Commercial Pig Populations Research Articles

Genome-wide association study of swine farrowing traits. Part II: Bayesian analysis of marker data1,2

Reproductive efficiency has a great impact on the economic success of pork (sus scrofa) production. Number born alive (NBA) and average piglet birth weight (ABW) contribute greatly to reproductive efficiency. To better understand the underlying genetics of birth traits, a genome-wide association study (GWAS) was undertaken. Samples of DNA were collected and tested using the Illumina PorcineSNP60 BeadChip from 1,152 first parity gilts. Traits included total number born (TNB), NBA, number born dead (NBD), number stillborn (NSB), number of mummies (MUM), total litter birth weight (LBW), and ABW. A total of 41,151 SNP were tested using a Bayesian approach. Beginning with the first 5 SNP on SSC1 and ending with the last 5 SNP on the SSCX, SNP were assigned to groups of 5 consecutive SNP by chromosome-position order and analyzed again using a Bayesian approach. From that analysis, 5-SNP groups were selected having no overlap with another 5-SNP groups and no overlap across chromosomes. These selected 5-SNP non-overlapping groups were defined as QTL. Of the available 8,814 QTL, 124 were found to be statistically significant (P < 0.01). Multiple testing was considered using the probability of false positives. Eleven QTL were found for TNB, 3 on SSC1, 3 on SSC4, 1 on SSC13, 1 on SSC14, 2 on SSC15, and 1 on SSC17. Statistical testing for NBA identified 14 QTL, 4 on SSC1, 1 on SSC4, 1 on SSC6, 1 on SSC10, 1on SSC13, 3 on SSC15, and 3 on SSC17. A single NBD QTL was found on SSC11. No QTL were identified for NSB or MUM. Thirty-three QTL were found for LBW, 3 on SSC1, 1 on SSC2, 1 on SSC3, 5 on SSC4, 2 on SSC5, 5 on SSC6, 3 on SSC7, 2 on SSC9, 1 on SSC10, 2 on SSC14, 6 on SSC15, and 2 on SSC17. A total of 65 QTL were found for ABW, 9 on SSC1, 3 on SSC2, 9 on SSC5, 5 on SSC6, 1 on SSC7, 2 on SSC8, 2 on SSC9, 3 on SSC10, 1 on SSC11, 3 on SSC12, 2 on SSC13, 8 on SSC14, 8 on SSC15, 1 on SSC17, and 8 on SSC18. Several candidate genes have been identified that overlap QTL locations among TNB, NBA, NBD, and ABW. These QTL when combined with information on genes found in the same regions should provide useful information that could be used for marker assisted selection, marker assisted management, or genomic selection applications in commercial pig populations.

Association between polymorphism in the FTO gene and growth and carcass traits in pig crosses

BackgroundIndependent studies have shown that several single nucleotide polymorphisms (SNP) in the human FTO (fat mass and obesity associated) gene are associated with obesity. SNP have also been identified in the pig FTO gene, among which some are associated with selected fat-deposition traits in F2 crosses and commercial populations. In this study, using both commercial pig populations and an experimental Meishan × Pietrain F2 population, we have investigated the association between one FTO SNP and several growth and carcass traits. Association analyses were performed with the FTO polymorphism either alone or in combination with polymorphisms in flanking loci.MethodsSNP (FM244720:g.400C>G) in exon 3 of porcine FTO was genotyped by PCR-RFLP and tested for associations with some growth, carcass and fat-related traits. Proportions of genetic variance of four pig chromosome 6 genes (FTO, RYR1, LIPE and TGFB1) on selected traits were evaluated using single- and multi-locus models.ResultsLinkage analysis placed FTO on the p arm of pig chromosome 6, approximately 22 cM from RYR1. In the commercial populations, allele C of the FTO SNP was significantly associated with back fat depth and allele G with muscling traits. In the Meishan × Pietrain F2 pigs, heterozygotes with allele C from the Pietrain sows and allele G from the Meishan boar were more significantly associated with fat-related traits compared to homozygotes with allele G from the Pietrain and allele G from the Meishan breed. In single- and multi-locus models, genes RYR1, TGFB1 and FTO showed high associations. The contribution in genetic variance from the polymorphism in the FTO gene was highest for back fat depth, meat area on the musculus longissimus lumborum et thoracis tissues and metabolite glucose-6-phosphate dehydrogenase.ConclusionsOur results show that in pig, FTO influences back fat depth in the commercial populations, while in the Meishan × Pietrain F2 pigs with a CG genotype, heterosis occurs for several fat-related traits.

