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Special Issue "Genomics for Sustainable Forestry - Selected Papers from IUFRO Genomics and Forest Tree Genetics Conference"

A special issue of Forests (ISSN 1999-4907).

Deadline for manuscript submissions: closed (1 September 2016)

Special Issue Editors

Guest Editor
Prof. Dr. John MacKay

Department of Plant Sciences, University of Oxford, Oxford, UK
Website | E-Mail
Phone: +44 (0)1865 275 088
Fax: +44 (0)1865 275 088
Interests: forest genomics; genetics and molecular biology; wood formation and genetics; insect resistance research; molecular markers, marker assisted selection
Guest Editor
Prof. Dr. Stephen P. DiFazio

Department of Biology, West Virginia University, Morgantown, West Virginia 26506, USA
Website | E-Mail

Special Issue Information

Dear Colleagues,

The age of genomics has infiltrated most biological disciplines, and Forestry is no exception. Genomic tools have led to fundamental insights about the ecology and evolutionary history of natural forests. Furthermore, genomics has actualized the promises of marker-aided selection by enabling whole genome prediction, which promises to revolutionize approaches to tree improvement. Genomic resources are reaching a critical mass for numerous species. We are now approaching an inflection point as forestry practitioners transition from the development of genomic resources as an end in itself, to application of genomics to problems of fundamental importance in forestry. This Special Issue will explore this transition through a series of papers focusing on the application of genomics approaches to diverse aspects of forestry research.

Dr. John MacKay
Dr. Stephen P. DiFazio
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 papers will be 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 1800 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
  • Adaptation
  • Sequencing
  • Population Structure

Published Papers (6 papers)

