# A comparison of five sets of overlapping and non-overlapping sliding windows for semen production traits in the Thai multibreed dairy population

## TL;DR

This study compares different SNP window sizes to understand genetic factors affecting semen traits in Thai dairy bulls.

## Contribution

The study introduces a comparison of overlapping and non-overlapping SNP windows for identifying shared genetic pathways in semen traits.

## Key findings

- Overlapping SNP windows identified more shared biological pathways and genes than non-overlapping windows.
- SW30 and SW50 overlapping windows detected the highest number of shared pathways and genes.
- The study provides insights into the genetic architecture of semen production traits in Thai multibreed dairy bulls.

## Abstract

This study compared five distinct sets of biological pathways and associated genes related to semen volume (VOL), number of sperm (NS), and sperm motility (MOT) in the Thai multibreed dairy population.

The phenotypic data included 13,533 VOL records, 12,773 NS records, and 12,660 MOT records from 131 bulls. The genotypic data consisted of 76,519 imputed and actual single nucleotide polymorphisms (SNPs) from 72 animals. The SNP additive genetic variances for VOL, NS, and MOT were estimated for SNP windows of one SNP (SW1), ten SNP (SW10), 30 SNP (SW30), 50 SNP (SW50), and 100 SNP (SW100) using a single-step genomic best linear unbiased prediction approach. The fixed effects in the model were contemporary group, ejaculate order, bull age, ambient temperature, and heterosis. The random effects accounted for animal additive genetic effects, permanent environment effects, and residual. The SNPs explaining at least 0.001% of the additive genetic variance in SW1, 0.01% in SW10, 0.03% in SW30, 0.05% in SW50, and 0.1% in SW100 were selected for gene identification through the NCBI database. The pathway analysis utilized genes associated with the identified SNP windows.

Comparison of overlapping and non-overlapping SNP windows revealed notable differences among the identified pathways and genes associated with the studied traits. Overlapping windows consistently yielded a larger number of shared biological pathways and genes than non-overlapping windows. In particular, overlapping SW30 and SW50 identified the largest number of shared pathways and genes in the Thai multibreed dairy population.

This study yielded valuable insights into the genetic architecture of VOL, NS, and MOT. It also highlighted the importance of assessing overlapping and non-overlapping SNP windows of various sizes for their effectiveness to identify shared pathways and genes influencing multiple traits.