The Imprinted Gene DIO3 Is a Candidate Gene for Litter Size in Pigs

Genomic imprinting is an important epigenetic phenomenon, which on the phenotypic level can be detected by the difference between the two heterozygote classes of a gene. Imprinted genes are important in both the development of the placenta and the embryo, and we hypothesized that imprinted genes might be involved in female fertility traits. We therefore performed an association study for imprinted genes related to female fertility traits in two commercial pig populations. For this purpose, 309 SNPs in fifteen evolutionary conserved imprinted regions were genotyped on 689 and 1050 pigs from the two pig populations. A single SNP association study was used to detect additive, dominant and imprinting effects related to four reproduction traits; total number of piglets born, the number of piglets born alive, the total weight of the piglets born and the total weight of the piglets born alive. Several SNPs showed significant () additive and dominant effects and one SNP showed a significant imprinting effect. The SNP with a significant imprinting effect is closely linked to DIO3, a gene involved in thyroid metabolism. The imprinting effect of this SNP explained approximately 1.6% of the phenotypic variance, which corresponded to approximately 15.5% of the additive genetic variance. In the other population, the imprinting effect of this QTL was not significant (), but had a similar effect as in the first population. The results of this study indicate a possible association between the imprinted gene DIO3 and female fertility traits in pigs.

Haplotype variation of toll-like receptor 3 among pig populations

The toll-like receptor 3 (TLR3) recognizes double-stranded RNA (dsRNA), the intermediate product of most virus during multiplication, and acts as a candidate gene for resistance to a large number of viral diseases. Variation in TLR3 may alter host immune response to dsRNA, as suggested by studies on other TLRs in humans and livestock. Here, the genetic variation in the coding sequence of porcine TLR3 gene was explored in animals belonging to western commercial and Chinese indigenous pig populations. Eight single nucleotide polymorphisms (SNPs), including four non-synonymous, were identified. Two non-synonymous fell in ligand binding region and potentially alter specificity of pathogen recognition. The 8 SNPs were found in 15 haplotypes, one of which segregated at high frequency in the whole sample. Departure from neutrality analysis highlighted the fact that demographic factors strongly influence the test. These data provide novel, informative genetic markers for future disease association studies.

