Unravelling the Genetic Mechanisms of Litter Traits in a Maternal Line of Pigs

Reproductive traits related to litter size are the main indicators of reproductive efficiency in pig production and are continuously evaluated for the selection of maternal lines. Several environmental and genetic factors are involved with the development of these traits. Genome-wide association studies (GWAS) allow a better understanding of the genetic control of complex traits, especially those with low heritability (h²). Therefore, this study aims to estimate the genetic parameters and to identify genomic regions and candidate genes associated with total number born (TNB), number born alive (NBA), and viable piglets at Day 5 (PV5) in a Large White female line. For this, 17,011 phenotypic records, 190,000 pedigree records, and 4366 animals genotyped with the Illumina 50 K and 80 K panels were used. Estimates of h², genetic (r_g) and phenotypic (r_p) correlations, and GWAS were performed with the BLUPF90 family programs. Positional candidate genes, their main biological processes, and networks were investigated using the Ensembl database and the BioMart, PANTHERdb, and STRING tools. The studied traits presented low h² estimates, but with high and positive r_g and r_p. In the GWAS, 14 significant genomic windows were identified for TNB, 10 for NBA, and 15 for PV5. These regions include 157 genes for TNB, 101 for NBA, and 140 for PV5, mapped across 10 different chromosomes. Among the genes located in those regions, the ESR1, THRB, SLIT2, and ZBTB2 were common to the three traits and are involved in processes of hormonal regulation, embryogenesis, immunity, and homeostasis. Moreover, 12 of those genes were new positional candidates for TNB, NBA, or PV5. Among them, we highlight the FSTL4, PAPPA, and TCF7 genes associated with PV5, which are involved with hormonal regulation, growth factors, and immunity, respectively. The SLIT2, MTHFD1L, OVOL2, SHB, and EXOSC3 genes, involved with embryogenesis and neurogenesis, were associated with TNB and NBA. Furthermore, uncharacterized genes, such as ENSSSCG00000058091, related to mitochondrial homeostasis, were associated with TNB, while ENSSSCG00000040472, related to protein synthesis, was identified for PV5. These new findings reveal common and exclusive genetic mechanisms that may influence important litter traits in pigs, helping the development of breeding strategies to optimise reproductive efficiency.