Whole-genome analysis reveals the hybrid formation of Chinese indigenous DHB pig following human migration

Construction of the porcine genome mobile element variations and investigation of its role in population diversity and gene expression

BACKGROUND

Mobile element variants (MEVs) have a significant and complex impact on genomic diversity and phenotypic traits. However, the quantity, distribution, and relationship with gene expression and complex traits of MEVs in the pig genome remain poorly understood.

RESULTS

We constructed the most comprehensive porcine MEV library based on high-depth whole genome sequencing (WGS) data from 747 pigs across 59 breeds worldwide. This database identified a total of 147,993 polymorphic MEVs, including 121,099 short interspersed nuclear elements (SINEs), 26,053 long interspersed nuclear elements (LINEs), 802 long terminal repeats (LTRs), and 39 other transposons, among which 54% are newly discovered. We found that MEVs are unevenly distributed across the genome and are strongly influenced by negative selection effects. Importantly, we identified 514, 530, and 584 candidate MEVs associated with population differentiation, domestication, and breed formation, respectively. For example, a significantly differentiated MEV is located in the ATRX intron between Asian and European pigs, whereas ATRX is also differentially expressed between Asian and European pigs in muscle tissue. In addition, we identified 4,169 expressed MEVs (eMEVs) significantly associated with gene expression and 6,914 splicing MEVs (sMEVs) associated with gene splicing based on RNA-seq data from 266 porcine liver tissues. These eMEVs and sMEVs explain 6.24% and 9.47%, respectively, of the observed cis-heritability and highlight the important role of MEVs in the regulation of gene expression. Finally, we provide a high-quality SNP-MEV reference haplotype panel to impute MEV genotypes from genome-wide SNPs. Notably, we identified a candidate MEV significantly associated with total teat number, demonstrating the functionality of this reference panel.

CONCLUSIONS

The present investigation demonstrated the importance of MEVs in pigs in terms of population diversity, gene expression and phenotypic traits, which may provide useful resources and theoretical support for pig genetics and breeding.

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.

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.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Whole Genome Screening Procures a Holistic Hold of the Russian Chicken Gene Pool Heritage and Demographic History

A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th-19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn (WL), were used along with other breeds representing the Russian gene pool. The characteristics of the genetic diversity and phylogenetic relationships of the native breeds of chickens were represented in comparison with foreign breeds. It was established that the studied native breeds demonstrate their own genetic structure that distinguishes them from foreign breeds, and from each other. For example, we previously made an assumption on what could cause the differences between two RW populations, RW1 and RW2. From the data obtained here, it was verified that WL was additionally crossed to RW2, unlike RW1. Thus, inherently, RW1 is a purer population of this improved Russian breed. A significant contribution of the gene pool of native breeds to the global genetic diversity of chickens was shown. In general, based on the results of a multilateral survey of this sample of breeds, it can be concluded that phylogenetic relationships based on their genetic structure and variability robustly reflect the known, previously postulated and newly discovered patterns of evolution of native chickens. The results herein presented will aid selection and breeding work using this gene pool.

Population Genetic Analysis of Six Chinese Indigenous Pig Meta-Populations Based on Geographically Isolated Regions

The diversification of indigenous pig breeds in China has resulted from multiple climate, topographic, and human cultural influences. The numerous indigenous pig breeds can be geographically divided into six meta-populations; however, their genetic relationships, contributions to genetic diversity, and genetic signatures remain unclear. Whole-genome SNP data for 613 indigenous pigs from the six Chinese meta-populations were obtained and analyzed. Population genetic analyses confirmed significant genetic differentiation and a moderate mixture among the Chinese indigenous pig meta-populations. The North China (NC) meta-population had the largest contribution to genetic and allelic diversity. Evidence from selective sweep signatures revealed that genes related to fat deposition and heat stress response (EPAS1, NFE2L2, VPS13A, SPRY1, PLA2G4A, and UBE3D) were potentially involved in adaptations to cold and heat. These findings from population genetic analyses provide a better understanding of indigenous pig characteristics in different environments and a theoretical basis for future work on the conservation and breeding of Chinese indigenous pigs.