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

Functional & Integrative Genomics - 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...     

Efficiency of genomic prediction for boar taint reduction in Danish Landrace pigs

Genetic selection against boar taint, which is caused by high skatole and androstenone concentrations in fat, is a more acceptable alternative than is the current practice of castration. Genomic predictors offer an opportunity to overcome the limitations of such selection caused by the phenotype being expressed only in males at slaughter, and this study evaluated different approaches to obtain such predictors. Samples from 1000 pigs were included in a design which was dominated by 421 sib pairs, each pair having one animal with high and one with low skatole concentration (≥0.3 μg/g). All samples were measured for both skatole and androstenone and genotyped using the Illumina SNP60 porcine BeadChip for 62 153 single nucleotide polymorphisms. The accuracy of predicting phenotypes was assessed by cross‐validation using six different genomic evaluation methods: genomic best linear unbiased prediction (GBLUP) and five Bayesian regression methods. In addition, this was compared to the accuracy of predictions using only QTL that showed genome‐wide significance. The range of accuracies obtained by different prediction methods was narrow for androstenone, between 0.29 (Bayes Lasso) and 0.31 (Bayes B), and wider for skatole, between 0.21 (GBLUP) and 0.26 (Bayes SSVS). Relative accuracies, corrected for h², were 0.54–0.56 and 0.75–0.94 for androstenone and skatole respectively. The whole‐genome evaluation methods gave greater accuracy than using only the QTL detected in the data. The results demonstrate that GBLUP for androstenone is the simplest genomic technology to implement and was also close to the most accurate method. More specialised models may be preferable for skatole.     

Genetic parameters for bone strength, osteochondrosis and meat percentage in Finnish Landrace and Yorkshire pigs

Osteochondrosis (OC) is a major factor causing joint problems that affect animal welfare and pork production profitability. Strong bones are also important in the slaughtering process, especially as broken bones can lead to rejections of parts of the carcass. In this study, 326 Finnish Yorkshire and 464 Finnish Landrace test station pigs were examined post mortem for bone strength and osteochondral lesions. The objective was to estimate genetic parameters for OC and bone strength and their genetic and phenotypic correlations with carcass meat percentage. Two formulas were used for lean meat percentage, the first one (Hennessy meat-%) comprising two fat thickness measurements and one muscle depth measurement, and the second one (test station meat-%) also including the weight of lean meat in ham. Finnish Yorkshire had stronger bones than Finnish Landrace on average, but also more OC in the proximal end of the humerus (36%) and the distal end of the femur (51%) than Finnish Landrace (29% and 31% OC in the humerus and femur, respectively). By using the data on both breeds, the OC heritability estimated was 0.05 in the humerus and 0.26 in the femur. The estimated heritability of bone strength was also moderate (0.26). Test station meat-% showed higher heritability (0.40) than meat-% based on the Hennessy formula (0.29). Genetic correlations between meat percentage and the other studied traits were weak and associated with high standard errors. The results show that a mild form of OC is common in both Finnish pig breeds; bone strength and OC in the distal end of the femur are moderately heritable and can be improved through selection; and selection for high meat percentage does not seem to affect bone strength or OC.     

The differential proliferative ability of satellite cells in Lantang and Landrace pigs

Here, for the first time, we evaluate the hypothesis that the proliferative abilities of satellite cells (SCs) isolated from Lantang (indigenous Chinese pigs) and Landrace pigs, which differ in muscle characteristics, are different. SCs were isolated from the longissimus dorsi muscle of neonatal Lantang and Landrace pigs. Proliferative ability was estimated by the count and proliferative activity of viable cells using a hemocytometer and MTT assay at different time points after seeding, respectively. Cell cycle information was detected by flow cytometry. Results showed that there was a greater (P<0.05) number of SCs in Lantang pigs compared with Landrace pigs after 72 h of culture. The percentage of cell population in S phase and G(2)/M phases in Lantang pigs were higher (P<0.05), while in G(0)/G(1) phase was lower (P<0.05) in comparison with the Landrace pigs. The mRNA abundances of MyoD, Myf5, myogenin and Pax7 in SCs from Lantang pigs were higher (P<0.05), while those of myostatin, Smad3 and genes in the mammalian target of rapamycin (mTOR) pathway (with the exception of 4EBP1) were lower (P<0.05) than the Landrace pigs. Protein levels of MyoD, myogenin, myostatin, S6K, phosphorylated mTOR and phosphorylated eIF4E were consistent with the corresponding mRNA abundance. Collectively, these findings suggested that SCs in the two breeds present different proliferative abilities, and the proliferative potential of SCs in Lantang pigs is higher than in Landrace pigs.     

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.     

