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  • 1
    Online Resource
    Online Resource
    Pollen contamination and mating patterns in a Douglas-fir seed orchard as measured by simple sequence repeat markers
    Canadian Science Publishing ; 2005
    In:  Canadian Journal of Forest Research Vol. 35, No. 7 ( 2005-07-01), p. 1592-1603
    Details
    In: Canadian Journal of Forest Research, Canadian Science Publishing, Vol. 35, No. 7 ( 2005-07-01), p. 1592-1603
    Abstract: Pollen contamination is detrimental to the genetic quality of seed orchard crops. Highly variable simple sequence repeat (SSR) markers make it possible to accurately measure pollen contamination and characterize patterns of within-orchard mating by directly identifying the male and female parent of each seed produced in the orchard. We used nine SSR markers to measure pollen contamination and characterize mating patterns based on seed samples collected in 3 years (1999, 2000, and 2003) from one block of a nonisolated, open-pollinated, clonal seed orchard of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) in western Oregon. Pollen contamination was consistently high across the 3 years (mean = 35.3%, range = 31.0%-41.3%) and appeared to result primarily from cross-pollination among the orchard blocks. Levels of pollen contamination varied substantially among clones and were higher in clones with early female receptivity (mean = 55.5%) than in those with either mid (mean = 36.4%) or late (mean = 28.3%) female receptivity. We detected low rates of self-pollination (mean = 1.8% per clone) and over 10-fold differences in the relative paternal contributions of the clones. There was a clear pattern of positive assortative mating with respect to floral phenology. This study illustrates that SSR markers are powerful tools for characterizing seed lots and improving the design and management of Douglas-fir seed orchards.
    Type of Medium: Online Resource
    ISSN: 0045-5067 , 1208-6037
    URL: Article
    DOI: 10.1139/x05-082
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 2005
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    SSG: 23
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  • 2
    Online Resource
    Online Resource
    Genomics-Enabled Management of Genetic Resources in Radiata Pine
    MDPI AG ; 2022
    In:  Forests Vol. 13, No. 2 ( 2022-02-10), p. 282-
    Details
    In: Forests, MDPI AG, Vol. 13, No. 2 ( 2022-02-10), p. 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) 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.
    Type of Medium: Online Resource
    ISSN: 1999-4907
    URL: Article
    DOI: 10.3390/f13020282
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2527081-3
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  • 3
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    Online Resource
    Genome‐wide association studies and prediction of 17 traits related to phenology, biomass and cell wall composition in the energy grass Miscanthus sinensis
    Wiley ; 2014
    In:  New Phytologist Vol. 201, No. 4 ( 2014-03), p. 1227-1239
    Details
    In: New Phytologist, Wiley, Vol. 201, No. 4 ( 2014-03), p. 1227-1239
    Abstract: Increasing demands for food and energy require a step change in the effectiveness, speed and flexibility of crop breeding. Therefore, the aim of this study was to assess the potential of genome‐wide association studies ( GWAS s) and genomic selection (i.e. phenotype prediction from a genome‐wide set of markers) to guide fundamental plant science and to accelerate breeding in the energy grass Miscanthus . We generated over 100 000 single‐nucleotide variants ( SNV s) by sequencing restriction site‐associated DNA ( RAD ) tags in 138 Micanthus sinensis genotypes, and related SNV s to phenotypic data for 17 traits measured in a field trial. Confounding by population structure and relatedness was severe in naïve GWAS analyses, but mixed‐linear models robustly controlled for these effects and allowed us to detect multiple associations that reached genome‐wide significance. Genome‐wide prediction accuracies tended to be moderate to high (average of 0.57), but varied dramatically across traits. As expected, predictive abilities increased linearly with the size of the mapping population, but reached a plateau when the number of markers used for prediction exceeded 10 000–20 000, and tended to decline, but remain significant, when cross‐validations were performed across subpopulations. Our results suggest that the immediate implementation of genomic selection in Miscanthus breeding programs may be feasible.
