利用高密度SNP检测不同猪品种间X染色体选择信号

在家猪的培育过程中,许多重要的经济性状受到过高强度的人工选择,高密度SNP标记为通过选择信号检测追踪这些性状经历的选择提供了可能,并能根据选择信号利用生物信息学寻找到与选择相关的基因。X染色体由于其特殊性,在传统的遗传分析中许多针对常染色体的方法往往不适用,需要采取特殊的方法,选择信号检测可以作为一种行之有效的方法对X染色体进行分析。文章利用长白、松辽黑猪和大白3个猪品种,通过品种间选择信号检测方法 XP-EHH,利用高密度SNP标记对X染色体进行选择信号检测,并通过生物信息学分析寻找选择信号区域内重要基因。在长白、松辽黑猪和大白3个品种中分别检测出29、13和15个选择信号区域,每个选择信号区域平均包含3.59、4.92、4.07个SNPs,长白和松辽黑猪、长白和大白有部分重叠选择信号区域,大白和松辽黑猪没有发现重叠选择信号区域。生物信息学分析发现各品种选择信号区域内有与繁殖、免疫等性状相关基因,其中部分在猪中尚未见报道,可作为研究猪相关性状的重要候选基因。     

Identification of Selection Footprints on the X Chromosome in Pig

Identifying footprints of selection can provide a straightforward insight into the mechanism of artificial selection and further dig out the causal genes related to important traits. In this study, three between-population and two within-population approaches, the Cross Population Extend Haplotype Homozygosity Test (XPEHH), the Cross Population Composite Likelihood Ratio (XPCLR), the F-statistics (Fst), the Integrated Haplotype Score (iHS) and the Tajima''s D, were implemented to detect the selection footprints on the X chromosome in three pig breeds using Illumina Porcine60K SNP chip. In the detection of selection footprints using between-population methods, 11, 11 and 7 potential selection regions with length of 15.62 Mb, 12.32 Mb and 9.38 Mb were identified in Landrace, Chinese Songliao and Yorkshire by XPEHH, respectively, and 16, 13 and 17 potential selection regions with length of 15.20 Mb, 13.00 Mb and 19.21 Mb by XPCLR, 4, 2 and 4 potential selection regions with length of 3.20 Mb, 1.60 Mb and 3.20 Mb by Fst. For within-population methods, 7, 10 and 9 potential selection regions with length of 8.12 Mb, 8.40 Mb and 9.99 Mb were identified in Landrace, Chinese Songliao and Yorkshire by iHS, and 4, 3 and 2 potential selection regions with length of 3.20 Mb, 2.40 Mb and 1.60 Mb by Tajima''s D. Moreover, the selection regions from different methods were partly overlapped, especially the regions around 22 ∼25 Mb were detected under selection in Landrace and Yorkshire while no selection in Chinese Songliao by all three between-population methods. Only quite few overlap of selection regions identified by between-population and within-population methods were found. Bioinformatics analysis showed that the genes relevant with meat quality, reproduction and immune were found in potential selection regions. In addition, three out of five significant SNPs associated with hematological traits reported in our genome-wide association study were harbored in potential selection regions.     

A genome‐wide scan for selection signatures in Yorkshire and Landrace pigs based on sequencing data

Pigs have experienced dramatic selection due to domestication, which has led to many different phenotypes when compared to their wild counterparts, especially in the last several decades. Currently, genome‐wide scans in both cattle and humans showing positive selection footprints have been investigated. However, few studies have focused on porcine selection footprints, particularly on a genome‐wide scale. Surveying for selection footprints across porcine genomes can be quite valuable for revealing the genetic mechanisms of phenotypic diversity. Here, we employed a medium sequencing depth (5–20x/site per individual, on average) approach called genotyping by genome reducing and sequencing (GGRS) to detect genome‐wide selection signatures of two domestic pig breeds (Yorkshire and Landrace) that have been under intensive selection for traits of muscle development, growth and behavior. The relative extended haplotype homozygosity test, which identifies selection signatures by measuring the characteristics of haplotypes’ frequency distribution within a single population, was also applied to identify potential positively selected regions. As a result, signatures of positive selection were found in each breed. However, most selection signatures were population specific and related to genomic regions containing genes for biological categories including brain development, metabolism, growth and olfaction. Furthermore, the result of the gene set enrichment analysis indicated that selected regions of the two breeds presented a different over‐representation of genes in the Gene Ontology annotations and Kyoto Encyclopedia of Genes and Genomes pathways. Our results revealed a genome‐wide map of selection footprints in pigs and may help us better understand the mechanisms of selection in pig breeding.     

