Dataset Information

Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand.

ABSTRACT: Anticipating the evolutionary responses of long-lived organisms, such as trees, to environmental changes, requires the assessment of genetic variation of adaptive traits in natural populations. To this end, high-density markers are needed to calculate genomic relatedness between individuals allowing to estimate the genetic variance of traits in wild populations. We designed a targeted capture-based, next-generation sequencing assay based on the highly heterozygous pedunculate oak (Quercus robur) reference genome, for the sequencing of 3 Mb of genic and intergenic regions. Using a mixed stand of 293 Q. robur and Q. petraea genotypes we successfully captured over 97% of the target sequences, corresponding to 0.39% of the oak genome, with sufficient depth (97×) for the detection of about 190,000 SNPs evenly spread over the targeted regions. We validated the technique by evaluating its reproducibility, and comparing the genomic relatedness of trees with their known pedigree relationship. We explored the use of the technique on other related species and highlighted the advantages and limitations of this approach. We found that 92.07% of target sequences in Q. suber and 70.36% of sequences in Fagus sylvatica were captured. We used this SNP resource to estimate genetic relatedness in the mixed oak stand. Mean pairwise genetic relatedness was low within each species with a few values exceeding 0.25 (half-sibs) or 0.5 (full-sibs). Finally, we applied the technique to a long-standing issue in population genetics of trees regarding the relationship between inbreeding and components of fitness. We found very weak signals for inbreeding depression for reproductive success and no signal for growth within both species.

SUBMITTER: Lesur I

PROVIDER: S-EPMC6053538 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Publications

Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand.

Lesur Isabelle I Alexandre Hermine H Boury Christophe C Chancerel Emilie E Plomion Christophe C Kremer Antoine A

Frontiers in plant science 20180713

Anticipating the evolutionary responses of long-lived organisms, such as trees, to environmental changes, requires the assessment of genetic variation of adaptive traits in natural populations. To this end, high-density markers are needed to calculate genomic relatedness between individuals allowing to estimate the genetic variance of traits in wild populations. We designed a targeted capture-based, next-generation sequencing assay based on the highly heterozygous pedunculate oak (<i>Quercus rob ...[more]

PMID: 30057586

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Project description:BackgroundThe Chinese Natural Forest Protection program has been conducted nationwide and has achieved resounding success. However, timber importation has increased; therefore, producing more domestic timber is critical to meet the demand for raw materials. Fertilization is one of the most effective silviculture practices used to improve tree and stand growth. However, determining the appropriate type and amount of elements is necessary for effective fertilization of big timber in different forest types and environmental conditions. Stoichiometric theory provides the criteria to assess nutrient limitation in plants and offers important insight into fertilizer requirements of forested ecosystems.MethodsNitrogen (N) and phosphorus (P) concentrations in plants' leaves, mineral soil, and litter were investigated in a mixed pine-oak stand.ResultsThe big timber rate for Pinus tabuliformis, Pinus armandii and Quercus aliena var. acutesserata is 57.71%, 22.79% and 2.78% of current existing individuals respectively. Foliar N and P concentrations were 9.08 and 0.88 mg g-1, respectively. The N:P in the plants was 10.30. N concentration and N:P in mineral soil decreased from 0-30 cm soil depth. For litter, N and P concentrations were 16.89 and 1.51 mg g-1, respectively, and N:P was 11.51. Concentrations of N and P in mineral soil and litter did not significantly affect plants'leaf concentrations. Similar result was also obtained between litter and mineral soil concentrations. Nitrogen storage in mineral soil was significantly correlated with foliar N:P in the plants.DiscussionFoliar N:P of dominant tree species and the plants, and foliar N concentration in Pinus tabuliformis and P. armandii, and foliar P concentration of P. armandii in the mixed pine-oak stand was lower than that in Chinese and other terrestrial plants. Foliar nutrients in the plants were not affected by soil nutrients. According to the criteria of nutrient limitation for plants, growth of dominant tree species was N limited; therefore, 1.49 t ha-1 pure N should be added to forest land to as fertilizer.

Project description:BackgroundEstimation of genetic relatedness, or kinship, is used occasionally for recreational purposes and in forensic applications. While numerous methods were developed to estimate kinship, they suffer from high computational requirements and often make an untenable assumption of homogeneous population ancestry of the samples. Moreover, genetic privacy is generally overlooked in the usage of kinship estimation methods. There can be ethical concerns about finding unknown familial relationships in third-party databases. Similar ethical concerns may arise while estimating and reporting sensitive population-level statistics such as inbreeding coefficients for the concerns around marginalization and stigmatization.ResultsHere, we present SIGFRIED, which makes use of existing reference panels with a projection-based approach that simplifies kinship estimation in the admixed populations. We use simulated and real datasets to demonstrate the accuracy and efficiency of kinship estimation. We present a secure federated kinship estimation framework and implement a secure kinship estimator using homomorphic encryption-based primitives for computing relatedness between samples in two different sites while genotype data are kept confidential. Source code and documentation for our methods can be found at https://doi.org/10.5281/zenodo.7053352.ConclusionsAnalysis of relatedness is fundamentally important for identifying relatives, in association studies, and for estimation of population-level estimates of inbreeding. As the awareness of individual and group genomic privacy is growing, privacy-preserving methods for the estimation of relatedness are needed. Presented methods alleviate the ethical and privacy concerns in the analysis of relatedness in admixed, historically isolated and underrepresented populations.Short abstractGenetic relatedness is a central quantity used for finding relatives in databases, correcting biases in genome wide association studies and for estimating population-level statistics. Methods for estimating genetic relatedness have high computational requirements, and occasionally do not consider individuals from admixed ancestries. Furthermore, the ethical concerns around using genetic data and calculating relatedness are not considered. We present a projection-based approach that can efficiently and accurately estimate kinship. We implement our method using encryption-based techniques that provide provable security guarantees to protect genetic data while kinship statistics are computed among multiple sites.

Dataset Information

Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand.

Publications

Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand.

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