Unraveling gene switches for the regulation of litter size through the study of swine with high and low prolificacy

Abstract

Between 2012 and 2022, the genetic potential for total number of born increased by 2.8 piglets per litter in commercial pigs, for which litter size ranges 13–16 piglets. Conversely, Alentejano pigs, a local breed from Portugal, has an average of 5 piglets, providing an opportunity to investigate different gene interactions related with litter size, and to characterize the biological mechanisms associated with this trait. The effect of breed and season in the gene expression levels of the uterus of Alentejano (AL) and commercial Landrace × Large White gilts was investigated at early gestation (N = 120). Three experimental conditions were established per breed, diestrous (not inseminated), estrous (inseminated), biopsy at d16 and at d30 in 2 seasons (bi-factorial design). Levels of triiodothyronine (T3), thyroxine (T4), progesterone, T3 and T4 in serum were measured using the chemiluminescence immunoassay method. Levels of cortisol in hair were measured by ELISA. During surgeries, count of corpus luteus was obtained and biopsies of uterine tissue were immediately washed in 1× PBS and preserved in Qiagen tissue preservative. Total RNA was extracted, quality was evaluated using fragment analyzer. RNA sequencing was performed generating libraries polyA enriched, paired-end of 150 bp (~40 M reads/sample). Breed and season effects in hormonal levels were investigated using a generalized linear model. Differential gene expression was analyzed using EdgeR, functional impact was analyzed using GeneMania. The effect of breed and season was significant, and T3 and T4 serum concentration are higher in AL gilts (P < 0.001). The results at gene level showed significant differences allowing to identify candidate genes for further downstream analyses. The identified gene networks reveal connections between the endocrinological and the neurological system. In conclusion, the study of breeds that have not been intensively selected for a given trait enables the investigation at molecular level of how genetic variation determines the epistasis and pleiotropic effects on polygenetic traits.