Copy number variants (CNVs) in primate species using array-based comparative genomic hybridization

A substantial amount of genomic variation is now known to exist in humans and other primate species. Single nucleotide polymorphisms (SNPs) are thought to represent the vast majority of genomic differences among individuals in a given primate species and comprise about 0.1% of the genomes of two humans. However, recent studies have now shown that structural variation msay account for as much as 0.7% of the genomic differences in humans, of which copy number variants (CNVs) are the largest component. CNVs are segments of DNA that can range in size from hundreds of bases to millions of base pairs in length and have different number of copies between individuals. Recent technological advancements in array technologies led to genome-wide identification of CNVs and consequently revealed thousands of variable loci in humans, comprising as much as 12% of the human genome [A.J. Iafrate, L. Feuk, M.N. Rivera, M.L. Listewnik, P.K. Donahoe, Y. Qi, S.W. Scherer, C. Lee, Nat. Genet. 36 (2004) 949–951, [3]]. CNVs in humans have already been associated with susceptibility to certain complex diseases, dietary adaptation, and several neurological conditions. In addition, recent studies have shown that CNVs can be successfully implemented in population genetics research, providing important insights into human genetic variation. Nevertheless, the important role of CNVs in primate evolution and genetic diversity is still largely unknown. This article aims to outline the strengths and weaknesses of current comparative genomic hybridization array technologies that have been employed to detect CNV variation and the applications of these techniques to primate genetic research.     

Morphometric evaluations of testicular tissues from azoospermic boars in Finnish Yorkshire and Landrace breeds

In 1996-2005, ejaculates of 2048 boars were collected. All boars were intended for use in artificial insemination or natural breeding and had two descended testes. Azoospermia was present in 16 of the 1097 Yorkshire boars (1.5%) and in 2 of the 951 Landrace boars (0.2%). The two most frequent diagnoses of azoospermia were arrested spermatogenesis at the pachytene spermatocyte stage (n=8) and segmental aplasia of the Wolffian ducts (n=7). Morphometric evaluations of testicular tissues of azoospermic boars were performed using an image analyzer. The morphometric evaluations revealed decreased portions and diameter of seminiferous tubule in tissue slides from the studied azoospermic boars compared with normal boars. The use of an image analyzer for morphometric evaluations of testicular tissues proved to be a good tool to characterize findings in testicular slides of azoospermic boars.     

Polymorphism analysis and supertype definition of swine leukocyte antigen class I molecules in three-way crossbred (Landrace,Duroc, and Yorkshire) pigs: implications for the vaccine development of African swine fever virus

正Dear Editor,Swine major histocompatibility complex (MHC) is a highly polymorphic gene in pigs and is also called swine leukocyte antigen (SLA)(Fan et al., 2018). SLA is divided into three major categories, SLA Ⅰ (SLA-1,-2,-3), SLA Ⅱ, and SLA Ⅲ(Smith et al., 2005). SLA Ⅰ plays an important role in cellular immunity which can eliminate viruses and other foreign     

Detecting copy number variation in the human genome using comparative genomic hybridization

Among human beings, it was once estimated that our genomes were 99.9% genetically identical. While this high level of genetic similarity helps to define us as a species, it is our genetic variation that contributes to our phenotypic diversity. As genomic technologies evolve to provide genome-wide analyses at higher resolution, we are beginning to appreciate that the human genome has a lot more variation than was once thought. Array-based comparative genomic hybridization (CGH) is one of these technologies that has recently revealed a newly appreciated type of genetic variation: copy number variation, in which thousands of regions of the human genome are now known to be variable in number between individuals. Some of these copy number variable regions have already been shown to predispose to certain common diseases, and others may ultimately have a significant impact on how each of us reacts to certain foods (e.g., allergic reactions), medications (e.g., pharmacogenomics), microscopic infections (i.e., immunity), and other aspects of our ever-changing environment.     

A two-nucleotide deletion renders the mannose-binding lectin 2 (MBL2) gene nonfunctional in Danish Landrace and Duroc pigs

The mannose-binding lectins (MBLs) are central components of innate immunity, facilitating phagocytosis and inducing the lectin activation pathway of the complement system. Previously, it has been found that certain single-nucleotide polymorphisms (SNPs) in porcine MBL1 and MBL2 (pMBL1, pMBL2) affect mRNA expression, serum concentration, and susceptibility to disease, but the combinatory effect of pMBL1 and pMBL2 genotypes needs further elucidation. In the present study, pMBL1 and pMBL2 alleles, combined pMBL haplotypes, and MBL-A concentration in serum were analyzed in purebred Landrace (N?=?30) and Duroc (N?=?10) pigs. Furthermore, the combined pMBL haplotypes of 89 Piètrain × (Large White × Landrace) crossbred pigs were studied, and the genotypes of 67 crossbreds challenged with Escherichia coli were compared to their individual disease records. In the purebred animals, three non-synonymous SNPs and a two-nucleotide deletion were detected in the coding sequence of pMBL2. The two-nucleotide deletion was present at a frequency of 0.88 in the Landrace pigs and 0.90 in the Duroc pigs, respectively. In the crossbreds, the T allele of the SNP G949T in pMBL1—previously shown to have profound effect on MBL-A concentration even in the heterozygote condition—was detected in 47 % of the animals. Finally, an association was found between low-producing MBL genotypes and low body weight on the day of weaning in the same animals.     

