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Several QTL regions affecting number of teats have been detected in commercial pig lines. In this study we follow the indirect effects of index selection on different QTL regions for number of teats in two maternal lines in 40K animals with imputed 555K SNP. In total, 3 QTL regions overlap between the two populations. For a QTL on Sus scrofa chromosome 7 (SSC7), the underlying functional variation affecting number of thoracic vertebrae located in the vertnin gene has also been genotyped showing an allelic substitution effect of nearly 0.4 teats in both lines. However, allele frequencies show an opposite trend at the vertnin gene locus in the two lines. Moreover, epistatic effects between two QTL regions on SSC7 and SSC12 are investigated at the molecular and phenotypic level.

De novo mutations arising in the germline add to genetic variation. The number of de novo mutations occurring every generation, especially structural variants, has not been well studied in most species, including livestock. We used whole-genome sequencing from 46 pig trios from two commercial lines to identify de novo structural variants (dnSVs) present in the offspring. We characterised these dnSV by identifying their parent-of-origin, predicting their causal mechanisms, and identifying their functional annotations. We identified four dnSVs, including two clusters of mutations. One of these clusters contained a deletion, and three duplications, one of which was inverted. This cluster was the only dnSV that could be phased and was located in the paternal haplotype of the proband. All four identified dnSVs were located within the introns of genes. Our study is the first of its kind to identify and characterise dnSVs using whole genome shotgun sequence data in pigs.

Genomics related research in animal breeding is usually performed by comparing genomic information to an existing reference genome. However, even if the reference genome is of high quality, the use of a single reference genome has clear drawbacks. Therefore, the breeding community is shifting towards the construction of a pan-genome for important agricultural species. In this study we produced a pig pangenome based on four different breeds (Landrace, Large White, Synthetic, Duroc) using the nanopore long read sequencing technology. We produced chromosome arm level assemblies comparable to the current Sus scrofa 11.1 reference genome. We identified between breed structural variation, which gives a unique insight in the genomic structural variation that define and differentiates breeds. The pig pan-genome will facilitate the discovery of novel variation providing a unique fundamental insight into breed genomic characteristics, which can subsequently be utilized for breeding.

The aim of this study was to perform genome-wide association analyses for backfat thickness and osteochondrosis in Landrace pigs and to fine map pleiotropic genomic regions. In order to characterise genomic regions, phenotypic information of 5,000 animals with osteochondrosis scored from CT images and 40,000 animals with backfat thickness scored from CT or ultrasound images were analysed. All animals were genotyped with a medium density SNP chip and a subset of them were genotyped with a high-density SNP chip as well, allowing for imputation. Two genomic loci were found in common for osteochondrosis and backfat thickness, one on chromosome 5 and one on chromosome 14. For both regions, an antagonistic relationship was found. Fine mapping using an impact score approach identified the CCND2 gene as the most likely causal gene on chromosome 5, whereas a mutation in CRTAC1 had the highest impact score in the chromosome 14 region.

The aim of this work was to identify functional variants potentially associated to complex phenotypes, to improve genomic selection. In this study, we combined genomics, transcriptomics and epigenomics data. First, we genotyped 100 pigs with the high-density genotyping array (with 660K markers). Then, we generated RNA-seq data on these animals in 4 biologically divergent tissues: liver, spleen, lung and muscle. We performed an expression GWAS (eGWAS) resulting in the identification of over 150,000 significant associations in each of the tissues. We were able to detect over 1,300 genes that showed a significant eGWAS associations. We also found an enrichment of eGWAS hits within regulatory elements such as enhancers and promoters, which indicates their pivotal role as drivers of phenotypic variation and thus are of highly relevance towards understanding the genetics of complex traits.

