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Genotyping-by-sequencing (GBS): a novel, efficient and cost-effective genotyping method for cattle using
Marcos De Donato1, Sunday O Peters, Sharon E Mitchell
1Department of Animal Science, Cornell University, Ithaca, New York, United States of America.
Plos One
|May 22, 2013
Summary
Genotyping-by-sequencing (GBS) adapted for cattle provides high-throughput SNP discovery at a lower cost. This method enables genomic selection and genome-wide association studies in cattle breeding programs.
Area of Science:
- Animal Genetics
- Genomics
- Biotechnology
Background:
- High-throughput genotyping is crucial for studying complex traits in animal improvement.
- The high cost of existing methods limits their large-scale application.
- Genotyping-by-sequencing (GBS) is a cost-effective method successfully used in plants.
Purpose of the Study:
- To adapt and evaluate the genotyping-by-sequencing (GBS) technique for cattle.
- To assess the feasibility of GBS for large-scale cattle genotyping and its cost-effectiveness.
Main Methods:
- Adapted plant GBS for 47 cattle from 7 breeds (taurine and indicine).
- Used Illumina HiSeq 2000 sequencing after DNA digestion and barcoding.
- Analyzed single nucleotide polymorphisms (SNPs) based on call rates and linkage.
Main Results:
- Identified 51,414 SNPs across autosomes and X chromosome with call rates >70%.
- Achieved an average SNP call rate of 86.5%, with 53% of loci >90%.
- GBS provided acceptable marker density for genomic selection at approximately one-third the cost of other technologies.
Conclusions:
- GBS is a novel, flexible, and high-throughput method suitable for cattle genotyping.
- The technique offers a cost-effective solution for genomic selection and genome-wide association studies in cattle.
- Brangus breed exhibited the highest genetic diversity among the studied populations.
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