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Research

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Open AccessCommunication Adaptive Variation and Introgression of a CONSTANS-Like Gene in North American Red Oaks
Forests 2017, 8(1), 3; https://doi.org/10.3390/f8010003
Received: 21 September 2016 / Revised: 9 December 2016 / Accepted: 13 December 2016 / Published: 22 December 2016
Cited by 4 | PDF Full-text (3135 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Oaks provide a model system to study maintenance of species identity by divergent selection since they maintain morphological differences and ecological adaptations despite interspecific hybridization. The genome of closely related interfertile oak species was shown to be largely homogeneous, with a few genomic [...] Read more.
Oaks provide a model system to study maintenance of species identity by divergent selection since they maintain morphological differences and ecological adaptations despite interspecific hybridization. The genome of closely related interfertile oak species was shown to be largely homogeneous, with a few genomic areas exhibiting high interspecific differentiation possibly as result of strong divergent selection. Previously, a genic microsatellite was identified as under strong divergent selection, being nearly fixed on alternative alleles in the two interfertile North American red oak species: Quercus rubra L. and Quercus ellipsoidalis E.J. Hill. Further genotyping in two other red oak species—Quercus velutina Lam. and Quercus coccinea Münchh.—revealed a similar bias for the Q. ellipsoidalis-specific allele. To further elucidate the basis of this differentiation, we sequenced the microsatellite in individuals from all four red oak species. Sequence variability was observed in the microsatellite motif which encodes a poly-Q repeat in a COL gene involved in phenology and growth. Furthermore, in neighboring (parapatric) Q. rubra/Q. ellipsoidalis populations, introgression of the Q. ellipsoidalis-specific allele into Q. rubra occurred at a lower rate than introgression of the Q. rubra-specific allele into Q. ellipsoidalis despite symmetric interspecific gene flow, indicating potential adaptive introgression. Introgression of adaptive alleles can be an important mechanism for rapid adaptation to new environmental conditions (e.g., climate change). Full article
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Open AccessArticle Identification and Target Prediction of MicroRNAs in Ulmus pumila L. Seedling Roots under Salt Stress by High-Throughput Sequencing
Forests 2016, 7(12), 318; https://doi.org/10.3390/f7120318
Received: 8 September 2016 / Revised: 30 November 2016 / Accepted: 9 December 2016 / Published: 20 December 2016
Cited by 1 | PDF Full-text (1812 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
MicroRNAs (miRNAs) are a class of endogenous small RNAs with important roles in plant growth, development, and environmental stress responses. Ulmus pumila L., a deciduous broadleaved tree species of northern temperate regions, is widely distributed in central and northern Asia and has important [...] Read more.
MicroRNAs (miRNAs) are a class of endogenous small RNAs with important roles in plant growth, development, and environmental stress responses. Ulmus pumila L., a deciduous broadleaved tree species of northern temperate regions, is widely distributed in central and northern Asia and has important economic and ecological value. With the spread and aggravation of soil salinization, salt stress has become a major abiotic stress affecting the normal growth and development of U. pumila. However, the influence of salt stress on U. pumila miRNA expression has not been investigated. To identify miRNAs and predict their target mRNA genes under salt stress, three small RNA libraries were generated and sequenced from roots of U. pumila seedlings treated with various concentrations of NaCl corresponding to no salt stress, light short-term salt stress, and medium-heavy long-term salt stress. Integrative analysis identified 254 conserved miRNAs representing 29 families and 49 novel miRNAs; 232 potential targets of the miRNAs were also predicted. Expression profiling of miRNAs between libraries was performed, and the expression of six miRNAs was validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Our findings provide an overview of potential miRNAs and corresponding targets involved in regulating U. pumila salt defense responses. These results lay the foundation for further research into molecular mechanisms involved in salt stress resistance in U. pumila and other Ulmaceae species. Full article
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Open AccessArticle Male Parent Identification of Triploid Rubber Trees (Hevea brasiliensis) and the Mechanism of 2n Gametes Formation
Forests 2016, 7(12), 301; https://doi.org/10.3390/f7120301
Received: 27 October 2016 / Revised: 23 November 2016 / Accepted: 24 November 2016 / Published: 7 December 2016
Cited by 1 | PDF Full-text (2318 KB) | HTML Full-text | XML Full-text
Abstract
Eight triploids were screened among offspring of the rubber tree clone GT1 × different clones by flow cytometry and chromosome counting. Twenty-five simple sequence repeat (SSR) markers were screened to identify the origin of 2n gametes, to determine the male parents of [...] Read more.
Eight triploids were screened among offspring of the rubber tree clone GT1 × different clones by flow cytometry and chromosome counting. Twenty-five simple sequence repeat (SSR) markers were screened to identify the origin of 2n gametes, to determine the male parents of these triploids, and to evaluate the mechanism of 2n gamete formation using band configurations and microsatellite DNA allele counting peak ratios (MAC-PR). The results showed that 2n gametes originated from the maternal rubber tree clone GT1, contributing the extra genome copy present in the triploids. It was confirmed that GT1 is able to produce a 2n megagametophyte spontaneously. Many male parents were shown to provide pollen for formation of triploid rubber trees, including clones RRIC 103, Yunyan 277-5, and three other clones. The second division restitution (SDR) was likely the main mechanism involved in formation of megagametophytes in GT1, as the rate of maternal heterozygosity restitution (HR) of all eight triploids varied from 27.78% to 75.00%, with a mean of 51.46%, and all 25 markers varied from 0% to 100%, with a mean of 51.69%. Elucidation of the origin and formation of 2n gametes will help optimize further sexual hybridization of polyploid rubber trees. Full article
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Open AccessArticle Perceived Acceptability of Implementing Marker-Assisted Selection in the Forests of British Columbia
Forests 2016, 7(11), 286; https://doi.org/10.3390/f7110286
Received: 11 October 2016 / Revised: 7 November 2016 / Accepted: 12 November 2016 / Published: 18 November 2016
Cited by 2 | PDF Full-text (2134 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The forest sector in British Columbia (BC) has faced a number of challenges over the past decade. In response to some of those challenges, the government has invested in forest genomic tools. Marker-assisted selection (MAS) is a biotechnological tool that flags desired traits [...] Read more.
The forest sector in British Columbia (BC) has faced a number of challenges over the past decade. In response to some of those challenges, the government has invested in forest genomic tools. Marker-assisted selection (MAS) is a biotechnological tool that flags desired traits on the genome. This tool may assist tree breeders with the early selection of preferred genotypes, reducing the breeding cycle and more accurately and efficiently selecting for improved qualities. However, there is a poor understanding of the perceived acceptability of implementing MAS. Semi-structured interviews and a questionnaire were employed across participants categorized into four groups. It was found that government and industry participants held positive perceptions towards MAS, supporting its use and continued research in BC, and identifying its benefits in forest regeneration and to tree breeders. Environmental non-governmental organizations (ENGOs) and First Nations attitudes lay between neutral and negative. Concerns were most strongly focused on environmental impacts, ecosystem degradation, and reduced genetic diversity, while identified benefits were specific to tree breeders and improved tree resiliency. It was concluded that before MAS can be successfully implemented, an appropriate setting must first be established through improved knowledge of biotechnology and its applications, well-defined policies, and strengthened engagement and consultation with First Nations. Full article
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Open AccessArticle Haploids in Conifer Species: Characterization and Chromosomal Integrity of a Maritime Pine Cell Line
Forests 2016, 7(11), 274; https://doi.org/10.3390/f7110274
Received: 4 September 2016 / Revised: 4 November 2016 / Accepted: 9 November 2016 / Published: 12 November 2016
PDF Full-text (1078 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Haploids are a valuable tool for genomic studies in higher plants, especially those with huge genome size and long juvenile periods, such as conifers. In these species, megagametophyte cultures have been widely used to obtain haploid callus and somatic embryogenic lines. One of [...] Read more.
Haploids are a valuable tool for genomic studies in higher plants, especially those with huge genome size and long juvenile periods, such as conifers. In these species, megagametophyte cultures have been widely used to obtain haploid callus and somatic embryogenic lines. One of the main problems associated with tissue culture is the potential genetic instability of the regenerants. Because of this, chromosomal stability of the callus and/or somatic embryos should also be assessed. To this end, chromosome counting, flow cytometry and genotyping using microsatellites have been reported. Here, we present an overview of the work done in conifers, with special emphasis on the production of a haploid cell line in maritime pine (Pinus pinaster L.) and the use of a set of molecular markers, which includes Single Nucleotide Polymorphisms (SNPs) and microsatellites or Single Sequence Repeats (SSRs), to validate chromosomal integrity confirming the presence of all chromosomic arms. Full article
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Review

