Inbreeding depression load for litter size in Entrepelado and Retinto Iberian pig varieties1

Analysis of Inbreeding Effects on Survival at Birth of Pannon White Rabbits Using the Inbreeding-Purging Model

Mating between related animals is an inevitable consequence of a closed population structure especially when it coincides with a small population size. As a result, inbreeding depression may be encountered especially when considering fitness traits. However, under certain circumstances, the joint effects of inbreeding and selection may at least partly purge the detrimental genes from the population. In the course of this study, our objective was to determine the status of purging and to quantify the magnitude of the eliminated genetic load for the survival at birth of Pannon White rabbit kits maintained in a closed nucleus population. The evolution of the survival at birth was evaluated by applying the PurgeR R package based on the inbreeding-purging model. In the period from 1992 to 2017, 22.718 kindling records were analyzed. According to the heuristic approach, the purging coefficient reached the maximum possible value of 0.5 when estimating between 1992 and 1997. Based on the expected fitness over generations and on the expressed opportunity of purging, the beneficial effects of purging could be expected after 10 generations. The proportion of the purged genetic load could be between 20% and 60%. While the results obtained are not entirely conclusive, they do raise the possibility that some of the inbreeding load was caused, at least in part, by genes that could be successfully removed from the population by purging.

Estimate of inbreeding depression on growth and reproductive traits in a Large White pig population

With the broad application of genomic information, SNP-based measures of estimating inbreeding have been widely used in animal breeding, especially based on runs of homozygosity. Inbreeding depression is better estimated by SNP-based inbreeding coefficients than pedigree-based inbreeding in general. However, there are few comprehensive comparisons of multiple methods in pigs so far, to some extent limiting their application. In this study, to explore an appropriate strategy for estimating inbreeding depression on both growth traits and reproductive traits in a Large White pig population, we compared multiple methods for the inbreeding coefficient estimation based on both pedigree and genomic information. This pig population for analyzing the influence of inbreeding was from a pig breeding farm in the Inner Mongolia of China. There were 26,204 pigs with records of age at 100 kg (AGE) and back-fat thickness at 100 kg (BF), and 6,656 sows with reproductive records of the total number of piglets at birth (TNB), and the number of alive piglets at birth (NBA), and litter weight at birth. Inbreeding depression affected growth and reproductive traits. The results indicated that pedigree-based and SNP-based inbreeding coefficients had significant effects on AGE, TNB, and NBA, except for BF. However, only SNP-based inbreeding coefficients revealed a strong association with inbreeding depression on litter weight at birth. Runs of homozygosity-based methods showed a slight advantage over other methods in the correlation analysis of inbreeding coefficients and estimation of inbreeding depression. Furthermore, our results demonstrated that the model-based approach (RZooRoH) could avoid miscalculations of inbreeding and inbreeding depression caused by inappropriate parameters, which had a good performance on both AGE and reproductive traits. These findings might improve the extensive application of runs of homozygosity analysis in pig breeding and breed conservation.

Photo Stimulation of Seminal Doses with Red LED Light from Duroc Boars and Resultant Fertility in Iberian Sows

Simple Summary

The main objective of breeding Iberian pigs is the production of high-quality dry cured meat products. As this breed shows a reduced litter size in comparison to the commercial breeds, some previous studies have reported the use of photostimulation of seminal doses as a method for improving the farrowing rate and litter size. The aim of this study was to explore whether the application of a photostimulation procedure to Duroc seminal doses has any beneficial effect on fertility and litter size. Semen samples were obtained from 38 fertile Duroc boars and the fertility study was conducted on two commercial farms using multiparous Iberian sows (farm A, n = 824; farm B, n = 2131), that were randomly assigned to LED (L) or control (C) groups. Post-cervical insemination took place 0 and 24 h after the diagnosis of estrus, with seminal doses from the same ejaculate and same treatment. The photostimulation of the seminal doses had no effect on the reproductive performance (farrowing rate: 91.72% C vs. 90.09% L, litter size: 8.71 ± 0.06 piglets C vs. 8.70 ± 0.05 L, p > 0.05).

