Population Genomics Analysis Revealed Origin and High-altitude Adaptation of Tibetan Pigs

Multiple Domestication Centers of the Indian Pig Population

The domestication of animals is a major milestone in human history and has been studied in various fields. Pig domestication, in particular, has been widely studied, and it is believed that India is one of at least six domestication centers. However, there is a lack of systematic studies using high-resolution genetic markers, including complete mitogenomes, to investigate the domestication and genetic roots of pigs in India. In the present study, we investigated the origin and evolution of Indian pigs using mitochondrial genetic data to complement archaeological data sets. The phylogenetic status of Indian pig breeds was determined by analyzing all available mitochondrial data, incorporating a global data set of 239 mitogenomes. The Bayesian and maximum likelihood tree analyses unveiled at least eight haplogroups diverging from three main branches, two of which are geographically restricted to India. We propose that the North Indian domestic haplogroup might represent an independent in situ domestication event in North India, probably dating before ∼5,000 YBP. An additional North East Indian domestic haplogroup is nested within a widespread Asian clade that also includes Indian mitogenomes from the Andaman and Nicobar Islands that diverged more recently from distinct East and Southeast Asian roots. In conclusion, we propose that North Indian farmers could have been responsible for the independent domestication of local wild boars giving rise to the current domestic lineage identified in North India. At least one additional domestic lineage arrived in India more recently and remained mainly localized in the northeast. Domestic mitogenomes from the Indian islands show a notable connection with pig populations from Vietnam, and their arrival might be related to Austroasiatic-speaking human populations. Overall, this study provides valuable insights into the complex dynamics of pig domestication in India.

Dissecting genomes of multiple yak populations: unveiling ancestry and high-altitude adaptation through whole-genome resequencing analysis

The present study was undertaken to elucidate the population structure and differentiation of Indian yak from Chinese and wild cohorts on genome-wide scale by identifying the selection sweeps and genomic basis of their adaptation across different comparisons while analyzing whole genome sequencing (WGS) data using latest bioinformatics tools. The study included 105 individuals from three distinct yak populations i.e., Indian yak (n = 29); Chinese yak (n = 61) and wild yak (n = 15), hypothesized to be related along the evolutionary timescale. Efficient variant calling and quality control in GATK and PLINK programs resulted in around 1 million (1,002,970) high-quality (LD-independent) SNPs with an average genotyping rate of 96.55%. The PCA, ADMIXTURE and TREEMIX analysis revealed stratification of the yak groups into three distinct clusters. The empirical distribution pattern of minor allele frequency (MAF) of SNPs on genome-wide scale was also elucidated for three yak cohorts revealing unique distribution across five different bins. The selection signature analysis revealed candidate genes that are important for the adaptation of Indian yak against harsh environmental conditions in their habitats. Under iHS analysis, several genes were identified to be under selection pressure in Indian yak including ABCA12, EXOC1, JUNB, KLF1, PRDX2, NANOS3, RFX1, RFX2, and CACNG7. On the other hand, across population analysis revealed the genes like NR2F2, OSBPL10, CIDEC, WFIKKN2, ADCY, THSD7A, ADGRB3, TRPC1, VASH2, and ABHD5 to be part of selective sweeps under these comparisons. A total of 53 genes were found common between intra- and inter-population selection signature analysis of Indian yak. Notably, the genes harbouring the SNPs under selection pressure were significant for adaptation traits including lipidogenesis, energy metabolism, thermogenesis, hair follicle formation, oxidation-reduction reactions, hypoxia and reproduction. These genes may be evaluated as candidate genes for livestock adaptation to harsh environmental conditions and to further the research and application in the present era of climate change.

Divergent adaptation to highland and tropical environments in Bolivian Creole cattle

Bolivian Creole cattle populations evolved under low levels of breeding management and, during more than 500 years of natural selection, became adapted to various environments such as the contrasting highland and subtropical environments. Recently, highland Creole cattle were crossbred with Holstein to improve dairy production. The aim of this research was to evaluate the divergent adaptation through selection footprints of Bolivian Creole cattle from Andean highland and tropical lowlands, and to evaluate the effect of Holstein introgression in highland Creole. For this purpose, 130 Creole cattle (75 highland, 55 lowland) and 88 Holstein were genotyped using a microarray. The database was used to determine population structure and admixture and detect selection sweeps using FST, Rsb, XP-EHH, and ROH. Ancestry inference suggested that selection peaks were not due to Holstein introgression. The NCBI database was used to retrieve genes from the common regions and then perform gene ontology analysis. The most prominent selection peaks were on BTA20 and BTA23 and included the PRLR (slick phenotype) and Class I and IIa BoLA genes. Other windows contained candidate genes for hypoxia (ANXA2, NDUFA4L2), angiogenesis and haematological parameters (ANXA2, CPLANE1, NRP1, NRP2), immune response (IL7R, IL6ST, IL31RA, C6, C7, STAT6, NKG2A, IRAK4, KLR, CLEC), oxidative stress (GSTA, HSD17B6) and morphological traits (PLAG1, CHCHD7, CAP2, ARL15). GO analysis revealed enrichment terms and pathways related to immune response, glutathione and retinol metabolism and reported QTLs for coat characteristics, immune response and tick resistance. The results suggest the complex mechanism in the adaptation of Bolivian Creole cattle to the contrasting highland and subtropical environments.

Gut microbiota profiles of sympatric snub-nosed monkeys and macaques in Qinghai-Tibetan Plateau show influence of phylogeny over diet

The unique environment of the Qinghai-Tibetan Plateau provides a great opportunity to study how primate intestinal microorganisms adapt to ecosystems. The 16S rRNA gene amplicon and metagenome analysis were conducted to investigate the correlation between gut microbiota in primates and other sympatric animal species living between 3600 and 4500 m asl. Results showed that within the same geographical environment, Macaca mulatta and Rhinopithecus bieti exhibited a gut microbiome composition similar to that of Tibetan people, influenced by genetic evolution of host, while significantly differing from other distantly related animals. The gut microbiota of plateau species has developed similar strategies to facilitate their hosts' adaptation to specific environments, including broadening its dietary niche and enhancing energy absorption. These findings will enhance our comprehension of the significance of primate gut microbiota in adapting to specific habitats.

The 1000 Chinese Indigenous Pig Genomes Project provides insights into the genomic architecture of pigs

Pigs play a central role in human livelihoods in China, but a lack of systematic large-scale whole-genome sequencing of Chinese domestic pigs has hindered genetic studies. Here, we present the 1000 Chinese Indigenous Pig Genomes Project sequencing dataset, comprising 1011 indigenous individuals from 50 pig populations covering approximately two-thirds of China's administrative divisions. Based on the deep sequencing (~25.95×) of these pigs, we identify 63.62 million genomic variants, and provide a population-specific reference panel to improve the imputation performance of Chinese domestic pig populations. Using a combination of methods, we detect an ancient admixture event related to a human immigration climax in the 13th century, which may have contributed to the formation of southeast-central Chinese pig populations. Analyzing the haplotypes of the Y chromosome shows that the indigenous populations residing around the Taihu Lake Basin exhibit a unique haplotype. Furthermore, we find a 13 kb region in the THSD7A gene that may relate to high-altitude adaptation, and a 0.47 Mb region on chromosome 7 that is significantly associated with body size traits. These results highlight the value of our genomic resource in facilitating genomic architecture and complex traits studies in pigs.

Genomic Insights into Pig Domestication and Adaptation: An Integrated Approach Using Genome-Wide Selection Analysis and Multiple Public Datasets

As a global focus of animal husbandry, pigs provide essential meat resources for humans. Therefore, analyzing the genetic basis of adaptability, domestication, and artificial selection in pigs will contribute to further breeding. This study performed a genome-wide selection sweep analysis to identify candidate genes related to domestication and adaptive selection via data from 2413 public genotypes. Two complementary statistical analyses, FST (fixation index) and XP-EHH (cross-population extended haplotype homozygosity) were applied. The results revealed that numerous candidate genes were associated with high-altitude adaptability (e.g., SIRPA, FRS2, and GRIN2B) and habitat temperature adaptability (e.g., MITF, PI3KC2A, and FRS2). In addition, candidate genes related to the domestic genetic imprint of indigenous pigs (e.g., TNR, NOCT, and SPATA5) and strong artificial selection pressure in commercial breeds (e.g., ITPR2, HSD17B12, and UGP2) were identified in this study. Specifically, some MHC-related genes (e.g., ZRTB12, TRIM26, and C7H6orf15) were also under selection during domestication and artificial selection. Additionally, a phylogenetic comparative analysis revealed that the genetic divergence between populations does not fully follow the geographical distribution and management history in the major histocompatibility complex region/major histocompatibility complex II haplotypes, unlike that of the genome-wide genotypes. Furthermore, the higher heterozygosity and haplotype alleles of MHC reduce the differences between populations. Briefly, this study not only helps promote the relative theoretical understanding of environmental adaptive selection and domestication but also provides a theoretical reference for disease-resistant breeding in pigs.

