Smooth Descent: A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors

Frontiers in Genetics

Genetics

Alejandro Thérèse Navarro¹  Corentin R. Clot¹  Peter M. Bourke¹  Eric van de Weg¹  Richard Finkers¹  Paul Arens¹  Chris Maliepaard² 

[1] Plant Breeding, Wageningen University & Research, Wageningen, Netherlands;null;

关键词: linkage mapping;    genotyping error;    identity by descent;    imputation;    polyploidy;   

DOI  :  10.3389/fgene.2023.1049988

 received in 2022-09-21, accepted in 2023-02-20,  发布年份 2023

来源: Frontiers

【 摘 要 】

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.

【 授权许可】

Unknown   
Copyright © 2023 Thérèse Navarro, Bourke, van de Weg, Clot, Arens, Finkers and Maliepaard.