초위성체 표지를 이용한 한국재래돼지 집단의 분자유전학적 고찰

초위성체(MS) 표지를 이용하여 한국재래돼지 집단의 각각의 분자유전학적 특성을 조사하고 그 평가를 통해 한국재래돼지에 대한 품종 및 계통분류의 기초를 마련하고자 본 연구를 수행하였다. 또한, 각 재래돼지 집단 내 및 집단간의 유전적 변이성을 확인하고, 그 분류 및 특성평가를 위한 MS 분석체계를 마련하여 국내 가축 유전자원 관리에 활용하고자 하였다. 국내 관리기관 및 농가에서 보유하고 있는 6개 재래돼지 집단을 중국의 4개 재래돼지 집단 및 외래종 돼지 7개 집단과 함께 분석하였다. 도합 17집단 648두를 대상으로 26개 MS 표지로 분석한 결과, 한국재래돼지 집단은 외래종과 중국재래돼지로부터 분자유전학적으로 별개의 집단으로 확연히 구분되는 것을 확인하였다. 한국재래돼지 집단의 기대이형접합도(<TEX>$H_E$</TEX>)는 0.65의 값을 보인 두 집단(B, D)을 제외한 나머지에서 0.48~0.55의 수준을 보여 전반적으로 외래종에 비해 낮았다. 한국재래돼지 집단간의 유전거리 또한 0.12~0.34 정도로 비교대상에 비하여 낮았다. 분석대상 한국재래돼지 6집단 중 세 개의 집단은 높은 유전적 균일도를 보였으나, 두 집단에서는 일부 집단의 혼입을, 나머지 하나의 집단에서는 둘 이상의 집단으로부터의 복잡한 혼입이 의심되는 매우 낮은 유전적 균일도를 확인하였다. 본 연구를 통하여 한국재래돼지 집단간의 유전적 차이 및 동질성, 그리고 집단내의 유전적 균일성을 확인하였다. 이러한 결과는 국내유전자원의 고유성을 인정할 수 있는 과학적인 근거로서, 국가수준의 가축유전자원 평가, 관리의 기초자료로 활용될 수 있을 것이다. The study was conducted to select and optimize microsatellite (MS) markers for evaluation of Korean native pig (KNP) populations in order to provide standard for the classification and breed definition of the indigenous breeds. The study also aimed to characterize and classify each KNP populations. A total of 648 pigs from 17 pig populations including six KNP, four Chinese native pig and four commercial pig populations were analyzed with 26 MS markers. KNP populations formed separate cluster from those of Chinese native pig and introduced pig populations. Expected heterozygosity (He) of KNP populations were 0.48~0.55 except two populations with 0.65. Genetic distances between KNP populations were relatively shorter: 0.12-0.34. Among six KNP populations, three showed high genetic uniformity, two showed lower uniformity and one showed high level of impurity and heterozygosity. The results can be used to evaluate and manage animal genetic resources at national scale.

A single nucleotide polymorphism set for paternal identification to reduce the costs of trait recording in commercial pig breeding1,2

In animal breeding, recording of correct pedigrees is essential to achieve genetic progress. Markers on DNA are useful to verify the on-farm pedigree records (parental verification) but can also be used to assign parents retrospectively (parental identification). This approach could reduce the costs of recording for traits with low incidence, such as those related to diseases or mortality. In this study, SNP were used to assign the true sires of 368 purebred animals from a Duroc-based sire line and 140 crossbred offspring from a commercial pig population. Some of the sires were closely related. There were 3 full sibs and 17 half sibs among the true fathers and 4 full sibs and 35 half sibs among all putative fathers. To define the number of SNP necessary, 5 SNP panels (40, 60, 80, 100, and 120 SNP) were assembled from the Illumina PorcineSNP60 Beadchip (Illumina, San Diego, CA) based on minor allele frequency (>0.3), high genotyping call rate (≥90%), and equal spacing across the genome. For paternal identification considering only the 66 true sires in the data set, 60 SNP resulted in 100% correct assignment of the sire. By including additional putative sires (n = 304), 80 SNP were sufficient for 100% correct assignment of the sire. The following criteria were derived to identify the correct sire for the current data set: the logarithm of odds (LOD) score for assigning the correct sire was ≥5, the number of mismatches was ≤1, and the difference in the LOD score between the first and the second most likely sire was >5. If the correct sire was not present among all putative sires, the mean LOD for the most likely sire was close to zero or negative when using 100 SNP. More SNP would be needed for paternal identification if the number of putative sires increased and the degree of relatedness was greater than in the data set used here. The threshold for the number of mismatches can be adjusted according to the practical situation to account for the trade-off between false negatives and false positives. The latter can be avoided efficiently, ensuring that the correct father is being sampled. Nevertheless, a restriction on the number of putative sires is advisable to reduce the risk of assigning close relatives.