Analysis of genetic evolutionary differences among four Tibetan pig populations in China

Tibetan pigs are a locally bred domestic pig breed originating from the Tibetan Plateau in China. They can be categorized into four distinct groups based on their geographical locations: Sichuan Tibetan pigs, Tibetan pigs from Tibet, Yunnan Tibetan pigs, and Gansu Tibetan pigs. This study aimed to explore population diversity, genetic structure and selection signals among Tibetan pigs in four Chinese national nature reserves. The results show that there is different observed heterozygosity among Tibetan pig populations (0.1957-0.1978). Ratio of runs of homozygosity (Froh) calculation of four Tibetan pig populations by runs of homozygosity (ROH) revealed the presence of inbreeding within the population (0.0336-0.0378). Analysis of the genetic structure demonstrated distinct population stratification among the four Tibetan pig populations, with each showing relatively independent evolutionary directions. Furthermore, Five methods (FST, Piratio, ROD, Tajima's D, XP-CLR) were used to artificially select evolutionary trajectories. The results mainly involved processes such as DNA repair, immune regulation, muscle fat deposition and adaptation to hypoxia. In conclusion, this study enhances our understanding of the genetic characteristics of Tibetan pig populations and provides a theoretical reference for the conservation of resources across different populations of Tibetan pigs.

Whole-genome sequencing and assessment of a novel protein- and gossypol-degrading Bacillus subtilis strain isolated from intestinal digesta of Tibetan Pigs

BACKGROUND

With the rapid development of animal husbandry, the demand for protein feed resources is increasing. Cottonseed meal (CSM) and soybean meal (SBM) are rich sources of protein. However, their application is limited due to the existence of anti-nutrients, which can be harmful to the digestion and absorption. A strain of Bacillus subtilis (Mafic-Y7) was isolated from digesta of intestines of Tibetan pigs. The strain showed high protease activity, which helps in degrading proteinic anti-nutritional factors in grain meal and in vitro degradation of free gossypol. In order to better understand this isolated strain, whole genome of Mafic-Y7 strain was sequenced and analyzed. Different effects on various grain meals were identified.

RESULT

The GC-depth Poisson distributions showed no bias suggesting high-quality genome assembly of Mafic-Y7. The whole genome sequencing showed that one chromosome with 4,248,845 base pairs(bp)and the genes total length with 3,736,524 bp was predicted in Mafic-Y7. Additionally, Mafic-Y7 possessed 4,254 protein-coding genes, and several protease genes were annotated by aligning them with databases. There are 55 protease genes, one phytase gene and one laccase gene were annotated in the gene sequence of Mafic-Y7. The average nucleotide identity between Mafic-Y7 and the GCA-000009045.1 homologous genome was 0.9938, suggesting a close genetic relationship between them at the species level. Compared with the closest four whole genomes, Mafic-Y7 was annotated the most abundant of protease genes (55 genes). The fermentation supernatant of Mafic-Y7 could increase the content of small peptides, water-soluble proteins, and acid-soluble proteins in vitro by 411%, 281% and 317% in SBM and 420%, 257% and 338% in CSM. After fermentation in grain meal by Mafic-Y7, the degradation rate of anti-nutritional factors in SBM, such as trypsin inhibitor, glycinin, and β-conglycinin was greater than 70%, and lectin was greater than 30%. The degradation rates of anti-nutritional factors in CSM, such as gossypol and phytic acid, were 82% and 26%, respectively.

Screening of functional genes for hypoxia adaptation in Tibetan pigs by combined genome resequencing and transcriptome analysis

The high-altitude, low-oxygen environment of the Qinghai-Tibet Plateau poses significant challenges for the introduction of superior livestock breeds. However, local plateau species have adapted to thrive and reproduce under these harsh conditions. Understanding the molecular mechanisms behind plateau animals' adaptation to low-oxygen environments is essential for breeding livestock suited to high-altitude regions. Tibetan pigs, which have undergone long-term natural selection and artificial breeding, have developed the ability to survive and reproduce in hypoxic environments. In this study, we conducted whole-genome resequencing of 30 Tibetan pigs from high-altitude regions and 30 Diannan small-ear pigs from low-altitude areas, to identify candidate genes that support Tibetan pigs' adaptation to hypoxic conditions through selection signal analysis. Additionally, we performed transcriptome sequencing on five tissues (heart, liver, spleen, lung, and bone marrow) from both Tibetan pigs and Diannan small-ear pigs to identify genes with significant differential expression between the two breeds. We then integrated the genomic and transcriptomic data by examining the expression of candidate genes identified in selection signal analysis across different tissues. The selection signal analysis identified 10 genes-HES4, ANGPT1, HIF3A, SPHK2, PCK2, RCN3, HIGD2A, DNM2, IRF9, and SRF-that were under positive selection in the Tibetan pig population and are associated with hypoxia adaptation. When combined with transcriptome data, we found that five of these genes-HIF3A, RCN3, HIGD2A, PCK2, and IRF9-exhibited differential expression. Through an integrated approach of selection signal and transcriptome analysis, we identified five key functional genes that contribute to the adaptation of Tibetan pigs to hypoxic environments. These findings offer new insights into the adaptability of plateau animals.

Genetic Adaptations of the Tibetan Pig to High-Altitude Hypoxia on the Qinghai-Tibet Plateau

The Tibetan Plateau's distinctive high-altitude environment, marked by extreme cold and reduced oxygen levels, presents considerable survival challenges for both humans and mammals. Natural selection has led to the accumulation of adaptive mutations in Tibetan pigs, enabling them to develop distinctive adaptive phenotypes. Here, we aim to uncover the genetic mechanisms underlying the adaptation of Tibetan pigs to high-altitude hypoxia. Therefore, we conducted a systematic analysis of 140 whole-genome sequencing (WGS) data points from different representing pig populations. Our analysis identified a total of 27,614,561 mutations, including 22,386,319 single-nucleotide variants (SNVs) and 5,228,242 insertions/deletions (INDELs, size < 50 bp). A total of 11% (2,678,569) of the SNVs were newly identified in our project, significantly expanding the dataset of genetic variants in Tibetan pigs. Compared to other pig breeds, Tibetan pigs are uniquely adapted to high-altitude environments, exhibiting the highest genetic diversity and the lowest inbreeding coefficient. Employing the composite of multiple signals (CMS) method, we scanned the genome-wide Darwinian positive selection signals and identified 32,499 Tibetan pig positively selected SNVs (TBPSSs) and 129 selected genes (TBPSGs), including 213 newly discovered genes. Notably, we identified eight genes (PHACTR1, SFI1, EPM2A, SLC30A7, NKAIN2, TNNI3K, and PLIN2) with strong nature selection signals. They are likely to improve cardiorespiratory function and fat metabolism to help Tibetan pigs become adapted to the high-altitude environment. These findings provide new insights into the genetic mechanisms of high-altitude adaptation and the adaptive phenotypes of Tibetan pigs.

Phylogenetic Relations and High-Altitude Adaptation in Wild Boar (Sus scrofa), Identified Using Genome-Wide Data

The Qinghai-Tibet Plateau (QTP) wild boar is an excellent model for investigating high-altitude adaptation. In this study, we analyzed genome-wide data from 93 wild boars compiled from various studies worldwide, including the QTP, southern and northern regions of China, Europe, Northeast Asia, and Southeast Asia, to explore their phylogenetic patterns and high-altitude adaptation based on genome-wide selection signal analysis and run of homozygosity (ROH) estimation. The findings demonstrate the alignment between the phylogenetic associations among wild boars and their geographical location. An ADMIXTURE analysis indicated a relatively close genetic relationship between QTP and southern Chinese wild boars. Analyses of the fixation index and cross-population extended haplotype homozygosity between populations revealed 295 candidate genes (CDGs) associated with high-altitude adaptation, such as TSC2, TELO2, SLC5A1, and SLC5A4. These CDGs were significantly overrepresented in pathways such as the mammalian target of rapamycin signaling and Fanconi anemia pathways. In addition, 39 ROH islands and numerous selective CDGs (e.g., SLC5A1, SLC5A4, and VCP), which are implicated in glucose metabolism and mitochondrial function, were discovered in QTP wild boars. This study not only assessed the phylogenetic history of QTP wild boars but also advanced our comprehension of the genetic mechanisms underlying the adaptation of wild boars to high altitudes.

Ssc-miR-101-3p inhibits hypoxia-induced apoptosis and inflammatory response in alveolar type-II epithelial cells of Tibetan pigs via targeting FOXO3

Tibetan pigs are a unique swine strain adapted to the hypoxic environment of the plateau regions in China. The unique mechanisms underlying the adaption by Tibetan pigs, however, are still elusive. Only few studies have investigated hypoxia-associated molecular regulation in the lung tissues of animals living in the plateau region of China. Our previous study reported that ssc-miR-101-3p expression significantly differed in the lung tissues of Tibetan pigs at different altitudes, suggesting that ssc-miR-101-3p plays an important role in the adaptation of Tibetan pigs to high altitude. To understand the underlying molecular mechanism, in this study, the target genes of ssc-miR-101-3p and their functions were analyzed via various methods including qRT-PCR and GO and KEGG pathway enrichment analyses. The action of ssc-miR-101-3p was investigated by culturing alveolar type-II epithelial cells (ATII) of Tibetan pigs under hypoxic conditions and transfecting ATII cells with vectors overexpressing or inhibiting ssc-miR-101-3p. Overexpression of ssc-miR-101-3p significantly increased the proliferation of ATII cells and decreased the expression of inflammatory and apoptotic factors. The target genes of ssc-miR-101-3p were significantly enriched in FOXO and PI3K-AKT signaling pathways required to mitigate lung injury. Further, FOXO3 was identified as a direct target of ssc-miR-101-3p. Interestingly, ssc-miR-101-3p overexpression reversed the damaging effect of FOXO3 in the ATII cells. In conclusion, ssc-miR-101-3p targeting FOXO3 could inhibit hypoxia-induced apoptosis and inflammatory response in ATII cells of Tibetan pigs. These results provided new insights into the molecular mechanisms elucidating the response of lung tissues of Tibetan pigs to hypoxic stress.

