Evidence map›Paper›PMID 40258473›Full record

ArticleJournal of advanced research2026

Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle.

Yahui Gao, Liu Yang, Kristen Kuhn, Wenli Li, Geoffrey Zanton, Mary Bowman, Pengju Zhao, Yang Zhou, Lingzhao Fang, John B Cole and 8 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of advanced research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing 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

7 citing papers in PubMed.

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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.

Yahui GaoState Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA. Electronic address: yahui.gao@scau.edu.cn.
Liu YangAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA. Electronic address: yangqism@gmail.com.
Kristen KuhnUSDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, USA. Electronic address: kristen.kuhn@usda.gov.
Wenli LiUS Dairy Forage Research Center, USDA-ARS, Madison, WI, USA. Electronic address: wenli.li@usda.gov.
Geoffrey ZantonUS Dairy Forage Research Center, USDA-ARS, Madison, WI, USA. Electronic address: geoffrey.zanton@usda.gov.
Mary BowmanAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA. Electronic address: mary.bowman@usda.gov.
Pengju ZhaoHainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya 572000, China. Electronic address: zhaopengju2014@gmail.com.
Yang ZhouKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China. Electronic address: yangzhou@mail.hzau.edu.cn.
Lingzhao FangQuantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, Denmark. Electronic address: lingzhao.fang@qgg.au.dk.
John B ColeCouncil on Dairy Cattle Breeding, 4201 Northview Dr, Bowie, MD 20716, USA; Department of Animal Sciences, Donald Henry Barron Reproductive and Perinatal Biology Research Program, and the Genetics Institute, University of Florida, Gainesville, FL 32611-0910, USA; Department of Animal Science, North Carolina State University, Raleigh, NC 27695-7621, USA. Electronic address: john.cole@uscdcb.com.
Benjamin D RosenAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA. Electronic address: ben.rosen@usda.gov.
Li MaDepartment of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA. Electronic address: lima@umd.edu.
Congjun LiAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA. Electronic address: congjun.li@usda.gov.
Ransom L BaldwinAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA. Electronic address: ransom.baldwin@usda.gov.
Curtis P Van TassellAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA. Electronic address: curt.vantassell@usda.gov.
Zhe ZhangState Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China. Electronic address: zhezhang@scau.edu.cn.
Timothy P L SmithUSDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, USA. Electronic address: tim.smith2@usda.gov.
George E LiuAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA. Electronic address: George.Liu@usda.gov.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

introductionMost SV studies in livestock rely on short-read sequencing, posing challenges in accurately characterizing large genomic variants due to their limited read length.

objectivesOur goal is to reveal structural variation and novel sequences specific to Holstein and Jersey cattle breeds using long-read and pan-genome analyses.

methodsWe sequenced 20 Holsteins and 8 Jersey cattle using PacBio HiFi to 20×, and integrated five read-based and one assembly-based SV caller to determine SVs.

resultsWe assembled the 28 genomes averaging 3.25 Gb with a contig N50 of 69.36 Mb and using the ARS-UCD1.2 reference, we acquired Holstein/Jersey SV catalogs with 74,068/54,689 events spanning 202/135 Mb (7.43 %/4.97 % of the genome). SVs were enriched in less conserved, non-coding, and non-regulatory regions. Comparing Holsteins with differing feed efficiency (FE), SVs unique to high FE were linked to energy metabolism and olfactory receptors, while those specific to low FE were associated with material transport. We constructed Holstein/Jersey pangenome graphs with 148,598/105,875 nodes and 208,891/147,990 edges, representing 47,028/37,137 biallelic and multi-allelic events, and 63.75/42.34 Mb of novel sequence. We observed SV count saturation with 20 Holsteins, while adding Jerseys significantly increased the SV count, highlighting breed-specific SV events.

conclusionOur long-read data and SV catalogs are valuable resources, revealing that the cattle genome is more complex than previously thought.

Indexed as

GenomeGenomicsGenomic Structural VariationAnimalsBreedingCattleGenetic VariationHigh-Throughput Nucleotide SequencingDairy cattleLinear genomeLong readPangenomeStructural variation

Identifiers

PMID40258473
PMCPMC12766236

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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 Socratic graph.