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

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

Detection of selection signatures in dairy and beef cattle using high-density genomic information

Background

Artificial selection for economically important traits in cattle is expected to have left distinctive selection signatures on the genome. Access to high-density genotypes facilitates the accurate identification of genomic regions that have undergone positive selection. These findings help to better elucidate the mechanisms of selection and to identify candidate genes of interest to breeding programs.

Results

Information on 705 243 autosomal single nucleotide polymorphisms (SNPs) in 3122 dairy and beef male animals from seven cattle breeds (Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental) were used to detect selection signatures by applying two complementary methods, integrated haplotype score (iHS) and global fixation index (F_ST). To control for false positive results, we used false discovery rate (FDR) adjustment to calculate adjusted iHS within each breed and the genome-wide significance level was about 0.003. Using the iHS method, 83, 92, 91, 101, 85, 101 and 86 significant genomic regions were detected for Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental cattle, respectively. None of these regions was common to all seven breeds. Using the F_ST approach, 704 individual SNPs were detected across breeds. Annotation of the regions of the genome that showed selection signatures revealed several interesting candidate genes i.e. DGAT1, ABCG2, MSTN, CAPN3, FABP3, CHCHD7, PLAG1, JAZF1, PRKG2, ACTC1, TBC1D1, GHR, BMP2, TSG1, LYN, KIT and MC1R that play a role in milk production, reproduction, body size, muscle formation or coat color. Fifty-seven common candidate genes were found by both the iHS and global F_ST methods across the seven breeds. Moreover, many novel genomic regions and genes were detected within the regions that showed selection signatures; for some candidate genes, signatures of positive selection exist in the human genome. Multilevel bioinformatic analyses of the detected candidate genes suggested that the PPAR pathway may have been subjected to positive selection.

Conclusions

This study provides a high-resolution bovine genomic map of positive selection signatures that are either specific to one breed or common to a subset of the seven breeds analyzed. Our results will contribute to the detection of functional candidate genes that have undergone positive selection in future studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0127-3) contains supplementary material, which is available to authorized users.     

Footprints of recent selection and variability in breed composition in the Göttingen Minipig genome

The Göttingen Minipig (GMP) developed at the University of Göttingen is a synthetic breed that is widely used in medical research and toxicology. It combines the high fertility of the Vietnamese potbellied pig, the low body weight of the Minnesota Minipig and the white coat colour of the German Landrace pig. The aim of this study was to find genomic regions that may have undergone selection since the creation of the breed in the 1960s. Therefore, the whole genome was screened for footprints of recent selection based on single nucleotide polymorphism (SNP) genotypes from the Illumina Porcine SNP60 BeadChip using two methods: the extended haplotype homozygosity (EHH) test and the estimation of the genomic proportion of the three original breeds at each SNP using a Bayesian approach. Local deviations from the average genome‐wide breed composition were tested with a permutation‐based empirical test. Results for a comprehensive whole‐genome scan for both methods are presented. Several regions showing the highest P‐values in the EHH test are related to breeding goals relevant in the GMP, such as growth (SOCS2, TXN, DDR2 and GRB10 genes) and white colour (PRLR gene). Additionally, the calculated proportion of the founder breeds diverged significantly in many regions from the pedigree‐based expectations and the genome average. The results provide a genome‐wide map of selection signatures in the GMP, which leads to a better understanding of selection that took place over the last decades in GMP breed development.     