Genetic characterization of Tibetan pigs adapted to high altitude under natural selection based on a large whole-genome dataset

The Qinghai-Tibet Plateau is a valuable genetic resource pool, and the high-altitude adaptation of Tibetan pigs is a classic example of the adaptive evolution of domestic animals. Here, we report the presence of Darwinian positive selection signatures in Tibetan pigs (TBPs) using 348 genome-wide datasets (127 whole-genome sequence datasets (WGSs) and 221 whole-genome single-nucleotide polymorphism (SNP) chip datasets). We characterized a high-confidence list of genetic signatures related response to high-altitude adaptation in Tibetan pigs, including 4,598 candidate SNPs and 131 candidate genes. Functional annotation and enrichment analysis revealed that 131 candidate genes are related to multiple systems and organs in Tibetan pigs. Notably, eight of the top ten novel genes, RALB, NBEA, LIFR, CLEC17A, PRIM2, CDH7, GK5 and FAM83B, were highlighted and associated with improved adaptive heart functions in Tibetan pigs high-altitude adaptation. Moreover, genome-wide association analysis revealed that 29 SNPs were involved in 13 candidate genes associated with at least one adaptive trait. In particular, among the top ten candidate genes, CLEC17A is related to a reduction in hemoglobin (HGB) in Tibetan pigs. Overall, our study provides a robust SNP/gene list involving genetic adaptation for Tibetan pig high-altitude adaptation, and it will be a valuable resource for future Tibetan pig studies.

Whole-genome analysis reveals distinct adaptation signatures to diverse environments in Chinese domestic pigs

BACKGROUND

Long-term natural and artificial selection has resulted in many genetic footprints within the genomes of pig breeds across distinct agroecological zones. Nevertheless, the mechanisms by which these signatures contribute to phenotypic diversity and facilitate environmental adaptation remain unclear.

RESULTS

Here, we leveraged whole-genome sequencing data from 82 individuals from 6 domestic pig breeds originating in tropical, high-altitude, and frigid regions. Population genetic analysis suggested that habitat isolation significantly shaped the genetic diversity and contributed to population stratification in local Chinese pig breeds. Analysis of selection signals revealed regions under selection for adaptation in tropical (55.5 Mb), high-altitude (43.6 Mb), and frigid (17.72 Mb) regions. The potential functions of the selective sweep regions were linked to certain complex traits that might play critical roles in different geographic environments, including fat coverage in frigid environments and blood indicators in tropical and high-altitude environments. Candidate genes under selection were significantly enriched in biological pathways involved in environmental adaptation. These pathways included blood circulation, protein degradation, and inflammation for adaptation to tropical environments; heart and lung development, hypoxia response, and DNA damage repair for high-altitude adaptation; and thermogenesis, cold-induced vasodilation (CIVD), and the cell cycle for adaptation to frigid environments. By examining the chromatin state of the selection signatures, we identified the lung and ileum as two candidate functional tissues for environmental adaptation. Finally, we identified a mutation (chr1: G246,175,129A) in the cis-regulatory region of ABCA1 as a plausible promising variant for adaptation to tropical environments.

CONCLUSIONS

In this study, we conducted a genome-wide exploration of the genetic mechanisms underlying the adaptability of local Chinese pig breeds to tropical, high-altitude, and frigid environments. Our findings shed light on the prominent role of cis-regulatory elements in environmental adaptation in pigs and may serve as a valuable biological model of human plateau-related disorders and cardiovascular diseases.

Application of RNA-Seq Technology for Screening Reproduction-Related Differentially Expressed Genes in Tibetan and Yorkshire Pig Ovarian Tissue

The purpose of this study was to explore and verify genes that regulate the reproductive traits of Tibetan pigs at the mRNA level. The ovarian tissues of Tibetan pigs (TPs) and Yorkshire pigs (YPs) were selected as research objects, and cDNA libraries of the ovarian tissue transcripts of Tibetan pigs and Yorkshire pigs were successfully constructed by the RNA-Seq technique. A total of 651 differentially expressed genes (DEGs) were screened, including 414 up-regulated genes and 237 down-regulated genes. Through GO and KEGG enrichment analysis, it was found that these differentially expressed genes were significantly enriched in cell process, reproductive process, reproduction, cell proliferation, binding, and catalytic activity, as well as oxidative phosphorylation, endocrine resistance, thyroid hormone, Notch, and other signal transduction pathways. Genes significantly enriched in pathways closely related to reproductive regulation were analyzed and selected, and the AR, CYP11A1, CYP17A1, INHBA, ARRB2, EGFR, ETS1, HSD17B1, IGF1R, MIF, SCARB1, and SMAD4 genes were identified as important candidate genes. Twelve differentially expressed genes related to reproduction were verified by RT-qPCR. The results showed that the expression of the AR, CYP17A1, EGFR, ETS1, IGF1R, and SMAD4 genes was significantly higher in Tibetan pigs than in Yorkshire pigs, while the expression of the CYP11A1, INHBA, ARRB2, HSD17B, MIF, and SCARB1 genes in Tibetan pigs was significantly lower than in Yorkshire pigs. The purpose of this study is to provide a theoretical basis for exploring the molecular mechanism of reproductive trait effect genes and the application of molecular breeding in Tibetan pigs.

Structural variant landscapes reveal convergent signatures of evolution in sheep and goats

BACKGROUND

Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution.

RESULTS

We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats.

CONCLUSIONS

Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.

Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups

Tibetan pig is a geographically isolated pig breed that inhabits high-altitude areas of the Qinghai-Tibetan plateau. At present, there is limited research on viral diseases in Tibetan pigs. This study provides a novel metagenomic exploration of the gut virome in Tibetan pigs (altitude ≈ 3000 m) across three critical developmental stages, including lactation, nursery, and fattening. The composition of viral communities in the Tibetan pig intestine, with a dominant presence of Microviridae phages observed across all stages of development, in combination with the previous literature, suggest that it may be associated with geographical locations with high altitude. Functional annotation of viral operational taxonomic units (vOTUs) highlights that, among the constantly increasing vOTUs groups, the adaptability of viruses to environmental stressors such as salt and heat indicates an evolutionary response to high-altitude conditions. It shows that the lactation group has more abundant viral auxiliary metabolic genes (vAMGs) than the nursery and fattening groups. During the nursery and fattening stages, this leaves only DNMT1 at a high level. which may be a contributing factor in promoting gut health. The study found that viruses preferentially adopt lytic lifestyles at all three developmental stages. These findings not only elucidate the dynamic interplay between the gut virome and host development, offering novel insights into the virome ecology of Tibetan pigs and their adaptation to high-altitude environments, but also provide a theoretical basis for further studies on pig production and epidemic prevention under extreme environmental conditions.

Landscape genomics reveals regions associated with adaptive phenotypic and genetic variation in Ethiopian indigenous chickens

Climate change is a threat to sustainable livestock production and livelihoods in the tropics. It has adverse impacts on feed and water availability, disease prevalence, production, environmental temperature, and biodiversity. Unravelling the drivers of local adaptation and understanding the underlying genetic variation in random mating indigenous livestock populations informs the design of genetic improvement programmes that aim to increase productivity and resilience. In the present study, we combined environmental, genomic, and phenotypic information of Ethiopian indigenous chickens to investigate their environmental adaptability. Through a hybrid sampling strategy, we captured wide biological and ecological variabilities across the country. Our environmental dataset comprised mean values of 34 climatic, vegetation and soil variables collected over a thirty-year period for 260 geolocations. Our biological dataset included whole genome sequences and quantitative measurements (on eight traits) from 513 individuals, representing 26 chicken populations spread along 4 elevational gradients (6-7 populations per gradient). We performed signatures of selection analyses ([Formula: see text] and XP-EHH) to detect footprints of natural selection, and redundancy analyses (RDA) to determine genotype-environment and genotype-phenotype-associations. RDA identified 1909 outlier SNPs linked with six environmental predictors, which have the highest contributions as ecological drivers of adaptive phenotypic variation. The same method detected 2430 outlier SNPs that are associated with five traits. A large overlap has been observed between signatures of selection identified by[Formula: see text]and XP-EHH showing that both methods target similar selective sweep regions. Average genetic differences measured by [Formula: see text] are low between gradients, but XP-EHH signals are the strongest between agroecologies. Genes in the calcium signalling pathway, those associated with the hypoxia-inducible factor (HIF) transcription factors, and sports performance (GALNTL6) are under selection in high-altitude populations. Our study underscores the relevance of landscape genomics as a powerful interdisciplinary approach to dissect adaptive phenotypic and genetic variation in random mating indigenous livestock populations.