The level of deleterious genetic variation in highly managed domestic populations is influenced by a variety of factors including mutation rate, effective population size, and artificial selection. Small populations enhance the risk of inbreeding depression, which negatively impacts individual fitness and population viability. Inbreeding depression has largely been attributed to the accumulation of recessive harmful mutations in the genome: inbreeding increases the probability of these mutations to become homozygous. Past population bottlenecks, including domestication, have been indicated as major driver of genetic load in populations. While lethal variants can quickly be purged from small populations, the frequency of slightly deleterious mutations is expected to rise due to less effective natural selection. Because of genetic hitch-hiking, mildly harmful mutations are thought to be over-represented in regions of the genome under selection. Recent advances in genome sequencing have opened exciting possibilities to actually measure the amount of harmful mutations in genomes. Using re-sequence data from 421 individuals, we provide an overview of the occurrence of deleterious mutations in individual pig genomes. An alternative approach to identify lethal variants in the genome, is offered by the vast amount of genotyped pedigreed individuals due to the widespread use of genomic selection in current breeding programs. This allows the identification of recessive deleterious variants by testing for statistical depletion, or even the absence, of specific haplotypes in homozygous state. We have used a combination of whole genome sequencing and 60K genotyping (23,800 individuals) to identify and characterize lethal variants segregating in three commercial pig breeding lines. Keywords: genome sequencing, lethal recessive, loss of function mutation, selective sweeps

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.

In a previous study, QTL for carcass composition and meat quality were identified in a commercial finisher cross. The main objective of the current study was to confirm and fine map the QTL on SSC4 and SSC11 by genotyping an increased number of individuals and markers and to analyze the data using a combined linkage and linkage disequilibrium analysis method. A modified version of the method excludes linkage disequilibrium information from the analysis, enabling the comparison of results based on linkage information only or results based on combined linkage and linkage disequilibrium information. Nine additional paternal half-sib families were genotyped for 18 markers, resulting in a total of 1,855 animals genotyped for 15 and 13 markers on SSC4 and SSC11, respectively. The QTL affecting meat color on SSC4 was confirmed, whereas the QTL affecting LM weight could not be confirmed. The combined linkage and linkage disequilibrium analysis resulted in the identification of new significant effects for 14 traits on the 2 chromosomes. Heritabilities of the QTL effects ranged from 1.8 to 13.2%. The analysis contributed to a more accurate positioning of QTL and further characterized their phenotypic effect. However, results showed that even greater marker densities are required to take full advantage of linkage disequilibrium information and to identify haplotypes associated with favorable QTL alleles

The use of DNA markers to evaluate genetic diversity is an important component of the management of animal genetic resources. The Food and Agriculture Organisation of the United Nations (FAO) has published a list of recommended microsatellite markers for such studies; however, other markers are potential alternatives. This paper describes results obtained with a set of amplified fragment length polymorphism (AFLP) markers as part of a genetic diversity study of European pig breeds that also utilized microsatellite markers. Data from 148 AFLP markers genotyped across samples from 58 European and one Chinese breed were analysed. The results were compared with previous analyses of data from 50 microsatellite markers genotyped on the same animals. The AFLP markers had an average within-breed heterozygosity of 0.124 but there was wide variation, with individual markers being monomorphic in 3¿98% of the populations. The biallelic and dominant nature of AFLP markers creates a challenge for their use in genetic diversity studies as each individual marker contains limited information and AFLPs only provide indirect estimates of the allelic frequencies that are needed to estimate genetic distances. Nonetheless, AFLP marker-based characterization of genetic distances was consistent with expectations based on breed and regional distributions and produced a similar pattern to that obtained with microsatellites. Thus, data from AFLP markers can be combined with microsatellite data for measuring genetic diversity.

