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

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

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

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

Spatial distribution of anti-Toxoplasma gondii antibody-positive wild boars in Gifu Prefecture, Japan.

Toxoplasma gondii is a globally wide-spread parasite that infects almost all species of mammals and birds, including humans. We studied the spatial distribution of individual T. gondii-seropositive wild boar in Gifu Prefecture (10,621 km2), Japan. Altogether, 744 wild boars were captured at 663 points around human settlements in Gifu Prefecture. Serum samples were collected after recording the exact capture locations, along with each wild boar's body length and sex. We then used a commercial enzyme-linked immunosorbent assay kit for swine to measure anti-T. gondii antibodies in these animals. Among the 744 wild boars, 169 tested positive for T. gondii (22.7%). No significant difference in T. gondii seroprevalence was observed between the mountainous northern region with high winter snow cover and the mild-wintered geographical plain of the southern part of the prefecture. In contrast, 8 of the 11 wild boars that were captured in a public park surrounded by residential areas showed T. gondii seropositivity (72.7%), a value significantly higher than those of the wild boar populations in the other prefecture areas. This in-depth analysis, which spans the big city suburbs and rural areas of a whole prefecture, explains the seroprevalence of zoonotic T. gondii in wild boar and has public health implications.

Androgen-Dependent Differences in the Amounts of CYP mRNAs in the Pig Kidney.

We previously reported androgen-dependent sex and breed differences in the amounts of mRNAs of CYP isoforms in the pig liver. To clarify whether there are such sex and breed differences in the kidney, we examined the amounts of several CYP mRNAs in the kidney using both sexes of 5-month-old Landrace, Meishan and/or their crossbred F1 (LM and ML) pigs. Significant sex differences in the amounts of several CYP mRNAs were found: male < female for CYP2A19 and CYP3A29; and male > female for CYP4A24/25 in all the breeds. Sex differences in the amount of CYP2B22 mRNA (male < female) and in CYP2C33 and CYP2C49 mRNAs (male > female) were also observed in all the breeds except Landrace pigs. Furthermore, a significant sex difference (male < female) in CYP3A46 mRNA was only found in LM and ML pigs. No significant sex differences were found in either Landrace or Meishan pigs for CYP1A1, CYP1A2 and CYP4B1 mRNAs. The amounts of CYP2C33 and CYP4A24/25 mRNAs in males were higher in Meishan pigs than in Landrace pigs. Additional experiments using pigs treated by castration and/or testosterone propionate indicated that sex and breed differences in the amounts of those CYP mRNAs were, at least in part, dependent on the levels of serum testosterone. Furthermore, the effects of androgen on the amounts of CYP mRNAs in the kidney did not necessarily correlate with those in the liver, suggesting that there is a tissue-selective factor responsible for the androgen-related expression of CYP genes.

Clear phylogeographic pattern and genetic structure of wild boar Sus scrofa population in Central and Eastern Europe.

The wild boar Sus scrofa is one of the widely spread ungulate species in Europe, yet the origin and genetic structure of the population inhabiting Central and Eastern Europe are not well recognized. We analysed 101 newly obtained sequences of complete mtDNA genomes and 548 D-loop sequences of the species and combined them with previously published data. We identified five phylogenetic clades in Europe with clear phylogeographic pattern. Two of them occurred mainly in western and central part of the continent, while the range of the third clade covered North-Eastern, Central and South-Eastern Europe. The two other clades had rather restricted distribution. In Central Europe, we identified a contact zone of three mtDNA clades. Population genetic structure reflected clear phylogeographic pattern of wild boar in this part of Europe. The contribution of lineages originating from the southern (Dinaric-Balkan) and eastern (northern cost of the Black Sea) areas to the observed phylogeographic pattern of the species in Central and Eastern Europe was larger than those from the regions located in southern France, Iberian, and Italian Peninsulas. The present work was the first mitogenomic analysis conducted in Central and Eastern Europe to study genetic diversity and structure of wild boar population.

Origin of the pork tapeworm Taenia solium in Bali and Papua, Indonesia.

