Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach
Abstract Background Experimental intercrosses between outbred founder populations are powerful resources for mapping loci that contribute to complex traits i.e. quantitative trait loci (QTL). Here, we present an approach and its accompanying software for high-resolution reconstruction of founder mos...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | deu |
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BMC
2019-08-01
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| Series: | Genetics Selection Evolution |
| Online Access: | http://link.springer.com/article/10.1186/s12711-019-0487-1 |
| _version_ | 1811328520748531712 |
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| author | Yanjun Zan Thibaut Payen Mette Lillie Christa F. Honaker Paul B. Siegel Örjan Carlborg |
| author_facet | Yanjun Zan Thibaut Payen Mette Lillie Christa F. Honaker Paul B. Siegel Örjan Carlborg |
| author_sort | Yanjun Zan |
| collection | DOAJ |
| description | Abstract Background Experimental intercrosses between outbred founder populations are powerful resources for mapping loci that contribute to complex traits i.e. quantitative trait loci (QTL). Here, we present an approach and its accompanying software for high-resolution reconstruction of founder mosaic genotypes in the intercross offspring from such populations using whole-genome high-coverage sequence data on founder individuals (~ 30×) and very low-coverage sequence data on intercross individuals (< 0.5×). Sets of founder-line informative markers were selected for each full-sib family and used to infer the founder mosaic genotypes of the intercross individuals. The application of this approach and the quality of the estimated genome-wide genotypes are illustrated in a large F2 pedigree between two divergently selected lines of chickens. Results We describe how we obtained whole-genome genotype data for hundreds of individuals in a cost- and time-efficient manner by using a Tn5-based library preparation protocol and an imputation algorithm that was optimized for this application. In total, 7.6 million markers segregated in this pedigree and, within each full-sib family, between 10.0 and 13.7% of these were fully informative, i.e. fixed for alternative alleles in the founders from the divergent lines, and were used for reconstruction of the offspring mosaic genotypes. The genotypes that were estimated based on the low-coverage sequence data were highly consistent (> 95% agreement) with those obtained using individual single nucleotide polymorphism (SNP) genotyping. The estimated resolution of the inferred recombination breakpoints was relatively high, with 50% of them being defined on regions shorter than 10 kb. Conclusions A method and software for inferring founder mosaic genotypes in intercross offspring from low-coverage whole-genome sequencing in pedigrees from heterozygous founders are described. They provide high-quality, high-resolution genotypes in a time- and cost-efficient manner. The software is freely available at https://github.com/CarlborgGenomics/Stripes. |
| first_indexed | 2024-04-13T15:27:34Z |
| format | Article |
| id | doaj.art-4a6429b99c6b4839aadf4991530fba97 |
| institution | Directory Open Access Journal |
| issn | 1297-9686 |
| language | deu |
| last_indexed | 2024-04-13T15:27:34Z |
| publishDate | 2019-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-4a6429b99c6b4839aadf4991530fba972022-12-22T02:41:28ZdeuBMCGenetics Selection Evolution1297-96862019-08-0151111110.1186/s12711-019-0487-1Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approachYanjun Zan0Thibaut Payen1Mette Lillie2Christa F. Honaker3Paul B. Siegel4Örjan Carlborg5Department of Medical Biochemistry and Microbiology, Uppsala UniversityDepartment of Medical Biochemistry and Microbiology, Uppsala UniversityDepartment of Medical Biochemistry and Microbiology, Uppsala UniversityDepartment of Animal and Poultry Sciences, Virginia Polytechnic Institute and State UniversityDepartment of Animal and Poultry Sciences, Virginia Polytechnic Institute and State UniversityDepartment of Medical Biochemistry and Microbiology, Uppsala UniversityAbstract Background Experimental intercrosses between outbred founder populations are powerful resources for mapping loci that contribute to complex traits i.e. quantitative trait loci (QTL). Here, we present an approach and its accompanying software for high-resolution reconstruction of founder mosaic genotypes in the intercross offspring from such populations using whole-genome high-coverage sequence data on founder individuals (~ 30×) and very low-coverage sequence data on intercross individuals (< 0.5×). Sets of founder-line informative markers were selected for each full-sib family and used to infer the founder mosaic genotypes of the intercross individuals. The application of this approach and the quality of the estimated genome-wide genotypes are illustrated in a large F2 pedigree between two divergently selected lines of chickens. Results We describe how we obtained whole-genome genotype data for hundreds of individuals in a cost- and time-efficient manner by using a Tn5-based library preparation protocol and an imputation algorithm that was optimized for this application. In total, 7.6 million markers segregated in this pedigree and, within each full-sib family, between 10.0 and 13.7% of these were fully informative, i.e. fixed for alternative alleles in the founders from the divergent lines, and were used for reconstruction of the offspring mosaic genotypes. The genotypes that were estimated based on the low-coverage sequence data were highly consistent (> 95% agreement) with those obtained using individual single nucleotide polymorphism (SNP) genotyping. The estimated resolution of the inferred recombination breakpoints was relatively high, with 50% of them being defined on regions shorter than 10 kb. Conclusions A method and software for inferring founder mosaic genotypes in intercross offspring from low-coverage whole-genome sequencing in pedigrees from heterozygous founders are described. They provide high-quality, high-resolution genotypes in a time- and cost-efficient manner. The software is freely available at https://github.com/CarlborgGenomics/Stripes.http://link.springer.com/article/10.1186/s12711-019-0487-1 |
| spellingShingle | Yanjun Zan Thibaut Payen Mette Lillie Christa F. Honaker Paul B. Siegel Örjan Carlborg Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach Genetics Selection Evolution |
| title | Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach |
| title_full | Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach |
| title_fullStr | Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach |
| title_full_unstemmed | Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach |
| title_short | Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach |
| title_sort | genotyping by low coverage whole genome sequencing in intercross pedigrees from outbred founders a cost efficient approach |
| url | http://link.springer.com/article/10.1186/s12711-019-0487-1 |
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