Simultaneous mapping of multiple gene loci with pooled segregants.
The analysis of polygenic, phenotypic characteristics such as quantitative traits or inheritable diseases remains an important challenge. It requires reliable scoring of many genetic markers covering the entire genome. The advent of high-throughput sequencing technologies provides a new way to evalu...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2013-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3575411?pdf=render |
| _version_ | 1811219945304883200 |
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| author | Jürgen Claesen Lieven Clement Ziv Shkedy Maria R Foulquié-Moreno Tomasz Burzykowski |
| author_facet | Jürgen Claesen Lieven Clement Ziv Shkedy Maria R Foulquié-Moreno Tomasz Burzykowski |
| author_sort | Jürgen Claesen |
| collection | DOAJ |
| description | The analysis of polygenic, phenotypic characteristics such as quantitative traits or inheritable diseases remains an important challenge. It requires reliable scoring of many genetic markers covering the entire genome. The advent of high-throughput sequencing technologies provides a new way to evaluate large numbers of single nucleotide polymorphisms (SNPs) as genetic markers. Combining the technologies with pooling of segregants, as performed in bulked segregant analysis (BSA), should, in principle, allow the simultaneous mapping of multiple genetic loci present throughout the genome. The gene mapping process, applied here, consists of three steps: First, a controlled crossing of parents with and without a trait. Second, selection based on phenotypic screening of the offspring, followed by the mapping of short offspring sequences against the parental reference. The final step aims at detecting genetic markers such as SNPs, insertions and deletions with next generation sequencing (NGS). Markers in close proximity of genomic loci that are associated to the trait have a higher probability to be inherited together. Hence, these markers are very useful for discovering the loci and the genetic mechanism underlying the characteristic of interest. Within this context, NGS produces binomial counts along the genome, i.e., the number of sequenced reads that matches with the SNP of the parental reference strain, which is a proxy for the number of individuals in the offspring that share the SNP with the parent. Genomic loci associated with the trait can thus be discovered by analyzing trends in the counts along the genome. We exploit the link between smoothing splines and generalized mixed models for estimating the underlying structure present in the SNP scatterplots. |
| first_indexed | 2024-04-12T07:34:16Z |
| format | Article |
| id | doaj.art-19ba8d7baeab4231bad2cb89376eb2d2 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-12T07:34:16Z |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-19ba8d7baeab4231bad2cb89376eb2d22022-12-22T03:41:58ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-0182e5513310.1371/journal.pone.0055133Simultaneous mapping of multiple gene loci with pooled segregants.Jürgen ClaesenLieven ClementZiv ShkedyMaria R Foulquié-MorenoTomasz BurzykowskiThe analysis of polygenic, phenotypic characteristics such as quantitative traits or inheritable diseases remains an important challenge. It requires reliable scoring of many genetic markers covering the entire genome. The advent of high-throughput sequencing technologies provides a new way to evaluate large numbers of single nucleotide polymorphisms (SNPs) as genetic markers. Combining the technologies with pooling of segregants, as performed in bulked segregant analysis (BSA), should, in principle, allow the simultaneous mapping of multiple genetic loci present throughout the genome. The gene mapping process, applied here, consists of three steps: First, a controlled crossing of parents with and without a trait. Second, selection based on phenotypic screening of the offspring, followed by the mapping of short offspring sequences against the parental reference. The final step aims at detecting genetic markers such as SNPs, insertions and deletions with next generation sequencing (NGS). Markers in close proximity of genomic loci that are associated to the trait have a higher probability to be inherited together. Hence, these markers are very useful for discovering the loci and the genetic mechanism underlying the characteristic of interest. Within this context, NGS produces binomial counts along the genome, i.e., the number of sequenced reads that matches with the SNP of the parental reference strain, which is a proxy for the number of individuals in the offspring that share the SNP with the parent. Genomic loci associated with the trait can thus be discovered by analyzing trends in the counts along the genome. We exploit the link between smoothing splines and generalized mixed models for estimating the underlying structure present in the SNP scatterplots.http://europepmc.org/articles/PMC3575411?pdf=render |
| spellingShingle | Jürgen Claesen Lieven Clement Ziv Shkedy Maria R Foulquié-Moreno Tomasz Burzykowski Simultaneous mapping of multiple gene loci with pooled segregants. PLoS ONE |
| title | Simultaneous mapping of multiple gene loci with pooled segregants. |
| title_full | Simultaneous mapping of multiple gene loci with pooled segregants. |
| title_fullStr | Simultaneous mapping of multiple gene loci with pooled segregants. |
| title_full_unstemmed | Simultaneous mapping of multiple gene loci with pooled segregants. |
| title_short | Simultaneous mapping of multiple gene loci with pooled segregants. |
| title_sort | simultaneous mapping of multiple gene loci with pooled segregants |
| url | http://europepmc.org/articles/PMC3575411?pdf=render |
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