs (AP-SVs). Notably, a 30-Mb hotspot for AP-SVs on chromosome X enriched for genes associated with Asian-pig-specific phenotypes is present in Asian domestic pig breeds, but absent in Asian wild boars, suggesting that Asian domestic breeds share a common ancestor. Interbreed transcriptomics reveals transcriptional suppression roles of AP-SVs in multiple tissues. Finally, transcriptional regulation in the intron of IGF2R is reported, as genomic SV (274-bp deletion) in Tibetan pig limits its growth compared to domestic pig breeds. In summary, this study provides insights regarding the genetic changes underlying pig domestication and presents a benchmark-setting resource for the utilization of agricultural valuable loci in Asian pigs.

Comparative Transcriptomic Analysis of Subcutaneous Adipose Tissue from Local Pig Breeds

When compared to modern lean-type breeds, Portuguese local Alentejano (AL) and Bísaro (BI) pig breeds present a high potential for subcutaneous and intramuscular fat (IMF) deposition which contributes for better meat quality. The aim of this work was to explore the genome function to better understand the underlying physiological mechanisms associated with body fat accretion. Dorsal subcutaneous fat samples were collected at slaughter from adult animals (n = 4 for each breed) with ~150 kg body weight. Total RNA was obtained and sequenced for transcriptome analysis using DESeq2. A total of 458 differentially expressed (DE) genes (q-value < 0.05) were identified, with 263 overexpressed in AL and 195 in BI. Key genes involved in de novo fatty acid biosynthesis, elongation and desaturation were upregulated in AL such as ACLY, FASN, ME1, ELOVL6 and SCD. A functional enrichment analysis of the DE genes was performed using Ingenuity Pathway Analysis. Cholesterol synthesis is suggested to be higher in AL via SREBF2, SCAP and PPARG, while lipolytic activity may be more active in BI through GH and AMPK signalling. Increased signalling of CD40 together with the predicted activation of INSIG1 and INSIG2 in BI suggests that this breed is more sensitive to insulin whereas the AL is less sensitive like the Iberian breed.

SLA-1 Genetic Diversity in Pigs: Extensive Analysis of Copy Number Variation, Heterozygosity, Expression, and Breed Specificity

Swine leukocyte antigens play indispensable roles in immune responses by recognizing a large number of foreign antigens and thus, their genetic diversity plays a critical role in their functions. In this study, we developed a new high-resolution typing method for pig SLA-1 and successfully typed 307 individuals from diverse genetic backgrounds including 11 pure breeds, 1 cross bred, and 12 cell lines. We identified a total of 52 alleles including 18 novel alleles and 9 SLA-1 duplication haplotypes, including 4 new haplotypes. We observed significant differences in the distribution of SLA-1 alleles among the different pig breeds, including the breed specific alleles. SLA-1 duplication was observed in 33% of the chromosomes and was especially high in the biomedical model breeds such as SNU (100%) and NIH (76%) miniature pigs. Our analysis showed that SLA-1 duplication is associated with the increased level of SLA-1 mRNA expression in porcine cells compared to that of the single copy haplotype. Therefore, we provide here the results of the most extensive genetic analysis on pig SLA-1.

[African swine fever]

African swine fever (ASF) is a hemorrhagic infectious disease of Suids, which is endemic in sub-Saharan area of African continent. ASF is usually circulating sub-symptomatically among wild species of Suidae family, such as warthogs and bush pigs, by mediating Ornithodoros soft ticks. Domestic pigs (Sus scrofa) are, however, highly sensitive to the infection and show severe clinical signs with a high mortality rate, resulting a huge impact on pork production. Currently, there is no treatment or vaccine available. The etiological agent, ASFV, is highly resistant to environmental conditions, and resides in unheated pork meat or pork meat products for a long period, which may be a chance of its long-distance spread. Since August 2018, ASFV has been circulating in East and Southeast Asian countries and may possibly be introduced into Japan. Here, I describe the outline of the disease and the etiology of the pathogen in order to remind the importance of "awareness" and "preparedness" for the disease.

