Genomic diversity evaluation of populus trichocarpa germplasm for rare variant genetic association studies

Genome-wide association studies are powerful tools to elucidate the genome-to-phenomerelationship. In order to explain most of the observed heritability of a phenotypic trait, asufficient number of individuals and a large set of genetic variants must be examined. Thedevelopment of high-throughput technologies and cost-efficient resequencing of completegenomes have enabled the genome-wide identification of genetic variation at large scale.As such, almost all existing genetic variation becomes available, and it is now possible toidentify rare genetic variants in a population sample. Rare genetic variants that were usuallyfiltered out in most genetic association studies are the most numerous genetic variationsacross genomes and hold great potential to explain a significant part of the missingheritability observed in association studies. Rare genetic variants must be identified withhigh confidence, as they can easily be confounded with sequencing errors. In this study,we used a pre-filtered data set of 1,014 purePopulus trichocarpaentire genomes toidentify rare and common small genetic variants across individual genomes. We comparedvariant calls betweenPlatypusandHaplotypeCallerpipelines, and we further applied strictqualityfilters for improved genetic variant identification. Finally, we only retained geneticvariants that were identified by both variant callers increasing calling confidence. Based onthese shared variants and after stringent qualityfiltering, we found high genomic diversity inP. trichocarpagermplasm, with 7.4 million small genetic variants. Importantly, 377k non-synonymous variants (5% of the total) were uncovered. We highlight the importance ofgenomic diversity and the potential of rare defective genetic variants in explaining asignificant portion ofP. trichocarpa's phenotypic variability in association genetics. Theultimate goal is to associate both rare and common alleles with poplar's wood quality traitsto support selective breeding for an improved bioenergy feedstock

Breeding without Breeding: Is a Complete Pedigree Necessary for Efficient Breeding?

Complete pedigree information is a prerequisite for modern breeding and the ranking of parents and offspring for selection and deployment decisions. DNA fingerprinting and pedigree reconstruction can substitute for artificial matings, by allowing parentage delineation of naturally produced offspring. Here, we report on the efficacy of a breeding concept called “Breeding without Breeding” (BwB) that circumvents artificial matings, focusing instead on a subset of randomly sampled, maternally known but paternally unknown offspring to delineate their paternal parentage. We then generate the information needed to rank those offspring and their paternal parents, using a combination of complete (full-sib: FS) and incomplete (half-sib: HS) analyses of the constructed pedigrees. Using a random sample of wind-pollinated offspring from 15 females (seed donors), growing in a 41-parent western larch population, BwB is evaluated and compared to two commonly used testing methods that rely on either incomplete (maternal half-sib, open-pollinated: OP) or complete (FS) pedigree designs. BwB produced results superior to those from the incomplete design and virtually identical to those from the complete pedigree methods. The combined use of complete and incomplete pedigree information permitted evaluating all parents, both maternal and paternal, as well as all offspring, a result that could not have been accomplished with either the OP or FS methods alone. We also discuss the optimum experimental setting, in terms of the proportion of fingerprinted offspring, the size of the assembled maternal and paternal half-sib families, the role of external gene flow, and selfing, as well as the number of parents that could be realistically tested with BwB

Data from: Exploration of genetic architecture through sib-ship reconstruction in advanced breeding population of Eucalyptus nitens

Accurate inference of relatedness between individuals in breeding population contributes to the precision of genetic parameter estimates, effectiveness of inbreeding management and the amount of genetic progress delivered from breeding programs. Pedigree reconstruction has been proven to be an efficient tool to correct pedigree errors and recover hidden relatedness in open pollinated progeny tests but the method can be limited by the lack of parental genotypes and the high proportion of alien pollen from outside the breeding population. Our study investigates the efficiency of sib-ship reconstruction in an advanced breeding population of Eucalyptus nitens with only partially tracked pedigree. The sib-ship reconstruction allowed the identification of selfs (4% of the sample) and the exploration of their potential effect on inbreeding depression in the traits studied. We detected signs of inbreeding depression in diameter at breast height and growth strain while no indications were observed in wood density, wood stiffness and tangential air-dry shrinkage. After the application of a corrected sib-ship relationship matrix, additive genetic variance and heritability were observed to increase where signs of inbreeding depression were initially detected. Conversely, the same genetic parameters for traits that appeared to be free of inbreeding depression decreased in size. It therefore appeared that greater genetic variance may be due, at least in part, to contributions from inbreeding in these studied populations rather than a removal of inbreeding as is traditionally thought

The Use of “Genotyping-by-Sequencing” to Recover Shared Genealogy in Genetically Diverse Eucalyptus Populations

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

Genotypic data

Data folder containing genotypes and their associated qualitative scores (GenTrain score and GenCall

Pedigree

Pedigree for the studied populatio

Phenotype file

File containing phenotypic data for the studied populatio

Graphical interpretation regarding the ordinal logistic regression for origin of father to explain egg puncture occurrence (E00).

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Spruce shoot weevil trial in the interior of British Columbia, Canada.

A) Photo to the left: emerging Pissodes strobi individual during the weevil rearing experiment (photo credit: Ward Strong); photo to the right: Kalamalka Research Station based Interior spruce weevil trial after thinning (photo credit: Val Ashley). B) Spatial distribution for classes of attack severity (upper left plot, A00), egg punctures occurrence (upper right plot, E00) in the year 2000, as well as for heights measured in cm at four years (bottom left plot, HT4 in the year 1998) and five years of age (bottom right plot, HT5 in the year 1999), respectively, on an individual tree basis within the experimental plot. Family plots are distinguished in the grid, where individual trees are indexed by row and column numbers. The plot outline of the entire trial on a family basis is provided in [33]. Forty-two controlled crosses were generated by mating resistant with resistant, resistant with susceptible, and susceptible with susceptible parents. The ranking in terms of weevil resistance of the individual Interior spruce parents is known and was done previously [13]. The evaluation of attacks was done following artificial weevil infestation of the spruce resistance trial. Height data from pre-attack years are shown. The colour code for ascending phenotypic values (that is for classes of attack severity, egg punctures occurrence, heights) is provided to the right of each plot outline. No formal statistical analysis on the spatial distribution of the weevil attack severity was attempted for this experiment designed as family-based plots where each plot contained 25 individuals of the same family.</p