Oestrogen receptor genotypes and litter size in Hungarian Large White pigs

Integration of multi-omics data reveals cis-regulatory variants that are associated with phenotypic differentiation of eastern from western pigs

Background

The genetic mechanisms that underlie phenotypic differentiation in breeding animals have important implications in evolutionary biology and agriculture. However, the contribution of cis-regulatory variants to pig phenotypes is poorly understood. Therefore, our aim was to elucidate the molecular mechanisms by which non-coding variants cause phenotypic differences in pigs by combining evolutionary biology analyses and functional genomics.

Results

We obtained a high-resolution phased chromosome-scale reference genome with a contig N50 of 18.03 Mb for the Luchuan pig breed (a representative eastern breed) and profiled potential selective sweeps in eastern and western pigs by resequencing the genomes of 234 pigs. Multi-tissue transcriptome and chromatin accessibility analyses of these regions suggest that tissue-specific selection pressure is mediated by promoters and distal cis-regulatory elements. Promoter variants that are associated with increased expression of the lysozyme (LYZ) gene in the small intestine might enhance the immunity of the gastrointestinal tract and roughage tolerance in pigs. In skeletal muscle, an enhancer-modulating single-nucleotide polymorphism that is associated with up-regulation of the expression of the troponin C1, slow skeletal and cardiac type (TNNC1) gene might increase the proportion of slow muscle fibers and affect meat quality.

Conclusions

Our work sheds light on the molecular mechanisms by which non-coding variants shape phenotypic differences in pigs and provides valuable resources and novel perspectives to dissect the role of gene regulatory evolution in animal domestication and breeding.

Polymorphism of candidate genes associated with reproductive performance in crossbred pigs

This investigation was done to analyze the polymorphism of 5 SNPs in candidate genes associated with reproductive performance in crossbred pig population by PCR-RFLP. The results revealed that out of 5 SNPs genotyped, 2 were polymorphic and 3 were monomorphic. Genotypic frequency of crossbred pigs were CC (100%) for ESR1; GG (21%), GT 65%) and TT (14%) for Prei3; CC (100%) for FSHβ; AA (100%) for OPN and CC (21%), CT (63%) and TT (16%) for CDK20 SNPs, respectively. Allelic frequencies for these SNPs {ESR1 (c.1227C>T), Prei3 (T802G), FSHβ (c.930A>G), OPN (c.425G>A) and CDK20 (T96C)} were 1.00 (C), 0.53 and 0.47 (G/T), 1.00 (C), 1.00 (A) and 0.52 and 0.48 (C/T), respectively. The least squares analysis revealed that both polymorphic SNPs had non-significant effect on litter traits. The values of PIC, heterozygosity and allelic diversity indicated that crossbred population under investigation was of intermediate diversity for both polymorphic SNP loci.

Genetic effect and combined genotype effect of ESR, FSHβ, CTNNAL1 and miR-27a loci on litter size in a Large White population

To select new Large White line with high number of piglets born, genotypes of estrogen receptor (ESR), the follicle stimulating hormone β subunit (FSHβ), catenin alpha like 1 (CTNNAL1) and miR-27a were tested in 472 Large White sows. The associations of different genotypes with litter size traits were also studied. The results showed ESR^BB and FSHβ^BB sows produced 0.41-1.49 more pigs per litter (p < .05) for total number born (TNB) and number born alive (NBA) than did other corresponding genotypes. TNB of CTNNAL1^CG sows is 0.50 more pigs per litter (p < .05) than that of CTNNAL1^GG sows with the dominance effect of 0.25 pigs per litter (p < .05). miR-27a^BB sows had a less estimated breeding value (EBV) to TNB and had a more number of mummified pigs (NM) than did miR-27a^AA or miR-27a^AB sows (p < .05). Therefore, ESR^B, FSHβ^B, CTNNAL1^G, miR-27a^A allele was favorable for litter size traits. Furthermore, combined genetic effect analysis showed ESR^AAFSHβ^BB, ESR^AACTNNAL1^CG, ESR^AAmiR-27a^AA, FSHβ^BBCTNNAL1^CC, FSHβ^BBmiR-27a^AA and CTNNAL1^CG miR-27a^AB was the favorable combined genotype for litter size traits. These results identified favorable alleles and genotypes for litter size traits and suggested a potential selection scheme for litter size in Large White pigs.

Single step genome-wide association studies based on genotyping by sequence data reveals novel loci for the litter traits of domestic pigs

In this study, data genotyping by sequence (GBS) was used to perform single step GWAS (ssGWAS) to identify SNPs associated with the litter traits in domestic pigs and search for candidate genes in the region of significant SNPs. After quality control, 167,355 high-quality SNPs from 532 pigs were obtained. Phenotypic traits on 2112 gilt litters from 532 pigs were recorded including total number born (TNB), number born alive (NBA), and litter weight born alive (LWB). A single-step genomic BLUP approach (ssGBLUP) was used to implement the genome-wide association analysis at a 5% genome-wide significance level. A total of 8, 23 and 20 significant SNPs were associated with TNB, NBA, and LWB, respectively, and these significant SNPs accounted for 62.78%, 79.75%, and 58.79% of genetic variance. Furthermore, 1 (SSC14: 16314857), 4 (SSC1: 81986236, SSC1: 66599775, SSC1: 161999013, and SSC1: 267883107), and 5 (SSC9: 29030061, SSC2: 32368561, SSC5: 110375350, SSC13: 45619882 and SSC13: 45647829) significant SNPs for TNB, NBA, and LWB were inferred to be novel loci. At SSC1, the AIM1 and FOXO3 genes were found to be associated with NBA; these genes increase ovarian reproductive capacity and follicle number and decrease gonadotropin levels. The genes SLC36A4 and INTU are involved in cell growth, cytogenesis and development were found to be associated with LWB. These significant SNPs can be used as an indication for regions in the Sus scrofa genome for variability in litter traits, but further studies are expected to confirm causative mutations.