Global distributions of zoonotic pathogens have been strongly affected by the history of human dispersal and domestication of livestock. The pork tapeworm Taenia solium is distributed worldwide as the cause of neurocysticercosis, one of the most serious neglected tropical diseases. T. solium has been reported in Indonesia but only endemic to restricted areas such as Bali and Papua. Previous studies indicated the distinctiveness of a mitochondrial haplotype confirmed in Papua, but only one isolate has been examined to date. In this study, genetic characterization of T. solium and pigs in Bali and Papua was conducted to clarify the distributional history of the parasite. Mitochondrial haplotype network analysis clearly showed that Indonesian T. solium comprises a unique haplogroup which was the first to diverge among Asian genotypes, indicating its single origin and the fact that it was not introduced in the recent past from other area in Asia in which it is endemic. Although phylogenetic analysis based on the mitochondrial D-loop revealed multiple origins of pigs in Bali and Papua, the majority of pigs belonged to the Pacific Clade, which is widely dispersed throughout the Island Southeast Asia (ISEA) and Oceania due to Neolithic human dispersal. Given the results of our network analysis, it is likely that the Pacific Clade pigs played a key role in the dispersal of T. solium. The data suggest that T. solium was introduced from mainland Asia into Western Indonesia, including Bali, by modern humans in the late Pleistocene, or in the early to middle Holocene along with the Pacific Clade pigs. Introduction into New Guinea most likely occurred in the late Holocene through the spread of Pacific Clade pigs. Over time, T. solium has been eradicated from most of Indonesia through the middle to modern ages owing to religious and cultural practices.

A large-scale comparison of meat quality and intramuscular fatty acid composition among three Chinese indigenous pig breeds.

Derived from the long historical natural and artificial selection, Chinese indigenous pigs have formed their own special meat characteristics. We herein systematically evaluated 14 meat characteristics and 15 fatty acid composition traits on three Chinese local pig breeds. The experimental pigs were produced by crossing design covering all sire genealogy and most of dam genealogy in each of the three breeds' seed conservation farms. All animals were reared in the same standardized housing and feeding conditions. A Comparison study showed that most of the investigated meat quality traits present significant differences among Bamaxiang, Erhualian and Laiwu breeds. While Erhualian pigs outperformed pH traits, the Laiwu pigs showed extremely high intramuscular fat content, better meat color and lower drip loss (P < .05). The highest contents of total saturated fatty acids and total polyunsaturated fatty acids were found in Laiwu and Erhualian, respectively. These results will benefit the future breeding utilization of these genetic resources for worldwide swine meat quality improvement.

Performance and carcass, loin and ham quality in crossbreds from three terminal sire lines.

This study was designed to compare performance, carcass and meat quality of crossbred of a hybrid sow x three sire lines, i.e. stress positive Belgian Piétrain (BP), stress negative French Piétrain (FP) and Canadian Duroc (CD). BP offspring had a significantly higher carcass yield (p < .001) and lean meat content (p < .001) in comparison with FP, which was higher than CD. BP offspring had significantly lower pH (p < .05), water-holding capacity (WHC) (p < .001) and intramuscular fat (IMF) (p < .001) content in the loin compared to FP and CD, but these meat quality parameters, with the exception of pH, were superior for CD as compared to FP. In accordance with loin quality, pHi, pHu, WHC and IMF of BP were significantly lower (p < .05) compared to CD in the fresh and cooked ham. Most often, FP offspring could not be differentiated from the other offspring, with the exception of cooking loss of the cooked ham. Trained and consumer taste panels resulted in no significant differences (p > .1) in sensory attributes, however, consumers preffered CD based on ranking.

Transcriptome profiling of porcine testis tissue reveals genes related to sperm hyperactive motility.

