Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled...

Area of Science:

• Animal Genetics
• Genomics
• Quantitative Trait Genetics

Background:

• The somatotrophic axis is crucial for animal growth, development, and fertility.
• Identifying genetic variants affecting these traits is important but challenging due to high sequencing costs.
• DNA pooling with target enrichment offers a cost-effective solution for large-scale genetic studies.

Purpose of the Study:

• To identify genetic polymorphisms and estimate allele frequency differences in 83 candidate genes of the somatotrophic axis.
• To investigate genetic variation related to fertility in Holstein-Friesian dairy bulls.
• To evaluate the efficacy of pooled DNA sequencing for genetic variant discovery.

Main Methods:

• Target enrichment and high-throughput sequencing of 83 candidate genes in 150 Holstein-Friesian dairy bulls.
• DNA samples were pooled from bulls divergent for genetic merit for fertility.
• Polymorphism discovery (SNPs and indels) and allele frequency estimation were performed.

Main Results:

• Over 4,135 SNPs and 893 indels were identified across the candidate genes.
• Significant allele frequency differences (P < 0.01) were found for 720 SNPs between high and low fertility groups.
• Genotyping of individual animals validated the allele frequency estimations from pooled DNA.

Conclusions:

• DNA pooling coupled with high-throughput sequencing is a viable strategy for polymorphism discovery and allele frequency estimation in livestock.
• This study characterized genetic variation in the somatotrophic axis, identifying variants potentially influencing fertility.
• This is the first report of targeted sequencing in livestock using divergent phenotypes for an economically important trait.