A unified DNA sequence and non‐DNA sequence mapping model of complex traits
Article Swipe
Yanru Zeng
,
Xuli Zhu
,
Chixiang Chen
,
Kalins Banerjee
,
Lidan Sun
,
Weiwu Yu
,
Bingsong Zheng
,
Rongling Wu
·
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.1111/tpj.14354
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.1111/tpj.14354
Summary Increasing evidence shows that quantitative inheritance is based on both DNA sequence and non‐ DNA sequence variants. However, how to simultaneously detect these variants from a mapping study has been unexplored, hampering our effort to illustrate the detailed genetic architecture of complex traits. We address this issue by developing a unified model of quantitative trait locus ( QTL ) mapping based on an open‐pollinated design composed of randomly sampling maternal plants from a natural population and their half‐sib seeds. This design forms a two‐level hierarchical platform for a joint linkage‐linkage disequilibrium analysis of population structure. The EM algorithm was implemented to estimate and test DNA sequence‐based effects and non‐ DNA sequence‐based effects of QTL s. We applied this model to analyze genetic mapping data from the OP design of a gymnosperm coniferous species, Torreya grandis , identifying 25 significant DNA sequence and non‐ DNA sequence QTL s for seedling height and diameter growth in different years. Results from computer simulation show that the unified model has good statistical properties and is powerful for QTL detection. Our model enables the tests of how a complex trait is affected differently by DNA ‐based effects and non‐ DNA sequence‐based transgenerational effects, thus allowing a more comprehensive picture of genetic architecture to be charted and quantified.
Related Topics
Concepts
Biology
Quantitative trait locus
Genetics
Linkage disequilibrium
Population
DNA sequencing
Computational biology
Sequence (biology)
DNA
Single-nucleotide polymorphism
Gene
Genotype
Sociology
Demography
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1111/tpj.14354
- https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/tpj.14354
- OA Status
- bronze
- Cited By
- 2
- References
- 47
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2941906771
All OpenAlex metadata
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https://openalex.org/W2941906771Canonical identifier for this work in OpenAlex
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https://doi.org/10.1111/tpj.14354Digital Object Identifier
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A unified
DNA sequence and non‐DNA sequence mapping model of complex traitsWork title - Type
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articleOpenAlex work type
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enPrimary language
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2019Year of publication
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2019-04-22Full publication date if available
- Authors
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Yanru Zeng, Xuli Zhu, Chixiang Chen, Kalins Banerjee, Lidan Sun, Weiwu Yu, Bingsong Zheng, Rongling WuList of authors in order
- Landing page
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https://doi.org/10.1111/tpj.14354Publisher landing page
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https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/tpj.14354Direct link to full text PDF
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YesWhether a free full text is available
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bronzeOpen access status per OpenAlex
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https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/tpj.14354Direct OA link when available
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Biology, Quantitative trait locus, Genetics, Linkage disequilibrium, Population, DNA sequencing, Computational biology, Sequence (biology), DNA, Single-nucleotide polymorphism, Gene, Genotype, Sociology, DemographyTop concepts (fields/topics) attached by OpenAlex
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2Total citation count in OpenAlex
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2022: 1, 2021: 1Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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