A two-step Bayesian network approach to identify key SNPs associated to multiple phenotypic traits in four purebred laying hen lines

Ismalia Bouba; Emiliano A Videla Rodriguez; V Anne Smith; Henry van den Brand; T Bas Rodenburg; Bram Visser

doi:10.1371/journal.pone.0297533

A two-step Bayesian network approach to identify key SNPs associated to multiple phenotypic traits in four purebred laying hen lines

PLoS One. 2024 Mar 28;19(3):e0297533. doi: 10.1371/journal.pone.0297533. eCollection 2024.

Authors

Ismalia Bouba^{1

2}, Emiliano A Videla Rodriguez³, V Anne Smith³, Henry van den Brand⁴, T Bas Rodenburg^{2

4}, Bram Visser¹

Affiliations

¹ Hendrix Genetics Research Technology & Services B.v, Hendrix Genetics, Boxmeer, North Brabant, The Netherlands.
² Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
³ School of Biology, University of St Andrews, St Andrews, Scotland, United Kingdom.
⁴ Adaptation Physiology Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, Gelderland, The Netherlands.

Abstract

When purebred laying hen chicks hatch, they remain at a rearing farm until approximately 17 weeks of age, after which they are transferred to a laying farm. Chicks or pullets are removed from the flocks during these 17 weeks if they display any rearing abnormality. The aim of this study was to investigate associations between single nucleotide polymorphisms (SNPs) and rearing success of 4 purebred White Leghorns layer lines by implementing a Bayesian network approach. Phenotypic traits and SNPs of four purebred genetic White Leghorn layer lines were available for 23,000 rearing batches obtained between 2010 and 2020. Associations between incubation traits (clutch size, embryo mortality), rearing traits (genetic line, first week mortality, rearing abnormalities, natural death, rearing success, pullet flock age, and season) and SNPs were analyzed, using a two-step Bayesian Network (BN) approach. Furthermore, the SNPs were connected to their corresponding genes, which were further explored in bioinformatics databases. BN analysis revealed a total of 28 SNPs associated with some of the traits: ten SNPs were associated with clutch size, another 10 with rearing abnormalities, a single SNP with natural death, and seven SNPs with first week mortality. Exploration via bioinformatics databases showed that one of the SNPs (ENAH) had a protein predicted network composed of 11 other proteins. The major hub of this SNP was CDC42 protein, which has a role in egg production and reproduction. The results highlight the power of BNs in knowledge discovery and how their application in complex biological systems can help getting a deeper understanding of functionality underlying genetic variation of rearing success in laying hens. Improved welfare and production might result from the identified SNPs. Selecting for these SNPs through breeding could reduce stress and increase livability during rearing.

Copyright: © 2024 Bouba et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

MeSH terms

Animal Husbandry / methods
Animals
Bayes Theorem
Chickens* / genetics
Female
Housing, Animal
Polymorphism, Single Nucleotide*

Grants and funding

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie [grant number 812777]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.