Evidence map›Paper›PMID 38515031›Full record

ArticleBMC genomics2024

Identification and characterization of structural variants related to meat quality in pigs using chromosome-level genome assemblies.

Daehong Kwon, Nayoung Park, Suyeon Wy, Daehwan Lee, Woncheoul Park, Han-Ha Chai, In-Cheol Cho, Jongin Lee, Kisang Kwon, Heesun Kim and 3 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 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
2.8field-weighted citation impact, top 10% of its field
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, 5 citations in OpenAlex.

  1. Review
  2. Review
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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

13 authors at 2 institutions in 1 country.

Daehong KwonDepartment of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
Nayoung ParkDepartment of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
Suyeon WyDepartment of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
Daehwan LeeDepartment of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
Woncheoul ParkAnimal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea.
Han-Ha ChaiAnimal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea.
In-Cheol ChoSubtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju, 63242, Republic of Korea.
Jongin LeeDepartment of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
Kisang KwonDepartment of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
Heesun KimDepartment of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
Youngbeen MoonDepartment of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
Juyeon KimDepartment of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
Jaebum KimDepartment of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea. jbkim@konkuk.ac.kr.
Konkuk University · KRNational Institute of Animal Science · KR

Funding

Ministry of Science and ICT, South Korea NRF-2021M3H9A2097134National Institute of Animal Science PJ01334302
6 · The paper itself

Abstract

backgroundMany studies have been performed to identify various genomic loci and genes associated with the meat quality in pigs. However, the full genetic architecture of the trait still remains unclear in part because of the lack of accurate identification of related structural variations (SVs) which resulted from the shortage of target breeds, the limitations of sequencing data, and the incompleteness of genome assemblies. The recent generation of a new pig breed with superior meat quality, called Nanchukmacdon, and its chromosome-level genome assembly (the NCMD assembly) has provided new opportunities.

resultsBy applying assembly-based SV calling approaches to various genome assemblies of pigs including Nanchukmacdon, the impact of SVs on meat quality was investigated. Especially, by checking the commonality of SVs with other pig breeds, a total of 13,819 Nanchukmacdon-specific SVs (NSVs) were identified, which have a potential effect on the unique meat quality of Nanchukmacdon. The regulatory potentials of NSVs for the expression of nearby genes were further examined using transcriptome- and epigenome-based analyses in different tissues.

conclusionsWhole-genome comparisons based on chromosome-level genome assemblies have led to the discovery of SVs affecting meat quality in pigs, and their regulatory potentials were analyzed. The identified NSVs will provide new insights regarding genetic architectures underlying the meat quality in pigs. Finally, this study confirms the utility of chromosome-level genome assemblies and multi-omics analysis to enhance the understanding of unique phenotypes.

Indexed as

GenomeGenomicsAnimalsChromosomesMeatPhenotypeSwineChromosome-level genome assemblyMeat qualityMulti-omics analysisNanchukmacdonStructural variation

Identifiers

PMID38515031
PMCPMC10956321
OpenAlexW4393052322

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

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.