Genetic basis of sow hyperprolificacy and litter size optimization based on a genome-wide association study.

Over the last few decades, there has been a constant increase in sow litter size, the consequences of which include parturition duration extension, an increase in the percentage of stillborn and hypoxic piglets, and increased variation in piglet birth weight, which reduces their vitality. As such, it seems clear that further increasing sow fertility will generate difficulties and costs in rearing numerous litters with low birth weights. Therefore, the current study aimed to analyze the genetic background of sow hyperprolifcacy using a genome-wide association study (GWAS). The research included 144 sows in the maternal component, divided into two equal groups. The first group (control) consisted of females giving birth to the optimal number of piglets in their third and fourth litters (14-16), while the second group (cases) included those with excessive litter size (>16). The analyzed sows were genotyped using Illumina's PorcineSNP60v2 BeadChip microarray, comprising 64,232 single nucleotide polymorphisms (SNPs). Statistical analysis using R included quality control of genotyping data and GWAS analysis based on five logistic regression models (dominant, codominant, overdominant, recessive, and log-additive) with a single SNP marker as the explanatory variable. On this basis, one SNP (SIRI0000069) was identified on chromosome seven within the EFCAB11 (EF-hand calcium binding domain 11) gene that had a statistically significant effect on sow hyperprolificacy. Additionally, ten SNPs (INRA0007631, ALGA0011600, ALGA0043433, ALGA0043428, M1GA0010535 ALGA00443338, ALGA0087116, MARC0056787, ALGA0112928, and ALGA0089047) had a relationship with the analyzed feature at a level close to significance, set at 1-5. These SNPs appear important since they are located on chromosomes on which a large number of quantitative trait loci (QTLs) and SNPs associated with reproductive characteristics, including litter size, have been identified.

Identification of SNP markers for canine mammary gland tumours in females based on a genome-wide association study - preliminary results.

Introduction: The development of genetic research over recent decades has enabled the discovery of new genetic markers, such as single nucleotide polymorphisms (SNPs). This, as well as the full sequencing of the dog genome, has enabled genome-wide association studies (GWAS) to be used in the search for genetic causes of canine mammary tumours (CMTs). Material and Methods: Genotypic data containing 175,000 SNPs, which had been obtained using the Illumina CanineHD BeadChip microarray technique, were available for analysis in this study. The data concerned 118 bitches, including 36 animals with CMT, representing various breeds and age groups. Statistical analysis was performed in two steps: quality control of genotyping data and genome-wide association analysis based on dominant, recessive, overdominant, codominant, and log-additive models with the single SNP effects. Results: A total of 40 different SNPs significantly associated with CMT appearance were detected. Moreover, twelve SNPs showed statistical significance in more than one model. Of all the significant SNPs, two, namely BICF2G630136001 in the overdominant model and TIGRP2P107898_rs9044787 in the log-additive model, reached the 5-8 significance level. The other SNPs were significant to a 1-5 level. Conclusion: In the group of SNPs indicated as significant in the GWAS analysis, several transpired to be localised within genes that may play an important role in CMT.

Insight into the Genetic Population Structure of Wild Red Foxes in Poland Reveals Low Risk of Genetic Introgression from Escaped Farm Red Foxes.

In this study we assessed the level of genetic introgression between red foxes bred on fur farms in Poland and the native wild population. We also evaluated the impact of a geographic barrier and isolation by distance on gene flow between two isolated subpopulations of the native red fox and their genetic differentiation. Nuclear and mitochondrial DNA was collected from a total of 308 individuals (200 farm and 108 wild red foxes) to study non-native allele flow from farm into wild red fox populations. Genetic structure analyses performed using 24 autosomal microsatellites showed two genetic clusters as being the most probable number of distinct populations. No strong admixture signals between farm and wild red foxes were detected, and significant genetic differentiation was identified between the two groups. This was also apparent from the mtDNA analysis. None of the concatenated haplotypes detected in farm foxes was found in wild animals. The consequence of this was that the haplotype network displayed two genetically distinct groups: farm foxes were completely separated from native ones. Neither the River Vistula nor isolation by distance had a significant impact on gene flow between the separated wild red fox subpopulations. The results of our research indicate a low probability of genetic introgression between farm and native red foxes, and no threat to the genetic integrity of this species.

How Selective Breeding Has Changed the Morphology of the American Mink (Neovison vison)-A Comparative Analysis of Farm and Feral Animals.

