Exclusion and Genomic Relatedness Methods for Assignment of Parentage Using Genotyping-by-Sequencing Data
Genotypes are often used to assign parentage in agricultural and ecological settings. Sequencing can be used to obtain genotypes but does not provide unambiguous genotype calls, especially when sequencing depth is low in order to reduce costs. In that case, standard parentage analysis methods no lon...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Oxford University Press
2019-10-01
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| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.119.400501 |
| _version_ | 1818356901313773568 |
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| author | Ken G. Dodds John C. McEwan Rudiger Brauning Tracey C. van Stijn Suzanne J. Rowe K. Mary McEwan Shannon M. Clarke |
| author_facet | Ken G. Dodds John C. McEwan Rudiger Brauning Tracey C. van Stijn Suzanne J. Rowe K. Mary McEwan Shannon M. Clarke |
| author_sort | Ken G. Dodds |
| collection | DOAJ |
| description | Genotypes are often used to assign parentage in agricultural and ecological settings. Sequencing can be used to obtain genotypes but does not provide unambiguous genotype calls, especially when sequencing depth is low in order to reduce costs. In that case, standard parentage analysis methods no longer apply. A strategy for using low-depth sequencing data for parentage assignment is developed here. It entails the use of relatedness estimates along with a metric termed excess mismatch rate which, for parent-offspring pairs or trios, is the difference between the observed mismatch rate and the rate expected under a model of inheritance and allele reads without error. When more than one putative parent has similar statistics, bootstrapping can provide a measure of the relatedness similarity. Putative parent-offspring trios can be further checked for consistency by comparing the offspring’s estimated inbreeding to half the parent relatedness. Suitable thresholds are required for each metric. These methods were applied to a deer breeding operation consisting of two herds of different breeds. Relatedness estimates were more in line with expectation when the herds were analyzed separately than when combined, although this did not alter which parents were the best matches with each offspring. Parentage results were largely consistent with those based on a microsatellite parentage panel with three discordant parent assignments out of 1561. Two models are investigated to allow the parentage metrics to be calculated with non-random selection of alleles. The tools and strategies given here allow parentage to be assigned from low-depth sequencing data. |
| first_indexed | 2024-12-13T20:04:34Z |
| format | Article |
| id | doaj.art-d60856b7d7ce403ebd26b1f1c98ec182 |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-13T20:04:34Z |
| publishDate | 2019-10-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-d60856b7d7ce403ebd26b1f1c98ec1822022-12-21T23:33:04ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362019-10-019103239324710.1534/g3.119.40050116Exclusion and Genomic Relatedness Methods for Assignment of Parentage Using Genotyping-by-Sequencing DataKen G. DoddsJohn C. McEwanRudiger BrauningTracey C. van StijnSuzanne J. RoweK. Mary McEwanShannon M. ClarkeGenotypes are often used to assign parentage in agricultural and ecological settings. Sequencing can be used to obtain genotypes but does not provide unambiguous genotype calls, especially when sequencing depth is low in order to reduce costs. In that case, standard parentage analysis methods no longer apply. A strategy for using low-depth sequencing data for parentage assignment is developed here. It entails the use of relatedness estimates along with a metric termed excess mismatch rate which, for parent-offspring pairs or trios, is the difference between the observed mismatch rate and the rate expected under a model of inheritance and allele reads without error. When more than one putative parent has similar statistics, bootstrapping can provide a measure of the relatedness similarity. Putative parent-offspring trios can be further checked for consistency by comparing the offspring’s estimated inbreeding to half the parent relatedness. Suitable thresholds are required for each metric. These methods were applied to a deer breeding operation consisting of two herds of different breeds. Relatedness estimates were more in line with expectation when the herds were analyzed separately than when combined, although this did not alter which parents were the best matches with each offspring. Parentage results were largely consistent with those based on a microsatellite parentage panel with three discordant parent assignments out of 1561. Two models are investigated to allow the parentage metrics to be calculated with non-random selection of alleles. The tools and strategies given here allow parentage to be assigned from low-depth sequencing data.http://g3journal.org/lookup/doi/10.1534/g3.119.400501parentagegenotyping-by-sequencingmismatch rategenomic relationship matrixexclusion |
| spellingShingle | Ken G. Dodds John C. McEwan Rudiger Brauning Tracey C. van Stijn Suzanne J. Rowe K. Mary McEwan Shannon M. Clarke Exclusion and Genomic Relatedness Methods for Assignment of Parentage Using Genotyping-by-Sequencing Data G3: Genes, Genomes, Genetics parentage genotyping-by-sequencing mismatch rate genomic relationship matrix exclusion |
| title | Exclusion and Genomic Relatedness Methods for Assignment of Parentage Using Genotyping-by-Sequencing Data |
| title_full | Exclusion and Genomic Relatedness Methods for Assignment of Parentage Using Genotyping-by-Sequencing Data |
| title_fullStr | Exclusion and Genomic Relatedness Methods for Assignment of Parentage Using Genotyping-by-Sequencing Data |
| title_full_unstemmed | Exclusion and Genomic Relatedness Methods for Assignment of Parentage Using Genotyping-by-Sequencing Data |
| title_short | Exclusion and Genomic Relatedness Methods for Assignment of Parentage Using Genotyping-by-Sequencing Data |
| title_sort | exclusion and genomic relatedness methods for assignment of parentage using genotyping by sequencing data |
| topic | parentage genotyping-by-sequencing mismatch rate genomic relationship matrix exclusion |
| url | http://g3journal.org/lookup/doi/10.1534/g3.119.400501 |
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