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Sequencing of mRNA from Whole Blood using Nanopore Sequencing
Published on: June 3, 2019
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Genomic prediction using low-coverage portable Nanopore sequencing.
Harrison J Lamb1, Ben J Hayes1, Imtiaz A S Randhawa2
1Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia.
Plos One
|December 15, 2021
Summary
Oxford Nanopore Technologies sequencing offers a portable and rapid method for calculating genomic breeding values in cattle. Low-coverage sequencing data correlated highly with SNP array data, showing potential for on-farm genomic prediction.
Area of Science:
- Genomics
- Animal Breeding
- Bioinformatics
Background:
- Polygenic traits, influenced by many genetic loci, are crucial in livestock, crops, and humans.
- Genomic breeding values (GBVs) and polygenic risk scores (PRS) are vital for predicting phenotypes and disease risk.
- SNP arrays are standard for genomic analysis, but genotyping-by-sequencing offers broader genome coverage.
Purpose of the Study:
- To evaluate the potential of Oxford Nanopore Technologies (ONT) portable sequencing for calculating GBVs in cattle.
- To compare GBVs derived from low-coverage ONT sequencing data with those from traditional SNP arrays.
Main Methods:
- Low-coverage whole-genome sequencing of cattle using ONT portable sequencers.
- Calculation of GBVs from ONT sequence data and SNP array data.
- Statistical comparison of GBVs obtained from both methods, with and without imputation.
Main Results:
- High correlations (>0.92 with imputation, >0.88 without) were observed between ONT-derived and SNP array-derived GBVs at 2X-4X coverage.
- Even at 0.5X average coverage, correlations ranged from 0.85 to 0.92 with imputation.
- ONT sequencing demonstrated strong potential for accurate genomic prediction.
Conclusions:
- ONT portable sequencing is a viable tool for on-farm genomic prediction in agriculture.
- Further validation in larger cattle populations is recommended to confirm these findings.
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