Evaluation of the porcine melanocortin 4 receptor (MC4R) gene as a positional candidate for a fatness QTL in a cross between Landrace and Hampshire

Melanocortin 4 receptor (MC4R) is expressed in the appetite-regulating areas of the brain where it is central in the regulation of feed intake and energy balance. A mutation in MC4R causing an Asp298Asn substitution has been associated with fatness, high daily gain and feed intake in the pig. In a previously performed genome scan based on a Hampshire x Landrace cross, we detected one quantitative trait loci (QTL) affecting carcass fat/meat ratio and one QTL affecting the biceps femoris muscle, both close to the position of MC4R on porcine chromosome 1. In this study, the two lines were found to be close to fixation for alternative alleles of the Asp298Asn polymorphism. Additional QTL analyses supported our hypothesis of MC4R as a positional candidate gene but only for the fat/meat QTL. The Asp298Asn polymorphism was also evaluated as a selection target for daily gain in a Danish pig breeding population that included four breeds (Hampshire, Duroc, Landrace and Yorkshire). Over a 12-year period (1990-2002), a significant increase in the allele frequency of 298Asn was found in Landrace and Duroc, whereas a non-significant decrease in the 298Asn allele frequency was observed in Yorkshire. The Hampshire breed was fixed for the 298Asn allele in 1990. The high 298Asn allele frequencies in Hampshire, Landrace and Duroc are most likely due to selection for daily gain, whereas selection for daily gain in the Yorkshire breed apparently focuses on other loci.     

Discovery of selection-driven genetic differences of Duroc,Landrace, and Yorkshire pig breeds by EigenGWAS and Fst analyses

Pigs are one of the earliest domesticated animals and multiple breeds have been developed to meet the various demands of consumers. EigenGWAS is a novel strategy to identify candidate genes that underlying population genetic differences and to infer candidate regions under selection as well. In this study, EigenGWAS and F_st analyses were performed using the public re-sequencing data of three typical commercial pig breeds, Duroc, Landrace and Yorkshire. The intersection of genome-wide significant SNPs detected by EigenGWAS and top-ranked 1% SNPs of F_st results were treated as signals under selection. Using the data of all three breeds, 3062 signals under selection were detected and the nearby genomic regions within 300 kb upstream and downstream covered 6.54% of whole genome. Pairs of breeds were analysed along with the pathway analysis. The gene function enrichment results indicated that many candidate genes located in the genomic regions of the signals under selection were associated with biological processes related to growth, metabolism, reproduction, sensory perception, etc. Among the candidate genes, the FSHB, AHR, PTHLH, KDR and FST genes were reported to be associated with reproductive performance; the KIT, KITLG, MITF, MC1R and EDNRB genes were previously identified to affect coat colour; the RETREG1, TXNIP, BMP5, PPARD and RBP4 genes were reported to be associated with lipid metabolism and growth traits. The identified genetic differences across the three commercial breeds will advance understanding of the artificial selection history of pigs and the signals under selection will suggest potential uses in pig genomic breeding programmes.     

A genome-wide scan for signatures of directional selection in domesticated pigs

Background

Animal domestication involved drastic phenotypic changes driven by strong artificial selection and also resulted in new populations of breeds, established by humans. This study aims to identify genes that show evidence of recent artificial selection during pig domestication.

Results

Whole-genome resequencing of 30 individual pigs from domesticated breeds, Landrace and Yorkshire, and 10 Asian wild boars at ~16-fold coverage was performed resulting in over 4.3 million SNPs for 19,990 genes. We constructed a comprehensive genome map of directional selection by detecting selective sweeps using an F_ST-based approach that detects directional selection in lineages leading to the domesticated breeds and using a haplotype-based test that detects ongoing selective sweeps within the breeds. We show that candidate genes under selection are significantly enriched for loci implicated in quantitative traits important to pig reproduction and production. The candidate gene with the strongest signals of directional selection belongs to group III of the metabolomics glutamate receptors, known to affect brain functions associated with eating behavior, suggesting that loci under strong selection include loci involved in behaviorial traits in domesticated pigs including tameness.

Conclusions

We show that a significant proportion of selection signatures coincide with loci that were previously inferred to affect phenotypic variation in pigs. We further identify functional enrichment related to behavior, such as signal transduction and neuronal activities, for those targets of selection during domestication in pigs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1330-x) contains supplementary material, which is available to authorized users.     

