Degree Type

Dissertation

Date of Award

2021

Degree Name

Doctor of Philosophy

Department

Animal Science

Major

Animal Breeding and Genetics (Quantitative Genetics)

First Advisor

Nick VL Serao

Abstract

The objective of this dissertation was to study potential indicator traits for reproductive performance in sows, including testis size, response (antibody and vaginal microbiome) to Porcine Reproductive and Respiratory Syndrome virus (PRRSV), and antibody response to other common infectious pathogens in swine (Mycoplasma hyopneumoniae, MH; swine Influenza A virus, IAV; porcine circovirus type 2, PCV2; and Actinobacillus pleropneumoniae, APP).To determine the effectiveness of measuring testis size in the sires to identify sows with superior reproduction, 161 Yorkshire and Landrace boars were measured for testis width and area, and 384 sows (daughters of 13 of the boars) had farrowing performance recorded. The heritability of testis size traits was high (~0.67). Larger testis width was associated with greater litter size without increasing piglet mortality. These results indicate the possibility of a phenotypic assessment of testis size in sires as a useful tool to cull boars for breeding, improving female performance and the possibility of indirect early selection for female reproductive performance traits in boars. The genetic basis of response to PRRSV vaccination, measured as sample-to-positive (S/P) ratio, was investigated. A total of 906 gilts had blood samples collected at ~50 days after a PRRSV vaccination. From those, 302 gilts had vaginal microbiome data collected at 4 and 52 days after the PRRSV vaccination, and 807 sows had farrowing performance collected. Heritability estimates of the relative abundance of the microbes varied from low to high (~0 – 0.60), and genomic regions were identified that were associated with several microbes, including a potential pleiotropic region on chromosome 12. Estimates of microbiability (i.e., the proportion of the phenotypic variance explained by the microbiome) for reproductive performance and antibody response to PRRSV were, in general, low (<0.15). However, the discriminant analyses revealed that the vaginal microbiota was able to classify gilts into groups of high and low antibody responders to PRRSV vaccination with a misclassification rate of less than 2%. Further, we identified eighteen microbes that were differentially abundant between the low and high reproductive performance sows. The discriminant analyses revealed that the vaginal microbiota was able to classify gilts into groups of high and low reproductive performance with a misclassification rate of less than 12%. Among the microbes that overlapped between these two analyses, Campylobacter, Bacteroides, Porphyromonas, Lachnospiraceae_unclassified, Prevotella, and Phascolarctobacterium are potential biomarkers for reproductive outcomes. In the same project, we investigated the genetic basis of antibody response to PRRSV vaccination, measured as sample-to-positive ratio (S/PVx), as a potential genetic indicator for reproductive performance in commercial sows. Estimates of heritability (~0.38) and genomic prediction accuracy (~0.60) were high. Based on a SNP-based and haplotype-based genome-wide association studies, we identified a major SNP on chromosome 7 with large effects on S/PVx along with several haplotypes on chromosomes 4, 7, and 9 associated with S/PVx. The SNP and haplotype on chromosome 7 were located in the Major Histocompatibility Complex (MHC). In addition, genomic regions with high levels of homozygosity or heterozygosity were associated with S/PVx. Also, S/PVx was favorably genetically correlated with reproductive performance in vaccinated commercial sows and non-infected purebred sows. For example, the genetic correlation of S/PVx with the number of piglets born alive was 0.61 and 0.50 in commercial and purebred sows, respectively. These results suggest that S/PVx could be used as an accurate and efficient genetic indicator to improve reproductive performance. We estimated the genetic correlation of S/PVx with antibody response following a natural PRRSV outbreak (S/POutbreak) to be 0.72, which shows that these two traits are under similar genetic control. In another project, antibody response to IAV, MH, PCV2, and APP were collected for ~2,300 sows in four time-points: at entry into a commercial sow farm, after post-acclimation, during parity 1, and during parity 2. Reproductive data from 1 to 4 parities were available on a subset of 2,000 sows. In general, the heritability estimates were low to moderate, depending on the pathogen and the time of antibody response. Estimates of heritability for antibody response to APP, IAV, MH, and PCV2 ranged from 0 to 0.76. The region on chromosome 14 (2 Mb) was associated with several serotypes of APP, explaining up to 4.3% of the genetic variance. In general, genomic prediction accuracies for antibody response were low to moderate. Estimates of genetic correlation of antibody response to infectious pathogens with lifetime reproductive traits varied with time of antibody collection. Estimates of genetic correlation of antibody responses to PRRSV and MH were mostly negative with lifetime performance, ranging from -0.85 to 0.70. Estimates of genetic correlation of antibody responses to PCV2 and APP MEAN were constantly positive with all reproductive traits, ranging from 0.03 to 0.97. In summary, there was a substantial genetic correlation of antibody response to infectious pathogens with reproductive performance depending on the time of antibody collection. It is worth to investigate this relationship at specific time-points after vaccination or infection as an alternative to select for resilience in commercial sows. In conclusion, we have identified several traits with the potential to be used for culling proposes (e.g., testis size and vaginal microbiome) and genetic selection (e.g., antibody response to PRRSV vaccination and to several other infectious pathogens). Several biomarkers associated with these traits were identified and could be used to improve farrowing performance phenotypically and genetically.

DOI

https://doi.org/10.31274/etd-20210609-145

Copyright Owner

Leticia M Pereira Sanglard

Language

en

File Format

application/pdf

File Size

365 pages

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