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  1. Article ; Online: Chasing genetic correlation breakers to stimulate population resilience to climate change

    Jaroslav Klápště / Emily J Telfer / Heidi S Dungey / Natalie J Graham

    Scientific Reports, Vol 12, Iss 1, Pp 1-

    2022  Volume 16

    Abstract: Abstract Global climate change introduces new combinations of environmental conditions, which is expected to increase stress on plants. This could affect many traits in multiple ways that are as yet unknown but will likely require the modification of ... ...

    Abstract Abstract Global climate change introduces new combinations of environmental conditions, which is expected to increase stress on plants. This could affect many traits in multiple ways that are as yet unknown but will likely require the modification of existing genetic relationships among functional traits potentially involved in local adaptation. Theoretical evolutionary studies have determined that it is an advantage to have an excess of recombination events under heterogeneous environmental conditions. Our study, conducted on a population of radiata pine (Pinus radiata D. Don), was able to identify individuals that show high genetic recombination at genomic regions, which potentially include pleiotropic or collocating QTLs responsible for the studied traits, reaching a prediction accuracy of 0.80 in random cross-validation and 0.72 when whole family was removed from the training population and predicted. To identify these highly recombined individuals, a training population was constructed from correlation breakers, created through tandem selection of parents in the previous generation and their consequent mating. Although the correlation breakers showed lower observed heterogeneity possibly due to direct selection in both studied traits, the genomic regions with statistically significant differences in the linkage disequilibrium pattern showed higher level of heretozygosity, which has the effect of decomposing unfavourable genetic correlation. We propose undertaking selection of correlation breakers under current environmental conditions and using genomic predictions to increase the frequency of these ’recombined’ individuals in future plantations, ensuring the resilience of planted forests to changing climates. The increased frequency of such individuals will decrease the strength of the population-level genetic correlations among traits, increasing the opportunity for new trait combinations to be developed in the future.
    Keywords Medicine ; R ; Science ; Q
    Subject code 333
    Language English
    Publishing date 2022-05-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Genomics-Enabled Management of Genetic Resources in Radiata Pine

    Jaroslav Klápště / Ahmed Ismael / Mark Paget / Natalie J. Graham / Grahame T. Stovold / Heidi S. Dungey / Gancho T. Slavov

    Forests, Vol 13, Iss 282, p

    2022  Volume 282

    Abstract: Traditional tree improvement is cumbersome and costly. Our main objective was to assess the extent to which genomic data can currently accelerate and improve decision making in this field. We used diameter at breast height (DBH) and wood density (WD) ... ...

    Abstract Traditional tree improvement is cumbersome and costly. Our main objective was to assess the extent to which genomic data can currently accelerate and improve decision making in this field. We used diameter at breast height (DBH) and wood density (WD) data for 4430 tree genotypes and single-nucleotide polymorphism (SNP) data for 2446 tree genotypes. Pedigree reconstruction was performed using a combination of maximum likelihood parentage assignment and matching based on identity-by-state (IBS) similarity. In addition, we used best linear unbiased prediction (BLUP) methods to predict phenotypes using SNP markers (GBLUP), recorded pedigree information (ABLUP), and single-step “blended” BLUP (HBLUP) combining SNP and pedigree information. We substantially improved the accuracy of pedigree records, resolving the inconsistent parental information of 506 tree genotypes. This led to substantially increased predictive ability (i.e., by up to 87%) in HBLUP analyses compared to a baseline from ABLUP. Genomic prediction was possible across populations and within previously untested families with moderately large training populations ( N = 800–1200 tree genotypes) and using as few as 2000–5000 SNP markers. HBLUP was generally more effective than traditional ABLUP approaches, particularly after dealing appropriately with pedigree uncertainties. Our study provides evidence that genome-wide marker data can significantly enhance tree improvement. The operational implementation of genomic selection has started in radiata pine breeding in New Zealand, but further reductions in DNA extraction and genotyping costs may be required to realise the full potential of this approach.
    Keywords tree breeding ; pedigree reconstruction ; genomic selection ; genomic prediction ; single-step BLUP ; Pinus radiata ; Plant ecology ; QK900-989
    Subject code 006
    Language English
    Publishing date 2022-02-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: The Use of “Genotyping-by-Sequencing” to Recover Shared Genealogy in Genetically Diverse Eucalyptus Populations

    Jaroslav Klápště / Rachael L. Ashby / Emily J. Telfer / Natalie J. Graham / Heidi S. Dungey / Rudiger Brauning / Shannon M. Clarke / Ken G. Dodds

    Forests, Vol 12, Iss 904, p

    2021  Volume 904

    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 ... ...

    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.
    Keywords genotyping-by-sequencing ; Eucalyptus ; genetic relatedness ; genotyping errors ; Plant ecology ; QK900-989
    Subject code 310
    Language English
    Publishing date 2021-07-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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