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Open AccessReview Thousand Cankers Disease Complex: A Forest Health Issue that Threatens Juglans Species across the U.S.
Forests 2016, 7(11), 260; https://doi.org/10.3390/f7110260
Received: 1 September 2016 / Revised: 26 October 2016 / Accepted: 29 October 2016 / Published: 3 November 2016
Cited by 3 | PDF Full-text (2415 KB) | HTML Full-text | XML Full-text
Abstract
Thousand Cankers Disease (TCD) is a disease complex wherein the fungus (Geosmithia morbida) is vectored by the walnut twig beetle (WTB, Pityophthorus juglandis). The disease causes mortality primarily of eastern black walnut (Juglans nigra), although other walnut and [...] Read more.
Thousand Cankers Disease (TCD) is a disease complex wherein the fungus (Geosmithia morbida) is vectored by the walnut twig beetle (WTB, Pityophthorus juglandis). The disease causes mortality primarily of eastern black walnut (Juglans nigra), although other walnut and wingnut (Pterocarya) species are also susceptible. Black walnut is native to the Eastern and Midwestern U.S. but is widely planted in western states. Total standing volume in both urban and forested settings is approximately 96 million cubic meters, and is valued at $539 billion. Although native to the Southwestern U.S., the range of WTB has expanded considerably. The spread of G. morbida coincides with that of WTB. TCD was introduced into Tennessee in 2010, and has spread to seven eastern states. Trees infected with TCD exhibit drought-like symptoms, making field detection difficult without molecular and/or morphological methods. The recently sequenced G. morbida genome will provide valuable research tools focused on understanding gene interactions between organisms involved in TCD and mechanisms of pathogenicity. With no chemical treatments available, quarantine and sanitation are preeminent options for slowing the spread of TCD, although biological control agents have been discovered. High levels of black walnut mortality due to TCD will have far-reaching implications for both eastern and western states. Full article
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