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

## TL;DR

This study uses a Bayesian network approach to find genetic markers linked to rearing success in laying hens, aiming to improve welfare and production.

## Contribution

A novel two-step Bayesian network method is applied to identify key SNPs associated with multiple traits in purebred laying hens.

## Key findings

- 28 SNPs were found to be associated with traits like clutch size, rearing abnormalities, and first week mortality.
- One SNP (ENAH) was connected to a protein network involving CDC42, which is important for reproduction and egg production.
- The Bayesian network approach proved effective in uncovering genetic factors influencing rearing success in laying hens.

## 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.