Genomic analyses provide insights into breed-of-origin effects from purebreds on three-way crossbred pigs

Crossbreeding is widely used aimed at improving crossbred performance for poultry and livestock. Alleles that are specific to different purebreds will yield a large number of heterozygous single-nucleotide polymorphisms (SNPs) in crossbred individuals, which are supposed to have the power to alter gene function or regulate gene expression. For pork production, a classic three-way crossbreeding system of Duroc × (Landrace × Yorkshire) (DLY) is generally used to produce terminal crossbred pigs with stable and prominent performance. Nonetheless, little is known about the breed-of-origin effects from purebreds on DLY pigs. In this study, we first estimated the distribution of heterozygous SNPs in three kinds of three-way crossbred pigs via whole genome sequencing data originated from three purebreds. The result suggested that DLY is a more effective strategy for three-way crossbreeding as it could yield more stably inherited heterozygous SNPs. We then sequenced a DLY pig family and identified 95, 79, 132 and 42 allele-specific expression (ASE) genes in adipose, heart, liver and skeletal muscle, respectively. Principal component analysis and unrestricted clustering analyses revealed the tissue-specific pattern of ASE genes, indicating the potential roles of ASE genes for development of DLY pigs. In summary, our findings provided a lot of candidate SNP markers and ASE genes for DLY three-way crossbreeding system, which may be valuable for pig breeding and production in the future.

Multiple Domestication Centers Revealed by the Geographical Distribution of Chinese Native Pigs

Previous studies have shown that Southeast Asian pigs were independently domesticated from local wild boars. However, the domestication of Chinese native pigs remains a subject of debate. In the present study, phylogenetic analysis of Chinese native pigs was performed by screening for haplotypes inferred from a phylogenetic tree of pig mitochondrial DNA (mtDNA) sequences based on sequence-specific mutations. A total of 2466 domestic pigs formed 124 haplotypes and were assigned to four clades. Clade A comprised pigs distributed mainly in the Qinghai-Tibet Plateau and its surrounding areas; these pigs clustered into three groups. The pigs of clade B were mainly from the Mekong River Basin in Yunnan Province and had been exposed to genetic infiltration from European populations. Clade C comprised pigs mainly from the middle and lower reaches of the Yangtze River. The pigs of clade D were distributed mainly at the intersection of Yunnan, Sichuan, and Gansu provinces east of the Hengduan Mountains (YSGH). Compared with wild boar, at least three domestication centers and one expansion center of pigs in China were detected. Among the four centers detected, two were for Tibetan pigs and were in the Qinghai-Tibet Plateau and at the YSGH intersection, and the other two were in the Mekong River Basin in Yunnan Province and the middle and downstream regions of the Yangtze River.

Genome editing in large animals: current status and future prospects

Large animals (non-human primates, livestock and dogs) are playing important roles in biomedical research, and large livestock animals serve as important sources of meat and milk. The recently developed programmable DNA nucleases have revolutionized the generation of gene-modified large animals that are used for biological and biomedical research. In this review, we briefly introduce the recent advances in nuclease-meditated gene editing tools, and we outline these editing tools’ applications in human disease modeling, regenerative medicine and agriculture. Additionally, we provide perspectives regarding the challenges and prospects of the new genome editing technology.

Characterization of Duck (Anas platyrhynchos) Short Tandem Repeat Variation by Population-Scale Genome Resequencing

