Functional genomics of reproduction in pigs: Are we there yet?

Authors: Nonneman, Danny - Dan; Lents, Clay

Submitted to: Molecular Reproduction and Development
Publication Type: Review Article
Publication Acceptance Date: 6/6/2022
Publication Date: 6/15/2022
Citation: Nonneman, D.J., Lents, C.A. 2022. Functional genomics of reproduction in pigs: Are we there yet?. Molecular Reproduction and Development. 90(7): 436-444. https://doi.org/10.1002/mrd.23625.
DOI: https://doi.org/10.1002/mrd.23625

Interpretive Summary: Reproductive efficiency in pigs has long been a critical area of management and research focus for scientists and the pork industry. Reproductive failure accounts for about 30% of sow removals and most of these are in lower parities, before sows have produced enough piglets to become profitable. Decades ago, it was realized that genetic selection for economically important traits could hasten genetic improvement. Genetic improvement for reproductive traits in pigs has been challenging because these traits are typically lowly heritable, sex-limited, and not realized until later in the animal’s life. Such traits, however, can be improved by selecting on the genetic variants, or DNA markers, that affect their phenotypic expression. Reproductive traits including age at puberty, ovulation rate, increased litter size or number born alive, teat number and testis size (sperm production) in males have been a focus for genetic improvement. Early genomic studies for reproductive traits indicated that genomic regions could be found for economically important traits and genes with large effects could be identified. A refinement of these studies using genome-wide associations with thousands of DNA markers has greatly improved the resolution and revealed that most reproductive traits are controlled by many genes with small effects. Identification of positional candidate genes and finding functional genetic variants within them can lead to a better understanding of the physiological components affecting the expression of these traits and will facilitate a greater understanding necessary to improve and optimize management strategies to maximize reproductive success of gilts and sows.

Technical Abstract: Reproductive failure is the main reason for culling females in swine herds and is both a financial and sustainability issue. Because reproductive traits are complex and lowly to moderately heritable, genomic selection within populations can achieve substantial genetic gain in reproductive efficiency. A better understanding of the physiological components affecting the expression of these traits will facilitate greater understanding of the genes affecting reproductive traits and is necessary to improve and optimize management strategies to maximize reproductive success of gilts and sows. Large-scale genotyping with single-nucleotide polymorphism (SNP) arrays are used for genome-wide association studies (GWAS) and have facilitated identification of positional candidate genes. Transcriptomic data can be used to weight SNP for GWAS and could lead to previously unidentified candidate genes. Resequencing and fine mapping of candidate genes are necessary to identify putative functional variants and some of these have been incorporated into new genotyping arrays. Sequence imputation and genotype by sequence are newer strategies that could reveal novel functional mutations. In this study, these approaches are discussed. Advantages and limitations are highlighted where additional research is needed.