Classic Selective Sweeps Revealed by Massive Sequencing in Cattle

Human driven selection during domestication and subsequent breed formation has likely left detectable signatures within the genome of modern cattle. The elucidation of these signatures of selection is of interest from the perspective of evolutionary biology, and for identifying domestication-related genes that ultimately may help to further genetically improve this economically important animal. To this end, we employed a panel of more than 15 million autosomal SNPs identified from re-sequencing of 43 Fleckvieh animals. We mainly applied two somewhat complementary statistics, the integrated Haplotype Homozygosity Score (iHS) reflecting primarily ongoing selection, and the Composite of Likelihood Ratio (CLR) having the most power to detect completed selection after fixation of the advantageous allele. We find 106 candidate selection regions, many of which are harboring genes related to phenotypes relevant in domestication, such as coat coloring pattern, neurobehavioral functioning and sensory perception including KIT, MITF, MC1R, NRG4, Erbb4, TMEM132D and TAS2R16, among others. To further investigate the relationship between genes with signatures of selection and genes identified in QTL mapping studies, we use a sample of 3062 animals to perform four genome-wide association analyses using appearance traits, body size and somatic cell count. We show that regions associated with coat coloring significantly (P<0.0001) overlap with the candidate selection regions, suggesting that the selection signals we identify are associated with traits known to be affected by selection during domestication. Results also provide further evidence regarding the complexity of the genetics underlying coat coloring in cattle. This study illustrates the potential of population genetic approaches for identifying genomic regions affecting domestication-related phenotypes and further helps to identify specific regions targeted by selection during speciation, domestication and breed formation of cattle. We also show that Linkage Disequilibrium (LD) decays in cattle at a much faster rate than previously thought.     

Signatures of Diversifying Selection in European Pig Breeds

Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, body size, reproduction, and behaviour. To better understand the relationship between genomic composition and phenotypic diversity arising from breed development, the genomes of 13 traditional and commercial European pig breeds were scanned for signatures of diversifying selection using the Porcine60K SNP chip, applying a between-population (differentiation) approach. Signatures of diversifying selection between breeds were found in genomic regions associated with traits related to breed standard criteria, such as coat colour and ear morphology. Amino acid differences in the EDNRB gene appear to be associated with one of these signatures, and variation in the KITLG gene may be associated with another. Other selection signals were found in genomic regions including QTLs and genes associated with production traits such as reproduction, growth, and fat deposition. Some selection signatures were associated with regions showing evidence of introgression from Asian breeds. When the European breeds were compared with wild boar, genomic regions with high levels of differentiation harboured genes related to bone formation, growth, and fat deposition.     

Enhancing Genome-Wide Copy Number Variation Identification by High Density Array CGH Using Diverse Resources of Pig Breeds

Copy number variations (CNVs) are important forms of genomic variation, and have attracted extensive attentions in humans as well as domestic animals. In the study, using a custom-designed 2.1 M array comparative genomic hybridization (aCGH), genome-wide CNVs were identified among 12 individuals from diverse pig breeds, including one Asian wild population, six Chinese indigenous breeds and two modern commercial breeds (Yorkshire and Landrace), with one individual of the other modern commercial breed, Duroc, as the reference. A total of 1,344 CNV regions (CNVRs) were identified, covering 47.79 Mb (∼1.70%) of the pig genome. The length of these CNVRs ranged from 3.37 Kb to 1,319.0 Kb with a mean of 35.56 Kb and a median of 11.11 Kb. Compared with similar studies reported, most of the CNVRs (74.18%) were firstly identified in present study. In order to confirm these CNVRs, 21 CNVRs were randomly chosen to be validated by quantitative real time PCR (qPCR) and a high rate (85.71%) of confirmation was obtained. Functional annotation of CNVRs suggested that the identified CNVRs have important function, and may play an important role in phenotypic and production traits difference among various breeds. Our results are essential complementary to the CNV map in the pig genome, which will provide abundant genetic markers to investigate association studies between various phenotypes and CNVs in pigs.     

Detection of signatures of selective sweeps in the Blonde d'Aquitaine cattle breed

Identifying recent positive selection signatures in domesticated animals could provide information on genome response to strong directional selection from domestication and artificial selection and therefore could help in identifying mutations responsible for improved traits. We used genotyping data generated using Illumina's BovineSNP50 Genotyping BeadChips to identify selection signatures in the Blonde d'Aquitaine breed, a well‐muscled French beef breed. For this purpose, we employed a hidden Markov model‐based test, which detects selection by studying local variations in the allele frequency spectrum along the genome, within a single population. Three regions containing selective sweeps were identified. Annotation of genes located within these regions revealed interesting candidate genes. For example, myostatin (also known as GDF8), a known muscle growth factor inhibitor, is located within the selection signature region found on chromosome 2. In addition, we have identified chromosomal regions that show some evidence of selection within QTL regions for economically important traits. The results of this study could help to better understand the mechanisms related to the selection of the Blonde d'Aquitaine breed.     

Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA

Background

Artificial selection has caused rapid evolution in domesticated species. The identification of selection footprints across domesticated genomes can contribute to uncover the genetic basis of phenotypic diversity.

Methodology/Main Findings

Genome wide footprints of pig domestication and selection were identified using massive parallel sequencing of pooled reduced representation libraries (RRL) representing ∼2% of the genome from wild boar and four domestic pig breeds (Large White, Landrace, Duroc and Pietrain) which have been under strong selection for muscle development, growth, behavior and coat color. Using specifically developed statistical methods that account for DNA pooling, low mean sequencing depth, and sequencing errors, we provide genome-wide estimates of nucleotide diversity and genetic differentiation in pig. Widespread signals suggestive of positive and balancing selection were found and the strongest signals were observed in Pietrain, one of the breeds most intensively selected for muscle development. Most signals were population-specific but affected genomic regions which harbored genes for common biological categories including coat color, brain development, muscle development, growth, metabolism, olfaction and immunity. Genetic differentiation in regions harboring genes related to muscle development and growth was higher between breeds than between a given breed and the wild boar.

Conclusions/Significance

These results, suggest that although domesticated breeds have experienced similar selective pressures, selection has acted upon different genes. This might reflect the multiple domestication events of European breeds or could be the result of subsequent introgression of Asian alleles. Overall, it was estimated that approximately 7% of the porcine genome has been affected by selection events. This study illustrates that the massive parallel sequencing of genomic pools is a cost-effective approach to identify footprints of selection.     

大白猪和通城猪全基因组选择性清扫分析

长期的人工选择使猪的生产性能得到显著提高,与选择相关的基因组区域也随之发生特定遗传变异表征(选择信号)。不同类型品种所受到选择强度不一,选择信号亦不相同,选择性清扫分析已逐渐成为选择信号的主要检测手段。文章基于商用型大白猪(n=45)和地方猪品种通城猪(n=45)的猪60K SNP芯片分型数据,借助遗传分化系数Fst法进行选择信号检测分析。利用gPLINK软件设定质控标准,共计34 304个SNPs被筛选出用于统计分析。使用Genepop软件包计算两个猪品种之间的遗传分化参数Fst,所得Fst平均值为0.3209。选取Fst>0.7036(即占总Fst值数目的 1%),共计344个SNPs被选择出来。SNP位置注释显示这些位点涉及到79个候选基因(Sus scrofa Build 9)。利用在线软件Ingenuity Pathway Analysis对候选基因的生物学通路进行网络分析,发现它们多与生长繁殖及免疫应答有关,如NCOA6、ERBB4、RUNX2和APOB等基因。研究结果为进行猪产肉、抗病等性状候选基因和致因突变深入挖掘提供了有益参考。     

Differential expression analysis of porcine MDH1, MDH2 and ME1 genes in adipose tissues

Malate dehydrogenases 1 and 2 (MDH1 and MDH2), and malic enzyme 1 (ME1) play important roles in the Krebs cycle for energy metabolism. The mRNA abundance changes of MDH1, MDH2 and ME1 genes were measured across six different adipose tissues from the leaner Landrace and fatty Rongchang pig breeds using quantitative real-time PCR. The mRNA of MDH1, MDH2 and ME1 was more abundant in fatty Rongchang pigs than in leaner Landrace pigs. In both breeds, females exhibited higher adipocyte volume and mRNA abundance of MDH1, MDH2 and ME1 compared with males. These values were higher in the subcutaneous adipose tissue compared with visceral adipose tissue. Furthermore, mRNA abundance changes of MDH1, MDH2 and ME1 have the remarked significant positive correlation with adipocyte volume across the six adipose tissue types. We conclude that there are breed-, gender- and tissue-specific expression patterns of ME1, MDH1 and MDH2, which highlight their potential as candidate genes for selecting for fat volume in pigs.     

