Low-Coverage Whole-Genome Sequencing Accelerates Genomic Selection in Livestock Breeding
With the completion of genome sequencing for many major agricultural species in recent years, advances in functional genomics and bioinformatics have transformed livestock and poultry breeding. Traditional breeding methods are increasingly being replaced by genomic selection.
Genomic selection uses molecular markers and advanced computational methods to identify animals with desirable traits more efficiently and accurately than conventional breeding approaches. However, high costs and technical barriers previously limited genomic selection to research collaborations within scientific institutes, with relatively little commercial adoption.
From research innovation to industry application
Based on the DNBSEQ-G400 genome sequencer*, the research team led by Professor Hu Xiaoxiang at China Agricultural University collaborated with Professor Wu Zhenfang’s team at South China Agricultural University to investigate the genetic architecture of economically important traits in pigs.
Using a low-coverage whole-genome sequencing strategy, the teams accelerated genomic analysis for breeding applications. The results of the research were published in the international journal GigaScience.
Professor Hu noted that earlier genotyping technologies were expensive for commercial breeding programmes. Around 2012, a 50K SNP chip for pigs cost between RMB 1000 and 1500, which limited adoption by agricultural enterprises.
Working with WENS Group, a leading Chinese agriculture and animal husbandry company, the research team applied the DNBSEQ-G400 sequencing platform to significantly reduce the cost of genotype analysis. Sequencing costs were reduced to approximately RMB 200 per sample.
Based on MGI’s DNBSEQ sequencing technology, the DNBSEQ-G400 platform not only lowered sequencing costs but also reduced duplication rates and improved detection accuracy for SNP and indel variants compared with other sequencing platforms. These improvements support the wider adoption of sequence-based genotyping in breeding programmes.
Low-coverage sequencing shows strong potential
In the study, researchers analysed 2,869 Duroc boars from a single breeding farm. The team developed an optimised Tn5-based low-coverage sequencing method to construct genomic libraries.
Whole-genome sequencing was performed on the DNBSEQ-G400 platform with an average sequencing depth of 0.73×. The BaseVar and STITCH methods were used for reference panel construction and genotype imputation.
To validate the accuracy of the low-coverage sequencing data, researchers compared the results with SNP chip analysis, high-depth sequencing and Fluidigm genotyping. Additional analyses evaluated how sample size and sequencing depth affected genotype accuracy.
The results demonstrated that low-coverage whole-genome sequencing can provide reliable genotyping data at significantly lower cost, making genomic selection more accessible for large-scale breeding programmes.
According to Professor Hu, low-coverage whole-genome sequencing has strong potential for broader applications across many species, including livestock, crops and aquatic animals.
The team is continuing research to apply the technology to the breeding of additional plant and animal varieties.
High-throughput gene sequencing technologies and whole-genome selection platforms are expected to play an increasingly important role in advancing breeding research, developing improved varieties and supporting the industrial application of biological breeding to drive agricultural modernisation.
*Unless otherwise informed, all sequencers and sequencing reagents are not available in Germany, USA, UK, Hong Kong, Sweden, Belgium and Italy.
