Reproductive productivity depend on a complex set of characteristics. The number of piglets at birth (Total number born, Litter size, TNB) and the number of alive piglets at birth (Total number born alive, NBA) are the main indicators of the reproductive productivity of sows in pig breeding. Great hopes are pinned on GWAS (Genome-Wide Association Studies) to solve the problems associated with studying the genetic architecture of reproductive traits of pigs. This paper provides an overview of international studies on SNP (Single nucleotide polymorphism) associated with TNB and NBA in pigs presented in PigQTLdb as “Genome map association”. Currently on the base of Genome map association results 306 SNPs associated with TNB (218 SNPs) and NBA (88 SNPs) have been identified and presented in the Pig QTLdb database. The results are based on research of pigs such as Large White, Yorkshire, Landrace, Berkshire, Duroc and Erhualian. The presented review shows that most SNPs found in chromosome areas where candidate genes or QTLs (Quantitative trait locus) have been identified. Further research in the given direction will allow to obtain new data that will become an impulse for creating breakthrough breeding technologies and increase the production efficiency in pig farming.

Intensive selection raises the efficiency of pig farming considerably, but it also promotes the accumulation of homozygosity, which can lead to an increase in inbreeding and the accumulation of deleterious variation. The analysis of segments homozygous-by-descent (HBD) and non-HBD segments in purebred and crossbred pigs is of great interest. Research was carried out on 657 pigs, of which there were Large White (LW, n = 280), Landrace (LR, n = 218) and F1 female (♂LR × ♀LW) (F1, n = 159). Genotyping was performed using the GeneSeek® GGP Porcine HD Genomic Profiler v1 (Illumina Inc., USA). To identify HBD segments and estimate autozygosity (inbreeding coefficient), we used the multiple HBD classes model. LW pigs exhibited 50,420 HBD segments, an average of 180 per animal; LR pigs exhibited 33,586 HBD segments, an average of 154 per animal; F1 pigs exhibited 21,068 HBD segments, an average of 132 per animal. The longest HBD segments in LW were presented in SSC1, SSC13 and SSC15; in LR, in SSC1; and in F1, in SSC15. In these segments, 3898 SNPs localized in 1252 genes were identified. These areas overlap with 441 QTLs (SSC1—238 QTLs; SSC13—101 QTLs; and SSC15—102 QTLs), including 174 QTLs for meat and carcass traits (84 QTLs—fatness), 127 QTLs for reproduction traits (100 QTLs—litter traits), 101 for production traits (69 QTLs—growth and 30 QTLs—feed intake), 21 QTLs for exterior traits (9 QTLs—conformation) and 18 QTLs for health traits (13 QTLs—blood parameters). Thirty SNPs were missense variants. Whilst estimating the potential for deleterious variation, six SNPs localized in the NEDD4, SEC11C, DCP1A, CCT8, PKP4 and TENM3 genes were identified, which may show deleterious variation. A high frequency of potential deleterious variation was noted for LR in DCP1A, and for LW in TENM3 and PKP4. In all cases, the genotype frequencies in F1 were intermediate between LR and LW. The findings presented in our work show the promise of genome scanning for HBD as a strategy for studying population history, identifying genomic regions and genes associated with important economic traits, as well as deleterious variation.

The most prospective and actual trend in farm animal breeding is studying gene polymorphisms affecting the productive traits. The objective of this investigation was to study the effect of polymorphisms in intron 1 of the swine POU1F1 gene on number of days to 100 kg (days to 100 kg), length of body (LB), backfat thickness (BF), and number of piglets born alive (NBA). Research was conducted on purebred pigs of Landrace (n = 80) and Duroc (n = 100) and crossbred pigs (Landrace × Large White) (n = 192). Insertions/deletions in intron 1 of the POU1F1 gene were defined by the PCR method. In Landrace the frequency of genotypes АА, АВ, and ВВ was 80.0%, 20.0%, and 0.0%; in crossbred pigs it was 63.0%, 29.0%, and 8.0%; and in Duroc it was 100.0%, 0.0%, and 0.0%, respectively. Significant effects of polymorphisms in intron 1 of the POU1F1 gene have been found in Landrace on days to 100 kg and LB and in crossbred pigs on LB and BF. The effect of the POU1F1 gene on NBA was not defined in our population. The obtained results show the possibility of using polymorphism in the 1st intron of the POU1F1 gene as a promising marker in breeding programs for improving growth and meat traits.