BACKGROUND: Sperm hyperactive motility has previously been shown to influence litter size in pigs, but little is known about the underlying biological mechanisms. The aim of this study was to use RNA sequencing to investigate gene expression differences in testis tissue from Landrace and Duroc boars with high and low levels of sperm hyperactive motility. Boars with divergent phenotypes were selected based on their sperm hyperactivity values at the day of ejaculation (day 0) (contrasts (i) and (ii) for Landrace and Duroc, respectively) and on their change in hyperactivity between day 0 and after 96 h liquid storage at 18 °C (contrast (iii)). RESULTS: RNA sequencing was used to measure gene expression in testis. In Landrace boars, 3219 genes were differentially expressed for contrast (i), whereas 102 genes were differentially expressed for contrast (iii). Forty-one differentially expressed genes were identified in both contrasts, suggesting a functional role of these genes in hyperactivity regardless of storage. Zinc finger DNLZ was the most up-regulated gene in contrasts (i) and (iii), whereas the most significant differentially expressed gene for the two contrasts were ADP ribosylation factor ARFGAP1 and solute carrier SLC40A1, respectively. For Duroc (contrast (ii)), the clustering of boars based on their gene expression data did not reflect their difference in sperm hyperactivity phenotypes. No results were therefore obtained for this breed. A case-control analysis of variants identified in the Landrace RNA sequencing data showed that SNPs in NEU3, CHRDL2 and HMCN1 might be important for sperm hyperactivity. CONCLUSIONS: Differentially expressed genes were identified in Landrace boars with high and low levels of sperm hyperactivity at the day of ejaculate collection and high and low change in hyperactivity after 96 h of sperm storage. The results point towards important candidate genes, biochemical pathways and sequence variants underlying sperm hyperactivity in pigs.

Development of a 64 SNV panel for breed authentication in Iberian pigs and their derived meat products.

Spanish legislation regulates the labelling of Iberian pig meat and dry-cured products, which are labelled as "Ibérico" or "100% Ibérico" when they come from Duroc x Iberian crossbred or Iberian purebred pigs. Although the analytical authentication of breed origin is not mandatory, a genetic diagnostic tool is demanded by producers and consumers. We have designed a 64 Single Nucleotide Variant genotyping panel displaying extreme allelic frequencies between Duroc and Iberian purebred samples. Average proportions of Iberian alleles of 0.99, 0.01, 0.77 and 0.48 were estimated by admixture clustering analysis of known origin samples, for Iberian and Duroc purebred, 75% Iberian and 50% Iberian classes, respectively. A supervised analysis with 1419 samples showed some overlapping between contiguous classes, but the calculated degrees of separability ranged from 0.800 to 0.996, exceeding the threshold value (0.70) for considering suitable for prediction. Therefore, this panel is a useful genetic tool to infer purebred or crossbred Iberian origin of live animals, meat and dry-cured products.

DNA methylation patterns vary in boar sperm cells with different levels of DNA fragmentation.

BACKGROUND: Sperm DNA integrity is considered essential for successful transmission of the paternal genome, fertilization and normal embryo development. DNA fragmentation index (DFI, %) has become a key parameter in the swine artificial insemination industry to assess sperm DNA integrity. Recently, in some elite Norwegian Landrace boars (boars with excellent field fertility records), a higher level of sperm DFI has been observed. In order to obtain a better understanding of this, and to study the complexity of sperm DNA integrity, liquid preserved semen samples from elite boars with contrasting DFI levels were examined for protamine deficiency, thiol profile and disulphide bonds. Additionally, the DNA methylation profiles of the samples were determined by reduced representation bisulphite sequencing (RRBS). RESULTS: In this study, different traits related to sperm DNA integrity were investigated (n = 18 ejaculates). Upon liquid storage, the levels of total thiols and disulphide bonds decreased significantly, while the DFI and protamine deficiency level increased significantly. The RRBS results revealed similar global patterns of low methylation from semen samples with different levels of DFI (low, medium and high). Differential methylation analyses indicated that the number of differentially methylated cytosines (DMCs) increased in the low-high compared to the low-medium and the medium-high DFI groups. Annotating the DMCs with gene and CpG features revealed clear differences between DFI groups. In addition, the number of annotated transcription starting sites (TSS) and associated pathways in the low-high comparison was greater than the other two groups. Pathway analysis showed that genes (based on the closest TSS to DMCs) corresponding to low-high DFI comparison were associated with important processes such as membrane function, metabolic cascade and antioxidant defence system. CONCLUSION: To our knowledge, this is the first study evaluating DNA methylation in boar sperm cells with different levels of DFI. The present study shows that sperm cells with varying levels of DNA fragmentation exhibit similar global methylation, but different site-specific DNA methylation signatures. Moreover, with increasing DNA fragmentation in spermatozoa, there is an increase in the number of potentially affected downstream genes and their respective regulatory pathways.