Short tandem repeats (STRs) are usually associated with genetic diseases and gene regulatory functions, and are also important genetic markers for analysis of evolutionary, genetic diversity and forensic. However, for the majority of STRs in the duck genome, their population genetic properties and functional impacts remain poorly defined. Recent advent of next generation sequencing (NGS) has offered an opportunity for profiling large numbers of polymorphic STRs. Here, we reported a population-scale analysis of STR variation using genome resequencing in mallard and Pekin duck. Our analysis provided the first genome-wide duck STR reference including 198,022 STR loci with motif size of 2–6 base pairs. We observed a relatively uneven distribution of STRs in different genomic regions, which indicates that the occurrence of STRs in duck genome is not random, but undergoes a directional selection pressure. Using genome resequencing data of 23 mallard and 26 Pekin ducks, we successfully identified 89,891 polymorphic STR loci. Intensive analysis of this dataset suggested that shorter repeat motif, longer reference tract length, higher purity, and residing outside of a coding region are all associated with an increase in STR variability. STR genotypes were utilized for population genetic analysis, and the results showed that population structure and divergence patterns among population groups can be efficiently captured. In addition, comparison between Pekin duck and mallard identified 3,122 STRs with extremely divergent allele frequency, which overlapped with a set of genes related to nervous system, energy metabolism and behavior. The evolutionary analysis revealed that the genes containing divergent STRs may play important roles in phenotypic changes during duck domestication. The variation analysis of STRs in population scale provides valuable resource for future study of genetic diversity and genome evolution in duck.

Improved, ACMG-compliant, in silico prediction of pathogenicity for missense substitutions encoded by TP53 variants

Clinical interpretation of germline missense variants represents a major challenge, including those in the TP53 Li-Fraumeni syndrome gene. Bioinformatic prediction is a key part of variant classification strategies. We aimed to optimize the performance of the Align-GVGD tool used for p53 missense variant prediction, and compare its performance to other bioinformatic tools (SIFT, PolyPhen-2) and ensemble methods (REVEL, BayesDel). Reference sets of assumed pathogenic and assumed benign variants were defined using functional and/or clinical data. Area under the curve and Matthews correlation coefficient (MCC) values were used as objective functions to select an optimized protein multisequence alignment with best performance for Align-GVGD. MCC comparison of tools using binary categories showed optimized Align-GVGD (C15 cut-off) combined with BayesDel (0.16 cut-off), or with REVEL (0.5 cut-off), to have the best overall performance. Further, a semi-quantitative approach using multiple tiers of bioinformatic prediction, validated using an independent set of nonfunctional and functional variants, supported use of Align-GVGD and BayesDel prediction for different strength of evidence levels in ACMG/AMP rules. We provide rationale for bioinformatic tool selection for TP53 variant classification, and have also computed relevant bioinformatic predictions for every possible p53 missense variant to facilitate their use by the scientific and medical community.

A genome scan for selection signatures in Taihu pig breeds using next-generation sequencing

Taihu pig breeds are the most prolific breeds of swine in the world, and they also have superior economic traits, including high resistance to disease, superior meat quality, high resistance to crude feed and a docile temperament. The formation of these phenotypic characteristics is largely a result of long-term artificial or natural selection. Therefore, exploring selection signatures in the genomes of the Taihu pigs will help us to identify porcine genes related to productivity traits, disease and behaviour. In this study, we used both intra-population (Relative Extend Haplotype Homozygosity Test (REHH)) and inter-population (the Cross-Population Extend Haplotype Homozygosity Test (XPEHH); F-STATISTICS, F ST ) methods to detect genomic regions that might be under selection process in Taihu pig breeds. As a result, we found 282 (REHH) and 112 (XPEHH) selection signature candidate regions corresponding to 159.78 Mb (6.15%) and 62.29 Mb (2.40%) genomic regions, respectively. Further investigations of the selection candidate regions revealed that many genes under these genomic regions were related to reproductive traits (such as the TLR9 gene), coat colour (such as the KIT gene) and fat metabolism (such as the CPT1A and MAML3 genes). Furthermore, gene enrichment analyses showed that genes under the selection candidate regions were significantly over-represented in pathways related to diseases, such as autoimmune thyroid and asthma diseases. In conclusion, several candidate genes potentially under positive selection were involved in characteristics of Taihu pig. These results will further allow us to better understand the mechanisms of selection in pig breeding.