A QTL study for carcass composition and meat quality traits was conducted on finisher pigs of a cross between a synthetic Pie¿train/Large White boar line and a commercial sow cross. The mapping population comprised 715 individuals evaluated for a total of 30 traits related to growth and fatness (4 traits), carcass composition (11 traits), and meat quality (15 traits). Offspring of 8 sires (n = 715) were used for linkage analysis and genotyped for 73 microsatellite markers covering 14 chromosomal regions representing approximately 50% of the pig genome. The regions examined were selected based on previous studies suggesting the presence of QTL affecting carcass composition or meat quality traits. Thirty-two QTL exceeding the 5% chromosome-wise significance level were identified. Among these, 5 QTL affecting 5 different traits were significant at the 1% chromosome-wise level. The greatest significance levels were found for a QTL affecting loin weight on SSC11 and a QTL with an effect on the Japanese color scale score of the loin on SSC4. About one-third of the identified QTL were in agreement with QTL previously reported. Results showed that QTL affecting carcass composition and meat quality traits segregated within commercial lines. Use of these results for marker-assisted selection offers opportunities for improving pork quality by within-line selection

Knowledge of farm animal genomes has increased enormously over the last decade. A large part if this information is publicly available for a variety of species and through specific databases such as for pigs; PiGBASE for mapping data, Pig EST Database, TIGR SsGI for genes and data on their expression patterns and the INRA Comparative and Cytogenetic mapping home pages. Potentially these databases provide comprehensive public repositories for genome research. However, these data are difficult to combine from the different sources or with private data, but also with genome data of model organisms. This strongly hinders comparative mapping and positional fine-mapping. A new pig genome database - PACE was set up in the Netherlands to enable integration of data from the different sources. For this, the widespread database system of AceDB has been adapted and links with existing farm animal databases but also databases like LocusLink, Genbank, MGI, GeneCards are included to facilitate an efficient comparative mapping with human and mouse. In addition published information on porcine QTL has been included. This database with more than 5000 genetic markers and loci and about 500 QTL¿s will be available publicly from July 2004

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A whole-genome scan was conducted using 132 microsatellite markers to identify chromosomal regions that have an effect on teat number. For this purpose, an experimental cross between Chinese Meishan pigs and five commercial Dutch pig lines was used. Linkage analyses were performed using interval mapping by regression under line cross models including a test for imprinting effects. The whole-genome scan revealed highly significant evidence for three quantitative trait loci (QTL) affecting teat number, of which two were imprinted. Paternally expressed (i.e., maternally imprinted) QTL were found on chromosomes 2 and 12. A Mendelian expressed QTL was found on chromosome 10. The estimated additive effects showed that, for the QTL on chromosomes 10 and 12, the Meishan allele had a positive effect on teat number, but, for the QTL on chromosome 2, the Meishan allele had a negative effect on teat number. This study shows that imprinting may play an important role in the expression of teat number.

To improve the comparative map for pig chromosome 2 and increase the gene density on this chromosome, a porcine bacterial artificial chromosome (BAC) library was screened with 17 microsatellite markers and 18 genes previously assigned to pig chromosome 2. Fifty-one BAC clones located in the region of a maternally imprinted quantitative trait locus for backfat thickness (BFT) were identified. From these BACs 372 kb were sample sequenced. The average read length of a subclone was 442 basepair (bp). Contig assembly analysis showed that every bp was sequenced 1.28 times. Subsequently, sequences were compared with sequences in the nucleotide databases to identify homology with other mammalian sequences. Sequence identity was observed with sequences derived from 35 BACs. The average percentage identity with human sequences was 87.6%, with an average length of 143 bp. In total, sample sequencing of all BACs resulted in sequence identity with 29 human genes, 13 human expressed sequence tags (ESTs), 17 human genomic clones, one rat gene, one porcine gene and nine porcine ESTs. Eighteen genes located on human chromosome 11 and 19, and seven genes from other human locations, one rat gene and one porcine gene were assigned to pig chromosome 2 for the first time. The new genes were added to the radiation hybrid map at the same position as the locus from which the BAC that was sequenced was derived. In total 57 genes were placed on the radiation hybrid map of SSC2p-q13.