    Type of Medium: Online Resource
    ISSN: 0028-646X , 1469-8137
    URL: Issue
    URL: Article
    DOI: 10.1111/nph.2014.201.issue-4
    DOI: 10.1111/nph.12621
    Language: English
    Publisher: Wiley
    Publication Date: 2014
    detail.hit.zdb_id: 208885-X
    detail.hit.zdb_id: 1472194-6
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  • 4
    Online Resource
    Online Resource
    Investigating the origins and evolution of a glyphosate‐resistant weed invasion in South America
    Wiley ; 2021
    In:  Molecular Ecology Vol. 30, No. 21 ( 2021-11), p. 5360-5372
    Details
    In: Molecular Ecology, Wiley, Vol. 30, No. 21 ( 2021-11), p. 5360-5372
    Abstract: The global invasion, and subsequent spread and evolution of weeds provides unique opportunities to address fundamental questions in evolutionary and invasion ecology. Amaranthus palmeri is a widespread glyphosate‐resistant (GR) weed in the USA. Since 2015, GR populations of A . palmeri have been confirmed in South America, raising questions about introduction pathways and the importance of pre‐ vs. post‐invasion evolution of GR traits. We used RAD‐sequencing genotyping to characterize genetic structure of populations from Brazil, Argentina, Uruguay and the USA. We also quantified gene copy number of the glyphosate target, 5‐enolpyruvyl‐3‐shikimate phosphate synthase ( EPSPS ), and the presence of an extrachromosomal circular DNA (eccDNA) replicon known to confer glyphosate resistance in USA populations. Populations in Brazil, Argentina and Uruguay were only weakly differentiated (pairwise F ST  ≤0.043) in comparison to USA populations (mean pairwise F ST  =0.161, range =0.068–0.258), suggesting a single major invasion event. However, elevated EPSPS copy number and the EPSPS replicon were identified in all populations from Brazil and Uruguay, but only in a single Argentinean population. These observations are consistent with independent in situ evolution of glyphosate resistance in Argentina, followed by some limited recent migration of the eccDNA‐based mechanism from Brazil to Argentina. Taken together, our results are consistent with an initial introduction of A . palmeri into South America sometime before the 1980s, and local evolution of GR in Argentina, followed by a secondary invasion of GR A . palmeri with the unique eccDNA‐based mechanism from the USA into Brazil and Uruguay during the 2010s.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    URL: Article
    DOI: 10.1111/mec.v30.21
    DOI: 10.1111/mec.16221
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2021
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    detail.hit.zdb_id: 1126687-9
    SSG: 12
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  • 5
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    Online Resource
    Allozyme variation, differentiation, and inbreeding in populations of Pinus mugo in Bulgaria
    Canadian Science Publishing ; 2004
    In:  Canadian Journal of Forest Research Vol. 34, No. 12 ( 2004-12-01), p. 2611-2617
    Details
    In: Canadian Journal of Forest Research, Canadian Science Publishing, Vol. 34, No. 12 ( 2004-12-01), p. 2611-2617
    Abstract: Genetic variation of 17 populations of Pinus mugo Turra was studied using 10 polymorphic allozyme loci. Polymorphism and gene diversity in these populations were comparable to mean values for gymnosperm species, but slightly lower than in pines with large and continuous ranges. We did not find significant interpopulation differentiation (F ST = 0.041) or isolation by distance, suggesting that gene flow might be extensive or that the time elapsed since the species range became fragmented has been too short for genetic differentiation to arise via genetic drift. We detected moderate and statistically significant levels of inbreeding (mean F IS = 0.252) for all loci in all populations. Although there are many possible explanations for this nonequilibrium population structure, we propose that the main reasons for its ubiquity are the peculiar growth form and reproductive biology of P. mugo, which promote excessive near-neighbor pollinations. Populations in Vitosha Mountain and western Stara Planina had the highest levels of inbreeding and the lowest observed heterozygosities. All populations in these mountains are small and isolated, but none of them is under a special regime of protection. Thus, the conservation status of P. mugo populations in Vitosha Mountain and western Stara Planina may deserve reevaluation. Future gene conservation efforts should focus on obtaining information on the genetic variation of adaptive traits in P. mugo.