Abstract

In pigs, it has been reported that increased farrowing rates and litter size have been induced by photostimulating the seminal doses for artificial insemination with red LED light. As the reproductive characteristics, production system, and outcome parameters of Iberian breed pigs are different from other commercial breeds, the aim of this study was to evaluate the possible effect of illuminating seminal doses from Duroc boars with red LED light and the fertility outcomes of Iberian females. Semen samples were obtained from 38 fertile Duroc boars. Photostimulation of the artificial insemination (AI) seminal doses was carried out by illuminating the samples with a red LED for 10 min, followed by 10 min of darkness, and finally 10 additional minutes of red light. The fertility study was conducted on two commercial farms using multiparous Iberian sows (farm A, n = 824; farm B, n = 2131), that were randomly assigned to LED (L) or control (C) groups. No differences were found between L and C groups in both farms (p > 0.05) for parity, pregnancy rate, duration of pregnancy, farrowing rate, and litter size (total, alive, and stillborn piglets). Farrowing rates in farm A were 88.8% (n = 383) for control and 89.6% (n = 441, p = 0.67) for the LED group. In farm B, farrowing rates were C:90.5% (n = 1030) and L: 90.1% (n = 1101, p = 0.48). In farm A, total born piglets were 8.69 ± 0.11 for C and 8.71 ± 0.11 for L (p = 0.87). In farm B, the results were 8.72 ± 0.7 for C and 8.70 ± 0.06 (p = 0.82) for L. Under the production conditions for the Iberian breed, the photostimulation with red LED light using Duroc pig seminal doses was not effective in improving the fertility of Iberian sows.

Fetal mortality associated with backfat thickness at first mating and first farrowing of the primiparous sows raised in a commercial herd in Thailand

This study aimed to investigate the fetal mortality, including stillborn piglets (SB) and mummified fetuses (MM), in relation to backfat thickness both at first mating (MBF) and at first farrowing (FBF) in 200 primiparous sows accommodated in a commercial breeding herd in Thailand. Backfat thickness of all pigs was measured at P2 position using an A-mode ultrasonography. Based on MBF, the gilts were classified into four groups: MBF1 (≤12.0 mm), MBF2 (>12.0-15.0 mm), MBF3 (>15.0-18.0 mm), and MBF4 (>18.0 mm). According to FBF, the primiparous sows were categorized into four classes: FBF1 (≤15.0 mm), FBF2 (>15.0-18.0 mm), FBF3 (>18.0-21.0 mm), and FBF4 (>21.0 mm). At farrowing, 174 litters were examined for percentage of SB and MM. The results indicated that mean MBF and FBF were 16.7 ± 0.3 mm and 19.6 ± 0.3 mm, respectively. Based on MBF, the pigs in MBF1 significantly possessed higher percentage of MM (13.8 ± 4.5%) than others; meanwhile, SB percentage was not different among groups (P > 0.05). According to FBF, the pigs in FBF4 farrowed the highest percentage of SB (9.1 ± 3.2%) than others, whereas MM percentage was not different among classes (P > 0.05). In summary, backfat thickness of the gilts should be one of the parameters to pay more attention since it is related to fetal mortality of the primiparous sows. The farmers should monitor the backfat thickness not only at the first mating time, but also along the gestation period in order to minimize fetal mortality in the primiparous sows.