Analysis and comparison of long non-coding RNAs expressed in the ovaries of Meishan and Yorkshire pigs.

LncRNAs comprise a vast majority of the RNAs transcribed from non-coding regions of mammalian genomes. Recently, lncRNAs have emerged as key regulators of a wide range of biological processes. In this study, we identified lncRNAs expressed in swine ovary tissue from Yorkshire and Meishan pigs. We obtained 3827 lncRNAs expressed from 4973 transcripts in swine ovary tissue, of which 510 were ovary specific, 192 were differentially expressed between Yorkshire and Meishan pigs and 38 were both ovary specific and differentially expressed. Furthermore, we randomly selected several differentially expressed and ovary-specific lncRNAs for verification by qRT-PCR and RT-PCR respectively. We also predicted the functions of the lncRNAs by analysing their nearest neighbouring protein-coding genes. Together, our results identify a series of ovary-associated lncRNAs for further experimental investigation of the functions of these genes in ovary development or for selection of candidate genes for breeding.

Comparison of microRNAs in adipose and muscle tissue from seven indigenous Chinese breeds and Yorkshire pigs.

Elucidation of the pig microRNAome is essential for interpreting functional elements of the genome and understanding the genetic architecture of complex traits. Here, we extracted small RNAs from skeletal muscle and adipose tissue, and we compared their expression levels between one Western breed (Yorkshire) and seven indigenous Chinese breeds. We detected the expression of 172 known porcine microRNAs (miRNAs) and 181 novel miRNAs. Differential expression analysis found 92 and 12 differentially expressed miRNAs in adipose and muscle tissue respectively. We found that different Chinese breeds shared common directional miRNA expression changes compared to Yorkshire pigs. Some miRNAs differentially expressed across multiple Chinese breeds, including ssc-miR-129-5p, ssc-miR-30 and ssc-miR-150, are involved in adipose tissue function. Functional enrichment analysis revealed that the target genes of the differentially expressed miRNAs are associated mainly with signaling pathways rather than metabolic and biosynthetic processes. The miRNA-target gene and miRNA-phenotypic traits networks identified many hub miRNAs that regulate a large number of target genes or phenotypic traits. Specifically, we found that intramuscular fat content is regulated by the greatest number of miRNAs in muscle tissue. This study provides valuable new candidate miRNAs that will aid in the improvement of meat quality and production.

Improving genomic prediction for two Yorkshire populations with a limited size using the single-step method.

In this study, we conducted genomic prediction for two Yorkshire purebred populations (Yichun and Chifeng) from two different provinces of China that both had a limited population size. Two growth traits (age adjusted to 100 kg weight, AGE; back-fat thickness adjusted to 100 kg weight, BF) and one reproduction trait (total number of piglets born, TNB) were analyzed with four prediction strategies: one-population BLUP, joint two-population BLUP, one-population single-step BLUP (SSBLUP) and joint two-population SSBLUP. Our results illustrate that accuracies of genomic estimated breeding values were improved for BF and TNB for the Yichun population and for BF for the Chifeng population by genomic prediction (one-population SSBLUP and joint two-population SSBLUP). The accuracy of TNB for the Yichun population was increased two fold when comparing the one-population SSBLUP to the one-population BLUP prediction. Meanwhile, prediction biases were dramatically reduced for AGE for the Yichun population and for TNB for the Chifeng population. The conclusions of this study are as follows: first, genomic prediction is useful for improving prediction accuracy for purebred pig breeding farms with a limited population size; second, joint genomic prediction for different populations of the same breed with certain genetic links has the trend to further improve prediction accuracy.

