Guide Wild Crop Relatives: Genomic and Breeding Resources: Forest Trees

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Through coresearch and the codevelopment of decision support tools and by capacity building, stakeholders will better define priorities, select methods and improve and implement practices and policies for TGR safeguarding. Through the adoption of model domestication pathways and decision-support tools, stakeholders will more widely and more effectively promote and apply new approaches to tree genetic improvement in combination with well-established existing methods.

This ensures faster, more targeted and better sustained genetic gains for a wide range of tree species. More efficient and inclusive tree planting material delivery options and support tools, developed through coresearch and through engagement with stakeholders, result in the upgrading and commercialization of input suppliers, including small and medium enterprises SMEs involving women and youth. This research includes genetic and phenotypic analysis and spatial mapping of patterns of tree genetic diversity.

It also includes discovering how the availability of tree genetic diversity conditions the wellbeing of rural people in forest and farm landscapes. Research seeks to reexamine the current mainstream theory governing TGR conservation practice, such as the contested assumption that the cultivation of trees for timber and commodities is sufficient to safeguard the related genetic resources. FTA seeks to determine the conditions when such current conventional wisdom holds and when it does not, based on particular production systems, landscapes and tree biologies. FTA also performs economic analyses to determine the option value provided by TGR for the future production of key tree products and services, to more adequately assess the value of land use for safeguarding of wild relatives of tree crops.

In addition, combining varied information sources on the location and value of, and threats to, TGR allows FTA to develop and out-scale spatially explicit safeguarding tools, such as online maps that indicate conservation priorities. Safeguarding research involves women in setting priorities based on their particular knowledge and future needs. FTA develops the procedures that can be applied to undertake this species prioritization in different contexts, as well as within the prioritized species, identifying the traits to focus on.

Research gives full attention to the involvement of women and youth in setting values, species priorities and traits for selection, particularly for tree foods that have a clear role in supporting family nutrition and the incomes of women. FTA also analyzes the utility of different methods, including advanced genomic and participatory approaches for tree domestication, and determines which methods work best in which context and for different objectives such as to enhance production, increase profitability, improve farm-level resilience or better support landscape restoration.

The full engagement of women in participatory domestication approaches and in business opportunities in value addition is supported through testing approaches that address the structural constraints that limit their participation. FTA provides a small range of well-worked pilot examples of domestication pathways that can serve as models for other tree species in similar contexts. FTA also provides a range of guidelines, training tools, online databases and maps to support tree domestication, which through promotion networks spread best practices globally.

Domestication covers the processes involved in bringing new trees into cultivation, as well as in the further enhancement of cultivation of trees already on the domestication pathway. Genetic gains can be high for trees because of their large gene pools and their limited or no previous histories of domestication. High variation in yield and food quality is, for example, observed in indigenous food trees such as Allanblackia species in Africa. Domestication work in FTA is linked to support for value chain development: for instance, through the development of a novel public—private collaborative platform to support domestication and market integration that has involved FTA and a wide range of partners, oil from the seed of the Allanblackia tree has now been incorporated into margarine production in Europe.

It advises on delivery system redesign and tests the efficacy of adjusted approaches.

Genetic Transformation of Forest Trees

FTA enquires whether annual crop delivery approaches can be adapted to trees, given the differing characteristics of trees with respect to annual crops time to maturity, fecundity, range of species, level of domestication, etc. Research considers how the involvement of entrepreneurial women and young entrepreneurs in delivery systems can be enhanced, seeking specific comparative advantages through understanding their existing knowledge, skills and experiences. FTA also explores how the few successful delivery systems that do exist for tree commodities can be extended to a wider range of trees.

A range of innovative decision-support tools that link planters with appropriate planting material, based on available sources, sites and the purpose of planting, is also being developed. Skip to content Now Playing! Home Research Flagships Flagship 1: Tree genetic resources. NEWS Using forests to support wellness.

When compared to existing imputation methods, LinkImpute had a similar run time and accuracy to Beagle, despite not requiring positional information for markers Money et al. As the ability to impute missing data without a reference genome improves, reduced representation sequencing techniques with high missing data, such as GBS, will continue to facilitate the discovery of new markers for genomics-assisted breeding in wild relatives. While there is opportunity for great improvement to elite perennial crops through genomics-assisted introgression of traits from wild relatives, many barriers remain.

Genomic tools designed for domesticated species are either not well-suited to more diverse wild relatives, or may be lacking completely. The same genetic divergence that has resulted in wild relatives harboring unique and desirable traits for breeding also results in difficulties in developing markers to introgress these traits into elite germplasm. However, given that DNA sequencing costs are likely to continue decreasing, it is essential that researchers begin planning for a future where the collection and analysis of DNA sequence data will not be the bottleneck to successful genetic mapping.

Especially for perennial breeders used to working on timescales of decades, the focus should be on the collection of high-quality phenotype data that can always be paired later with genotype data as it becomes available. Now is the time to establish GWAS and linkage mapping populations that will enable powerful genetic mapping in a future where genotyping costs are negligible and the available genomic analysis tools are far superior to those available today. Although the primary focus of this review is the use of genomics, it is worth noting that there are several difficulties unrelated to genomics that may limit the use of improvement using wild relatives.