Genome-wide SNP data unveils the globalization of domesticated pigs

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies

Uncovering genetic variation through resequencing is limited by the fact that only sequences with similarity to the reference genome are examined. Reference genomes are often incomplete and cannot represent the full range of genetic diversity as a result of geographical divergence and independent demographic events. To more comprehensively characterize genetic variation of pigs (Sus scrofa), we generated de novo assemblies of nine geographically and phenotypically representative pigs from Eurasia. By comparing them to the reference pig assembly, we uncovered a substantial number of novel SNPs and structural variants, as well as 137.02-Mb sequences harboring 1737 protein-coding genes that were absent in the reference assembly, revealing variants left by selection. Our results illustrate the power of whole-genome de novo sequencing relative to resequencing and provide valuable genetic resources that enable effective use of pigs in both agricultural production and biomedical research.

Age-Related 1H NMR Characterization of Cerebrospinal Fluid in Newborn and Young Healthy Piglets

When it comes to neuroscience, pigs represent an important animal model due to their resemblance with humans’ brains for several patterns including anatomy and developmental stages. Cerebrospinal fluid (CSF) is a relatively easy-to-collect specimen that can provide important information about neurological health and function, proving its importance as both a diagnostic and biomedical monitoring tool. Consequently, it would be of high scientific interest and value to obtain more standard physiological information regarding its composition and dynamics for both swine pathology and the refinement of experimental protocols. Recently, proton nuclear magnetic resonance (¹H NMR) spectroscopy has been applied in order to analyze the metabolomic profile of this biological fluid, and results showed the technique to be highly reproducible and reliable. The aim of the present study was to investigate in both qualitative and quantitative manner the composition of Cerebrospinal Fluid harvested form healthy newborn (5 days old-P5) and young (30-P30 and 50-P50 days old) piglets using ¹H NMR Spectroscopy, and to analyze any possible difference in metabolites concentration between age groups, related to age and Blood-Brain-Barrier maturation. On each of the analyzed samples, 30 molecules could be observed above their limit of quantification, accounting for 95–98% of the total area of the spectra. The concentrations of adenine, tyrosine, leucine, valine, 3-hydroxyvalerate, 3-methyl-2-oxovalerate were found to decrease between P05 and P50, while the concentrations of glutamine, creatinine, methanol, trimethylamine and myo-inositol were found to increase. The P05-P30 comparison was also significant for glutamine, creatinine, adenine, tyrosine, leucine, valine, 3-hydroxyisovalerate, 3-methyl-2-oxovalerate, while for the P30-P50 comparison we found significant differences for glutamine, myo-inositol, leucine and trimethylamine. None of these molecules showed at P30 concentrations outside the P05 –P50 range.

A report to an academy: On carnophallogocentrism, pigs and meat-writing

How can organisational studies theory respond to the call of nonhuman animals? This article argues there is ‘too much humanism’ in organisational studies and defines the problem as originating in language practices. The example of factory-farmed pigs is used to illustrate the argument. Derrida’s term carnophallogocentrism is used to suggest that ethical thinking about the animal be moved from face-to-face encounters through the eyes to the mouth and that by adopting methods used in literature and ‘feminist dog-writing’ ways can be found to co-constitute human and nonhuman species in academic writing practices. The term meat-writing is offered as a practice of challenging carnophallogocentrism.

Evolutionary patterns of Toll-like receptor signaling pathway genes in the Suidae

BACKGROUND

The Toll-like receptor (TLR) signaling pathway constitutes an essential component of the innate immune system. Highly conserved proteins, indicative of their critical roles in host survival, characterize this pathway. Selective constraints could vary depending on the gene's position within the pathway as TLR signaling is a sequential process and that genes downstream of the TLRs may be more selectively constrained to ensure efficient immune responses given the important role of downstream genes in the signaling process. Thus, we investigated whether gene position influenced protein evolution in the TLR signaling pathway of the Suidae. The members of the Suidae examined included the European Sus scrofa (wild boar), Asian Sus scrofa (wild boar), Sus verrucosus, Sus celebensis, Sus scebifrons, Sus barbatus, Babyrousa babyrussa, Potamochoerus larvatus, Potamochoerus porcus and Phacochoerus africanus.

