2015
DOI: 10.1186/s12864-015-2252-3
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Construction of relatedness matrices using genotyping-by-sequencing data

Abstract: BackgroundGenotyping-by-sequencing (GBS) is becoming an attractive alternative to array-based methods for genotyping individuals for a large number of single nucleotide polymorphisms (SNPs). Costs can be lowered by reducing the mean sequencing depth, but this results in genotype calls of lower quality. A common analysis strategy is to filter SNPs to just those with sufficient depth, thereby greatly reducing the number of SNPs available. We investigate methods for estimating relatedness using GBS data, includin… Show more

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Cited by 126 publications
(213 citation statements)
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“…High implementation costs will likely moderate the practical application of the selection in GS scenarios that were investigated in this simulation study, particularly the cost of parentage testing and genomic selection. The cost of genomic technology is dropping rapidly and the expectation is that prices will further decrease, with encouraging possibilities developed in the area of genotyping by sequencing (GBS) [26]. Reduction in genotyping costs and policies which restrict genotyping to animals for which the most benefit can be generated, will likely be a key to achieve higher adoption of recording efforts and genotyping among producers.…”
Section: Discussionmentioning
confidence: 99%
“…High implementation costs will likely moderate the practical application of the selection in GS scenarios that were investigated in this simulation study, particularly the cost of parentage testing and genomic selection. The cost of genomic technology is dropping rapidly and the expectation is that prices will further decrease, with encouraging possibilities developed in the area of genotyping by sequencing (GBS) [26]. Reduction in genotyping costs and policies which restrict genotyping to animals for which the most benefit can be generated, will likely be a key to achieve higher adoption of recording efforts and genotyping among producers.…”
Section: Discussionmentioning
confidence: 99%
“…) for use in paternity and relatedness studies, including genotyping by sequencing (GBS; Dodds et al . ), restriction site‐associated DNA sequencing (RAD‐seq; Senn et al . ; Kess et al .…”
Section: Discussionmentioning
confidence: 99%
“…Genotyping‐by‐sequencing, including library preparation, was performed at Genomnz Animal Genomics Group (AgResearch). Procedures followed Dodds et al () after Elshire et al (), with the following modifications. Briefly, genomic DNA was digested with PstI and MspI restriction enzymes (NEB R140L and R0106L; New England Biolabs).…”
Section: Methodsmentioning
confidence: 99%