Microsatellite-based characterization of Southern African domestic pigs (&lt;i&gt;Sus scrofa domestica&lt;/i&gt;)

This paper details genetic characterization and trends from a microsatellite-based study of genetic diversity on southern African pig populations. A total of 351 pigs from three commercial breeds and three indigenous populations were genotyped at 39 loci. Differences among the levels of genetic diversity in populations correlated well with known population histories. In commercial breeds, heterozygosity was higher in the well established SA Landrace and Large White breeds (0.580 and 0.636) compared to the Duroc breed, established more recently (0.531). In indigenous populations, the highest heterozygosity levels were found in the Mozambican and South African populations (0.692 and 0.634) with a lower value of 0.531 in a smaller Namibian population. A hierarchical division of total genetic diversity revealed a high between-population component of 17.9%. FST- and RST-based analysis confirmed high levels of differentiation, with pair-wise comparisons between breeds indicating significant differentiation in 20 out of 21 comparisons. Results from an assignment test confirmed results from FST and RST and suggested a true genetic structure with significant differentiation between most populations sampled, but with little differentiation among the commercial SA Landrace and Large White breeds. The results are discussed with reference to known historical information on commercial and indigenous pig populations. This paper also presents new data on the optimization of microsatellite markers for application in Sus scrofa domestica.Keywords: Genetic diversity, domestic pig, microsatellites, indigenous breeds

Association analysis of PPARGC1A mutations with meat quality parameters in a commercial hybrid pig population

Peroxisome proliferator-activated receptor &amp;gamma; coactivator 1&amp;alpha; (PPARGC1A) is a promising candidate gene for selection on meat and carcass quality traits in the pig industry. In the pig, several SNPs have been reported in both coding and regulatory regions of this gene, some of which were associated with fat characteristics, but none of these associations have been confirmed and many SNPs have not yet been evaluated. Therefore, 18 PPARGC1A SNPs were genotyped in 65 slaughter pigs of a commercial hybrid population and used in an association analysis with multiple muscle and carcass traits. Several SNPs located in the 3'UTR and exon 8 and 9 of PPARGC1A were significantly (P &amp;lt; 0.05&amp;ndash;0.001) associated with various carcass composition, tenderness and muscle fibre traits. They could potentially serve as DNA selection markers, if their impact was to be confirmed by a functional analysis.

Detection of multiple quantitative trait loci and their pleiotropic effects in outbred pig populations

BackgroundSimultaneous detection of multiple QTLs (quantitative trait loci) may allow more accurate estimation of genetic effects. We have analyzed outbred commercial pig populations with different single and multiple models to clarify their genetic properties and in addition, we have investigated pleiotropy among growth and obesity traits based on allelic correlation within a gamete.MethodsThree closed populations, (A) 427 individuals from a Yorkshire and Large White synthetic breed, (B) 547 Large White individuals and (C) 531 Large White individuals, were analyzed using a variance component method with one-QTL and two-QTL models. Six markers on chromosome 4 and five to seven markers on chromosome 7 were used.ResultsPopulation A displayed a high test statistic for the fat trait when applying the two-QTL model with two positions on two chromosomes. The estimated heritabilities for polygenic effects and for the first and second QTL were 19%, 17% and 21%, respectively. The high correlation of the estimated allelic effect on the same gamete and QTL test statistics suggested that the two separate QTL which were detected on different chromosomes both have pleiotropic effects on the two fat traits. Analysis of population B using the one-QTL model for three fat traits found a similar peak position on chromosome 7. Allelic effects of three fat traits from the same gamete were highly correlated suggesting the presence of a pleiotropic QTL. In population C, three growth traits also displayed similar peak positions on chromosome 7 and allelic effects from the same gamete were correlated.ConclusionDetection of the second QTL in a model reduced the polygenic heritability and should improve accuracy of estimated heritabilities for both QTLs.