RESULTS

A total of 33 TLR signaling pathway genes in the Suidae were retrieved from resequencing data. The evolutionary parameter ω (dn/ds) had an overall mean of 0.1668 across genes, indicating high functional conservation within the TLR signaling pathway. A significant relationship was inferred for the network parameters gene position, number of protein-protein interactions, protein length and the evolutionary parameter dn (nonsynonymous substitutions) such that downstream genes had lower nonsynonymous substitution rates, more interactors and shorter protein length than upstream genes. Gene position was significantly correlated with the number of protein-protein interactions and protein length. Thus, the polarity in the selective constraint along the TLR signaling pathway was due to the number of molecules a protein interacted with and the protein's length.

CONCLUSION

Results indicate that the level of selective constraints on genes within the TLR signaling pathway of the Suidae is dependent on the gene's position and network parameters. In particular, downstream genes evolve more slowly as a result of being highly connected and having shorter protein lengths. These findings highlight the critical role of gene network parameters in gene evolution.

Genetic divergence in domesticated and non-domesticated gene regions of barley chromosomes

Little is known about the genetic divergence in the chromosomal regions with domesticated and non-domesticated genes. The objective of our study is to examine the effect of natural selection on shaping genetic diversity of chromosome region with domesticated and non-domesticated genes in barley using 110 SSR markers. Comparison of the genetic diversity loss between wild and cultivated barley for each chromosome showed that chromosome 5H had the highest divergence of 35.29%, followed by 3H, 7H, 4H, 2H, 6H. Diversity ratio was calculated as (diversity of wild type – diversity of cultivated type)/diversity of wild type×100%. It was found that diversity ratios of the domesticated regions on 5H, 1H and 7H were higher than those of non-domesticated regions. Diversity ratio of the domesticated region on 2H and 4H is similar to that of non-domesticated region. However, diversity ratio of the domesticated region on 3H is lower than that of non-domesticated region. Averaged diversity among six chromosomes in domesticated region was 33.73% difference between wild and cultivated barley, and was 27.56% difference in the non-domesticated region. The outcome of this study advances our understanding of the evolution of crop chromosomes.

A genome scan for selection signatures in pigs

Identifying signatures of selection can provide a straightforward insight into the mechanism of artificial selection and further uncover the causal genes related to the phenotypic variation. Based on Illumina Porcine60KSNP chip data, four complementary methods, Long-Range Haplotype (LRH), Tajima’s D, Cross Population Extend Haplotype Homozygosity Test (XPEHH) and F_ST, were implemented in this study to detect the selection signatures in the whole genome of one typical Chinese indigenous breed, Rongchang, one Chinese cultivated breed, Songliao, and two western breeds, Landrace and Yorkshire. False Discovery Rate (FDR) was implemented to control the false positive rates. In our study, a total of 159, 127, 179 and 159 candidate selection regions with average length of 0.80 Mb, 0.73 Mb, 0.78 Mb and 0.73 Mb were identified in Landrace, Rongchang, Songliao and Yorkshire, respectively, that span approximately 128.00 Mb, 92.38 Mb, 130.30 Mb and 115.40 Mb and account for approximately 3.74–5.33% of genome across all autosomes. The selection regions of 11.52 Mb shared by Landrace and Yorkshire were the longest when chosen pairs from the pool of the four breeds were examined. The overlaps between Yorkshire and Songliao, approximately 9.20 Mb, were greater than those of Yorkshire and Rongchang. Meanwhile, the overlaps between Landrace and Songliao were greater than those of Landrace and Rongchang but less than those of Songliao and Ronchang. Bioinformatics analysis showed that the genes/QTLs relevant to fertility, coat color, and ear morphology were found in candidate selection regions. Some genes, such as LEMD3, MC1R, KIT, TRHR etc. that were reported under selection, were confirmed in our study, and this analysis also demonstrated the diversity of breeds.

