Skip to main content
ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #415273
Research Project: Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: A pilot detection and associate study of gene presence-absence variation in Holstein cattle

Author
item BOSCHIERO, CLARISSA - University Of Maryland
item Neupane, Mahesh
item YANG, LIU - University Of Maryland
item Schroeder, Steven - Steve
item Tuo, Wenbin
item MA, LI - University Of Maryland
item Baldwin, Ransom - Randy
item Van Tassell, Curtis - Curt
item Liu, Ge - George

Submitted to: Animals
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/26/2024
Publication Date: 6/28/2024
Citation: Boschiero, C., Neupane, M., Yang, L., Schroeder, S.G., Tuo, W., Ma, L., Baldwin, R.L., Van Tassell, C.P., Liu, G. 2024. A pilot detection and associate study of gene presence-absence variation in Holstein cattle. Animals. 14(13):1921. https://doi.org/10.3390/ani14131921.
DOI: https://doi.org/10.3390/ani14131921

Interpretive Summary: PAV, or presence-absence variation, means that some individuals have certain genes, while others don't in one species. We used computer tools to detect PAVs and study their impacts on Holstein cattle traits. These findings address gaps in our understanding and lay the groundwork for integrating PAV into future animal breeding programs as an assessment or prediction tool. Farmers, scientists, and policy planners who need to improve animal health and production based on genome enabled animal selection will benefit from this study.

Technical Abstract: Presence-absence variations (PAVs) represent an important form of structural variation (SV), wherein a genomic segment containing one or more genes is present in some individuals but absent in others. While PAVs have been extensively studied in plants, research in animals, particularly cattle, remains limited. This study identified PAVs in 173 Holstein bulls using whole genome sequencing data and assessed their associations with 46 economically important traits. Out of 28,772 evaluated genes, an average of 98.06% were present and 1.94% were absent in the 173 animals. A total of 1,793 genes were found to be absent in at least one animal, including olfactory receptor (OR) and other protein-coding gene families, tRNAs, microRNAs, as well as uncharacterized genes. Core genes (present in all individuals) comprised 93.77% of the gene pool, while variable genes included 928 softcore (present in 95-99% of individuals), 494 shell (present in 5-94%), and 371 cloud genes (present in < 5%). Cloud genes were enriched in functions associated with hormonal and antimicrobial activities, while shell genes were enriched in immune functions. As expected, principal component analysis (PCA) and phylogenetic analysis of gene PAVs showed high genetic similarity among the Holstein cattle, with only a few animals clustering separately. PAV-based genome-wide association studies (GWAS) identified associations between gene PAVs and 15 traits including milk, fat and protein yields, and those related to health (metritis) and reproduction. Associations were found on multiple chromosomes, illustrating important associations on BTA15 and 7, involving OR and immune-related genes, respectively. By examining the PAVs at the population level, the results of this research provided crucial insights into the genetic structures underlying the complex traits of Holstein cattle.