A whole-genome association study for litter size and litter weight traits in pigs

A whole-genome association study was performed using the PorcineSNP60 BeadChip and Bayesian statistical method Bayes B for litter size and litter weight traits in sows from a divergent selection experiment for residual feed intake. A total of 12 traits of litter size and litter weight at birth and weaning were included for the first two parities. We report associations of informative QTL and genes associated with each trait. Different QTL and genes had impact on traits in first and second parity. Most of the important multiple trait genomic regions in first parity were found to be associated with litter weight traits at birth. Genes in the identified regions are involved in implantation and placenta (e.g. PPP3CA, ARHGEF17, KLF17 and RNU5A-1) and in energy metabolism (e.g., UCP2/3, MRPL48, GLO1, and MKK6). The QTL associated with litter size at birth and weaning contained genes involved in embryo development and energy balance during lactation (e.g. SCO1, SEMA5A, and ABHD5). Most of the important multiple trait genomic regions for second parity were found to be associated with litter size traits at birth. The regions contain genes for endometrium, placenta and embryonic development (e.g. ZCCHC7, RG9MTD3, LRIG3, TIGD1, and TCP-1). The QTL that contained genes related to placenta, embryonic development and long-term stress (e.g. FTL, NT5C3, and AVL9) were associated with litter weight traits at birth. Further validation studies on larger populations will improve our understanding of the complex genetic basis of litter size and weight traits.