A Pilot Detection and Associate Study of Gene Presence-Absence Variation in Holstein Cattle
Open accessAbstract
Presence-absence variations (PAVs) are important structural variations, 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 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 cattle genes (from the longest transcripts), a total of 26,979 (93.77%) core genes were identified (present in all individuals), 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. PAV-based genome-wide association studies identified associations between gene PAVs and 16 traits including milk, fat, and protein yields, as well as traits related to health and reproduction. Associations were found on multiple chromosomes, illustrating important associations on cattle chromosomes 7 and 15, involving olfactory receptor 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.
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The linear model fundamentally fails to capture the full genetic diversity, such as SVs and PAVs, particularly in non-reference populations like Bos indicus.
“While invaluable, this linear model fundamentally fails to capture the full genetic diversity, such as SVs and presence/absence variations (PAVs) [182], particularly in non-reference populations like Bos indicus [180].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [182]
The Discussion (no page given) says the linear reference genome assembly constrained detection of PAVs, and the Introduction identifies PAVs as a form of SV. It does not establish that the linear model fundamentally fails to capture SVs generally. The Bos indicus clause carries a different citation, so it is not assessed against this source. (LLM, conf=0.84)
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References 82 · Cited by 5
- Authors
- Boschiero, C., Neupane, M., Yang, L., Schroeder, S. G., Tuo, W., Ma, L., Baldwin, R. L., Van Tassell, C. P., & Liu, G. E.
- Affiliations
- Agricultural Research Service (US)
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
- University of Maryland, College Park (US)
- Corresponding author
- Liu, George E.
- ORCID
- Venue
- Animals
- Publisher
- MDPI AG
- Published
- 2024-06-28
- Volume
- 14
- Issue
- 13
- Pages
- 1921
- ISSN
- 2076-2615 (ISSN-L)
- PMC
- PMC11240624
- OpenAlex
- W4400209420
- Cited by
- 5
- References
- 82
- Citations by year
- 2026: 4 · 2025: 1
- FWCI
- 1.33
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Animals (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- U.S. Department of Agriculture (8042-31000-112-000-D, 8042-31000-113-000-D, 8042-32000-116-000-D, 2019-67015-29321, 2021-67015-33409)
- AFRI (8042-31000-112-000-D, 8042-31000-113-000-D, 8042-32000-116-000-D, 2019-67015-29321, 2021-67015-33409)
- USDA National Institute of Food and Agriculture (8042-31000-112-000-D, 8042-31000-113-000-D, 8042-32000-116-000-D, 2019-67015-29321, 2021-67015-33409)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- presence/absence variation, Holstein cows, structural variants, genome-wide association study, milk yield, fat yield, protein yield, reproductive traits, immune-related genes, olfactory receptor genes
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