Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
4.5
2.9
Journals
Forests
Special Issues
Using Genomic Information in Forest Tree Breeding, Restoration, and Conservation:...
share announcement

Using Genomic Information in Forest Tree Breeding, Restoration, and Conservation: Separating Hype from Reality

A special issue of Forests (ISSN 1999-4907). This special issue belongs to the section "Genetics and Molecular Biology".

Deadline for manuscript submissions: 14 June 2024 | Viewed by 17329

Special Issue Editors

Dr. Gancho Slavov

E-Mail Website
Guest Editor
Radiata Pine Breeding Company, Rotorua, New Zeland
Interests: genetic variation within and among populations; quantitative traits; adaptation to climate change; genome-wide association studies; genomic prediction; tree improvement and conservation
Dr. Glenn T. Howe

E-Mail Website
Guest Editor
Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
Interests: physiological and ecological genetics of forest trees; genomics of forest trees; quantitative genetics and tree breeding; forest responses to climate change and management responses
Dr. Jaroslav Klápště

E-Mail Website
Guest Editor
Quantitative Genomics Team, Scion (New Zealand Forest Research Institute), Rotorua, New Zealand
Interests: forest tree breeding; genotype by environment interaction; multi-trait evaluation and selection strategies; genomic selection; inheritance of complex traits; simulation studies

Special Issue Information

Dear Colleagues,

Large-scale genomic information has already changed forest genetics, and new approaches are on the horizon. However, rapid advances have widened the gulf between researchers and the users of genomic information. This Special Issue of Forests aims to review the latest research on forest tree genomics and facilitate dialog among researchers and expert practitioners. We seek review articles, short perspective papers, and contributions describing original research and applications of structural, functional, evolutionary/comparative, quantitative/population, and ecological/landscape genomics in forest trees. Research on non-forest species (e.g., fruit trees or agricultural/energy crops) is encouraged, if implications for forest trees are clear. Our goal is to ‘connect-the-dots’ between genomic research and application. Thus, your paper should include a discussion of the timeline and steps involved in translating genomic research into operational activities in ways that are clear to knowledgeable practitioners. We also encourage papers that describe downstream applications and priority needs for genomic information from a user’s perspective. Papers from breeders, conservationists, ecologists, and physiologists are particularly relevant. Our submission, peer-review, and publication processes are designed to achieve a comprehensive overview of the topic that incorporates diverse perspectives. By first sending us a short overview of your proposed paper, we can fill topic-area gaps as needed. The submissions themselves will be evaluated by external reviewers, and once a paper is accepted, it will be shared among other authors. These interactions will help us to develop an integrated Special Issue with critical analysis of ongoing debates.

Dr. Gancho Slavov
Dr. Glenn T. Howe
Dr. Jaroslav Klápště
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Forests is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genomics
  • genomic selection
  • pedigree reconstruction
  • management of genetic diversity
  • inbreeding depression
  • resistance to pests and pathogens
  • genome-wide association studies (GWAS)
  • gene/genome editing
  • biotechnology
  • climate change adaptation
  • assisted migration
  • tree improvement

Published Papers (6 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review, Other

19 pages, 17436 KiB  
Article
Genomics-Enabled Management of Genetic Resources in Radiata Pine
by Jaroslav Klápště, Ahmed Ismael, Mark Paget, Natalie J. Graham, Grahame T. Stovold, Heidi S. Dungey and Gancho T. Slavov
Forests 2022, 13(2), 282; https://doi.org/10.3390/f13020282 - 10 Feb 2022
Cited by 4 | Viewed by 2235
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Using Genomic Information in Forest Tree Breeding, Restoration, and Conservation: Separating Hype from Reality)
►▼ Show Figures

