A Pilot Detection and Associate Study of Gene Presence-Absence Variation in Holstein Cattle

Area of Science:

• Genomics
• Animal Genetics
• Bioinformatics

Background:

• Presence-absence variations (PAVs) are crucial structural variations impacting gene content.
• PAV research in cattle is limited compared to plants.
• Understanding PAVs is vital for improving economically important traits in livestock.

Purpose of the Study:

• To identify PAVs in Holstein bulls using whole-genome sequencing data.
• To investigate the association of PAVs with 46 economically important traits in cattle.
• To explore the functional enrichment of variable gene categories (softcore, shell, cloud).

Main Methods:

• Whole-genome sequencing of 173 Holstein bulls.
• Identification and classification of genes into core, softcore, shell, and cloud categories.
• PAV-based genome-wide association studies (GWAS) for trait associations.

Main Results:

• Identified 26,979 core genes and variable genes (softcore, shell, cloud).
• Cloud genes are enriched in hormonal and antimicrobial functions; shell genes in immune functions.
• Discovered associations between PAVs and 16 traits, including milk yield, fat, protein, health, and reproduction, notably on chromosomes 7 and 15.

Conclusions:

• PAVs significantly contribute to genetic variation and trait diversity in Holstein cattle.
• PAV-based GWAS provides valuable insights into the genetic architecture of complex traits.
• This research highlights the importance of considering PAVs for cattle breeding and genetic improvement programs.