Partition of genetic trends by origin in Landrace and Large-White pigs

The objective of this study was to analyse the effectiveness of genetic improvement via domestic selection and import for backfat thickness and time on test in a conventional pig breeding programme for Landrace (L) and Large-White (LW) breeds. Phenotype data was available for 25 553 L and 10 432 LW pigs born between 2002 and 2012 from four large-scale farms and 72 family farms. Pedigree information indicated whether each animal was born and registered within the domestic breeding programme or has been imported. This information was used for defining the genetic groups of unknown parents in a pedigree and the partitioning analysis. Breeding values were estimated using a Bayesian analysis of an animal model with and without genetic groups. Such analysis enabled full Bayesian inference of the genetic trends and their partitioning by the origin of germplasm. Estimates of genetic group indicated that imported germplasm was overall better than domestic and substantial changes in estimates of breeding values was observed when genetic group were fitted. The estimated genetic trends in L were favourable and significantly different from zero by the end of the analysed period. Overall, the genetic trends in LW were not different from zero. The relative contribution of imported germplasm to genetic trends was large, especially towards the end of analysed period with 78% and 67% in L and from 50% to 67% in LW. The analyses suggest that domestic breeding activities and sources of imported animals need to be re-evaluated, in particular in LW breed.     

Comparison of microRNAs in the intramuscular adipose tissue from Jinhua and Landrace pigs

MicroRNA (miRNA) is critically involved in lipogenesis occurring in various body parts of humans and animals. In this study, to further investigate the role and distribution of miRNA in porcine intramuscular adipose tissue, small RNAs were extracted from Jinhua and Landrace pigs to identify the expression profiles of miRNAs. miRNA expression profiles revealed that 558 miRNAs including 287 known and 271 novel miRNAs were identified, and 220 of them showed differential expression in the pigs. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis suggested that the target genes of the differentially expressed miRNAs were involved in fatty metabolism. In conclusion, the current study reveals the active participation of miRNAs in the regulation of adipogenesis in the intramuscular adipose tissue of Jinhua and Landrace pigs.     

Detecting changes in the relative expression of KRAS2 splice variants using polymerase colonies

Because splice variants of a gene with multiple isoforms give rise to proteins with different functions, it seems plausible that changes in the expression levels of the splice variants could be a contributing factor to disease. In fact, recent examples in the literature clearly illustrate that altered expression levels of splice variants may play an important role in disease. Furthermore, these works demonstrate that changes in expression levels could potentially be used to (1) monitor disease progression, (2) diagnose disease, and/or (3) determine disease state. In this work an immobilized form of PCR, known as polony technology, was adapted to quantify the relative expression levels of splice variants. Specifically, the relative expression levels of the two splice variants of the oncogene K-ras, namely, K-RAS2A and K-RAS2B, were determined using polony technology.     

Aneuploidy detection in pigs using comparative genomic hybridization: from the oocytes to blastocysts

Data on the frequency of aneuploidy in farm animals are lacking and there is the need for a reliable technique which is capable of detecting all chromosomes simultaneously in a single cell. With the employment of comparative genomic hybridization coupled with the whole genome amplification technique, this study brings new information regarding the aneuploidy of individual chromosomes in pigs. Focus is directed on in vivo porcine blastocysts and late morulas, 4.7% of which were found to carry chromosomal abnormality. Further, ploidy abnormalities were examined using FISH in a sample of porcine embryos. True polyploidy was relatively rare (1.6%), whilst mixoploidy was presented in 46.8% of embryos, however it was restricted to only a small number of cells per embryo. The combined data indicates that aneuploidy is not a prevalent cause of embryo mortality in pigs.     

Bayesian analysis of response to selection: a case study using litter size in Danish Yorkshire pigs

Implementation of a Bayesian analysis of a selection experiment is illustrated using litter size [total number of piglets born (TNB)] in Danish Yorkshire pigs. Other traits studied include average litter weight at birth (WTAB) and proportion of piglets born dead (PRBD). Response to selection for TNB was analyzed with a number of models, which differed in their level of hierarchy, in their prior distributions, and in the parametric form of the likelihoods. A model assessment study favored a particular form of an additive genetic model. With this model, the Monte Carlo estimate of the 95% probability interval of response to selection was (0.23; 0.60), with a posterior mean of 0.43 piglets. WTAB showed a correlated response of -7.2 g, with a 95% probability interval equal to (-33.1; 18.9). The posterior mean of the genetic correlation between TNB and WTAB was -0.23 with a 95% probability interval equal to (-0.46; -0.01). PRBD was studied informally; it increases with larger litters, when litter size is >7 piglets born. A number of methodological issues related to the Bayesian model assessment study are discussed, as well as the genetic consequences of inferring response to selection using additive genetic models.