Figure 1

14 pages, 1747 KiB  
Article
Development and Validation of a 36K SNP Array for Radiata Pine (Pinus radiata D.Don)
by Natalie Graham, Emily Telfer, Tancred Frickey, Gancho Slavov, Ahmed Ismael, Jaroslav Klápště and Heidi Dungey
Forests 2022, 13(2), 176; https://doi.org/10.3390/f13020176 - 24 Jan 2022
Cited by 10 | Viewed by 3354
Abstract
Radiata pine (Pinus radiata D.Don) is one of the world’s most domesticated pines and a key economic species in New Zealand. Thus, the development of genomic resources for radiata pine has been a high priority for both research and commercial breeding. Leveraging [...] Read more.
Radiata pine (Pinus radiata D.Don) is one of the world’s most domesticated pines and a key economic species in New Zealand. Thus, the development of genomic resources for radiata pine has been a high priority for both research and commercial breeding. Leveraging off a previously developed exome capture panel, we tested the performance of 438,744 single nucleotide polymorphisms (SNPs) on a screening array (NZPRAD01) and then selected 36,285 SNPs for a final genotyping array (NZPRAD02). These SNPs aligned to 15,372 scaffolds from the Pinus taeda L. v. 1.01e assembly, and 20,039 contigs from the radiata pine transcriptome assembly. The genotyping array was tested on more than 8000 samples, including material from archival progenitors, current breeding trials, nursery material, clonal lines, and material from Australia. Our analyses indicate that the array is performing well, with sample call rates greater than 98% and a sample reproducibility of 99.9%. Genotyping in two linkage mapping families indicated that the SNPs are well distributed across the 12 linkage groups. Using genotypic data from this array, we were also able to differentiate representatives of the five recognized provenances of radiata pine, Año Nuevo, Monterey, Cambria, Cedros and Guadalupe. Furthermore, principal component analysis of genotyped trees revealed clear patterns of population structure, with the primary axis of variation driven by provenance ancestry and the secondary axis reflecting breeding activities. This represents the first commercial use of genomics in a radiata pine breeding program. Full article
(This article belongs to the Special Issue Using Genomic Information in Forest Tree Breeding, Restoration, and Conservation: Separating Hype from Reality)
►▼ Show Figures

Figure 1

Review

Jump to: Research, Other

25 pages, 2759 KiB  
Review
Twelve Years into Genomic Selection in Forest Trees: Climbing the Slope of Enlightenment of Marker Assisted Tree Breeding
by Dario Grattapaglia
Forests 2022, 13(10), 1554; https://doi.org/10.3390/f13101554 - 23 Sep 2022
Cited by 24 | Viewed by 4992
Abstract
Twelve years have passed since the early outlooks of applying genomic selection (GS) to forest tree breeding, initially based on deterministic simulations, soon followed by empirical reports. Given its solid projections for causing a paradigm shift in tree breeding practice in the years [...] Read more.
Twelve years have passed since the early outlooks of applying genomic selection (GS) to forest tree breeding, initially based on deterministic simulations, soon followed by empirical reports. Given its solid projections for causing a paradigm shift in tree breeding practice in the years to come, GS went from a hot, somewhat hyped, topic to a fast-moving area of applied research and operational implementation worldwide. The hype cycle curve of emerging technologies introduced by Gartner Inc. in 1995, models the path a technology takes in terms of expectations of its value through time. Starting with a sudden and excessively positive “peak of inflated expectations” at its introduction, a technology that survives the “valley of disappointment” moves into maturity to climb the “slope of enlightenment”, to eventually reach the “plateau of productivity”. Following the pioneering steps of GS in animal breeding, we have surpassed the initial phases of the Gartner hype cycle and we are now climbing the slope of enlightenment towards a wide application of GS in forest tree breeding. By merging modern high-throughput DNA typing, time-proven quantitative genetics and mixed-model analysis, GS moved the focus away from the questionable concept of dissecting a complex, polygenic trait in its individual components for breeding advancement. Instead of trying to find the needle in a haystack, i.e., the “magic” gene in the complex and fluid genome, GS more efficiently and humbly “buys the whole haystack” of genomic effects to predict complex phenotypes, similarly to an exchange-traded fund that more efficiently “buys the whole market”. Tens of studies have now been published in forest trees showing that GS matches or surpasses the performance of phenotypic selection for growth and wood properties traits, enhancing the rate of genetic gain per unit time by increasing selection intensity, radically reducing generation interval and improving the accuracy of breeding values. Breeder-friendly and cost-effective SNP (single nucleotide polymorphism) genotyping platforms are now available for all mainstream plantation forest trees, but methods based on low-pass whole genome sequencing with imputation might further reduce genotyping costs. In this perspective, I provide answers to why GS will soon become the most efficient and effective way to carry out advanced tree breeding, and outline a simple pilot demonstration project that tree breeders can propose in their organization. While the fundamental properties of GS in tree breeding are now solidly established, strategic, logistics and financial aspects for the optimized adoption of GS are now the focus of attentions towards the plateau of productivity in the cycle, when this new breeding method will become fully established into routine tree improvement. Full article
(This article belongs to the Special Issue Using Genomic Information in Forest Tree Breeding, Restoration, and Conservation: Separating Hype from Reality)
►▼ Show Figures