Genes located on a SSC17 meat quality QTL region are associated with growth in outbred pig populations

The objective of this study was to evaluate the effect of markers developed in eight genes, located in a previously detected meat quality QTL region on SSC17, on growth, fat and meat quality traits collected in commercial pig populations of different genetic backgrounds. The genes had been previously mapped to SSC17 as part of a fine-mapping effort. Association analyses were conducted between each marker and the available phenotypic traits. Results showed that three genes (CTSZ, CSTF1 and C20orf43) were significantly associated with the growth traits. In addition, CTSZ also impacted on meat colour, with the less favourable genotype for growth being associated with darker meat. The differences observed between genotypes were substantial and may be of economic importance to pig producers. These markers may be useful for selecting for faster growth or improved meat quality.

Role of Wild Suids in the Epidemiology of African Swine Fever

There is presently no vaccine to combat African swine fever (ASF), a viral hemorrhagic fever of domestic pigs that causes up to 100% morbidity and mortality in naive, commercial pig populations. In its endemic setting, ASF virus cycles between asymptomatic warthogs and soft ticks, with persistence in exotic locations being ascribed to the almost global distribution of susceptible soft tick and suid hosts. An understanding of the role played by diverse hosts in the epidemiology of this multi-host disease is crucial for effective disease control. Unlike the intensively studied Ornithodoros tick vector, the role of many wild suids remains obscure, despite growing recognition for suid-exclusive virus cycling, without the agency of the argasid tick, at some localities. Because the four wild suid genera, Phacochoerus, Potamochoerus, Hylochoerus, and Sus differ from each other in taxonomy, distribution, ecology, reservoir host potential, virus shedding, ASF symptomology, and domestic-pig contact potential, their role in disease epidemiology is also varied. This first consolidated summary of ASF epidemiology in relation to wild suids summarizes current knowledge and identifies information gaps and future research priorities crucial for formulating effective disease control strategies.

Toll‐like receptor 4genetic diversity among pig populations

The transmembrane glycoprotein encoded by the Toll-like receptor 4 gene (TLR4) acts as the transducing subunit of the lipopolysaccharide receptor complex of mammals, which is a major sensor of infections by Gram-negative bacteria. As variation in TLR4 may alter host immune response to lipopolysaccharide, the association between TLR4 polymorphisms and immune traits of the respiratory and gut systems has important implications for livestock. Here, a sequence dataset from 259 animals belonging to commercial and traditional European pig populations, consisting of 4305 bp of TLR4, including the full transcribed region, a portion of intron 2 and the putative promoter region, was used to explore genetic variation segregating at the TLR4 locus. We identified 34 single nucleotide polymorphisms, 17 in the coding sequence and 17 in the non-coding region. Five non-synonymous mutations clustered within, or in close proximity to, the hypervariable domain of exon 3. In agreement with studies in other mammals, a major exon 3 haplotype segregated at high frequency in the whole sample of 259 pigs, while variants carrying non-synonymous substitutions showed frequencies ranging between 0.6% and 8.7%. Although results on exon 3 provided suggestive evidence for purifying selection occurring at the porcine TLR4 gene, the analysis of both coding and non-coding regions highlighted the fact that demographic factors strongly influence the tests of departure from neutrality. The phylogenetic analysis of TLR4 identified three clusters of variation (ancestral, Asian, European), supporting the evidence of Asian introgression in European main breeds and the well documented history of pig breed domestication previously identified by mtDNA analysis.