Genomic analysis on pygmy hog reveals extensive interbreeding during wild boar expansion.

Wild boar (Sus scrofa) drastically colonized mainland Eurasia and North Africa, most likely from East Asia during the Plio-Pleistocene (2-1Mya). In recent studies, based on genome-wide information, it was hypothesized that wild boar did not replace the species it encountered, but instead exchanged genetic materials with them through admixture. The highly endangered pygmy hog (Porcula salvania) is the only suid species in mainland Eurasia known to have outlived this expansion, and therefore provides a unique opportunity to test this hybridization hypothesis. Analyses of pygmy hog genomes indicate that despite large phylogenetic divergence (~2 My), wild boar and pygmy hog did indeed interbreed as the former expanded across Eurasia. In addition, we also assess the taxonomic placement of the donor of another introgression, pertaining to a now-extinct species with a deep phylogenetic placement in the Suidae tree. Altogether, our analyses indicate that the rapid spread of wild boar was facilitated by inter-specific/inter-generic admixtures.

Genome-wide identification and comparison of mRNAs, lncRNAs and circRNAs in porcine intramuscular, subcutaneous, retroperitoneal and mesenteric adipose tissues.

Many types of RNAs, including messenger RNAs (mRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs), play crucial roles in regulating fat cell differentiation and tissue development. However, the expression profiles of these RNAs in different adipose tissues are still largely unknown. To shed light on this issue, we performed a transcriptome analysis of mRNAs, lncRNAs and circRNAs obtained from intramuscular adipose tissue, subcutaneous adipose tissue, retroperitoneal adipose tissue and mesenteric adipose tissue of Chinese Erhualian pigs. A number of differentially expressed mRNAs, lncRNAs and circRNAs were identified among the four adipose tissues. Tissue-specific analysis indicated that circRNAs exhibited the highest tissue specificity among mRNAs, lncRNAs and circRNAs, whereas intramuscular adipose tissue had the most tissue-specific genes among the four adipose tissues. Gene Ontology analysis showed that differentially expressed mRNAs among groups were involved mainly in lipid metabolism and immune inflammatory response processes. Furthermore, the co-expression network construction of mRNAs-lncRNAs revealed that several important lncRNAs, such as MSTRG.426159 and MSTRG.604206, might associate with lipid metabolic process. Taken together, these data provide a genome-wide resource of mRNAs, lncRNAs and circRNAs potentially involved in porcine fat metabolism, thus improving understanding of their function in diverse adipose tissues.

Three-dimensional tooth surface texture analysis on stall-fed and wild boars (Sus scrofa).

Categorizing the archaeological remains of Sus scrofa as domesticated "pigs" or wild "boars" is often difficult because of their morphological and genetic similarities. For this purpose, we tested whether feeding ecological change of S. scrofa that accompanied their domestication can be detected based on the three-dimensional texture created on the tooth enamel surface by mastication. We scanned the lower tooth surface of one wild and one stall-fed populations of modern S. s. leucomystax and one wild population of S. s. riukiuanus by using a confocal laser microscope. The average body weight of S. s. leucomystax is twice as heavier as that of S. s. riukiuanus. The textures were quantified using the industrial "roughness" standard, ISO 25178, to prevent inter-observer errors and to distinguish small differences that were difficult to detect by two dimensional image observation. The values of parameters related to height and volume were significantly larger in the stall-fed population. Twenty parameters differed significantly between the stall-fed and wild population of S. s. leucomystax, which indicated that the feeding ecological difference affected the ISO parameters of the two boar populations. Six parameters also differed between the wild populations of S. s. leucomystax and S. s. riukiuanus. Surprisingly, no parameter differed between the populations of stall-fed S. s. leucomystax and wild S. s. riukiuanus. Consumption of hard nuts and/or agricultural fruits and crops by the wild population of S. s. riukiuanus may have produced a tooth surface texture similar to that of the stall-fed population of S. s. leucomystax. Further analysis of S. s. riukiuanus with a known diet is necessary to conclude whether ISO parameters reflect the dietary transition accompanying the domestication of Sus (e.g., wild, semi-domestic, and domestic). Until then, caution is needed in discriminating domesticated populations from wild populations that mainly feed on hard objects.