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.

Identification of Selection Signatures and Candidate Genes Related to Environmental Adaptation and Economic Traits in Tibetan Pigs

Tibetan pigs are indigenous to the Qinghai-Tibet Plateau and have been the subject of extensive genomic research primarily focused on their adaptation to high altitudes. However, genetic modifications associated with their response to low-altitude acclimation have not been thoroughly explored. To investigate the genetic basis underlying the low-altitude acclimation of Tibetan pigs, we generated and analyzed genotyping data of Tibetan pigs that inhabit high-altitude regions (average altitude 4000 m) and Tibetan pigs that have inhabited nearby low-altitude regions (average altitude 500 m) for approximately 20 generations. We found that the highland and lowland Tibetan pigs have distinguishable genotype and phenotype variations. We identified 46 and 126 potentially selected SNPs associated with 29 and 56 candidate genes in highland and lowland Tibetan pigs, respectively. Candidate genes in the highland Tibetan pigs were involved in immune response (NFYC and STAT1) and radiation (NABP1), whereas candidate genes in the lowland Tibetan pigs were related to reproduction (ESR2, DMRTA1, and ZNF366), growth and development (NTRK3, FGF18, and MAP1B), and blood pressure regulation (CARTPT). These findings will help to understand the mechanisms of environmental adaptation in Tibetan pigs and offer valuable information into the genetic improvement of Tibetan pigs pertaining to low-altitude acclimation and economic traits.

Cloning, expression analysis and localization of DAZL gene implicated in germ cell development of male Hezuo pig

Deleted in azoospermia-like (DAZL) is essential for mammalian testicular function and spermatogenesis. To explore the molecular characterization, expression patterns, and cellular localization of the DAZL in Hezuo pig testes, testicular tissue was isolated from Hezuo pig at five development stages including 30 days old (30 d), 90 days old (90 d), 120 days old (120 d), 180 days old (180 d), and 240 days old (240 d). DAZL cDNA was first cloned using the RT-PCR method, and its molecular characterization was analyzed using relevant bioinformatics software. Subsequently, the expression patterns and cellular localization of DAZL were evaluated using quantitative real-time PCR (qRT-PCR), Western blot, and immunohistochemistry. The cloning and sequence analysis showed that the Hezuo pig DAZL cDNA fragment contained 888 bp open reading frame (ORF) capable of encoding 295 amino acid residues and exhibited high identities with some other mammals. The qRT-PCR and Western blot results indicated that DAZL was specifically expressed in Hezuo pig testes, and DAZL levels of both mRNA and protein were expressed at all five reproductive stages of Hezuo pig testes, with extremely significant higher expression levels in 90 d, 120 d, 180 d, and 240 d than those in 30 d (p < 0.01). Additionally, immunohistochemistry results revealed that DAZL protein was mainly localized in gonocytes at 30 d testes, primary spermatocytes, and spermatozoon at other developmental stages, and Leydig cells throughout five development stages. Together, these results suggested that DAZL may play an important role by regulating the proliferation or differentiation of gonocytes, development of primary spermatocytes and spermatozoon, and functional maintenance of Leydig cells in testicular development and spermatogenesis of Hezuo pig. Nevertheless, the specific regulatory mechanisms underlying these phenomena still requires further investigated and verified.

Identification and analysis of circRNAs in the prefrontal cortices of wild boar and domestic pig

Domestication caused significant differences in morphology and behavior between wild and domestic pigs. However, the regulatory role of circRNA in this event is unclear. Here, we analyzed circRNA expression patterns in the prefrontal cortices of wild boar and domestic pigs to determine the potential role of circRNAs in domestication. We identified a total of 11,375 circRNAs and found that 349 and 354 circRNAs were up-regulated in wild boar and Rongchang pig, respectively. Functional enrichment analysis showed that host genes of significantly highly-expressed circRNAs in wild boar were significantly enriched in neural synapse-related categories and the categories of 'regulation of defense response (p = 0.028)' and 'neural retina development (p = 4.32 × 10-3)'. Host genes of significantly highly-expressed circRNAs in Rongchang pig were specifically involved in 'chordate embryonic development (p = 2.38 × 10-4)'. Additionally, we constructed circRNA-miRNA-mRNA regulatory axes in wild boar and Rongchang pig and found more regulatory axes in wild boar that potentially regulate synaptic activities. We identified multiple circRNAs that may be related to domesticated characteristics, such as ssc_circ_6179 (ssc_circ_6179-ssc-miR-9847-HRH3, related to aggression) and ssc_circ_3027 (ssc_circ_3027-ssc-miR-4334-5p-HCRTR1, related to attention). This study provides a resource for further investigation of the molecular basis of pig domestication.

Molecular characterization, expression patterns and cellular localization of BCAS2 gene in male Hezuo pig

Background

Breast carcinoma amplified sequence 2 (BCAS2) participates in pre-mRNA splicing and DNA damage response, which is implicated in spermatogenesis and meiosis initiation in mouse. Nevertheless, the physiological roles of BCAS2 in the testes of large mammals especially boars remain largely unknown.

Methods

In this study, testes were collected from Hezuo pig at three development stages including 30 days old (30 d), 120 days old (120 d), and 240 days old (240 d). BCAS2 CDS region was firstly cloned using RT-PCR method, and its molecular characteristics were identified using relevant bioinformatics software. Additionally, the expression patterns and cellular localization of BCAS2 were analyzed by quantitative real-time PCR (qRT-PCR), Western blot, immunohistochemistry and immunofluorescence.

Results

The cloning and sequence analysis indicated that the Hezuo pig BCAS2 CDS fragment encompassed 678 bp open reading frame (ORF) capable of encoding 225 amino acid residues, and possessed high identities with some other mammals. The results of qRT-PCR and Western blot displayed that BCAS2 levels both mRNA and protein were age-dependent increased (p < 0.01). Additionally, immunohistochemistry and immunofluorescence results revealed that BCAS2 protein was mainly observed in nucleus of gonocytes at 30 d testes as well as nucleus of spermatogonia and Sertoli cells at 120 and 240 d testes. Accordingly, we conclude that BCAS2 is critical for testicular development and spermatogenesis of Hezuo pig, perhaps by regulating proliferation or differentiation of gonocytes, pre-mRNA splicing of spermatogonia and functional maintenance of Sertoli cells, but specific mechanism still requires be further investigated.

Genomic selection analysis of morphological and adaptation traits in Chinese indigenous dog breeds

The significant morphological differences and abundant germplasm resources of Chinese indigenous dog breeds can be attributed to the diverse geographical environment, including plateaus, mountains, and a long history of raising dogs. The combination of both natural and artificial selection during the past several thousand years has led to hundreds of dog breeds with distinct morphological traits and environmental adaptations. China is one of the earliest countries to domesticate dogs and there are more than 50 ancient indigenous dog breeds. In this study, the run of homozygosity (ROH) and proportion of the autosomal genome covered by ROHs (FROH) were calculated for 10 dog breeds that are the most representative Chinese indigenous dogs based on 170K SNP microarray. The results of FROH showed that the Chuandong hound dogs (HCSSC) have the highest level of inbreeding among the tested breeds. The inbreeding in HCSSC occurred more recently than the Liangshan dogs (SCLSQ) dogs because of more numbers of long ROHs in HCSSC dogs, and the former also have higher inbreeding degree. In addition, there are significant differences in the inbreeding degree among different subpopulations of the same breed, such as the Thin dogs from Shaanxi and Shandong province. To explore genome-wide selection signatures among different breeds, including coat color, ear shape, and altitude adaptability, we performed genome selection analyses of FST and cross population extended haplotype homozygosity (XP-EHH). For the coat color, the FST analysis between Xiasi dogs (XSGZ) and HCSSC dogs was performed and identified multiple genes involved in coat color, hair follicle, and bone development, including MC1R, KITLG, SOX5, RSPO2, and TBX15. For the plateau adaptability, we performed FST and XP-EHH analyses between dogs from Tibet (Tibetan Mastiffs and Nyingchi dogs) and plain regions (Guangxi Biwei dogs GXBWQ and Guandong Sharpei dogs). The results showed the EPAS1 gene in dogs from Tibet undergo strong selection. Multiple genes identified for selection signals based on different usage of dogs. Furthermore, the results of ear shape analyses showed that MSRB3 was likely to be the main gene causing the drop ear of domestic dogs. Our study provides new insights into further understanding of Chinese indigenous dogs.

Comparative Analysis of Structural Composition and Function of Intestinal Microbiota between Chinese Indigenous Laiwu Pigs and Commercial DLY Pigs

Intestinal microbiota has an important impact on pig phenotypes. Previous studies mainly focused on the microbiota of feces and worldwide farmed commercial pigs, while research on the microbiota of various intestinal sections and indigenous pig breeds is very limited. This study aimed to characterize and compare the biogeography of intestinal microbiota in pigs of one Chinese indigenous breed and one commercial crossbred. In this study, we sequenced the microbiota of six intestinal segments in the grown-up pigs of a Chinese indigenous breed, Laiwu pigs, and the worldwide farmed crossbred Duroc × Landrace × Yorkshire (DLY) pigs by 16S rRNA sequencing, characterized the biogeography of intestinal microbiota, and compared the compositional and functional differences between the two breeds. The results showed that there were obvious differences in microbial structure and abundance between the small and large intestines. Laiwu pigs had higher large intestinal diversity than DLY pigs, while DLY pigs had higher small intestinal diversity than Laiwu pigs. Moreover, some specific bacterial taxa and Kyoto Encyclopedia of Genes and Genomes pathways were found to be related to the high fat deposition and good meat quality of Laiwu pigs and the high growth speed and lean meat rate of DLY pigs. This study provides an insight into the shifts in taxonomic composition, microbial diversity, and functional profile of intestinal microbiota in six intestinal segments of Laiwu and DLY pigs, which would be essential for exploring the potential influence of the host's genetic background on variation in microbiota composition and diversity.