Gene networks for total number born in pigs across divergent environments

For reproductive traits such as total number born (TNB), variance due to different environments is highly relevant in animal breeding. In this study, we aimed to perform a gene-network analysis for TNB in pigs across different environments using genomic reaction norm models. Thus, based on relevant single-nucleotide polymorphisms and linkage disequilibrium blocks across environments obtained from GWAS, different sets of candidate genes having biological roles linked to TNB were identified. Network analysis across environment levels resulted in gene interactions consistent with known mammal's fertility biology, captured relevant transcription factors for TNB biology and pointing out different sets of candidate genes for TNB in different environments. These findings may have important implication for animal production, as optimal breeding may vary depending on later environments. Based on these results, genomic diversity was identified and inferred across environments highlighting differential genetic control in each scenario.

Association of BF, RBP4, and ESR2 Genotypes with Litter Size in an Autochthonous Pig Population

The aim of the present study was to determine any potential association of the BF, RBP4, and ESR2 genes with reproduction traits in an autochthonous Greek pig population. The PCR-RFLP methodology was implemented for genotyping purposes of the examined genes. No deviation from the Hardy-Weinberg equilibrium was observed for the examined loci, while the B allele noted to be the more frequent in all analyzed genes. In addition, sows with the AA genotype of BF gene found to produce significantly lower numbers of the total born piglets (TNB) and number of piglets born alive (TNA), while the respective BB genotype significantly exceeded in TNB and NBA traits compared to the other two genotypes (P < 0.001). In the case of RBP4 gene, sows with the AB genotype noted to have significant higher values of TNB and NBA in regard to the respective homozygous genotypes (AA or BB), while the BB genotype showed intermediate results (P < 0.001). There were no statistical differences between the BB genotype and the AB genotype of ESR2 locus in regard to the examined traits. However, a noticeable superiority (P < 0.01) of the BB genotype compared to the homozygous AA genotype, adding almost 2 piglets/litter in TNB and NBA trait, was found.

ABBREVIATIONS

TNB: Total number of born piglets; NBA: Number of piglets born alive.

A genome-wide linkage analysis for reproductive traits in F2 Large White × Meishan cross gilts

Female reproductive performance traits in pigs have low heritabilities thus limiting improvement through traditional selective breeding programmes. However, there is substantial genetic variation found between pig breeds with the Chinese Meishan being one of the most prolific pig breeds known. In this study, three cohorts of Large White × Meishan F2 cross-bred pigs were analysed to identify quantitative trait loci (QTL) with effects on reproductive traits, including ovulation rate, teat number, litter size, total born alive and prenatal survival. A total of 307 individuals were genotyped for 174 genetic markers across the genome. The genome-wide analysis of the trait-recorded F2 gilts in their first parity/litter revealed one QTL for teat number significant at the genome level and a total of 12 QTL, which are significant at the chromosome-wide level, for: litter size (three QTL), total born alive (two QTL), ovulation rate (four QTL), prenatal survival (one QTL) and teat number (two QTL). Further support for eight of these QTL is provided by results from other studies. Four of these 12 QTL were mapped for the first time in this study: on SSC15 for ovulation rate and on SSC18 for teat number, ovulation rate and litter size.

QTL and candidate genes for fecundity in sows

Fecundity in pigs is a trait of major economic interest but low heritability. For the improvement of fecundity, genetic markers for selection are desirable and therefore, several searches for genetic variation influencing fecundity have been performed. The aim of this review is to compare and to evaluate all published QTL analyses and candidate gene approaches concerning reproductive traits in sows. For this purpose, we present a comprehensive cytogenetic map comprising 54 QTL and 11 candidate genes with influence on reproductive traits. The evaluation and comparison of the results showed similarities, but also marked differences among studies. Reasons for different results are multicausal and are due to differences between resource populations, number of evaluated animals, mating systems, measured phenotypical traits and environmental influences. We could show that chromosome 8 and to a lower extend chromosome 7 are the most important chromosomes with regard to reproductive traits in pigs. For further research, fine mapping of the identified QTL regions is necessary in order to confirm and to narrow the most likely chromosomal intervals. Although difficult to perform, an advance would be a standardization of the experimental setup in particular, in respect to the collection of phenotypic data. Furthermore, we suggest to publish the information on further identified QTL and candidate genes as comprehensive and accurate as possible in order to allow a more transparent comparison and collation of the results.

Study on the Association Between Estrogen Receptor Gene (ESR) and Reproduction Traits in Landrace Pigs

To study the potential use of estrogen receptor gene (ESR) as a genetic marker to improve the reproductive traits of pigs, the genotypes of the ESR PCR product digested by Pvu II were determined in 2,239 litters from 612 Landrace sows. The data of the first, second, and later parities were separately evaluated. Although the frequency of the B allele was much lower than that of the A allele, likelihood ratio test showed that the gene frequencies were in Hardy-Weinberg equilibrium. The effects of ESR of different parities were not equal. In summary, the sows with the BB genotype showed better performance for total number of piglets born (TNB) and number of piglets born alive (NBA), but had a lower average piglet weight at birth (AWB). It was concluded that ESR could be used as a marker for the selection of litter size in the Landrace population.