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Related Experiment Video

Updated: Jul 28, 2025

Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood

Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood

Published on: November 28, 2018

The SWine IMputation (SWIM) haplotype reference panel enables nucleotide resolution genetic mapping in pigs.

Rongrong Ding^1,2,3, Rodrigo Savegnago^2,4, Jinding Liu^2,5

¹College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China.

Communications Biology

|May 30, 2023

Summary

Researchers developed a pig haplotype panel from 2259 whole genome-sequenced animals. This resource significantly improves genotype imputation accuracy, enhancing genetic mapping resolution for livestock genetic improvement.

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Last Updated: Jul 28, 2025

Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood

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Published on: November 19, 2013

Area of Science:

Animal Genetics
Genomics
Quantitative Trait Loci (QTL) analysis

Background:

Genetic mapping in pigs is crucial for animal genetic improvement but hindered by low-resolution genotyping.
Advances in high-throughput genotyping have not fully overcome the challenge of sparse variant data in pigs.

Purpose of the Study:

To develop a high-quality reference haplotype panel for pigs to improve genotype imputation accuracy.
To enhance the resolution of genetic mapping in pigs for better identification of genes influencing economically important traits.

Main Methods:

Constructed a reference haplotype panel using whole genome sequencing data from 2259 pigs across 44 breeds.
Optimized genotype imputation by evaluating software and breed composition for the panel.
Validated imputation accuracy using concordance rates and r-squared values.

Main Results:

Achieved an average genotype concordance rate exceeding 96% with the developed panel.
Obtained a non-reference concordance rate of 88% and an imputation accuracy (r²) of 0.85.
Demonstrated significant improvement in genetic mapping resolution through case studies using the imputed genotypes.

Conclusions:

The developed pig reference haplotype panel substantially enhances genotype imputation accuracy and genetic mapping resolution.
This resource, accessible via a public web server, is expected to accelerate genetic improvement in pigs.
Facilitates the identification of genes and alleles responsible for economically important traits in swine populations.