High-Altitude Andean H194R HIF2A Allele Is a Hypomorphic Allele

For over 10,000 years, Andeans have resided at high altitude where the partial pressure of oxygen challenges human survival. Recent studies have provided evidence for positive selection acting in Andeans on the HIF2A (also known as EPAS1) locus, which encodes for a central transcription factor of the hypoxia-inducible factor pathway. However, the precise mechanism by which this allele might lead to altitude-adaptive phenotypes, if any, is unknown. By analyzing whole genome sequencing data from 46 high-coverage Peruvian Andean genomes, we confirm evidence for positive selection acting on HIF2A and a unique pattern of variation surrounding the Andean-specific single nucleotide variant (SNV), rs570553380, which encodes for an H194R amino acid substitution in HIF-2α. Genotyping the Andean-associated SNV rs570553380 in a group of 299 Peruvian Andeans from Cerro de Pasco, Peru (4,338 m), reveals a positive association with increased fraction of exhaled nitric oxide, a marker of nitric oxide biosynthesis. In vitro assays show that the H194R mutation impairs binding of HIF-2α to its heterodimeric partner, aryl hydrocarbon receptor nuclear translocator. A knockin mouse model bearing the H194R mutation in the Hif2a gene displays decreased levels of hypoxia-induced pulmonary Endothelin-1 transcripts and protection against hypoxia-induced pulmonary hypertension. We conclude the Andean H194R HIF2A allele is a hypomorphic (partial loss of function) allele.

Metagenome and metabolome insights into the energy compensation and exogenous toxin degradation of gut microbiota in high-altitude rhesus macaques (Macaca mulatta)

There have been many reports on the genetic mechanism in rhesus macaques (RMs) for environmental adaptation to high altitudes, but the synergistic involvement of gut microbiota in this adaptation remains unclear. Here we performed fecal metagenomic and metabolomic studies on samples from high- and low-altitude populations to assess the synergistic role of gut microbiota in the adaptation of RMs to high-altitude environments. Microbiota taxonomic annotation yielded 7471 microbiota species. There were 37 bacterial species whose abundance was significantly enriched in the high-altitude populations, 16 of which were previously reported to be related to the host's dietary digestion and energy metabolism. Further functional gene enrichment found a stronger potential for gut microbiota to synthesize energy substrate acetyl-CoA using CO2 and energy substrate pyruvate using oxaloacetate, as well as a stronger potential to transform acetyl-CoA to energy substrate acetate in high-altitude populations. Interestingly, there were no apparent differences between low-altitude and high-altitude populations in terms of genes enriched in the main pathways by which the microbiota consumed the three energy substrates, and none of the three energy substrates were detected in the fecal metabolites. These results strongly suggest that gut microbiota plays an important energy compensatory role that helps RMs to adapt to high-altitude environments. Further functional enrichment after metabolite source analysis indicated the abundance of metabolites related to the degradation of exogenous toxins was also significantly higher in high-altitude populations, which suggested a contributory role of gut microbiota to the degradation of exogenous toxins in wild RMs adapted to high-altitude environments.

Divergence of Liver Lipidomes in Tibetan and Yorkshire Pigs Living at Different Altitudes

The Tibetan pig is a characteristic breed of the Qinghai-Tibet Plateau with distinct physiological and meat quality attributes. The liver lipid profile can offer an important perspective to explore the uniqueness of Tibetan pigs. A quantitative comparison of liver lipidomes revealed significant differences in the lipid profiles between Tibetan and Yorkshire pigs raised at different altitudes. The abundance of lipids in the livers of pigs raised at a high altitude was higher than that of pigs raised at a lower altitude, whereas the abundance of lipids in the livers of Yorkshire pigs was higher than that of Tibetan pigs raised at the same altitude. Of the 1101 lipids identified, 323 and 193 differentially abundant lipids (DALs) were identified in the pairwise comparisons of Tibetan and Yorkshire pigs raised at different altitudes, respectively. The DALs of Tibetan pigs consisted mainly of 161 triglycerides, along with several acylcarnitines, represented by carnitine C2:0, and significant changes in the abundance of some phospholipids. The DALs of Yorkshire pigs were more complex, with significant increases in the abundance of triglycerides, cholesteryl esters, and free fatty acids, and decreases in the abundance of some phospholipids. This research provides strong theoretical and data support for the high-quality development of the highland livestock industry.

Ssc-miR-141 Attenuates Hypoxia-Induced Alveolar Type II Epithelial Cell Injury in Tibetan Pigs by Targeting PDCD4

The Tibetan pig is an endemic economic animal in the plateau region of China, and has a unique adaptation mechanism to the plateau hypoxic environment. Research into microRNAs (miRNAs) involved in the mechanism underlying hypoxia adaptation of Tibetan pig is very limited. Therefore, we isolated alveolar type II epithelial (ATII) cells from the lungs of the Tibetan pig, cultured them in normoxia/hypoxia (21% O₂; 2% O₂) for 48 h, and performed high-throughput sequencing analysis. We identified a hypoxic stress-related ssc-miR-141 and predicted its target genes. The target genes of ssc-miR-141 were mainly enriched in mitogen-activated protein kinase (MAPK), autophagy-animal, and Ras signaling pathways. Further, we confirmed that PDCD4 may serve as the target gene of ssc-miR-141. Real-time quantitative polymerase chain reaction (RT-qPCR) analysis was performed to confirm the expression levels of ssc-miR-141 and PDCD4, and a dual-luciferase gene reporter system was used to verify the targeted linkage of ssc-miR-141 to PDCD4. The results showed that the expression level of ssc-miR-141 in the hypoxia group was higher than that in the normoxia group, while the expression level of PDCD4 tended to show the opposite trend and significantly decreased under hypoxia. These findings suggest that ssc-miR-141 is associated with hypoxia adaptation and provide a new insight into the role of miRNAs from ATII cells of Tibetan pig in hypoxia adaptation.

Remodeling of the microbiota improves the environmental adaptability and disease resistance in Tibetan pigs

Introduction

The establishment of intestinal microbiota and the maintenance of its equilibrium structure plays an important role in Tibetan pigs during different growth stages. Understanding the structure and function of the intestinal microbiota at different growth stages of Tibetan pigs can provide a theoretical basis for guiding nutritional regulation and feeding management in different stages.

Methods

Fecal samples were collected from the Tibetan piglets at different growth stages, and the 16S rRNA was sequenced to analyze the changes of intestinal microbiota.

Results

Alpha and Beta diversity indexes showed that the diversity of the intestinal microbiota did not change during the three growth stages, and the main components of intestinal microbiota were not significantly different. At the phylum level, Firmicutes and Bacteroidetes were dominant and abundant at different growth stages and were not restricted by age. At the genus level, Streptococcus, Lactobacillus, and Bifidobacterium were the most dominant in the TP10d and TP40d groups, Streptococcus was the most dominant in the TP100d group, followed by Treponema_2 and Lactobacillus. Fusobacteria, Gluconobacter, and Synergistetes were found to be specific genera of 10-day-old Tibetan piglets by LEfSe combined with LDA score. The change of diet made Tenericutes and Epsilonbacteraeota, which are closely related to digestive fiber, become specific bacteria at the age of 40 days. With the consumption of oxygen in the intestine, obligate anaerobes, such as Verrucomicrobia, Fibrobacter, and Planctomycetes, were the characteristic genera of 100 days. KEGG function prediction analysis showed that the intestinal microbiota function of Tibetan pigs changed dynamically with the growth and development of Tibetan piglets.

Discussion

In conclusion, the structure and composition of the intestinal microbiota of Tibetan pigs are significantly different at different growth and development stages, which plays an important role in their immune performance.

First detection and complete genome analysis of porcine circovirus-like virus P1 and porcine circovirus-2 in yak in China

Porcine circovirus-like virus P1, like porcine circovirus type 2 (PCV2), is a potential pathogen of post-weaning multisystemic wasting syndrome in swine. Yaks are a valuable species and an iconic symbol of the Tibet Plateau which is the highest and largest plateau in the world. In this study, a total of 105 yak diarrheal samples, collected from 13 farms in Linzhi in the Tibet Plateau from January 2019 to December 2021, that were screened for P1 and PCV2 by polymerase chain reaction, 10.48% (n = 11) were positive for P1, 4.76% (n = 5) for PCV2, and 5.71% (n = 6) were positive for coinfection of P1 and PCV2. In addition, the whole genomes of eight P1 strains and eight PCV2 strains were sequenced. Alignment of deduced amino acid sequences of P1 ORF1 and PCV2 ORF2 gene revealed that ON012566 had one unique amino acid mutation at residues 137 (T to P). This mutation has important implication for the study of virus virulence, tissue tropism, and immune response. Phylogenetic analysis shows that the yak-origin P1 strains in this study with cattle-origin P1 reference strains were grouped into one cluster. The yak-origin PCV2 (ON012566) and a buffalo-origin PCV2 (KM116514) reference strain clustered in the same branch in the PCV2b regions. Meanwhile, the remaining PCV2 strains and buffalo-origin PCV2 reference strain (ON012565) clustered in the PCV2d regions. To summarize, to our knowledge, this is the first report on the molecular prevalence and genome characteristics of P1 and PCV2 in yaks in the world and will contribute to further study of the molecular epidemiology, source, and evolution of P1 and PCV2 strains.

