Abstract
The recovery of genealogy in both natural and captive populations is critical for any decision in the management of genetic resources. It allows for the estimation of genetic parameters such as heritability and genetic correlations, as well as defining an optimal mating design that maintains a large effective population size. We utilised “genotyping-by-sequencing” (GBS) in combination with bioinformatics tools developed specifically for GBS data to recover genetic relatedness, with a focus on parent-offspring relationships in a Eucalyptus nitens breeding population as well as recognition of individuals representing other Eucalyptus species and putative hybrids. We found a clear advantage on using tools specifically designed for data of highly variable sequencing quality when recovering genetic relatedness. The parent-offspring relatedness showed a significant response to data filtering from 0.05 to 0.3 when the standard approach (G1) was used, while it oscillated around 0.4 when the specifically designed method (G5) was implemented. Additionally, comparisons with commonly used tools demonstrated vulnerability of the relatedness estimates to incorrect imputation of missing data when shallow sequencing information and genetically distant individuals are present in the population. In turn, these biased imputed genotypes negatively affected the estimation of genetic relatedness between parents and offspring. Careful filtering for both genetic outliers and shallowly sequenced markers led to improvements in estimations of genetic relatedness. Alternatively, a method that avoided missing data imputation and took sequence depth into consideration improved the accuracy of parent-offspring relationship coefficients where sequencing data quality was highly variable.
Highlights
Genetic relatedness [1], defined as twice the probability that alleles from each of a pair of individuals are identical by descent (IBD) [2], and its accuracy, is considered one of the essential factors of any quantitative genetic analysis [3,4]
We investigated the effect of the inclusion of other Eucalyptus species to the population on call rates
The efficiency of pedigree reconstruction depends on the availability of genetic fingerprints for all possible parents contributing to the gene pool [68,69], which can be a crucial limitation especially in multi-generational forest tree breeding populations
Summary
Genetic relatedness [1], defined as twice the probability that alleles from each of a pair of individuals are identical by descent (IBD) [2], and its accuracy, is considered one of the essential factors of any quantitative genetic analysis [3,4]. The first attempts to improve relatedness estimations through the employment of DNA information arose with the development of highly polymorphic molecular markers (i.e., microsatellites (simple sequence repeats—SSR)) in concert with pedigree reconstruction approaches [8]. There are two main approaches undertaken for reducing complexity when generating forest tree genomic resources: (1) exome capture-based [24,25,26] or (2) reduced genome representation sequencing methodologies such as genotyping-by-sequencing (GBS-RE-RRS) [27,28,29,30], Restriction site
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