Inference of polyploid origin and inheritance mode from population genomic data
- Author
- Alison Dawn Scott, Jozefien D. Van de Velde and Polina Novikova (UGent)
- Organization
- Abstract
- Whole-genome duplications yield varied chromosomal pairing patterns, ranging from strictly bivalent to multivalent, resulting in disomic and polysomic inheritance modes. In the bivalent case, homeologous chromosomes form pairs, where in a multivalent pattern all copies are homologous and are therefore free to pair and recombine. As sufficient sequencing data is more readily available than high-quality cytological assessments of meiotic behavior or population genetic assessment of allelic segregation, especially for non-model organisms, bioinformatics approaches to infer origins and inheritance modes of polyploids using short-read sequencing data are attractive. Here we describe two such approaches, where the first is based on distributions of allelic read depth at heterozygous sites within an individual, as the expectations of such distributions are different for disomic and polysomic inheritance modes. The second approach is more laborious and based on a phylogenetic assessment of partially phased haplotypes of a polyploid in comparison to the closest diploid relatives. We discuss the sources of deviations from expected inheritance patterns, advantages and pitfalls of both methods, effects of mating types on the performance of the methods, and possible future developments.
- Keywords
- Disomic, tetrasomic, polysomic, and mixed inheritance modes, Homeologous exchanges, selfing, outcrossing, Polyploidy, Rediploidization
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-01K76J7M6R7SQY8V5WM50X2YPQ
- MLA
- Scott, Alison Dawn, et al. “Inference of Polyploid Origin and Inheritance Mode from Population Genomic Data.” Polyploidy : Methods and Protocols, vol. 2545, Springer, 2023, pp. 279–95, doi:10.1007/978-1-0716-2561-3_15.
- APA
- Scott, A. D., Van de Velde, J. D., & Novikova, P. (2023). Inference of polyploid origin and inheritance mode from population genomic data. In Polyploidy : methods and protocols (Vol. 2545, pp. 279–295). https://doi.org/10.1007/978-1-0716-2561-3_15
- Chicago author-date
- Scott, Alison Dawn, Jozefien D. Van de Velde, and Polina Novikova. 2023. “Inference of Polyploid Origin and Inheritance Mode from Population Genomic Data.” In Polyploidy : Methods and Protocols, 2545:279–95. New York: Springer. https://doi.org/10.1007/978-1-0716-2561-3_15.
- Chicago author-date (all authors)
- Scott, Alison Dawn, Jozefien D. Van de Velde, and Polina Novikova. 2023. “Inference of Polyploid Origin and Inheritance Mode from Population Genomic Data.” In Polyploidy : Methods and Protocols, 2545:279–295. New York: Springer. doi:10.1007/978-1-0716-2561-3_15.
- Vancouver
- 1.Scott AD, Van de Velde JD, Novikova P. Inference of polyploid origin and inheritance mode from population genomic data. In: Polyploidy : methods and protocols. New York: Springer; 2023. p. 279–95.
- IEEE
- [1]A. D. Scott, J. D. Van de Velde, and P. Novikova, “Inference of polyploid origin and inheritance mode from population genomic data,” in Polyploidy : methods and protocols, vol. 2545, New York: Springer, 2023, pp. 279–295.
@incollection{01K76J7M6R7SQY8V5WM50X2YPQ,
abstract = {{Whole-genome duplications yield varied chromosomal pairing patterns, ranging from strictly bivalent to multivalent, resulting in disomic and polysomic inheritance modes. In the bivalent case, homeologous chromosomes form pairs, where in a multivalent pattern all copies are homologous and are therefore free to pair and recombine. As sufficient sequencing data is more readily available than high-quality cytological assessments of meiotic behavior or population genetic assessment of allelic segregation, especially for non-model organisms, bioinformatics approaches to infer origins and inheritance modes of polyploids using short-read sequencing data are attractive. Here we describe two such approaches, where the first is based on distributions of allelic read depth at heterozygous sites within an individual, as the expectations of such distributions are different for disomic and polysomic inheritance modes. The second approach is more laborious and based on a phylogenetic assessment of partially phased haplotypes of a polyploid in comparison to the closest diploid relatives. We discuss the sources of deviations from expected inheritance patterns, advantages and pitfalls of both methods, effects of mating types on the performance of the methods, and possible future developments.}},
author = {{Scott, Alison Dawn and Van de Velde, Jozefien D. and Novikova, Polina}},
booktitle = {{Polyploidy : methods and protocols}},
isbn = {{9781071625606}},
issn = {{1064-3745}},
keywords = {{Disomic, tetrasomic, polysomic, and mixed inheritance modes,Homeologous exchanges, selfing, outcrossing,Polyploidy,Rediploidization}},
language = {{eng}},
pages = {{279--295}},
publisher = {{Springer}},
series = {{Methods in molecular biology (MIMB)}},
title = {{Inference of polyploid origin and inheritance mode from population genomic data}},
url = {{http://doi.org/10.1007/978-1-0716-2561-3_15}},
volume = {{2545}},
year = {{2023}},
}
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