Alternative splicing signature of alveolar type II epithelial cells of Tibetan pigs under hypoxia-induced

Alternative splicing (AS) allows the generation of multiple transcript variants from a single gene and affects biological processes by generating protein diversity in organisms. In total, 41,642 AS events corresponding to 9,924 genes were identified, and SE is the most abundant alternatively spliced type. The analysis of functional categories demonstrates that alternatively spliced differentially expressed genes (DEGs) were enriched in the MAPK signaling pathway and hypoxia-inducible factor 1 (HIF-1) signaling pathway. Proteoglycans in cancer between the normoxic (21% O2, TN and LN) and hypoxic (2% O2, TL and LL) groups, such as SLC2A1, HK1, HK2, ENO3, and PFKFB3, have the potential to rapidly proliferate alveolar type II epithelial (ATII) cells by increasing the intracellular levels of glucose and quickly divert to anabolic pathways by glycolysis intermediates under hypoxia. ACADL, EHHADH, and CPT1A undergo one or two AS types with different frequencies in ATII cells between TN and TL groups (excluding alternatively spliced DEGs shared between normoxic and hypoxic groups), and a constant supply of lipids might be obtained either from the circulation or de novo synthesis for better growth of ATII cells under hypoxia condition. MCM7 and MCM3 undergo different AS types between LN and LL groups (excluding alternatively spliced DEGs shared between normoxic and hypoxic groups), which may bind to the amino-terminal PER-SIM-ARNT domain and the carboxyl terminus of HIF-1α to maintain their stability. Overall, AS and expression levels of candidate mRNAs between Tibetan pigs and Landrace pigs revealed by RNA-seq suggest their potential involvement in the ATII cells grown under hypoxia conditions.

Plateau Adaptation Gene Analyses Reveal Transcriptomic, Proteomic, and Dual Omics Expression in the Lung Tissues of Tibetan and Yorkshire Pigs

Elevated environments such as plateaus are often classified as low oxygen environments. The hypoxic adaptation mechanisms utilized by organisms in these conditions are not well understood. To address this, the differentially expressed genes (DEGs) involved in hypoxia adaptation were assessed using two pig breeds (Tibetan pig [TP] and Yorkshire sow [YY]). Genes related to lung tissue responses to hypoxia were assessed using transcriptomic (using RNA-seq) and proteomic (using iTRAQ) analysis. A total of 1021 DEGs were screened out. In the iTRAQ omics data, a total of 22,100 peptides were obtained and 4518 proteins were found after filtering. A total of 271 differentially expressed proteins [DEPs] were screened using the conditions of p < 0.05; FC ≤ 0.833; and FC ≥ 1.2. A total of 14 DEGs at the mRNA and protein levels were identified and found to be associated with regulation of the inflammatory response; blood particles; and MAPK cascade response regulation. Among the DEGs, six were associated with hypoxia adaptation function (mitochondria and glycolysis) in pigs. The results of this study identify novel candidate genes involved in porcine hypoxia adaptation mechanisms.

Healthy Gut Microbiome Composition Enhances Disease Resistance and Fat Deposition in Tibetan Pigs

The gut microbiota is involved in a range of physiological processes in animals, and modulating the microbiome composition is considered a novel target for identifying animal traits. Tibetan pigs show better fat deposition and disease resistance compared to Yorkshire pigs. However, studies investigating the correlation between favorable characteristics in Tibetan pigs and the gut microbial community remain scarce. In the current study, 1,249,822 high-quality sequences were obtained by amplicon sequencing of the colon contents of Tibetan and Yorkshire pigs. We found that at the boundary level, the abundance and relative abundance of colon bacterial community in Tibetan pigs were higher than that in Yorkshire pigs (P &gt; 0.05). Phylum level, Firmicutes were the dominant colonic microflora of Tibetan and Yorkshire pigs, and the ratio of Firmicutes to Bacteroides in Tibetan pigs was slightly higher than in Yorkshire pigs. Actinobacteria and Spirobacteria were significantly higher in Tibetan pigs than in Yorkshire pigs (P &lt; 0.05). At the genus level, the relative abundance of Bifidobacterium, Lactobacillus, and Bacteriologist, which are related to disease resistance, was significantly higher than that in Yorkshire pigs in Yorkshire pigs. In conclusion, the composition and abundance of colonic intestinal microflora in Tibetan pigs were closely related to their superior traits. Bifidobacteria, Ruminococcaceae, and Family-XIII-AD3011-Group are conducive to improving disease resistance in Tibetan pigs. Lactobacillus and Solobacterium were observed to be the main bacterial communities involved in fat deposition in Tibetan pigs. This study will provide a new reference for the development and utilization of Tibetan pigs in future.

Transcriptomics-Based Study of Differentially Expressed Genes Related to Fat Deposition in Tibetan and Yorkshire Pigs

Fat deposition traits are one of the key factors in pig production and breeding. The fat deposition capacity of pigs mainly affects the quality of pork and pig productivity. The aim of this study was to analyze the differential expression of mRNA levels in dorsal adipose tissue of Tibetan and York pigs at different growth stages using transcriptomic data to estimate key genes that regulate fat deposition in pigs. The results showed that a total of 32,747 positively expressed genes were present in the dorsal adipose tissue of the two breeds. Differentially expressed gene (DEG) screening of multiple combinations between the two breeds yielded 324 DEGS. Gene ontology (GO) biofunctional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these DEGS were mainly involved in lipid metabolic pathways, steroid biosynthetic pathways and lipid biosynthetic processes, sterol biosynthetic processes, brown adipocyte differentiation, and other pathways related to lipid deposition and metabolism. The results showed that ACACA, SLC2A4 and THRSP genes positively regulated the lipid deposition ability and CHPT1 gene negatively regulated the lipid deposition ability in pigs. The results of this experiment suggest a theoretical basis for further studies on the regulatory mechanisms of fat deposition in pigs.

Effect of a Plateau Environment on the Oxidation State of the Heart and Liver through AMPK/p38 MAPK/Nrf2-ARE Signaling Pathways in Tibetan and DLY Pigs

This study evaluated the effect of a plateau environment on the heart and liver oxidation state of Tibetan pigs (TPs) and DLY pigs through analyzing AMPK, p38 MAPK, and Nrf2 signaling pathways. Twelve 120-day-old TPs and twelve 120-day-old DLY pigs were randomly divided into two groups in a plateau environment for three weeks. Exposed to a plateau environment, TPs exhibited a lower (p < 0.05) malondialdehyde level but higher (p < 0.05) glutathione, superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and total antioxidant capacity (T-AOC) activities in the liver and heart than those observed in DLY pigs. TPs also showed higher (p < 0.05) mRNA levels of SOD and GSH-Px in the liver and heart compared with those of DLY pigs. The TPs showed higher (p < 0.05) mRNA and protein levels of AMPK and Nrf2 in the liver and heart compared with those of DLY pigs. Furthermore, TPs showed higher (p < 0.05) mRNA and protein levels of p38 MAPK in the heart and higher mRNA levels of p38 MAPK in the liver compared with those of DLY pigs under a plateau environment. In summary, TPs possess a stronger antioxidant capacity in the heart and liver than that of DLY pigs in a plateau environment through AMPK/p38 MAPK/Nrf2-ARE signaling pathways.

Genome-Wide Selection Sweep between Wild and Local Pigs from Europe for the Investigation of the Hereditary Characteristics of Domestication in Sus Scrofa

The phenotypic characteristics of existing domestic pigs (DPs) greatly differ from those of wild boar (WB) populations thousands of years ago. After thousands of years of human domestication, WB and DP have diverged greatly in terms of genetics. Theoretically, worldwide local pigs have independent contributions from their local WBs at the beginning of Sus scrofa domestication. The investigation of the vicissitude of the heredity material between domestic populations and their wild ancestors will help in further understanding the domestication history of domestic animals. In the present study, we performed a genome-wide association scan (GWSA) and phylogeny estimation with a total of 1098 public European Illumina 60K single nucleotide polymorphism data, which included 650 local DPs and 448 WBs. The results revealed that the phylogenetic relationship of WBs corresponds to their geographical distribution and carries large divergence with DPs, and all WB breeds (e.g., HRWB, SBWB, and TIWB) presents a closely linkage with the middle WB (e.g., HRWB, and PLWB). In addition, 64 selected candidate genes (e.g., IDH2, PIP5K1B, SMARCA2, KIF5C, and TJP2) were identified from GWSA. A total of 63 known multiple biological functional pathways were annotated by 22 genes, and ubiquinone and other terpenoid-quinone biosynthesis pathways that belong to the metabolism of cofactors and vitamins were significantly enriched (p < 0.05). The most frequent (28.57%) pathways were classified under metabolism. We confirmed that the middle European WB has made an important genetic contribution to the entire European WB populations. A series of selected genes discovered from this study provides the scientific community with a deeper understanding of the heredity performance of metabolism and emotion and the real purpose behind domestication.

