A tetrasomic inheritance model and likelihood‐based method for mapping quantitative trait loci in autotetraploid species

Abstract

Dissecting the genetic architecture of quantitative traits in autotetraploid species is a methodologically challenging task, but a pivotally important goal for breeding globally important food crops, including potato and blueberry, and ornamental species such as rose. Mapping quantitative trait loci (QTLs) is now a routine practice in diploid species but is far less advanced in autotetraploids, largely due to a lack of analytical methods that account for the complexities of tetrasomic inheritance. We present a novel likelihood-based method for QTL mapping in outbred segregating populations of autotetraploid species. The method accounts properly for sophisticated features of gene segregation and recombination in an autotetraploid meiosis. It may model and analyse molecular marker data with or without allele dosage information, such as that from microarray or sequencing experiments. The method developed outperforms existing bivalent-based methods, which may fail to model and analyse the full spectrum of experimental data, in the statistical power of QTL detection, and accuracy of QTL location, as demonstrated by an intensive simulation study and analysis of data sets collected from a segregating population of potato (Solanum tuberosum). The study enables QTL mapping analysis to be conducted in autotetraploid species under a rigorous tetrasomic inheritance model.

Accounting for polysomic inheritance in quantitative trait loci mapping of autopolyploids

“…We recently became aware of an inaccurate reference to our work published in your journal which we would like to discuss here in order to rectify the record. The statement in question asserted that '… the method described in Bourke et al (2019) lacks an essential component; that is, genetic linkage analysis between quantitative trait locus (QTLs) and surrounding markers for QTL mapping in an outbred autotetraploid segregating population, as we have presented here' (Chen et al, 2021). We would like to briefly explain why we think this assertion is incorrect.…”

A Brief History of the Impact of Potato Genetics on the Breeding of Tetraploid Potato Cultivars for Tuber Propagation

“…In practice we need a lot of computing power to reach this conclusion. Computer software is now available to do this at the tetraploid level for each linkage group separately in a full sib family, either assuming no double reduction (TetraploidSNPMap, Hackett et al 2017) or taking account of quadrivalents and double reduction (Chen et al 2020). It is also available for Genome Wide Association Studies (GWAS) on a diverse set of genotypes in a collection of interest to the breeder, where QTLs for more traits and better mapping resolution were anticipated (R package GWASpoly, Rosyara et al 2016).…”

Mapping quantitative trait loci in autotetraploids under a genuine tetrasomic model

“…recently argued that the comment made in Chen et al (2021), which was in fact first published online in January 2020, 'the method described in Bourke et al (2019) lacks an essential component; that is, genetic linkage analysis between quantitative trait loci (QTLs) and surrounding markers for QTL mapping in an outbred autotetraploid segregating population', is incorrect. I explain here why the comment we made is adequate and correct on the basis of facts and statistical principles.…”

“…This much pre-dates the literature cited by Bourke et al (2024). Bourke et al (2024) state, referring to Chen et al (2021), 'In the test dataset with their package, the function QvMethod took over 17 h to detect a single QTL in a mapping population of 300 individuals carrying 20 markers along a single chromosome (using a desktop computer with 32 Gb RAM and an Intel Xeon W-2133 3.6 GHz processor). No significance thresholds were returned with the results.…”

“…However, no such term as 'posterior genotype probability' is found and nor is the relevant material for the calculation present in Bourke et al (2021). Bourke et al (2024) attempted to depreciate the work presented in Chen et al (2021) as 'a theoretical exercise' because it 'requires that the users already know the rate of double reduction at each locus'. This is misleading, because the data presented in Chen et al (2021) suffices to estimate the double reduction parameters using the method I developed and published more than 20 years ago (Luo et al, 2000), which was also cited in Chen et al (2021).…”