In this study, we performed a comparative analysis of the morphological traits between feral (n = 43) and farm (n = 200) individuals of the American mink in Poland to address the question of how multigenerational intensive selective breeding has morphologically differentiated these two populations. Nine body measurements and two proportion coefficients were obtained using adult individuals. The significance of differences between population means was assessed using the Wilcoxon test for independent samples, while the Kruskal-Wallis test was used to compare sex-population groups. Spearman's correlation coefficients between measurements were estimated for each population. We also performed Principal Component Analysis (PCA) to identify the variables that were most closely correlated with variation in the trait measurements and to investigate the morphological differences between farm and feral minks. We found that the farm minks exhibited significantly higher mean values for eight out of eleven studied traits. Moreover, significant changes in forelimb length, with no concomitant changes in hindlimb length, were accompanied by differences in body shape: trapezoidal in feral minks and rectangular in farm minks. The PCA suggested an almost complete separation of the two populations and indicated that sexes were quite separate; farm males in particular constitute a wholly discrete cluster. Such a clear differentiation between the two populations and sexes over a period of several decades highlights the intensity of selective breeding in shaping the morphology of these animals.

Admixture analyses and phylogeographic relationships reveal complete genetic distinctiveness of Polish farm and wild red foxes (Vulpes vulpes) and the North American origin of farm-bred individuals.

A number of studies showed that many mtDNA haplotypes were shared among contemporary farm red foxes bred on different continents and the historical wild red foxes of North American origin. Therefore, in this study, the population genetic structure and phylogeographic relationships of Polish red foxes kept on fur farms and their wild conspecifics were investigated to assess the ancestry of the farm red foxes in Poland. A total of 330 tissue samples (200 from farm foxes and 130 from wild foxes) were used for the genetic analyses. Thirty microsatellite loci and two regions of mtDNA were used to assess the level of admixture between farm- and wild red foxes, to construct haplotype networks and create a phylogenetic tree. The genetic structure analysis clearly indicated two genetic clusters as being the most probable number of genetically distinct populations. The fixation index revealed a significant genetic distance between the farm- and wild red fox populations (FST  = 0.27, p < 0.05). Haplotype networks based on frequencies showing relationships between concatenated haplotypes of Polish farm- and wild red foxes and the constructed phylogenetic tree clearly indicated two genetically distinct groups. The results of this study provide strong evidence confirming the North American origin of red foxes bred on Polish farms and the genetic distinctiveness of both studied populations.

Microsatellite polymorphism and its association with body weight and selected morphometrics of farm red fox (Vulpes vulpes L.).

Polymorphism of 30 canine-derived microsatellites was studied in a group of 200 red foxes kept on 2 Polish farms. 22 out of 30 microsatellites were selected to study association between marker genotypes and body weight (BW), body length (BL), body circumference (BC), tail length (TL), ear height (EH), length of the right front limb (FRLL), length of the right rear limb (RRLL), length of the right front foot (FRFL) and length of the right rear foot (RRFL). A total of 112 alleles and 243 genotypes were found at 22 autosomal microsatellite loci. Three monomorphic loci deemed as uninformative were excluded from the study. The association between marker genotypes and the studied traits was analysed using general linear model (GLM) procedure and least squares means (LSM). Linkage disequilibrium (LD) was estimated to assess non-random association between microsatellite loci. Out of 19 microsatellites studied four markers showed no association with the studied traits, three markers had a significant effect on one trait, and another three markers had significant effect on two traits. Among ten microsatellites with significant effect on four economically important traits (BW, BL, BC, TL) four were associated with two characters: marker FH2613 with BW and BC, marker FH2097withBL and BC, marker ZUBECA6 with BW and BC, whereas marker REN75M10 was associated with BL and TL. The strongest LD (r(2) ranged from 0.15 to 0.33) was estimated between nine loci with significant effect on economically important traits (BW, BL, BC, TL).

Statistical aspects of genetic association testing in small samples, based on selective DNA pooling data in the arctic fox.

We analysed data from a selective DNA pooling experiment with 130 individuals of the arctic fox (Alopex lagopus), which originated from 2 different types regarding body size. The association between alleles of 6 selected unlinked molecular markers and body size was tested by using univariate and multinomial logistic regression models, applying odds ratio and test statistics from the power divergence family. Due to the small sample size and the resulting sparseness of the data table, in hypothesis testing we could not rely on the asymptotic distributions of the tests. Instead, we tried to account for data sparseness by (i) modifying confidence intervals of odds ratio; (ii) using a normal approximation of the asymptotic distribution of the power divergence tests with different approaches for calculating moments of the statistics; and (iii) assessing P values empirically, based on bootstrap samples. As a result, a significant association was observed for 3 markers. Furthermore, we used simulations to assess the validity of the normal approximation of the asymptotic distribution of the test statistics under the conditions of small and sparse samples.