Revealing genetic relationships between compounds affecting boar taint and reproduction in pigs.
ABSTRACT Boar taint is characterized by an unpleasant taste or odor in intact male pigs and is primarily attributed to increased concentrations of androstenone and skatole and to a lesser extent by increased indole. The boar taint compounds skatole and indole are produced by gut bacteria, metabolized in the liver, and stored in the fat tissue. Androstenone, on the other hand, is synthesized in the testis along with testosterone and estrogens, which are known to be important factors affecting fertility. The main goal of this study was to investigate the relationship between genetic factors involved in the primary boar taint compounds in an attempt to discover ways to reduce boar taint without decreasing fertility-related compounds. Heritabilities and genetic correlations between traits were estimated for compounds related to boar taint (androstenone, skatole, indole) and reproduction (testosterone, 17β-estradiol, and estrone sulfate). Heritabilities in the range of 0.47 to 0.67 were detected for androstenone concentrations in both fat and plasma, whereas those for skatole and indole were slightly less (0.27 to 0.41). The genetic correlations between androstenone in plasma and fat were extremely high (0.91 to 0.98) in Duroc and Landrace. In addition, genetic correlations between androstenone (both plasma and fat) and the other sex steroids (estrone sulfate, 17β-estradiol, and testosterone) were very high, in the range of 0.80 to 0.95. Furthermore, a genome-wide association study (GWA) and a combined linkage disequilibrium and linkage analysis (LDLA) were conducted on 1,533 purebred Landrace and 1,027 purebred Duroc to find genome regions involved in genetic control of the boar taint compounds androstenone, skatole, and indole, and sex hormones related to fertility traits. Up to 3,297 informative SNP markers were included for both breeds, including SNP from several boar taint candidate genes. From the GWA study, we found that altogether 27 regions were significant at a genome-wide level (P < 0.05) and an additional 7 regions were significant at a chromosomal level. From the LDLA study, 7 regions were significant on a genome-wide level and an additional 7 regions were significant at a chromosomal level. The most convincing associations were obtained in 6 regions affecting skatole and indole in fat on chromosomes 1, 2, 3, 7, 13, and 14, 1 region on chromosome 6 affecting androstenone in plasma only, and 5 regions on chromosomes 3, 4, 13, and 15 affecting androstenone, testosterone, and estrogens.
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ABSTRACT: One of the primary factors contributing to boar taint is the level of androstenone in porcine adipose tissues. A majority of the studies performed to identify candidate biomarkers for the synthesis of androstenone in testis tissues follow a reductionist approach, identifying and studying the effect of biomarkers individually. Although these studies provide detailed information on individual biomarkers, a global picture of changes in metabolic pathways that lead to the difference in androstenone synthesis is still missing. The aim of this work was to identify major pathways and interactions influencing steroid hormone synthesis and androstenone biosynthesis using an integrative approach to provide a bird's eye view of the factors causing difference in steroidogenesis and androstenone biosynthesis. For this purpose, we followed an analysis procedure merging together gene expression data from boars with divergent levels of androstenone and pathway mapping and interaction network retrieved from KEGG database. The interaction networks were weighted with Pearson correlation coefficients calculated from gene expression data and significant interactions and enriched pathways were identified based on these networks. The results show that 1,023 interactions were significant for high and low androstenone animals and that a total of 92 pathways were enriched for significant interactions. Although published articles show that a number of these enriched pathways were activated as a result of downstream signaling of steroid hormones, we speculate that the significant interactions in pathways such as glutathione metabolism, sphingolipid metabolism, fatty acid metabolism and significant interactions in cAMP-PKA/PKC signaling might be the key factors determining the difference in steroidogenesis and androstenone biosynthesis between boars with divergent androstenone levels in our study. The results and assumptions presented in this study are from an in-silico analysis done at the gene expression level and further laboratory experiments at genomic, proteomic or metabolomic level are necessary to validate these findings.PLoS ONE 03/2014; 9(3):e91077. · 3.53 Impact Factor
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ABSTRACT: Androstenone is one of the major compounds responsible for boar taint, a pronounced urine-like odor produced when cooking boar meat. Several studies have identified quantitative trait loci (QTL) for androstenone level on Sus scrofa chromosome (SSC) 6. For one of the candidate genes in the region SULT2A1, a difference in expression levels in the testis has been shown at the protein and RNA level. Haplotypes were predicted for the QTL region and their effects were estimated showing that haplotype 1 was consistently related with a lower level, and haplotype 2 with a higher level of androstenone. A recombinant haplotype allowed us to narrow down the QTL region from 3.75 Mbp to 1.94 Mbp. An RNA-seq analysis of the liver and testis revealed six genes that were differentially expressed between homozygotes of haplotypes 1 and 2. Genomic sequences of these differentially expressed genes were checked for variations within potential regulatory regions. We identified one variant located within a CpG island that could affect expression of SULT2A1 gene. An allele-specific expression analysis in the testis did not show differential expression between the alleles of SULT2A1 located on the different haplotypes in heterozygous animals. However a synonymous mutation C166T (SSC6: 49,117,861 bp in Sscrofa 10.2; C/T) was identified within the exon 2 of SULT2A1 for which the haplotype 2 only had the C allele which was higher expressed than the T allele, indicating haplotype-independent allelic-imbalanced expression between the two alleles. A phylogenetic analysis for the 1.94 Mbp region revealed that haplotype 1, associated with low androstenone level, originated from Asia. Differential expression could be observed for six genes by RNA-seq analysis. No difference in the ratio of C:T expression of SULT2A1 for the haplotypes was found by the allele-specific expression analysis, however, a difference in expression between the C over T allele was found for a variation within SULT2A1, showing that the difference in androstenone levels between the haplotypes is not caused by the SNP in exon 2.BMC Genetics 01/2014; 15(1):4. · 2.36 Impact Factor
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ABSTRACT: As one of the main breeding selection criteria, external appearance has special economic importance in the hog industry. In this study, an Illumina Porcine SNP60 BeadChip was used to conduct a genome-wide association study (GWAS) in 605 pigs of the F2 generation derived from a Large White × Minzhu intercross. Traits under study were abdominal circumference (AC), body height (BH), body length (BL), cannon bone circumference (CBC), chest depth (CD), chest width (CW), rump circumference (RC), rump width (RW), scapula width (SW), and waist width (WW). A total of 138 SNPs (the most significant being MARC0033464) on chromosome 7 were found to be associated with BH, BL, CBC, and RC (P-value = 4.15E-6). One SNP on chromosome 1 was found to be associated with CD at genome-wide significance levels. The percentage phenotypic variance of these significant SNPs ranged from 0.1-25.48%. Moreover, a conditional analysis revealed that the significant SNPs were derived from a single quantitative trait locus (QTL) and indicated additional chromosome-wide significant association for 25 SNPs on SSC4 (BL, CBC) and 9 SNPs on SSC7 (RC). Linkage analysis revealed two complete linkage disequilibrium haplotype blocks that contained seven and four SNPs, respectively. In block 1, the most significant SNP, MARC0033464, was present. Annotations from pig reference genome suggested six genes (GRM4, HMGA1, NUDT3, RPS10, SPDEF and PACSIN1) in block 1 (495 kb), and one gene (SCUBE3) in block 3 (124 kb). Functional analysis indicated that HMGA1 and SCUBE3 genes are the potential genes controlling BH, BL, and RC in pigs, with an application in breeding programs. We screened several candidate intervals and genes based on SNP location and gene function, and predicted their function using bioinformatics analyses.PLoS ONE 08/2014; 9(8):e103766. · 3.53 Impact Factor