Gene coexpression networks reveal key drivers of phenotypic divergence in porcine muscle

Background

Domestication of the wild pig has led to obese and lean phenotype breeds, and evolutionary genome research has sought to identify the regulatory mechanisms underlying this phenotypic diversity. However, revealing the molecular mechanisms underlying muscle phenotype variation based on differentially expressed genes has proved to be difficult. To characterize the mechanisms regulating muscle phenotype variation under artificial selection, we aimed to provide an integrated view of genome organization by weighted gene coexpression network analysis.

Results

Our analysis was based on 20 publicly available next-generation sequencing datasets of lean and obese pig muscle generated from 10 developmental stages. The evolution of the constructed coexpression modules was examined using the genome resequencing data of 37 domestic pigs and 11 wild boars. Our results showed the regulation of muscle development might be more complex than had been previously acknowledged, and is regulated by the coordinated action of muscle, nerve and immunity related genes. Breed-specific modules that regulated muscle phenotype divergence were identified, and hundreds of hub genes with major roles in muscle development were determined to be responsible for key functional distinctions between breeds. Our evolutionary analysis showed that the role of changes in the coding sequence under positive selection in muscle phenotype divergence was minor.

Conclusions

Muscle phenotype divergence was found to be regulated by the divergence of coexpression network modules under artificial selection, and not by changes in the coding sequence of genes. Our results present multiple lines of evidence suggesting links between modules and muscle phenotypes, and provide insights into the molecular bases of genome organization in muscle development and phenotype variation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1238-5) contains supplementary material, which is available to authorized users.

Genome sequencing and analysis of Mangalica, a fatty local pig of Hungary

BACKGROUND

Mangalicas are fatty type local/rare pig breeds with an increasing presence in the niche pork market in Hungary and in other countries. To explore their genetic resources, we have analysed data from next-generation sequencing of an individual male from each of three Mangalica breeds along with a local male Duroc pig. Structural variations, such as SNPs, INDELs and CNVs, were identified and particular genes with SNP variations were analysed with special emphasis on functions related to fat metabolism in pigs.

RESULTS

More than 60 Gb of sequence data were generated for each of the sequenced individuals, resulting in 11× to 19× autosomal median coverage. After stringent filtering, around six million SNPs, of which approximately 10% are novel compared to the dbSNP138 database, were identified in each animal. Several hundred thousands of INDELs and about 1,000 CNV gains were also identified. The functional annotation of genes with exonic, non-synonymous SNPs, which are common in all three Mangalicas but are absent in either the reference genome or the sequenced Duroc of this study, highlighted 52 genes in lipid metabolism processes. Further analysis revealed that 41 of these genes are associated with lipid metabolic or regulatory pathways, 49 are in fat-metabolism and fatness-phenotype QTLs and, with the exception of ACACA, ANKRD23, GM2A, KIT, MOGAT2, MTTP, FASN, SGMS1, SLC27A6 and RETSAT, have not previously been associated with fat-related phenotypes.

CONCLUSIONS

Genome analysis of Mangalica breeds revealed that local/rare breeds could be a rich source of sequence variations not present in cosmopolitan/industrial breeds. The identified Mangalica variations may, therefore, be a very useful resource for future studies of agronomically important traits in pigs.

Identification of selection signatures in livestock species

The identification of regions that have undergone selection is one of the principal goals of theoretical and applied evolutionary genetics. Such studies can also provide information about the evolutionary processes involved in shaping genomes, as well as physical and functional information about genes/genomic regions. Domestication followed by breed formation and selection schemes has allowed the formation of very diverse livestock breeds adapted to a wide variety of environments and with special characteristics. The advances in genomics in the last five years have enabled the development of several methods to detect selection signatures and have resulted in the publication of a considerable number of studies involving livestock species. The aims of this review are to describe the principal effects of natural/artificial selection on livestock genomes, to present the main methods used to detect selection signatures and to discuss some recent results in this area. This review should be useful also to research scientists working with wild animals/non-domesticated species and plant biologists working with breeding and evolutionary biology.