First, in order to make use of wild relatives for breeding, new germplasm must be collected. While some wild relative collections are well-characterized and actively in use, such as those described in this review, there are likely many benefits of wild germplasm that remain undiscovered. A focus on the collection and characterization of wild germplasm is the first step towards discovering which relatives and traits will be useful for breeding, and thus be exploitable through genomics. Among the major barriers to improved characterization of wild germplasm are the locations where such germplasm may be found.

Often, wild relatives must be collected from locations that are difficult to access, and thus collecting new wild germplasm can be an expensive and time-consuming process. For example, wild cacao is found in the tropical rainforests of South America Lachenaud et al. There are also compulsory quarantine requirements when transferring material between political boundaries.

Several decades may pass between the collection of wild germplasm and their use by growers Lachenaud et al. Finally, it is important to consider the cultural and financial ramifications of collecting wild relatives. In the past, germplasm has been collected from farmers and communities without compensation or recognition. In such a scenario, seeds may be taken from one country and used to benefit the private sector in another country. While there is ample opportunity for commercial crops to benefit from wild relatives, it is necessary that farmers and communities which have preserved wild relatives receive adequate credit and compensation for use of such resources Montenegro, The introgression of valuable wild traits into domesticated crops can only occur when breeders have access to these relatives through gene banks.

The collection of new samples for marker discovery poses a major limitation to establishing such collections. Wild relatives are very under-represented in gene bank collections. Future collection of germplasm is also threatened due to habitat destruction and climate change Maxted et al. As the power of genomic tools increases, genomics will become increasingly effective for introgression of wild traits into perennial crops. However, the ability to exploit wild relatives for breeding requires that this diversity be protected for future use through gene banks and habitat conservation.

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Preservation of wild relatives will require a complex approach across many environments on a local, national and international scale Montenegro, It is crucial to begin exhaustive sampling and extensive evaluation of wild germplasm for all major perennial crops, an enormously expensive and time-consuming undertaking. However, such projects are essential to ensuring a safe and secure future food supply as clonally propagated cultivars continue to be threatened by a constantly evolving environment.

An essential step toward the adoption of genomic markers from wild relatives will be methods that accelerate the juvenile period in order to increase the efficiency of backcrossing progeny to domesticated germplasm. While the use of genomics-assisted breeding can increase the efficiency of selecting for traits of interest and decrease the number of plants that must be propagated, the long juvenile period of many perennials still poses a constraint on the rate of crop improvement.

A solution to the problem of long juvenile periods has been found in grapes. In comparison to the 2—5 years of juvenility generally required for grapes, the Vvgai1 mutant produces fruit 2 months after germination. For example, recent work used microvines to aide in QTL identification for traits such as berry acidity Houel et al. In apple, an early flowering transgenic line containing the BpMADS4 gene from silver birch Betula pendula was combined with MAS to pyramid resistance to apple scab, powdery mildew, and fire blight Flachowsky et al.

However, while transgenic lines are incredibly helpful for decreasing the generation time while breeding, it is often desirable to have a final cultivar for release that does not contain the transgene and is not considered a GMO. Thus, once the rapid cycling of generations is completed, a non-GMO tree possessing desirable traits from wild relatives—but not the transgene—can easily be selected Flachowsky et al.

The creation of similar mutants in other species, which reduce the juvenile phase in long-lived perennials, will be essential to the efficient application of MAS. As an alternative to transgenics, virus-induced gene silencing VIGS can also be used to shorten the juvenile phase in perennials. VIGS uses a viral vector to infect a plant with a particular gene, resulting in an RNA-mediated defense which silences expression of the gene within the plant Lu et al. As genes involved in flowering are identified in other perennials, VIGS could be used to silence these genes and thus shorten the juvenile period Yamagishi et al.

ALSV has several other valuable characteristics which make it attractive for use in breeding. The virus was not detected in neighboring trees in an orchard where it had been present since , suggesting there was no vector for transmission present in the sampled orchard and horizontal transmission via pollen did not occur Nakamura et al.

Finally, ALSV can be eliminated from an infected tree using high temperature, allowing for vegetative propagation of that tree and resulting in fruit exempt from restrictions on GMOs Yamagishi et al.

Wild Crop Relatives: Genomic and Breeding Resources: Forest Trees - Google книги

Therefore, VIGS is a promising method for reducing the juvenile phase in perennials, allowing for a shorter generation time and thus facilitating backcrossing when breeding with wild relatives. The ability to genotype plants using MAS at the earliest stage of development will allow for the least amount of time and resources to be spent propagating plants which do not carry the marker of interest. While extraction of DNA from seeds is possible for several plants, in perennials it is generally required that plants germinate in order to collect DNA from leaf tissue.

Many tree fruits and nuts require a seed dormancy period of up to 12 weeks at low temperatures prior to germination. The development and improvement of methods which overcome seed dormancy could decrease the time prior to genotyping and the generation time between crosses. Several techniques for overcoming seed dormancy include the dissection of embryos and application of bioactive gibberellins or nitric oxide van Nocker and Gardiner, Work describing the non-destructive ability to extract DNA from seeds, although recently published in soybean, has been limited so far Al-Amery et al.

