Genomic regions possibly associated with anestrus in gilts.

To this study 239 Landrace x Large White F1 gilts with approximately 230 days from a commercial pig production farm with high sanitary status, located in the Santa Catarina state, Brazil. For DNA extraction, ear tissue were collected from 150 gilts detected with anestrus. The absence of estrus, vulva edema and hyperemia and three consecutive dosages of progesterone below 2.5 ng/mL in an 7 days interval were used to classify the gilts in anestrus (case group). An additional 150 samples were collected from gilts in estrus in a contemporary group, with same line, age, weight, time spent in the fourth place (control group). To be considered in estrus, gilts should be with ovary in luteal phase, and progesterone level above 2.5 ng/mL. To RNA extraction, 20 gilts (10 from each group) were transported to a slaughterhouse where estrus and anestrus were confirmed and hypothalamus and hypophyses samples were collected. DNA extraction and genotyping with PorcineSNP50 BeadChip (Illumina, EUA) from the 300 samples were performed at Neogen (Indaiatuba, São Paulo, Brazil). After received the genotypes, quality control was performed using PLINK v1.9 software. SNPs with call rate below 98%, with significant deviations (p< 1x10-6) from the Hardy-Weinberg equilibrium, and with minor allele frequencies (MAF) lower than 5% and samples with call rates lower than 90% were excluded. For animals, the relationship between animals was estimated based on the genome wide IBD sharing and those samples with more than ±3 standard deviations of heterozygosity and identity by descent - IBD ≥ 98% were also removed. A multidimensional scaling (MDS) analysis was used to detect population structure in PLINK v1.9 software. The linkage disequilibrium (LD) between SNP pairs with a maximum distance of 5 Mb was measured by r2 values for each chromosome using the --indeppairwise parameter in PLINK v1.9 software. An extra genome wide association was also performed using gemma software.