Genomics and systems biology of boar taint and meat quality in pigs

TY - ABST

T1 - Genomics and systems biology of boar taint and meat quality in pigs

AU - Drag, Markus

AU - Kogelman, Lisette JA

AU - Meinert, Lene

AU - Maribo, Hanne

AU - Kadarmideen, Haja N

PY - 2015

Y1 - 2015

N2 - Boar taint (BT) is an offensive odour or taste of cooked porcine meat which may occur in entire male pigs due to skatole and androstenone accumulation in the adipose tissue. To avoid BT, surgical castration of young piglets is performed but castration is undesirable due to animal welfare concerns, economic losses associated with castrated pigs and a ban on castration in the EU effective by 2018. The main objective of the PhD project is to unravel the underlying mechanisms of BT at the genomic, transcriptomic and phenotypic levels as well as its connection with sensory meat quality (SMQ) in order to enable optimized breeding strategies as alternative to castration. Male pigs with different genetic merit of BT were selected and tissue from liver and testes were subjected to transcriptomic profiling by stranded paired end RNA-Seq which produced ~30 mio. reads per sample. The reads were subjected to quality control by FASTQC and later pre-processed with Cutadapt and Trimmomatic. The reads were mapped with STAR aligner which resulted in ~87% uniquely mapped reads per sample. Post-processing quality control with Qualimap revealed ~51% of reads mapped in the exonic region and a mean mapping quality of ~52. Gene expression levels were quantified by HTseq. Genotypic profiling by 60K Porcine SNPchip was performed and selected cuts from fore-end, loin, ham and backfat of the pigs was subjected to SMQ assessments. Combining SNPchip, RNA-seq and SMQ data will reveal causative genes, co-expression networks and find biomarkers for BT phenotypes. Candidate biomarkers will be validated by qPCR and intended for use in optimized breeding strategies to avoid BT without compromising SMQ in a non-castration scenario.

AB - Boar taint (BT) is an offensive odour or taste of cooked porcine meat which may occur in entire male pigs due to skatole and androstenone accumulation in the adipose tissue. To avoid BT, surgical castration of young piglets is performed but castration is undesirable due to animal welfare concerns, economic losses associated with castrated pigs and a ban on castration in the EU effective by 2018. The main objective of the PhD project is to unravel the underlying mechanisms of BT at the genomic, transcriptomic and phenotypic levels as well as its connection with sensory meat quality (SMQ) in order to enable optimized breeding strategies as alternative to castration. Male pigs with different genetic merit of BT were selected and tissue from liver and testes were subjected to transcriptomic profiling by stranded paired end RNA-Seq which produced ~30 mio. reads per sample. The reads were subjected to quality control by FASTQC and later pre-processed with Cutadapt and Trimmomatic. The reads were mapped with STAR aligner which resulted in ~87% uniquely mapped reads per sample. Post-processing quality control with Qualimap revealed ~51% of reads mapped in the exonic region and a mean mapping quality of ~52. Gene expression levels were quantified by HTseq. Genotypic profiling by 60K Porcine SNPchip was performed and selected cuts from fore-end, loin, ham and backfat of the pigs was subjected to SMQ assessments. Combining SNPchip, RNA-seq and SMQ data will reveal causative genes, co-expression networks and find biomarkers for BT phenotypes. Candidate biomarkers will be validated by qPCR and intended for use in optimized breeding strategies to avoid BT without compromising SMQ in a non-castration scenario.

M3 - Conference abstract in proceedings

SP - 79

BT - International Symposium on Animal Functional Genomics - 2015 Proceedings

T2 - International Symposium on Animal Functional Genomics

Y2 - 27 July 2015 through 29 July 2015

ER -