Smooth Descent: A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors.
genotyping error
identity by descent
imputation
linkage mapping
polyploidy
Journal
Frontiers in genetics
ISSN: 1664-8021
Titre abrégé: Front Genet
Pays: Switzerland
ID NLM: 101560621
Informations de publication
Date de publication:
2023
2023
Historique:
received:
21
09
2022
accepted:
20
02
2023
entrez:
20
3
2023
pubmed:
21
3
2023
medline:
21
3
2023
Statut:
epublish
Résumé
Linkage mapping is an approach to order markers based on recombination events. Mapping algorithms cannot easily handle genotyping errors, which are common in high-throughput genotyping data. To solve this issue, strategies have been developed, aimed mostly at identifying and eliminating these errors. One such strategy is SMOOTH, an iterative algorithm to detect genotyping errors. Unlike other approaches, SMOOTH can also be used to impute the most probable alternative genotypes, but its application is limited to diploid species and to markers heterozygous in only one of the parents. In this study we adapted SMOOTH to expand its use to any marker type and to autopolyploids with the use of identity-by-descent probabilities, naming the updated algorithm Smooth Descent (SD). We applied SD to real and simulated data, showing that in the presence of genotyping errors this method produces better genetic maps in terms of marker order and map length. SD is particularly useful for error rates between 5% and 20% and when error rates are not homogeneous among markers or individuals. With a starting error rate of 10%, SD reduced it to ∼5% in diploids, ∼7% in tetraploids and ∼8.5% in hexaploids. Conversely, the correlation between true and estimated genetic maps increased by 0.03 in tetraploids and by 0.2 in hexaploids, while worsening slightly in diploids (∼0.0011). We also show that the combination of genotype curation and map re-estimation allowed us to obtain better genetic maps while correcting wrong genotypes. We have implemented this algorithm in the R package Smooth Descent.
Identifiants
pubmed: 36936433
doi: 10.3389/fgene.2023.1049988
pii: 1049988
pmc: PMC10014611
doi:
Types de publication
Journal Article
Langues
eng
Pagination
1049988Informations de copyright
Copyright © 2023 Thérèse Navarro, Bourke, van de Weg, Clot, Arens, Finkers and Maliepaard.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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