Swine

Consistent litters or a genetic lottery? The genomic drivers of litter size variability in Landrace pigs

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Abstract

Traditional pig breeding programs prioritize the genetic enhancement of economically valuable traits related to production and reproduction. Beyond this conventional focus, selection for uniformity would be particularly beneficial for reproductive traits in pigs. The reproductive phenotypes of litter size and its variability are characterized by low heritability and substantial genomic complexity. Many genome-wide association studies (GWAS) have been conducted in pigs to systematically identify chromosomal regions and candidate genes underlying the genetic basis of litter traits, which is crucial for accelerating genetic improvement. To improve the power and reliability of genome-wide association studies (GWAS), whole-genome sequencing (WGS) data is used. Thus, the purpose of this study was to use WGS data to investigate the genetic architecture underlying variation of litter size in a Landrace pig population. We used ~160,00 litter records on the total number born (TNB) from ~40,000 sequenced Landrace sows. Since the original phenotypic data were skewed, we performed a Box-Cox transformation (bcTNB). Initially, variance components and heritability were estimated using ASReml for TNB and bcTNB. Based on the residuals from these models, the phenotypic variability was obtained as the log-transformed variance of residuals (LnVar_TNB and LnVar_bcTNB). Variance components were subsequently estimated for both variability traits. Lastly, LnVar_TNB and LnVar_bcTNB were evaluated in a GWAS run in GCTA using a mixed model, with ~30,000,000 SNPs available for all sows. Our previous study, 660K SNP-chip data, identified significant genomic regions on SSC3, SSC10, and SSC13 associated with litter size variability. That analysis highlighted STAG3, ESRRG, and MFN1, genes involved in gametogenesis and embryonic development, as strong positional candidates. Thus, this study aims to determine if these associations are confirmed using whole-genome sequencing and whether the increased marker density allows for more precise fine-mapping of the signals in these regions. In conclusion, this study confirms that litter size variability (LnVar_bcTNB), derived from Box-Cox transformed data, is a heritable trait, providing a robust quantitative basis for further analysis. The high resolution of WGS data not only validated the genomic regions previously associated with variability on SSC3, SSC10, and SSC13, but also allowed for precise fine-mapping of these loci, substantially strengthening the candidacy of STAG3, ESRRG, and MFN1.

Keywords: 2026

How to Cite:

Boshove, A., CieleÅ„, G., Derks, M. & Sell-Kubiak, E., (2026) “Consistent litters or a genetic lottery? The genomic drivers of litter size variability in Landrace pigs”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286038. doi: https://doi.org/10.31274/wcgalp.23843

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