Capped hock affects the exterior of pedigree pigs, making them unsalable and resulting in a negative impact on the efficiency of pig-breeding centers. The purpose of this paper was to carry out pilot studies aimed at finding genomic regions and genes linked to the capped hock in pigs. The studies were carried out on Landrace pigs (n = 75) and Duroc pigs (n = 70). To identify genomic regions linked to capped hock in pigs, we used smoothing FST statistics. Genotyping was performed with GeneSeek® GGP Porcine HD Genomic Profiler v1 (Illumina Inc, San Diego, CA, USA). The research results showed 70 SNPs linked to capped hock in Landrace (38 SNPs) and Duroc (32 SNPs). The identified regions overlapped with QTLs related with health traits (blood parameters) and meat and carcass traits (fatness). In total, 31 genes were identified (i.e., 17 genes in Landrace, 14 genes in Durocs). Three genes appeared in both the Landrace and Duroc groups, including A2ML1 (SSC5), ROBO2 (SSC13), and MSI1 (SSC14). We identified genomic regions directly or indirectly linked to capped hock, which thus might contribute to identifying genetic variants and using them as genetic markers in pig breeding.

The aim of the work was to conduct GWAS for Total Number Born (TNB) based on the Gradient Boosting Machine (GBM) algorithm, taking into account additive and dominance effects. The study population consisted of 218 Landrace sows. DNA samples were genotyped using GGP HD Porcine. After filtering, 40358 SNPs are left for further analysis. The target variable is the Total Number Born estimated from the third farrow. To assess the additive (model A) and dominant (model D), the coding 0/1/2 and 0/1/0 were used, respectively. Based on the test results, the top 50 SNPs were selected for each of the models in accordance with the relative importance. Of the top 50 SNPs determined by model D, 36 SNPs were identified based on model A (of which 14 SNPs were included in the top of model A). However, the top 14 SNPs for Model D showed relative importance = 0 for Model A. The genes identified in Models A and D are responsible for Molecular functions: binding (GO: 0005488), catalytic activity (GO: 0003824), and transcriptional regulator activity (GO: 0140110); Biological process: cellular process (GO: 0009987), biological regulation (GO: 0065007), metabolic process (GO: 0008152); Cellular component: part of a cell (GO: 0044464) and a cell (GO: 0005623). Further research will allow a more detailed study of the genetic electrical energy of fertility traits in pigs. The results showed that the dominance effects has additional value for genomic effects that control pig fertility. This research was performed with financial support from the Russian Science Foundation (RSF) 19-76-10012.

We formed three samples: Landrace (L, n = 86), Large White (LW, n = 120), and Duroc pigs (D, n = 140). Three traits investigated: the mean daily gain (ADG), early maturity (DAY100) and limb condition (LEG; good/bad). The PPARD (rs80828473) and VRTN (rs343248943) genes were selected. The effects of genotypes PPARD on ADG and DAY100 were determined in Duroc by the association with these traits. Pigs D of AA, comparing to GG had better ADG by 82.3 (P = 0.01) and DAY100 by 6.5 (P = 0.05). Pigs L with the AA genotype, comparing to the GG genotype, had the best ADGs by 101.0 (P = 0.05) and DAY100 by 13.1 (P = 0.04). The effect of the PPARD in LW is unknown as AA genotype was not detected in LW. For the VRTN gene D pigs of the AG and GG genotype comparing to the AA genotype had the best ADGs by 49.1 (P = 0.03) and 56.5 (P = 0.09); DAY100 by 4.8 (P = 0.03) and 9.7 (P = 0.005). Pigs D of AA genotype (P = 0.01) had the best limbs conformation but demonstrated lower productivity. In Landrace pigs, no differences in ADG and DAY100 associated with the VRTN genotypes were found. The possible reason is the low frequency of the GG genotype in this group. Regarding to the limbs the desired genotype in pigs L is AA (P = 0.05). In Large white pigs a positive effect of the AG genotype on ADG and DAY100 was found, comparing to the AA genotype it was 100.6 g (P = 0.02) and 11.7 days. (P = 0.01). The effect of the VRTN different genotypes on the LW limbs has not been found. Research was performed with the Russian Foundation for Basic Research financial support 19-016-00068 A.