The Porcine Mitochondrial Transcription Factor a Gene: Molecular Characterization, Radiation Hybrid Mapping and Genetic Diversity among 12 Pig Breeds

Problem statement: Mitochondrial transcription factor A (TFAM) is a nucleus-encoded protein that is a key activator of mitochondrial transcription as well as a major participant in mitochondrial genome replication. Genomic characterization of the porcine TFAM gene is, therefore, necessary to determine its involvement in regulation of fat depots and meat quality traits in pigs. Approach: Genomic DNA sequence was determined using a comparative in silico annotation approach. RT-PCR was used for analysis of alternative splicing. Genome location was determined using Radiation Hybrid (RH) mapping. Genetic marker was identified by sequencing and genotyped by the PCR-RFLP method with SacI. GENEPOP version 3.3 software was used for statistic analysis. Results: We determined both full-length cDNA and genomic DNA sequences of the porcine TFAM gene. Gene expression analysis revealed an alternative 5’ splice site, which excludes exon 4 of the pig gene. We assigned this gene to porcine chromosome 14 (SSC14). A G/A substitution was detected in intron 1 of porcine TFAM gene and genotyped on a total of 252 animals, including 165 from seven Chinese and 87 from five Western pig breeds. The Bayesian analysis via MCMC (Markov chain Monte Carlo) revealed that these two groups of pigs were well separated at this locus during the breed history; 95% of the posterior difference of TFAM allelic frequency between these two pig groups was greater than zero. Conclusion/Recommendations: All these data provided basic genomic information needed for further functional characterization of the porcine TFAM gene. Because marked differences in fat and lean tissue deposition exist between Western and Chinese pig breeds, the G557A mutation in the TFAM gene deserves further evaluation to determine its phenotypic effect on fattening and carcass traits in commercial pig populations.

Polymorphism ofMC4RAsp298Asn site and its relationship with backfat thickness in commercial pigs

AbstractMelanocortin-4 receptor (MC4R) is a member of the superfamily of G-protein-coupled receptors (GPCRs), which affects body weight, energy homeostasis and food intake in humans and mice. In this study, the Asp298Asn polymorphism of theMC4Rgene was investigated in Laiwu, Yorkshire×Laiwu and commercial cross-bred pig populations using polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP), and the relationship of this mutation with backfat thickness was analysed. The results indicated that only genotype 11 exists in 33 individuals of Laiwu pigs, and three genotypes (11, 12 and 22) were detected in Yorkshire×Laiwu and commercial cross-bred populations. The distributions of allele and genotype frequencies in Yorkshire×Laiwu and commercial cross-bred populations were similar, with the frequency of allele 1 being higher than that of allele 2. In commercial cross-bred pigs, the mean backfat thickness of individuals with genotype 22 was significantly higher than that of individuals with genotypes 12 (P&lt;0.01) and 11 (P&lt;0.05). This study provides evidence that the Asp298Asn polymorphism of theMC4Rgene is associated with backfat thickness in commercial cross-bred pigs with Western pigs as parental lines and, therefore, can be used as a DNA marker for breeding in such populations of pigs.

돼지 품종의 경제형질 관련 후보유전자의 단일염기 다형성에 관한 연구

돼지 2번 염색체의 육질 관련 양적 경제형질에 관한 연구보고가 몇몇 이루어 지고 있다. 양돈업계에서 DNA 기술을 이용한 염색체 정보를 활용하기 위해 본 연구에서는 13개의 후보 유전자에서 생성된 중합효소연쇄반응(PCR) 생성물을 비교 재서열 함으로써 단일염기변이(SNP) 표지들을 개발했다. 11개의 중합효소연쇄반응 생성물에서 296 bp마다 에서 평균 하나의 SNP, 총 34개의 SNP를 발견하였다. 또한 11개의 SNP에 대한 PCR 제한효소길이 절편길이 다형성(RFLP) 분석을 전개한 후, 이를 대한민국 상업돈 4품종 개체군의 유전자형을 분석하는데 활용하였다. 본 연구는 유용한 단일염기변이를 식별하고 돼지 개체군 내 경제적으로 중요한 특성들과 SNP의 연관성을 확인하는 데 그 목적이 있다. Several studies reported quantitative trait loci (QTL) for meat quality on porcine chromosome 2. For application of the chromosomal information to pig industry through using DNA technology, single nucleotide polymorphism (SNP) markers are developed by comparative re-sequencing of polymerase chain reaction (PCR) products of 13 candidate genes. A total of 34 SNPs were identified in 11 PCR products, an average of one SNP in every 296 bp.PCR restriction fragment length polymorphism (RFLP) assays were developed for 11 SNPs and used to genotype four commercial pig populations in Korea. The SNP markers were used to map candidate genes in QTL and to clarify the relevance of SNP and quantitative traits.