Linkage disequilibrium pattern and genome-wide association mapping for meat traits in multiple porcine F2 crosses.

In the present study, data from four F2 crosses were analysed and used to study the linkage disequilibrium (LD) structure within and across the crosses. Genome-wide association analyses (GWASes) for conductivity and dressing out meat traits were conducted using single-marker and Bayesian multi-marker models using the pooled data from all F2 crosses. Porcine F2 crosses generated from the distantly related founder breeds Wild Boar, Piétrain and Meishan, as well as from a porcine F2 cross from the closely related founder breed Piétrain and an F1 Large White × Landrace cross were pooled. A total of 2572 F2 animals were genotyped using a 62K SNP chip. The positions of the SNPs were based on genome assembly Sscrofa11.1. After post-alignment and genotype filtering, approximately 50K SNPs were usable for LD studies and GWASes. The main findings of the present study are that the breakdown of LD was faster in crosses from closely related founder breeds compared to crosses from distantly related founders. The fastest breakdown of LD was observed by pooling the data. Based on the single-marker results and LD structure, clusters and windows were built for 1-Mb intervals. For conductivity and dressing out, 183 and 191 nominal significant associations respectively and six and five clusters respectively were found. Dominance was important for conductivity, and considering dominance in GWASes improved the mapping signals. Most clear signals were found for conductivity on SSC6, 8 and 15 and for dressing out on SSC2 and 7. Considering dominance might contribute to the accuracy of genomic selection and serve as a guide for choosing mating pairs with good combining abilities. However, further research is needed to investigate if dominance is also important in crossbreed pig breeding schemes.

Genetic relationships among Vietnamese local pigs investigated using genome-wide SNP markers.

Vietnam is one of the most important countries for pig domestication, and a total of 26 local breeds have been reported. In the present study, genetic relationships among the various pig breeds were investigated using 90 samples collected from local pigs (15 breeds) in 15 distantly separated, distinct areas of the country and six samples from Landrace pigs in Hanoi as an out-group of a common Western breed. All samples were genotyped using the Illumina Porcine SNP60 v2 Genotyping BeadChip. We used 15 160-15 217 SNPs that showed a high degree of polymorphism in the Vietnamese breeds for identifying genetic relationships among the Vietnamese breeds. Principal components analysis showed that most pigs indigenous to Vietnam formed clusters correlated with their original geographic locations. Some Vietnamese breeds formed a cluster that was genetically related to the Western breed Landrace, suggesting the possibility of crossbreeding. These findings will be useful for the conservation and management of Vietnamese local pig breeds.

The genetic diversity and population structures of indigenous pig breeds in Zhejiang Province revealed by GGRS sequencing.

Chinese indigenous pigs in Zhejiang Province are well known for their high fecundity. In order to verify breed subdivision at the genomic level, we investigated genetic diversity and population structure of seven breeds and made comparisons with three Western pig breeds using next-generation sequencing data. Parameters obtained from allelic richness and proportion of polymorphic markers indicated that the genetic diversity of the Chinese indigenous pigs was higher than that of the Western pigs, with the highest and lowest values found in the Chaluand and the Landrace pigs respectively. Both neighbor-joining tree and principal components analysis could distinguish breeds from one another and structure analysis showed less differentiation among Western pigs than among the Chinese pigs. The average linkage disequilibrium decay over distance was significantly less in the Chinese pigs compared with the Western pigs, ranging from 188.2 to 280.6 kb for the Chinese pigs and 680.3 to 752.8 kb for the Western breeds and showing an average r2 threshold value of 0.3. Results obtained from high-density SNP comparison over the whole genome on genetic diversity and population structure were in agreement with the current breed classification of the pigs in Zhejiang Province. More importantly, the results presented here advances our current understanding of the genomic biology of Chinese indigenous pigs in Zhejiang Province and allows for implementation of conservation strategies in additional breeds.