    Type of Medium: Online Resource
    ISSN: 0045-5067 , 1208-6037
    URL: Article
    DOI: 10.1139/x04-127
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 2004
    detail.hit.zdb_id: 1473096-0
    SSG: 23
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Genetic relationships between spring emergence, canopy phenology, and biomass yield increase the accuracy of genomic prediction in Miscanthus
    Oxford University Press (OUP) ; 2017
    In:  Journal of Experimental Botany Vol. 68, No. 18 ( 2017-11-02), p. 5093-5102
    Details
    In: Journal of Experimental Botany, Oxford University Press (OUP), Vol. 68, No. 18 ( 2017-11-02), p. 5093-5102
    Type of Medium: Online Resource
    ISSN: 0022-0957 , 1460-2431
    URL: Article
    DOI: 10.1093/jxb/erx339
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2017
    detail.hit.zdb_id: 1466717-4
    SSG: 12
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  • 7
    Online Resource
    Online Resource
    Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations
    Springer Science and Business Media LLC ; 2014
    In:  Nature Genetics Vol. 46, No. 10 ( 2014-10), p. 1089-1096
    Details
    In: Nature Genetics, Springer Science and Business Media LLC, Vol. 46, No. 10 ( 2014-10), p. 1089-1096
    Type of Medium: Online Resource
    ISSN: 1061-4036 , 1546-1718
    URL: Article
    DOI: 10.1038/ng.3075
    RVK:
    XA 10000
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2014
    detail.hit.zdb_id: 1494946-5
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Population structure and history of the Welsh sheep breeds determined by whole genome genotyping
    Springer Science and Business Media LLC ; 2015
    In:  BMC Genetics Vol. 16, No. 1 ( 2015-12)
    Details
    In: BMC Genetics, Springer Science and Business Media LLC, Vol. 16, No. 1 ( 2015-12)
    Type of Medium: Online Resource
    ISSN: 1471-2156
    URL: Article
    DOI: 10.1186/s12863-015-0216-x
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2015
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    detail.hit.zdb_id: 3058779-7
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    Population genomics of selectively neutral genetic structure and herbicide resistance in UK populations of Alopecurus myosuroides
    Wiley ; 2021
    In:  Pest Management Science Vol. 77, No. 3 ( 2021-03), p. 1520-1529
    Details
    In: Pest Management Science, Wiley, Vol. 77, No. 3 ( 2021-03), p. 1520-1529
    Abstract: Alopecurus myosuroides (blackgrass) is a major weed in Europe with known resistance to multiple herbicide modes of action. In the UK, there is evidence that blackgrass has undergone a range expansion. In this paper, genotyping‐by‐sequencing and population‐level herbicide resistance phenotypes are used to explore spatial patterns of selectively neutral genetic variation and resistance. We also perform a preliminary genome‐wide association study (GWAS) and genomic prediction analysis to evaluate the potential of these approaches for investigating nontarget site herbicide resistance. RESULTS Blackgrass was collected from 47 fields across the British Isles and up to eight plants per field population ( n = 369) were genotyped by Restriction site‐associated DNA (RAD)‐sequencing. A total of 20 426 polymorphic loci were identified and used for population genetic analyses. Phenotypic assays revealed significant variation in herbicide resistance between populations. Population structure was weak ( F ST = 0.024–0.048), but spatial patterns were consistent with an ongoing westward and northward range expansion. We detected strong and consistent Wahlund effects ( F IS = 0.30). There were no spatial patterns of herbicide resistance or evidence for confounding with population structure. Using a combination of population‐level GWAS and genomic prediction we found that the top 20, 200, and 2000 GWAS loci had higher predictive abilities for fenoxaprop resistance compared to all markers. CONCLUSION There is likely extensive human‐mediated gene flow between field populations of the weed blackgrass at a national scale. The lack of confounding of adaptive and neutral genetic variation can enable future, more extensive GWAS analyses to identify the genetic architecture of evolved herbicide resistance. © 2020 Society of Chemical Industry
    Type of Medium: Online Resource
    ISSN: 1526-498X , 1526-4998
    URL: Issue
    URL: Article
    DOI: 10.1002/ps.v77.3
    DOI: 10.1002/ps.6174
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 2003455-6
    SSG: 12
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  • 10
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    Online Resource
    Gene-Editing for Production Traits in Forest Trees: Challenges to Integration and Gene Target Identification
    MDPI AG ; 2022
    In:  Forests Vol. 13, No. 11 ( 2022-11-10), p. 1887-
    Details
    In: Forests, MDPI AG, Vol. 13, No. 11 ( 2022-11-10), p. 1887-
    Abstract: Gene-editing methods, particularly CRISPR, provide extraordinary opportunities for scientific insights and applications in the life sciences. However, the prospects for near-term applications to commercial forestry appear limited. Loss-of-function phenotypes that can be imparted by mutation of one or a few conserved genes offer the best opportunities in the near term. For traits with complex inheritance, there is insufficient science to guide gene-editing efforts, and Genome-Wide Association Studies (GWASs), without strong validation, typically cannot provide high-confidence gene identification. Other obstacles include the difficulty of transformation in many important genotypes, difficulties of transient editing or complete editor removal, and complexity of use in breeding programs. Gene edits that cause loss-of-function traits will generally be recessive, and thus not be expressed among outbred progeny, so vegetative propagules (clones) will be required in most cases. There are also important societal constraints, such as strict regulations for field trials in most countries, and market certification systems that do not allow any kinds of recombinant DNA-modified trees, including those produced by gene-editing, in certified production forests. We conclude that gene-editing applications will be extremely limited for the foreseeable future (i.e., at least 10 years). Nevertheless, gene-editing is a very powerful scientific tool that will be widely used by molecular forest scientists and can lead to important applications in the longer term, if research advances are made on key fronts and regulatory and market obstacles greatly attenuated.
    Type of Medium: Online Resource
    ISSN: 1999-4907
    URL: Article
    DOI: 10.3390/f13111887
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2527081-3
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