Association of a new mobile element in predicted promoter region of ATP-binding cassette transporter 12 gene (ABCA12) with pig production traits

Accelerated discovery of functional genomic variation in pigs

The genotype-phenotype link is a major research topic in the life sciences but remains highly complex to disentangle. Part of the complexity arises from the number of genes contributing to the observed phenotype. Despite the vast increase of molecular data, pinpointing the causal variant underlying a phenotype of interest is still challenging. In this study, we present an approach to map causal variation and molecular pathways underlying important phenotypes in pigs. We prioritize variation by utilizing and integrating predicted variant impact scores (pCADD), functional genomic information, and associated phenotypes in other mammalian species. We demonstrate the efficacy of our approach by reporting known and novel causal variants, of which many affect non-coding sequences. Our approach allows the disentangling of the biology behind important phenotypes by accelerating the discovery of novel causal variants and molecular mechanisms affecting important phenotypes in pigs. This information on molecular mechanisms could be applicable in other mammalian species, including humans.

The SSC15 QTL-Rich Region Mutations Affecting Intramuscular Fat and Production Traits in Pigs

One of the more interesting regions in the pig genome is on chromosome 15 (115,800,000-122,100,000, SSC15, Sus scrofa 11.1) that has high quantitative trait locus (QTL) density associated with fattening, slaughter and meat quality characteristics. The SSC15 region encodes over 80 genes and a few miRNA sequences where potential genetic markers can be found. The goal of the study was to evaluate the effects of SSC15 mutations associated with villin 1 (VIL1), tensin 1 (TNS1), obscurin-like 1 (OBSL1) genes and with one long non-coding RNA (lncRNA) on productive pig traits and to enrich the genetic marker pool in further selection purpose. The potential genetic markers were identified using the targeted enrichment DNA sequencing (TEDNA-seq) of chromosome 15 region. The selected mutations were genotyped by using HRM, PCR and PCRRFLP methods. The association study was performed using the general linear model (GLM) in the sas program that included over 600 pigs of 5 Polish populations. The rs332253419 VIL1 mutation shows a significant effect on intramuscular fat (IMF) content in Duroc population where AA pigs had a 16% higher level than heterozygotes. The IMF content is also affected by the OBSL1 mutation, and the differences between groups are even up to 30%, but it is strongly dependent on breed factor. The OBSL1 mutation also significantly influences the meat yellowness, backfat thickness and pH level. The performed study delivers valuable information that could be highly useful during the development of the high-throughput genotyping method for further selection purposes in pigs. The OBSL1 and VIL1 mutations seem to be the most promising DNA marker showing a high effect on IMF level.

Detection of genetic variants between different Polish Landrace and Puławska pigs by means of RNA-seq analysis

Variant calling analysis based on RNA sequencing data provides information about gene variants. RNA-seq is cheaper and faster than is DNA sequencing. However, it requires individual hard filters during data processing due to post-transcriptional modifications such as splicing and RNA editing. In the present study, RNA-seq transcriptome data on two Polish pig breeds (Puławska, PUL, n = 8, and Polish Landrace, PL, n = 8) were included. The pig breeds are significantly different with regard to meat qualities such as texture, water exudation, growth traits and fat content in carcasses. A total of 2451 significant mutations were identified by a chi square tests, and functional analysis was carried out using Panther, KEGG and Kobas. Interesting missense gene variants and mutations located in regulatory regions were found in a few genes related to fatty acid metabolism and lipid storage such as ACSL5, ALDH3A2, FADS1, SCD, PLA2G12A and ATGL. A validation of mutational influences on pig traits was performed for ALDH3A2, ATGL, PLA2G12A and MYOM1 variants using association analysis including 215 pigs of the PL and PUL breeds. The ALDH3A2ENSSSCT00000019636.2:c.470T>C polymorphism was found to affect the weight of the ham and loin eye area. In turn, an ENSSSCT00000004091.2:c.2836G>A MYOM1 mutation, which could be implicated in myofibrillar network organisation, had an effect on meatiness and loin texture parameters. The study aimed to estimate the usefulness of RNA-seq results for a purpose other than differentially expressed gene analysis. The analysis performed indicated interesting gene variants that could be used in the future as markers during selection.

The effect of QTL-rich region polymorphisms identified by targeted DNA-seq on pig production traits

The aim of the present study was to analyse the effect of PLCD4, PECR, FN1 and PNKD mutations on pig productive traits and tested the usefulness of targeted enrichment DNA sequencing method as tool for preselection of genetic markers. The potential genetic markers for pig productive traits were identified by using targeted enrichment DNA sequencing of chromosome 15 region that is QTL-rich. The selected mutations were genotyped by using HRM, Sanger sequencing and PCR-ACRS methods. The association study was performed by using GLM model in SAS program and included over 500 pigs of 5 populations maintained in Poland. The variation (C/T) of PLCD4 gene affected feed conversion, intramuscular fat and water exudation. The PNKD mutations were associated with texture parameters measured after cooking. In turn, the variation rs792423408 (C/T) in the FN1 gene influenced toughness measured in semimembranosus muscle and growth traits that was observed particularly in Duroc breed. Summarizing, the investigated gene variants delivered valuable information that could be used during developing SNP microarray for genomic estimated breeding value procedure in pigs. Moreover, the study showed that the TEDNA-seq method could be used to preselect the molecular markers associated with pig traits. However, the further association study that included large number animal populations is necessary.

Deep sequencing of a QTL-rich region spanning 128-136Mbp of pig chromosome 15

The present study shows the characterization of the chromosome 15 (SSC15) region that is highly rich in quantitative traits loci (QTLs) associated with pork quality, growth performance, fat and meat carcass contents. The analytic method that was utilized included targeted enrichment DNA sequencing and RNA hybridisation probes. The research included two pig breeds (Puławska and Polish Landrace) that are significantly different in terms of carcass and meat quality features. Filtered sequences were aligned to the Sscrofa10.2 assembly genome with the STAR aligner and GATK HaplotypeCaller was used for identified gene variants in SSC15 region. In Puławska pigs, which were characterized by high meat quality, mutations were predominantly observed in non-coding regions such as introns and intergenic regions. The highest over 50% frequencies of alternate alleles were identified in the introns of TNS1, VIL1 and USP37 genes. In the upstream gene regions of the Polish Landrace pigs, were observed more mutations than in the upstream gene regions of Puławska. The present study showed interesting gene variant panel that could be analyzed in the further association studies in order to understand the impact on important productive pig traits.