Gut Bacterial Composition and Functional Potential of Tibetan Pigs Under Semi-Grazing

Gut bacterial community plays a key role in maintaining host health. The Tibetan pig (Sus scrofa), an ancient breed in China, has been known for its high adaptability to harsh environments and for its meat quality. To understand the underlying mechanisms facilitating to shape these unique features, in this study, 16S rRNA sequencing using pigs feces and subsequent bacterial functional prediction were performed. Also, the gut bacteria of two other breeds of pigs, Barkshire and Landrace, were examined for comparison. It was revealed that the structure of bacterial community in Tibetan pigs appeared to be more complex; the relative abundances of dominant bacterial families varied inversely with those of the other pigs, and the proportion of Firmicutes in Tibetan pigs was lower, but Bacteroides, Fibrobacterota, Lachnospiraceae, Oscillospiraceae, and Ruminococcaceae were higher. Bacterial functional prediction revealed that the dominant flora in the Tibetan pigs was more correlated with functions regulating the hosts’ immune and inflammatory responses, such as NOD-like_receptor_signaling_pathway and vitamin metabolism. In addition, in Tibetan pigs, the taxonomic relationships in the gut bacteria on day 350 were closer than those on earlier stages. Furthermore, gender played a role in the composition and function of bacterial inhabitants in the gut; for boars, they were more correlated to drug resistance and xenobiotics metabolism of the host compared to the sows. In sum, our preliminary study on the gut bacterial composition of the Tibetan pigs provided an insight into the underlying host–microorganism interactions, emphasizing the role of intestinal bacteria in the context of modulating the host’s immune system and host development.

Molecular detection and phylogenetic analysis of porcine circovirus type 3 in Tibetan pigs on the Qinghai-Tibet Plateau of China

Background

Porcine circovirus type 3 (PCV3) has been confirmed to infect pigs, posing a health risk and making pigs more susceptible to other pathogens. After the first report of PCV3 infection in the United States, its prevalence was determined in pigs suffering from clinical digestive or respiratory diseases in several other regions, including the Sichuan and Gansu provinces of China. In this study, we describe the frequency of PCV3 detection in Tibetan pigs inhabiting three different provinces surrounding the Qinghai-Tibet Plateau of China.

Methods

A total of 316 samples from diarrheic animals and 182 samples from healthy animals were collected in a randomized manner. Conventional PCR was applied for PCV3 DNA detection. The conserved regions of the PCV3 gene were analyzed with MEGA 7.1 software to design specific primers to sequence entire Cap genes in PCV3 strains, and the sequences were then used to confirm the subtypes of PCV3 in the positive samples. Prediction of the amino acid sequences by nucleotide sequence translation was also performed to compare the point mutations in the entire Cap protein. Twenty PCV3 whole-genomic sequences were used for genome phylogenetic analyses of PCV3 and sequence alignments with 22 other reference strains.

Results

We found that the prevalence of the virus was significantly higher in samples from pigs with diarrhoea than that in samples from healthy pigs. Phylogenetic analysis of Cap proteins demonstrated that the 20 PCV3 strains formed three clades, including PCV3a (8/20, 40.00%), PCV3b (5/20, 25%) and PCV3c (7/20, 35.00%). The complete genome sequence revealed that these strains formed one branch in the phylogenetic tree. Sequence analysis showed that the Cap proteins of the 20 different viral strains shared between 95.84 and 99.18% nucleotide identity. Cap protein sequence analyses showed that the positivity rate of PCV3a was highest in the samples from pigs with diarrhoea. In comparison, PCV3c was the most elevated subtype in the healthy samples. There was no mutation at a specific site in the amino acid sequences of the entire Cap protein from different PCV3 subtype strains from heathy samples. There was a mutation at site 113 in PCV3a, site 129 in PCV3b, and site 116 in PCV3c.

Conclusion

Our present data provide evidence that PCV3 is prevalent in Tibetan pigs at high altitudes in China, and the higher prevalence rates of the PCV3a and PCV3b subtypes in samples from pigs with diarrhoea further indicate that the genotypes should not be neglected during surveys of the pathogenicity of PCV3. Phylogenetic and genetic diversity analyses suggested that the continuous evolution, adaptation and mechanisms of pathogenicity of PCV3 in Tibetan pigs living in this special environment should be further studied.

Integrative Analysis of the lncRNA-Associated ceRNA Regulatory Network Response to Hypoxia in Alveolar Type II Epithelial Cells of Tibetan Pigs

The function of alveolar type II epithelial (ATII) cells is severely hampered by oxygen deficiency, and understanding the regulatory mechanisms controlling responses to hypoxia may assist in relieving injury induced by hypoxia. In this study, we cultured ATII cells from Tibetan pigs and Landrace pigs under hypoxic and normoxic environments to screen for differentially expressed (DE) lncRNAs, DEmiRNAs, and construct their associated ceRNA regulatory networks in response to hypoxia. Enrichment analysis revealed that target genes of DElncRNAs of Tibetan pigs and Landrace pig between the normoxic (TN, LN) and hypoxic (TL, LL) groups significantly enriched in the proteoglycans in cancer, renal cell carcinoma, and erbB signaling pathways, while the target genes of DEmiRNAs were significantly enriched in the axon guidance, focal adhesion, and mitogen-activated protein kinase (MAPK) signaling pathways. Hypoxia induction was shown to potentially promote apoptosis by activating the focal adhesion/PI3K-Akt/glycolysis pathway. The ssc-miR-20b/MSTRG.57127.1/ssc-miR-7-5p axis potentially played a vital role in alleviating hypoxic injury by regulating ATII cell autophagy under normoxic and hypoxic conditions. MSTRG.14861.4-miR-11971-z-CCDC12, the most affected axis, regulated numerous RNAs and may thus regulate ATII cell growth in Tibetan pigs under hypoxic conditions. The ACTA1/ssc-miR-30c-3p/MSTRG.23871.1 axis is key for limiting ATII cell injury and improving dysfunction and fibrosis mediated by oxidative stress in Landrace pigs. Our findings provide a deeper understanding of the lncRNA/miRNA/mRNA regulatory mechanisms of Tibetan pigs under hypoxic conditions.

The genomic basis of high-elevation adaptation in wild house mice (Mus musculus domesticus) from South America

Understanding the genetic basis of environmental adaptation in natural populations is a central goal in evolutionary biology. The conditions at high elevation, particularly the low oxygen available in the ambient air, impose a significant and chronic environmental challenge to metabolically active animals with lowland ancestry. To understand the process of adaptation to these novel conditions and to assess the repeatability of evolution over short timescales, we examined the signature of selection from complete exome sequences of house mice (Mus musculus domesticus) sampled across two elevational transects in the Andes of South America. Using phylogenetic analysis, we show that house mice colonized high elevations independently in Ecuador and Bolivia. Overall, we found distinct responses to selection in each transect and largely nonoverlapping sets of candidate genes, consistent with the complex nature of traits that underlie adaptation to low oxygen availability (hypoxia) in other species. Nonetheless, we also identified a small subset of the genome that appears to be under parallel selection at the gene and SNP levels. In particular, three genes (Col22a1, Fgf14, and srGAP1) bore strong signatures of selection in both transects. Finally, we observed several patterns that were common to both transects, including an excess of derived alleles at high elevation, and a number of hypoxia-associated genes exhibiting a threshold effect, with a large allele frequency change only at the highest elevations. This threshold effect suggests that selection pressures may increase disproportionately at high elevations in mammals, consistent with observations of some high-elevation diseases in humans.

Transcriptome and Metabolome Integration Provides New Insights Into the Regulatory Networks of Tibetan Pig Alveolar Type II Epithelial Cells in Response to Hypoxia

Tibetan pigs show a widespread distribution in plateau environments and exhibit striking physiological and phenotypic differences from others pigs for adaptation to hypoxic conditions. However, the regulation of mRNAs and metabolites as well as their functions in the alveolar type II epithelial (ATII) cells of Tibetan pigs remain undefined. Herein, we carried out integrated metabolomic and transcriptomic profiling of ATII cells between Tibetan pigs and Landrace pigs across environments with different oxygen levels to delineate their signature pathways. We observed that the differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs) profiles displayed marked synergy of hypoxia-related signature pathways in either Tibetan pigs or Landrace pigs. A total of 1,470 DEGs shared between normoxic (TN, ATII cells of Tibetan pigs were cultured under 21% O₂; LN, ATII cells of Landrace pigs were cultured under 21% O₂) and hypoxic (TL, ATII cells of Tibetan pigs were cultured under 2% O₂; LL, ATII cells of Landrace pigs were cultured under 2% O₂) groups and 240 DAMs were identified. Functional enrichment assessment indicated that the hypoxia-related genes and metabolites were primarily involved in glycolysis and aldosterone synthesis and secretion. We subsequently constructed an interaction network of mRNAs and metabolites related to hypoxia, such as guanosine-3′, 5′-cyclic monophosphate, Gly-Tyr, and phenylacetylglycine. These results indicated that mitogen-activated protein kinase (MAPK) signaling, aldosterone synthesis and secretion, and differences in the regulation of MCM and adenosine may play vital roles in the better adaptation of Tibetan pigs to hypoxic environments relative to Landrace pigs. This work provides a new perspective and enhances our understanding of mRNAs and metabolites that are activated in response to hypoxia in the ATII cells of Tibetan pigs.

