Evidence map›Paper›PMID 42399265›Full record

ArticleNature communications2026

Pangenome-based structural variant imputation enables large-scale genotype-phenotype studies in dairy cattle.

Liu Yang, Junjian Wang, Kristen Kuhn, Wenli Li, Geoffrey Zanton, Mahesh Neupane, Clarissa Boschiero, John B Cole, Bingjie Li, Congjun Li and 8 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
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

18 authors.

Liu Yang *Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.ORCID http://orcid.org/0000-0002-4179-8587
Junjian Wang *Department of Animal Science, North Carolina State University, Raleigh, NC, USA.ORCID http://orcid.org/0000-0003-4824-9617
Kristen KuhnUSDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, USA.ORCID http://orcid.org/0009-0009-9498-8788
Wenli LiUS Dairy Forage Research Center, USDA-ARS, Madison, WI, USA.
Geoffrey ZantonUS Dairy Forage Research Center, USDA-ARS, Madison, WI, USA.ORCID http://orcid.org/0000-0002-6946-540X
Mahesh NeupaneAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.
Clarissa BoschieroAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.
John B ColeDepartment of Animal Science, North Carolina State University, Raleigh, NC, USA.ORCID http://orcid.org/0000-0003-1242-4401
Bingjie LiDepartment of Animal and Veterinary Sciences, Scotland's Rural College, Midlothian, UK.ORCID http://orcid.org/0000-0002-8528-1889
Congjun LiAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.
Ransom L Baldwin ViAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.ORCID http://orcid.org/0000-0002-0753-4377
Curtis P Van TassellAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.ORCID http://orcid.org/0000-0002-8416-2087
Benjamin D RosenAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.ORCID http://orcid.org/0000-0001-9395-8346
Timothy P L SmithUSDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, USA.
Jicai JiangDepartment of Animal Science, North Carolina State University, Raleigh, NC, USA. jicai_jiang@ncsu.edu.ORCID http://orcid.org/0000-0001-6890-7539
Lingzhao FangQuantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, Denmark. lingzhao.fang@qgg.au.dk.ORCID http://orcid.org/0000-0003-1103-3679
Li MaDepartment of Animal and Avian Sciences, University of Maryland, College Park, MD, USA. lima@umd.edu.ORCID http://orcid.org/0000-0003-1038-1081
George E LiuAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA. George.Liu@usda.gov.ORCID http://orcid.org/0000-0003-0192-6705

Funding

United States Department of Agriculture | National Institute of Food and Agriculture (NIFA) 2019-67015-29321United States Department of Agriculture | National Institute of Food and Agriculture (NIFA) 2021-67015-33409
6 · The paper itself

Abstract

Pangenomes of several species have been assembled recently, facilitating the detection and genotyping of structural variants. As part of the FarmGTEx Project, we previously constructed a Holstein pangenome (H20D) based on 40 phased haploid assemblies. Here, we use this breed specific pangenome to genotype 93,059 structural variants from whole-genome sequences of 1,571 cattle. We then develop a Holstein pangenome variation imputation reference panel we name HolPIP. Leveraging HolPIP, we impute 86.65% (68,354/78,886) of structural variants for 50,299 bulls with Beagle R² ≥ 0.8. Using these imputed structural variants and phenotypes for 43 complex traits, we conduct GWAS, identifying 1,225 structural variant-trait associations. We next use fine-mapping to prioritize 32 high-confidence candidate structural variants, including a 75-bp deletion in ANKRD11 linked to dairy form, rump width, and stature, as well as an insertion in DHX32 associated with RNA metabolism. Compared to SNPs across various functional annotations, structural variants show a stronger genome-wide enrichment across most complex traits in cattle, suggesting that structural variants may have an important contribution to the genetic basis of dairy traits.

Indexed as

GenomeAnimalsCattleChromosome MappingDairyingGenome-Wide Association StudyGenotypeMalePhenotypePolymorphism, Single NucleotideQuantitative Trait Loci

Identifiers

PMID42399265
PMCPMC13469606

What OpenQuestion holds

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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.