Genome-wide association analysis to identify SNP markers affecting teat numbers in an F2 intercross population between Landrace and Korean native pigs

Most reproductive traits have low heritability and are greatly affected by environmental factors. Teat number and litter size are traits related to the reproduction ability of pigs. To identify quantitative trait loci (QTLs) for teat number traits, a genome-wide association study (GWAS) was conducted using an F2 intercross between Landrace and Korean native pigs. Genotype analysis was performed using the porcine SNP 60 K beadchip. The GWAS was performed using a mixed-effects model and linear regression approach. When a genome-wide threshold was determined using the Bonferroni method (P = 1.61 × 10(-6)), 38 single nucleotide polymorphism (SNP) markers in pig chromosome 7 (SSC7) were significantly associated with three teat number traits (total teat number, left teat number, and right teat number). Among these, SNPs in 5 genes (HDDC3, LOC100156276, LOC100155863, ANPEP, SCAMP2) were selected for further study based primarily on their statistical significance. A significant association was detected in SCAMP2 g.25280 G>A for total teat number (P = 2.0 × 10(-12)), HDDC3 g.1319 G>A SNP for left teat number (P = 2.3 × 10(-7)), and SCAMP2 g.14198 G>A for right teat number (P = 4.7 × 10(-12)). These results provide valuable information about the selective breeding for desirable teat numbers in pigs.

Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication

Domesticated organisms have experienced strong selective pressures directed at genes or genomic regions controlling traits of biological, agricultural or medical importance. The genome of native and domesticated pigs provide a unique opportunity for tracing the history of domestication and identifying signatures of artificial selection. Here we used whole-genome sequencing to explore the genetic relationships among the European native pig Berkshire and breeds that are distributed worldwide, and to identify genomic footprints left by selection during the domestication of Berkshire. Numerous nonsynonymous SNPs-containing genes fall into olfactory-related categories, which are part of a rapidly evolving superfamily in the mammalian genome. Phylogenetic analyses revealed a deep phylogenetic split between European and Asian pigs rather than between domestic and wild pigs. Admixture analysis exhibited higher portion of Chinese genetic material for the Berkshire pigs, which is consistent with the historical record regarding its origin. Selective sweep analyses revealed strong signatures of selection affecting genomic regions that harbor genes underlying economic traits such as disease resistance, pork yield, fertility, tameness and body length. These discoveries confirmed the history of origin of Berkshire pig by genome-wide analysis and illustrate how domestication has shaped the patterns of genetic variation.

Human–carnivore conflict over livestock in the eastern part of the Serengeti ecosystem, with a particular focus on the African wild dogLycaon pictus

During 2007–2009 we conducted a survey of attacks by wild carnivores on the livestock of the Maasai and Sonjo tribes in the eastern Serengeti ecosystem of northern Tanzania. Local enumerators systematically recorded incidents of carnivore predation on livestock and their data were quantified by us, with the aid of District Game Officers or trusted local people. The annual rate of attack by African wild dogsLycaon pictuswas significantly higher (1.42 animals per 1,000 livestock) in the Sonjo tribal area than in the Maasai tribal area (0.72 animals per 1,000 livestock). In the Maasai tribal area there was a significant amount of predation by leopardsPanthera pardusand spotted hyaenasCrocuta crocuta. In both tribal areas sheepOvis ariesand goatsCapra aegagrus hircuswere subject to predation more frequently than cattle. Attacks on livestock by wild dogs occurred most frequently in the afternoon and evening, whereas other carnivores generally attacked livestock at night. Sheep and goats were most frequently attacked by most carnivores during the long rainy season. CattleBos primigeniuswere most frequently attacked by wild dogs and leopards during the long dry season and by lionsPanthera leoduring the long rainy season, whereas spotted hyaenas killed cattle most frequently during the short rainy season.