Allelic variation of the porcine α-1,3-galactosyltransferase 1 (GGTA1) gene

The alpha-1,3-galactosyltransferase 1 enzyme (GGTA1) produces the alpha-Gal epitopes, responsible for pig-to-human hyperacute xenograft rejection. Recently, efforts have been directed at inactivating the porcine GGTA1 gene in order to reduce hyperacute rejection. As very little is known about the genetic variability of this key gene among pig breeds, we investigated the variation in its nucleotide sequence, by amplification of the entire coding region with the use of polymerase chain reaction followed by DNA sequencing. Eight commercial pig populations were analysed and 17 single nucleotide polymorphisms (SNPs) were detected: 11 in intronic regions and 6 in the 3' untranslated region (UTR). No SNPs change the encoded protein; however, 8 of these SNPs may alter the transcriptional regulation and pre-mRNA splicing of GGTA1.

Investigation of Single Nucleotide Polymorphisms in Porcine Chromosome 2 Quantitative Trait Loci for Meat Quality Traits

Several studies have reported quantitative trait loci (QTL) for meat quality on porcine chromosome 2 (http://www.animalgenome.org/QTLdb/pig.html). For application of the molecular genetic information to the pig industry through marker-assisted selection, single nucleotide polymorphism (SNP) markers were analyzed by comparative re-sequencing of polymerase chain reaction (PCR) products of 13 candidate genes with DNA from commercial pig breeds such as Berkshire, Yorkshire, Landrace, Duroc and Korean Native pig. A total of 34 SNPs were identified in 15 PCR products producing an average of one SNP in every 253 bp. PCR restriction fragment length polymorphism (RFLP) assays were developed for 11 SNPs and used to investigate allele frequencies in five commercial pig breeds in Korea. Eight of the SNPs appear to be fixed in at least one of the five pig breeds, which indicates that different selection among pig breeds might be applied to these SNPs. Polymorphisms detected in the PTH, CSF2 and FOLR genes were chosen to genotype a Berkshire-Yorkshire pig breed reference family for linkage and association analyses. Using linkage analysis, PTH and CSF2 loci were mapped to pig chromosome 2, while FOLR was mapped to pig chromosome 9. Association analyses between SNPs in the PTH, CSF2 and FOLR suggested that the CSF2 MboII polymorphism was significantly associated with several pork quality traits in the Berkshire and Yorkshire crossed F2 pigs. Our current findings provide useful SNP marker information to fine map QTL regions on pig chromosome 2 and to clarify the relevance of SNP and quantitative traits in commercial pig populations.

Empirical Bayes factor analyses of quantitative trait loci for gestation length in Iberian × Meishan F2 sows

The aim of this study was to investigate chromosomal regions affecting gestation length in sows. An experimental F2 cross between Iberian and Meishan pig breeds was used for this purpose and we genotyped 119 markers covering the 18 porcine autosomal chromosomes. Within this context, we have developed a new empirical Bayes factor (BF) approach to compare between nested models, with and without the quantitative trait loci (QTL) effect, and after including the location of the QTL as an unknown parameter in the model. This empirical BF can be easily calculated from the output of a Markov chain Monte Carlo sampling by averaging conditional densities at the null QTL effects. Linkage analyses were performed in each chromosome using an animal model to account for infinitesimal genetic effects. Initially, three QTL were detected at chromosomes 6, 8 and 11 although, after correcting for multiple testing, only the additive QTL located in cM 110 of chromosome 8 remained. For this QTL, the allelic effect of substitution of the Iberian allele increased gestation length in 0.521 days, with a highest posterior density region at 95% ranged between 0.121 and 0.972 days. Although future studies are necessary to confirm if detected QTL is relevant and segregating in commercial pig populations, a hot-spot on the genetic regulation of gestation length in pigs seems to be located in chromosome 8.

