ArticleGigaScience2021
Accelerated deciphering of the genetic architecture of agricultural economic traits in pigs using a low-coverage whole-genome sequencing strategy.
Article in GigaScience, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 2 of them syntheses that pooled it.
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Who cites it
55 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Pooled it
- Genome-Wide Association Study Meta-Analysis Elucidates Genetic Structure and Identifies Candidate Genes of Teat Number Traits in Pigs.International journal of molecular sciences · 2023Pooled it
- PGS-GS: a framework integrating polygenic scores and genomic selection in animal breeding.Briefings in bioinformatics · 2026Article
- Low-Coverage Whole-Genome Resequencing in Livestock and Poultry: Statistical Foundations, Applications and Future Directions.Biology · 2026Review
- Genome-wide association study reveals putative genetic determinants of longitudinal immune responses to avian influenza and Newcastle disease in chickens.Genetics, selection, evolution : GSE · 2026Article
- Integrated Analysis of SNPs and Structural Variations via High-depth Whole-genome Sequencing Reveals the Genetic Architecture and Optimizes Genomic Prediction in Chickens.Poultry science · 2026Article
- The influence of structural variants from 2445 pigs on gene expression and complex traits.Nature communications · 2026Article
- Article
- Improving genomic prediction accuracy of complex traits by integrating massive types of functional annotation information.Nature communications · 2026Article
- Genes and Gene Functions Associated with Morphological, Productive, Reproductive, and Carcass Quality Traits in Pigs: A Functional Bioinformatics Approach.Current issues in molecular biology · 2026Article
- Egg-laying ChickenGTEx resource deciphers context-specific regulatory effects on fertility traits.Nature communications · 2025Article
- Single-nucleus transcriptome profiling of skeletal muscle in Diqing Tibetan pigs with distinct body sizes.BMC genomics · 2025Article
- Integrative multi-omics analysis deciphers the regulatory mechanisms of egg weight traits in chickens.Poultry science · 2025Article
- The impact of haplotypes derived from Chinese pigs on genetic variation and economic traits in the Duroc breed.Genetics, selection, evolution : GSE · 2025Article
- Multi-omics integration reveals Chr1 associated QTL mediating backfat thickness in pigs.Journal of animal science and biotechnology · 2025Article
- Fine mapping genetic variants affecting birth weight in sheep: a GWAS of 3007 individuals using low-coverage whole genome sequencing.Journal of animal science and biotechnology · 2025Article
- Genome-wide analyses reveal intricate genetic mechanisms underlying egg production efficiency in chickens.Journal of animal science and biotechnology · 2025Article
- Rapid Identification of the SNP Mutation in theAnimals : an open access journal from MDPI · 2025Article
- GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes.Genomics, proteomics & bioinformatics · 2025Article
- Mapping the regulatory genetic landscape of complex traits using a chicken advanced intercross line.Nature communications · 2025Article
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundUncovering the genetic architecture of economic traits in pigs is important for agricultural breeding. However, high-density haplotype reference panels are unavailable in most agricultural species, limiting accurate genotype imputation in large populations. Moreover, the infinitesimal model of quantitative traits implies that weak association signals tend to be spread across most of the genome, further complicating the genetic analysis. Hence, there is a need to develop new methods for sequencing large cohorts without large reference panels.
resultsWe describe a Tn5-based highly accurate, cost- and time-efficient, low-coverage sequencing method to obtain 11.3 million whole-genome single-nucleotide polymorphisms in 2,869 Duroc boars at a mean depth of 0.73×. On the basis of these single-nucleotide polymorphisms, a genome-wide association study was performed, resulting in 14 quantitative trait loci (QTLs) for 7 of 21 important agricultural traits in pigs. These QTLs harbour genes, such as ABCD4 for total teat number and HMGA1 for back fat thickness, and provided a starting point for further investigation. The inheritance models of the different traits varied greatly. Most follow the minor-polygene model, but this can be attributed to different reasons, such as the shaping of genetic architecture by artificial selection for this population and sufficiently interconnected minor gene regulatory networks.
conclusionsGenome-wide association study results for 21 important agricultural traits identified 14 QTLs/genes and showed their genetic architectures, providing guidance for genetic improvement harnessing genomic features. The Tn5-based low-coverage sequencing method can be applied to large-scale genome studies for any species without a good reference panel and can be used for agricultural breeding.
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