Evolutionary physiology at 30+: Has the promise been fulfilled?: Advances in Evolutionary Physiology: Advances in Evolutionary Physiology

Three decades ago, interactions between evolutionary biology and physiology gave rise to evolutionary physiology. This caused comparative physiologists to improve their research methods by incorporating evolutionary thinking. Simultaneously, evolutionary biologists began focusing more on physiological mechanisms that may help to explain constraints on and trade-offs during microevolutionary processes, as well as macroevolutionary patterns in physiological diversity. Here we argue that evolutionary physiology has yet to reach its full potential, and propose new avenues that may lead to unexpected advances. Viewing physiological adaptations in wild animals as potential solutions to human diseases offers enormous possibilities for biomedicine. New evidence of epigenetic modifications as mechanisms of phenotypic plasticity that regulate physiological traits may also arise in coming years, which may also represent an overlooked enhancer of adaptation via natural selection to explain physiological evolution. Synergistic interactions at these intersections and other areas will lead to a novel understanding of organismal biology.

High-altitude adaptation in vertebrates as revealed by mitochondrial genome analyses

The high-altitude environment may drive vertebrate evolution in a certain way, and vertebrates living in different altitude environments might have different energy requirements. We hypothesized that the high-altitude environment might impose different influences on vertebrate mitochondrial genomes (mtDNA). We used selection pressure analyses and PIC (phylogenetic independent contrasts) analysis to detect the evolutionary rate of vertebrate mtDNA protein-coding genes (PCGs) from different altitudes. The results showed that the ratio of nonsynonymous/synonymous substitutions (dN/dS) in the mtDNA PCGs was significantly higher in high-altitude vertebrates than in low-altitude vertebrates. The seven rapidly evolving genes were shared by the high-altitude vertebrates, and only one positive selection gene (ND5 gene) was detected in the high-altitude vertebrates. Our results suggest the mtDNA evolutionary rate in high-altitude vertebrates was higher than in low-altitude vertebrates as their evolution requires more energy in a high-altitude environment. Our study demonstrates the high-altitude environment (low atmospheric O2 levels) drives vertebrate evolution in mtDNA PCGs.

The Expression Regulatory Network in the Lung Tissue of Tibetan Pigs Provides Insight Into Hypoxia-Sensitive Pathways in High-Altitude Hypoxia

To adapt to a low-oxygen environment, Tibetan pigs have developed a series of unique characteristics and can transport oxygen more effectively; however, the regulation of the associated processes in high-altitude animals remains elusive. We performed mRNA-seq and miRNA-seq, and we constructed coexpression regulatory networks of the lung tissues of Tibetan and Landrace pigs. HBB, AGT, COL1A2, and EPHX1 were identified as major regulators of hypoxia-induced genes that regulate blood pressure and circulation, and they were enriched in pathways related to signal transduction and angiogenesis, such as HIF-1, PI3K-Akt, mTOR, and AMPK. HBB may promote the combination of hemoglobin and oxygen as well as angiogenesis for high-altitude adaptation in Tibetan pigs. The expression of MMP2 showed a similar tendency of alveolar septum thickness among the four groups. These results indicated that MMP2 activity may lead to widening of the alveolar wall and septum, alveolar structure damage, and collapse of alveolar space with remarkable fibrosis. These findings provide a perspective on hypoxia-adaptive genes in the lungs in addition to insights into potential candidate genes in Tibetan pigs for further research in the field of high-altitude adaptation.

Vascular characteristics and expression of hypoxia genes in Tibetan pigs' hearts

Background

Tibetan pigs have exhibited unique characteristics from low‐altitudes pigs and adapted well to the Qinghai‐Tibet Plateau.

Objectives

The current study was undertaken to investigate the hypoxic adaptation of heart in Tibetan pigs.

Methods

The hearts of Tibetan pigs and Landrace pigs raised at high or low altitudes were compared using 3D casting technology, scanning electron microscopy and real‐time quantitative PCR (qRT‐PCR).

Results

We found that the ratio of the major axis to the minor axis and the density of the heart were significantly higher in Tibetan pigs than in Landrace pigs (p < 0.05). Tibetan pigs had larger diameters and higher densities of arterioles than Landrace pigs (p < 0.05), and these features have a similar variation with the expression of vascular endothelial growth factor (VEGF). The cardiac expression levels of hypoxia‐inducible factor‐1α (HIF‐1α) and endothelial nitric oxide synthase (eNOS) were significantly higher in pigs reared at high altitudes than in those reared at low altitudes (p < 0.05). In contrast, Egl nine homolog 1 (EGLN1) had the opposite trend with respect to HIF‐1α and eNOS and was related to red blood cell (RBC) counts. Notably, the expressions of erythropoietin (EPO) and endothelial PAS domain‐containing protein 1 (EPAS1) were significantly higher in Landrace pigs kept at high altitudes than in the others (p < 0.05) and were associated with haemoglobin.

Conclusions

These findings show that the regulation of the heart function of Tibetan pigs in a hypoxic environment is manifested at various levels to ensure the circulation of blood under extreme environmental conditions.

The evolutionary and physiological significance of the Hif pathway in teleost fishes

The hypoxia-inducible factor (HIF) pathway is a key regulator of cellular O2 homeostasis and an important orchestrator of the physiological responses to hypoxia (low O2) in vertebrates. Fish can be exposed to significant and frequent changes in environmental O2, and increases in Hif-α (the hypoxia-sensitive subunit of the transcription factor Hif) have been documented in a number of species as a result of a decrease in O2. Here, we discuss the impact of the Hif pathway on the hypoxic response and the contribution to hypoxia tolerance, particularly in fishes of the cyprinid lineage, which includes the zebrafish (Danio rerio). The cyprinids are of specific interest because, unlike in most other fishes, duplicated paralogs of the Hif-α isoforms arising from a teleost-specific genome duplication event have been retained. Positive selection has acted on the duplicated paralogs of the Hif-α isoforms in some cyprinid sub-families, pointing to adaptive evolutionary change in the paralogs. Thus, cyprinids are valuable models for exploring the evolutionary significance and physiological impact of the Hif pathway on the hypoxic response. Knockout in zebrafish of either paralog of Hif-1α greatly reduces hypoxia tolerance, indicating the importance of both paralogs to the hypoxic response. Here, with an emphasis on the cardiorespiratory system, we focus on the role of Hif-1α in the hypoxic ventilatory response and the regulation of cardiac function. We explore the effects of the duration of the hypoxic exposure (acute, sustained or intermittent) on the impact of Hif-1α on cardiorespiratory function and compare relevant data with those from mammalian systems.

Recent progress in research on the gut microbiota and highland adaptation on the Qinghai-Tibet Plateau

Microbial communities that inhabit the host's intestine influence many aspects of the host's health and bear the adaptive potential to alterations in harsh environments and diets. The Qinghai-Tibet Plateau represents one of the harshest environments in the world. Preliminary progress has been made in identifying the communities of gut microbes in Indigenous Tibetans and non-human animals. However, due to the complexity of microbial communities, the effects of gut microbes on the host's health and high-plateau adaptation remain unexplained. Herein, we review the latest progress in identifying factors affecting the gut microbiota of native Tibetans and non-human animals and highlight the complex interactions between the gut microbiota, health and highland adaptation, which provides a basis for exploring the correlations between the gut microbiota and clinical indexes in native highland residents and travellers, as well as developing microbiota-based strategies to mitigate health risks for tourists and treatments for mountain sickness during high-altitude travel in the future.

Characteristics of Tibetan pig lung tissue in response to a hypoxic environment on the Qinghai-Tibet Plateau

To adapt to the plateau environment, Tibetan pigs' lungs have developed a unique physiological mechanism during evolution. The vascular corrosion casting technique and scanning electron microscopy were used to understand arterial architecture. Blood physiological index and quantitative real-time PCR (qRT-PCR) were used for assessing whether the lung can regulate the body through anatomical, physiological and molecular mechanisms to adapt to hypoxic environments. Our study showed that the lungs of Tibetan pigs were heavier and wider and that the pulmonary arteries were thicker and branched and had a denser vascular network than those of Landrace pigs. The hemoglobin (HGB), mean corpuscular hemoglobin concentration (MCHC) values of high-altitude pigs were significantly higher than those of low-altitude pigs. The expression levels of HIF- 1α , EPAS1, EPO and VEGF, but not those of eNOSand EGLN1, were significantly higher in the lungs of high-altitude pigs than in those from pigs at a lower altitude ( P<0.05 ). These findings and a comprehensive analysis help elucidate the pulmonary mechanism of hypoxic adaptation in pigs.

Genomics of Adaptations in Ungulates

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