ArticleScientific reports2017
Imputation-Based Whole-Genome Sequence Association Study Rediscovered the Missing QTL for Lumbar Number in Sutai Pigs.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers, 2 of them syntheses that pooled it.
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Who cites it
33 citing papers in PubMed, 2 syntheses or guidelines pooled it, 67 citations in OpenAlex.
- A meta-analysis of genome-wide association studies revealed significant QTL and candidate genes for loin muscle area in three breeding pigs.Scientific reports · 2025Pooled it
- False positive findings during genome-wide association studies with imputation: influence of allele frequency and imputation accuracy.Human molecular genetics · 2021Pooled it
- Imputed whole genome sequence based association pinpoints genetic architecture of labour dystocia of pigs using multi-breed populations.Genetics, selection, evolution : GSE · 2026Article
- An Advanced Entropy Approach for Minimizing False Discoveries in Imputation-Based Association Analyses.Research square · 2025Article
- Integrative analysis of genome and transcriptome reveals a novel regulator for pork intramuscular fat content.Genetics, selection, evolution : GSE · 2025Article
- GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes.Genomics, proteomics & bioinformatics · 2025Article
- Whole-Genome Resequencing of Ujimqin Sheep Identifies Genes Associated with Vertebral Number.Animals : an open access journal from MDPI · 2024Article
- Advancements in Genetic Marker Exploration for Livestock Vertebral Traits with a Focus on China.Animals : an open access journal from MDPI · 2024Review
- Increased Accuracy of Genomic Prediction Using Preselected SNPs from GWAS with Imputed Whole-Genome Sequence Data in Pigs.Animals : an open access journal from MDPI · 2023Article
- Imputation of low-density marker chip data in plant breeding: Evaluation of methods based on sugar beet.The plant genome · 2022Article
- PHARP: a pig haplotype reference panel for genotype imputation.Scientific reports · 2022Article
- Development and validation of a horse reference panel for genotype imputation.Genetics, selection, evolution : GSE · 2022Article
- An imputed whole-genome sequence-based GWAS approach pinpoints causal mutations for complex traits in a specific swine population.Science China. Life sciences · 2022Article
- Exploring the optimal strategy of imputation from SNP array to whole-genome sequencing data in farm animals.Frontiers in genetics · 2022Article
- Imputation to whole-genome sequence and its use in genome-wide association studies for pork colour traits in crossbred and purebred pigs.Frontiers in genetics · 2022Article
- Genomic Prediction Using LD-Based Haplotypes in Combined Pig Populations.Frontiers in genetics · 2022Article
- Increasing calling accuracy, coverage, and read-depth in sequence data by the use of haplotype blocks.PLoS genetics · 2021Article
- Accelerated deciphering of the genetic architecture of agricultural economic traits in pigs using a low-coverage whole-genome sequencing strategy.GigaScience · 2021Article
- Soybean (Glycine max) Haplotype Map (GmHapMap): a universal resource for soybean translational and functional genomics.Plant biotechnology journal · 2021Article
- A Single-Step Genome Wide Association Study on Body Size Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs.Frontiers in genetics · 2021Article
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8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Resequencing a number of individuals of various breeds as reference population and imputing the whole-genome sequences of individuals that were genotyped with medium-density chips to perform an association study is a very efficient strategy. Previously, we performed a genome-wide association study (GWAS) of lumbar number using 60K SNPs from the porcine Illumina chips in 418 Sutai pigs and did not detect any significant signals. Therefore, we imputed the whole-genome sequences of 418 Sutai individuals from 403 deeply resequenced reference individuals and performed association tests. We identified a quantitative trait locus (QTL) for lumbar number in SSC1 with a P value of 9.01E-18 that was close to the potential causative gene of NR6A1. The result of conditioning on the top SNP association test indicated that only one QTL was responsible for this trait in SSC1. The linkage disequilibrium (LD) drop test result for the condition of the reported potential causative mutation (c.575T > C missense mutation of NR6A1) indicated that this mutation was probably not the underlying mutation that affected lumbar number in our study. As the first trial of imputed whole-genome sequence GWAS in swine, this approach can be also powerful to investigate complex traits in pig like in human and cattle.
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