Graphical abstract

Other

Jump to: Research, Review

12 pages, 738 KiB  
Perspective
Will Genomic Information Facilitate Forest Tree Breeding for Disease and Pest Resistance?
by Richard A. Sniezko, Jennifer Koch, Jun-Jun Liu and Jeanne Romero-Severson
Forests 2023, 14(12), 2382; https://doi.org/10.3390/f14122382 - 06 Dec 2023
Viewed by 1000
Abstract
Forest trees are beleaguered by the ever-increasing onslaught of invasive pests and pathogens, with some species in danger of functional extinction. Recent successes in developing resistant populations using traditional tree breeding assures that some of the affected species will persist in future forests. [...] Read more.
Forest trees are beleaguered by the ever-increasing onslaught of invasive pests and pathogens, with some species in danger of functional extinction. Recent successes in developing resistant populations using traditional tree breeding assures that some of the affected species will persist in future forests. However, the sheer number of threatened species requires increases in breeding efficiency. The time is right to consider how the use of genomic resources might aid breeding efforts in the next 20 years. Any operational benefit of genomic resources will be minimal without closer collaboration between tree breeders, forest managers, and genomic researchers. We reflect here on what attributes were responsible for the success of traditional resistance breeding programs and whether advances in genomics can realistically accelerate breeding. We conclude that the use of genomics to directly advance resistance breeding efforts in the next 20 years will be limited. Major obstacles will include factors such as the undomesticated nature of most tree species, the quantitative genetic nature of resistance in many species, and the lack of adequate funding to accelerate and more fully develop genomic resources. Despite these limitations, genomic tools have potential to help increase our understanding of the nature of resistance, and the genetic variability in the host, which can aid in the deployment of resistant populations and may assist in marker-assisted selection, particularly for major gene resistance. Full article
(This article belongs to the Special Issue Using Genomic Information in Forest Tree Breeding, Restoration, and Conservation: Separating Hype from Reality)
10 pages, 716 KiB  
Perspective
Genomic Tools in Applied Tree Breeding Programs: Factors to Consider
by Ross W. Whetten, Keith J. S. Jayawickrama, W. Patrick Cumbie and Gustavo S. Martins
Forests 2023, 14(2), 169; https://doi.org/10.3390/f14020169 - 17 Jan 2023
Cited by 5 | Viewed by 1880
Abstract
The past three decades have seen considerable research into the molecular genetics and genomics of forest trees, and a variety of new tools and methods have emerged that could have practical applications in applied breeding programs. Applied breeders may lack specialized knowledge required [...] Read more.
The past three decades have seen considerable research into the molecular genetics and genomics of forest trees, and a variety of new tools and methods have emerged that could have practical applications in applied breeding programs. Applied breeders may lack specialized knowledge required to evaluate claims made about the advantages of new methods over existing practices and are faced with the challenge of deciding whether to invest in new approaches or continue with current practices. Researchers, on the other hand, often lack experience with constraints faced by applied breeding programs and may not be well-equipped to evaluate the suitability of the method they have developed to a particular program. Our goal here is to outline social, biological, and economic constraints relevant to applied breeding programs to inform researchers, and to summarize some new methods and how they may address those constraints to inform breeders. The constraints faced by programs breeding tropical species grown over large areas in relatively uniform climates with rotations shorter than 10 years differ greatly from those facing programs breeding boreal species deployed in many different environments, each with relatively small areas, with rotations of many decades, so different genomic tools are likely to be appropriate. Full article
(This article belongs to the Special Issue Using Genomic Information in Forest Tree Breeding, Restoration, and Conservation: Separating Hype from Reality)
13 pages, 1025 KiB  
Perspective
Gene-Editing for Production Traits in Forest Trees: Challenges to Integration and Gene Target Identification
by Steven H. Strauss, Gancho T. Slavov and Stephen P. DiFazio
Forests 2022, 13(11), 1887; https://doi.org/10.3390/f13111887 - 10 Nov 2022
Cited by 4 | Viewed by 1910
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Using Genomic Information in Forest Tree Breeding, Restoration, and Conservation: Separating Hype from Reality)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-6

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Author: Dario Grattapaglia
Working Title: How will genomic information facilitate genomic selection and tree breeding, including advantages and disadvantages versus other forms of MAS?

Authors: Steven Strauss, Stephen DiFazio, Gancho Slavov
Title: How will genomic information facilitate the use of gene editing for tree breeding?

Author: Nicholas Ukrainetz
Working Title: How will genomic information facilitate climate change adaptation (e.g., species and population-level assisted migration)?

Author: Richard Sniezko 
Working Title: How will genomic information facilitate breeding for disease resistance or disease management?

Author: Ross Whetten 
Working Title: What are priorities for genomics research from an industry perspective?<false,>6. Genome sequencing and annotation

Author: Jill Wegrzyn 
Working Title: How will genome sequencing and annotation facilitate forest tree breeding, restoration, and conservation?

Author: Zander Myburg
Working Title: How will physiological and developmental genomics contribute to forest tree breeding, restoration, and conservation?

Author: TBA
Working Title: How will genomic information facilitate forest conservation and ecosystem management?

Author: Steve Hanley
Working Title: How will genomic information from non-tree crops contribute to forest conservation and ecosystem management?

Back to TopTop