Use of Genome Sequencing for Improved Pig Breeding

Over the last decades major advances in the use of sequence data to improve pig breeding have been achieved. A key achievement was the publication of the pig reference genome and subsequent design of selection single-nucleotide polymorphism (SNP) chips to implement genomic selection. This chapter outlines major advances and future use of genome sequencing for improved pig breeding. It discusses that the breeding community will shift from the use of a single reference genome to a more comprehensive pig pangenome that better covers structural variation. In addition, the impact of deleterious variation and subsequent purging strategies is discussed. It is predicted that the functional genomic information published by the Functional Annotation of Animal Genomes (FAANG) consortium will aid in the discovery of functionally important (regulatory) variation. More specifically, regulatory variants can be discovered with large-scale gene expression data sets to discover expression quantitative trait loci (eQTLs). The annotation can be further improved by mapping regulatory regions in the genome by using-large scale epigenomic data sets that assess chromatin modifications and methylation states. The discovered functional variation can subsequently be used to improve pig breeding by adding functional markers to the selection chips, significantly improving prediction accuracies. Together, the chapter provides a comprehensive overview of the current status and future steps in the use of genome sequencing for pig breeding.