Evidence map›Paper›PMID 38998033›Full record

ArticleAnimals : an open access journal from MDPI2024

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

Clarissa Boschiero, Mahesh Neupane, Liu Yang, Steven G Schroeder, Wenbin Tuo, Li Ma, Ransom L Baldwin, Curtis P Van Tassell, George E Liu

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Animals : an open access journal from MDPI, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Clarissa BoschieroAnimal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.ORCID 0000-0002-6575-5266
Mahesh NeupaneAnimal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.ORCID 0000-0003-0849-4642
Liu YangAnimal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.
Steven G SchroederAnimal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.
Wenbin TuoAnimal Parasitic Diseases Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.ORCID 0000-0002-3764-8981
Li MaDepartment of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA.ORCID 0000-0003-1038-1081
Ransom L BaldwinAnimal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.ORCID 0000-0002-0753-4377
Curtis P Van TassellAnimal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.ORCID 0000-0002-8416-2087
George E LiuAnimal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.ORCID 0000-0003-0192-6705

Funding

USDA National Institute of Food and Agriculture 2019-67015-29321USDA National Institute of Food and Agriculture 2021-67015-33409
6 · The paper itself

Abstract

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.

Indexed as

genomeHolsteinolfactory receptorpresence-absence variation (PAV)

Identifiers

PMID38998033
PMCPMC11240624

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.