Frequency of the HAL-1843 mutation of the ryanodine receptor gene in dead and nonambulatory-noninjured pigs on arrival at the packing plant1

Four Midwestern packing plants (designated as plants A, B, C, and D) were visited on 53 occasions, and tissue samples were collected postmortem from a total of 2,019 pigs to determine the frequency of the HAL-1843 mutation of the ryanodine receptor gene in dead (DOA), nonambulatory-noninjured (NANI), and normal animals. The sampled pigs came from approximately 130,000 animals from 454 farms and were transported on 861 trailer loads, with an average of 152 pigs/load and an average pig live BW/load of 125 (SD 7.02) kg/pig. Frequency of animals with the HAL-1843 mutation was low, with only 2.7% of the pigs being either homozygous recessives (nn, 0.45%) or carriers (Nn, 2.3%) for the mutation and 97.3% of the pigs being homozygous for the normal allele (NN). The mutation was present in all 3 classes of pig, with 1.8% of normal, 1.8% of NANI, and 4.7% of DOA animals having at least 1 copy. Two of the plants (A and C) had a greater frequency (P < 0.05) of carrier (3.7 and 3.5 vs. 1.1 and 1.0 for plants A and C vs. B and D, respectively) and homozygous recessive (1.0 and 0.9 vs. 0.0 and 0.0, respectively) animals than the others (plants B and D). There was a greater frequency (P < 0.05) of carriers in DOA animals than in the normal or NANI pigs (3.7 vs. 1.7 and 1.5 for DOA vs. normal and NANI, respectively). The 55 pigs that had at least 1 copy of the mutation came from 53 farms; therefore, the mutation was relatively widespread, being present in approximately 11% of the farms sampled. Although the HAL-1843 mutation is still present in commercial pig populations in the United States, its low frequency in DOA and NANI pigs suggests that it is not a major cause of these transport losses.

Single nucleotide polymorphisms for pig identification and parentage exclusion

Single nucleotide polymorphisms (SNPs) have become an important type of marker for commercial diagnostic and parentage genotyping applications as automated genotyping systems have been developed that yield accurate genotypes. Unfortunately, allele frequencies for public SNP markers in commercial pig populations have not been available. To fulfil this need, SNP markers previously mapped in the USMARC swine reference population were tested in a panel of 155 boars that were representative of US purebred Duroc, Hampshire, Landrace and Yorkshire populations. Multiplex assay groups of 5-7 SNP assays/group were designed and genotypes were determined using Sequenom's massarray system. Of 80 SNPs that were evaluated, 60 SNPs with minor allele frequencies >0.15 were selected for the final panel of markers. Overall identity power across breeds was 4.6 x 10(-23), but within-breed values ranged from 4.3 x 10(-14) (Hampshire) to 2.6 x 10(-22) (Yorkshire). Parentage exclusion probability with only one sampled parent was 0.9974 (all data) and ranged from 0.9594 (Hampshire) to 0.9963 (Yorkshire) within breeds. Sire exclusion probability when the dam's genotype was known was 0.99998 (all data) and ranged from 0.99868 (Hampshire) to 0.99997 (Yorkshire) within breeds. Power of exclusion was compared between the 60 SNP and 10 microsatellite markers. The parental exclusion probabilities for SNP and microsatellite marker panels were similar, but the SNP panel was much more sensitive for individual identification. This panel of SNP markers is theoretically sufficient for individual identification of any pig in the world and is publicly available.