Signatures of selection in five Italian cattle breeds detected by a 54K SNP panel

In this study we used a medium density panel of SNP markers to perform population genetic analysis in five Italian cattle breeds. The BovineSNP50 BeadChip was used to genotype a total of 2,935 bulls of Piedmontese, Marchigiana, Italian Holstein, Italian Brown and Italian Pezzata Rossa breeds. To determine a genome-wide pattern of positive selection we mapped the F _st values against genome location. The highest F _st peaks were obtained on BTA6 and BTA13 where some candidate genes are located. We identified selection signatures peculiar of each breed which suggest selection for genes involved in milk or meat traits. The genetic structure was investigated by using a multidimensional scaling of the genetic distance matrix and a Bayesian approach implemented in the STRUCTURE software. The genotyping data showed a clear partitioning of the cattle genetic diversity into distinct breeds if a number of clusters equal to the number of populations were given. Assuming a lower number of clusters beef breeds group together. Both methods showed all five breeds separated in well defined clusters and the Bayesian approach assigned individuals to the breed of origin. The work is of interest not only because it enriches the knowledge on the process of evolution but also because the results generated could have implications for selective breeding programs.     

SNP genotypes reveal breed substructure,selection signatures and highly inbred regions in Piétrain pigs

The Piétrain pig originates from the Belgian village Piétrain some time between 1920 and 1950. Owing to its superior conformation, the Piétrain has spread worldwide since the 1960s. As initial population sizes were limited and close inbreeding was commonplace, the breed’s genetic diversity has been questioned. Therefore, this study examines Piétrain breed substructure, diversity and selection signatures using SNP data in comparison with Duroc, Landrace and Large White populations. Principal component analysis indicated three subpopulations, and F_ST analysis showed that US Piétrains differ most from European Piétrains. Average inbreeding based on runs of homozygosity (ROH) segments larger than 4 Mb ranged between 16.7 and 20.9%. The highest chromosomal inbreeding levels were found on SSC8 (42.7%). ROH islands were found on SSC8, SSC15 and SSC18 in all Piétrain populations, but numerous population-specific ROH islands were also detected. Moreover, a large ROH island on SSC8 (34–126 Mb) appears nearly fixed in all Piétrain populations, with a unique genotype. Chromosomal ROH patterns were similar between Piétrain populations. This study shows that Piétrain populations are genetically diverging, with at least three genetically distinct populations worldwide. Increasing genetic diversity in local Piétrain populations by introgression from other Piétrain populations seems to be only limited. Moreover, a unique 90 Mb region on SSC8 appeared largely fixed in the Piétrain breed, indicating that fixation was already present before the 1960s. We believe that strong selection and inbreeding during breed formation fixed these genomic regions in Piétrains. Finally, we hypothesize that independent coat color selection may have led to large ROH pattern similarities on SSC8 between unrelated pig breeds.     

SIM1基因第8外显子的SNP对猪背膘厚的影响

采用PCR-SSCP方法检测了约克夏、杜洛克、皮特兰、长白猪、嘉兴黑猪和金华猪6个品种共169头猪的SIM1基因外显子8的SNP及其基因型频率。结果共发现CC、CT、TT 3种基因型, 其基因型频率在国内外猪品种之间具有较大差异。其中, 国内猪种嘉兴黑猪和金华猪只存在TT基因型, 而国外猪种约克夏、杜洛克、皮特兰、长白猪则都存在3种基因型。用最小二乘法分析SNP对长白猪、约克夏猪和杜洛克猪的背膘厚的效应的结果表明, 纯合基因型个体的背膘厚大于杂合基因型个体。SIM1基因型对国外猪种背膘厚有显著效应(P< 0.05), 并且不同部位效应不同。     

Identifying candidate positive selection genes in Korean imported pig breeds

Domestication and artificial selection have modified the genome landscape of the pig. The identification of selection signatures in the genome can help to elucidate the selection mechanisms and uncover the causal genes related to the phenotypic variations between domestic pig breeds. We scanned the genomes of Korean imported pig breeds against native breeds using Z-transformed Fst (ZF_ST) and Heterozygosity (ZH_p) statistics to search for the signatures of positive selection. We identified 411 (ZF_ST?=?175; ZH_p?=?256) putatively selected genes in commercial breeds. The gene regions identified were harboring those related to immunity, coat color, reproduction function and other traits. Several genes (e.g., PLSCR4, AGTR1 and CORIN) were related to reproduction traits such as fertility, ovulation rate, and uterine function. This study revealed genes which improve our understanding of the biological mechanisms of higher litter sizes, the phenotype of interest, in higher litter pig breeds.