Luzhong mutton sheep: inbreeding and selection signatures

Intense artificial selection has been imposed to Luzhong mutton sheep population in the past years. Improvements on growth and reproductive performance are two breeding goals in the present herd. Although some progresses were phenotypically observed possibly due to inbreeding induced by strong selection in terms of these traits, the genomic evaluation was poorly understood. Therefore, a high-density SNP array was used to characterize the pattern of runs of homozygosity (ROH), estimate inbreeding and inbreeding depressions on early growth performance and litter size based upon ROH, and scan positive selection signatures of recent population. Consequently, a low inbreeding level was observed which had negative effects on litter size, but not on early growth performance. And 160 genes were under selection, of which some were reported to be linked to several traits of sheep including body weight, litter size, carcass and meat quality, milk yield and composition, fiber quality and health, and the top genes were associated with growth (growth hormone [GH]- growth hormone receptor [GHR]- Insulin-like growth factor 1 [IGF1] axis) and litter size (bone morphogenic proteins [BMPs]-associated). The effectiveness of previous breeding measures was highlighted, but purging selection was proposed to alleviate the inbreeding depression on litter size, providing some genomic insights to breeding management of Luzhong mutton sheep.

Maternal Transmission Ratio Distortion in Two Iberian Pig Varieties

Transmission ratio distortion (TRD) is defined as the allele transmission deviation from the heterozygous parent to the offspring from the expected Mendelian genotypic frequencies. Although TRD can be a confounding factor in genetic mapping studies, this phenomenon remains mostly unknown in pigs, particularly in traditional breeds (i.e., the Iberian pig). We aimed to describe the maternal TRD prevalence and its genomic distribution in two Iberian varieties. Genotypes from a total of 247 families (dam and offspring) of Entrepelado (n = 129) and Retinto (n = 118) Iberian varieties were analyzed. The offspring were sired by both ungenotyped purebred Retinto and Entrepelado Iberian boars, regardless of the dam variety used. After quality control, 16,246 single-nucleotide polymorphisms (SNPs) in the Entrepelado variety and 9744 SNPs in the Retinto variety were analyzed. Maternal TRD was evaluated by a likelihood ratio test under SNP-by-SNP, adapting a previous model solved by Bayesian inference. Results provided 68 maternal TRD loci (TRDLs) in the Entrepelado variety and 24 in the Retinto variety (q < 0.05), with mostly negative TRD values, increasing the transmission of the minor allele. In addition, both varieties shared ten common TRDLs. No strong evidence of biological effects was found in genes with TRDLs. However, some biological processes could be affected by TRDLs, such as embryogenesis at different levels and lipid metabolism. These findings could provide useful insight into the genetic mechanisms to improve the swine industry, particularly in traditional breeds.

Genetic Association between Swine Leukocyte Antigen Class II Haplotypes and Reproduction Traits in Microminipigs

The effects of swine leukocyte antigen (SLA) molecules on numerous production and reproduction performance traits have been mainly reported as associations with specific SLA haplotypes that were assigned using serological typing methods. In this study, we intended to clarify the association between SLA class II genes and reproductive traits in a highly inbred population of 187 Microminipigs (MMP), that have eight different types of SLA class II haplotypes. In doing so, we compared the reproductive performances, such as fertility index, gestation period, litter size, and number of stillbirth among SLA class II low resolution haplotypes (Lrs) that were assigned by a polymerase chain reaction-sequence specific primers (PCR-SSP) typing method. Only low resolution haplotypes were used in this study because the eight SLA class II high-resolution haplotypes had been assigned to the 14 parents or the progenitors of the highly inbred MMP herd in a previous publication. The fertility index of dams with Lr-0.13 was significantly lower than that of dams with Lr-0.16, Lr-0.17, Lr-0.18, or Lr-0.37. Dams with Lr-0.23 had significantly smaller litter size at birth than those with Lr-0.17, Lr-0.18, or Lr-0.37. Furthermore, litter size at weaning of dams with Lr-0.23 was also significantly smaller than those dams with Lr-0.16, Lr-0.17, Lr-0.18, or Lr-0.37. The small litter size of dams with Lr-0.23 correlated with the smaller body sizes of these MMPs. These results suggest that SLA class II haplotypes are useful differential genetic markers for further haplotypic and epistatic studies of reproductive traits, selective breeding programs, and improvements in the production and reproduction performances of MMPs.