In such a scenario, only the seeds with the desired trait would be germinated, greatly improving the efficiency and decreasing the cost of each breeding cycle. To facilitate DNA sequence mapping and marker discovery for wild relatives, improvement of genomic resources is needed. As such, there is an urgent need for reference genomes in wild species, or the development of pan-genome sequences that include sequence from both wild and domesticated relatives.

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  • To characterize the pan-genome of poplar, recent work performed genome-wide analysis of structural variation in three intercrossable poplar species Pinosio et al. Similar efforts are required in most other perennial species. Resequencing of wild germplasm, in combination with de novo assembly, will not only improve our understanding of the domestication history of perennial crops, but also enable the genetic mapping of important traits that can be used for genomics-assisted breeding.

    While this review focuses on the potential of genomics-assisted breeding, and in particular MAS, it is worth noting that these tools will always be used in combination with traditional evaluation of cultivars when selecting new varieties.

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    • Breeders will always grow and evaluate plants prior to commercial release, but genomics can speed up reaching that final evaluation. Moreover, there are certainly cases where MAS may not even be desirable. For example, when selecting for red fruit flesh in apple, the same anthocyanin-regulating transcription factor often leads to red foliage and therefore trees with this trait can be easily identified before fruit production Chagne et al.

      However, there is also a paralogous gene for red fruit flesh color where red foliage does not occur and MAS could be valuable in those instances Chagne et al. Due to the cost and labor expense of MAS, previous work selecting for downy and powdery mildew resistance in grape included both phenotypic and marker-assisted selection. The initial population of interest consisted of plants inoculated with downy mildew. Seedlings resistant to downy mildew were then screened for powdery mildew resistance.

      Finally, the 20 seedlings resistant to both diseases were tested using MAS, resulting in a final reduction to only four seedlings Eibach et al. In this case, while phenotype selection was effective, MAS allowed for an improved reduction in the number of seedlings. When applying MAS to perennial crops, the greatest cost-savings will occur if testing occurs at the seed or seedling stage. MAS is particularly useful for traits that are difficult, expensive, or time-consuming to phenotype, such as fruit traits and disease resistance. To be of use, the markers must be economical to discover as well as test.

      Thus, while low cost MAS can facilitate the introgression of specific traits of interest from wild relatives, it will ultimately only be useful when the cost of phenotyping is higher than the cost of discovering markers and genotyping Luby and Shaw, While the cost and speed of collecting genomic data has continued to decrease, phenotyping remains slow and expensive Burleigh et al.

      Given that high-quality phenotype data is required for well-powered QTL analyses, the improvement of phenotyping technologies is a major area of current research interest. The development of new, high-throughput HT phenotyping technologies has begun, including advances in image analysis and robotics Furbank and Tester, Improvement to phenotyping technologies will aid in the characterization of wild germplasm, a task which is particularly challenging due to the high level of diversity present.

      Thus far, HT phenotyping technologies have focused on annual crops such as rice Tanger et al. One example of a technology useful for wild relatives is Field Book, an open-source application for collecting field data that eliminates the need to transcribe handwritten notes Rife and Poland, As phenotyping technology for perennial crops and wild relatives improves, so will the ability to detect markers which can be exploited for genomics-assisted breeding. Thus, phenotyping of wild relatives, while expensive, is a necessary task. Additionally, good quality phenotype data will continue to have value in the future.

      Phenotype data can be collected now but analyzed in the future when, for example, the cost of whole genome sequencing is no longer prohibitive. Ultimately, although genomics-assisted breeding has been used to introgress traits from wild relatives into perennial crops in the past, there are still many areas in which future work is required to improve this process.

      The use of genomic tools such as those which reduce the generation time for long-lived perennial crops and allow for DNA extraction from seeds—and the continued development of such tools—are two crucial steps in facilitating the use of MAS in perennials. To make use of markers in breeding, they must first be discovered, and as such improvement to genetic mapping techniques and resources will be necessary.

      Finally, MAS is especially valuable for the introgression of multiple traits as well as those that are difficult or expensive to phenotype. However, the usefulness of MAS relies on the ability to discover and genotype markers for less than the cost of phenotyping all progeny. As technology improves and the cost of marker discovery decreases, it will become increasingly feasible to introgress useful traits from wild relatives into elite perennial cultivars, resulting in the much-needed improvement of crops that may have been clonally propagated for centuries. There are clearly many traits such as disease resistance, fruit quality, and rootstock characteristics which would benefit domesticated perennials but are locked in undesirable, wild germplasm.

      Use of MAS can enable breeders to unlock the potential of wild germplasm by facilitating selection at an early stage of development—or even as a seed—allowing for less time and money to be spent growing plants which will inevitably be discarded. However, when crossing wild relatives and elite cultivars there are certain limitations and difficulties. Often many generations of backcrossing are required to decrease linkage drag and other wild characteristics.

      Use of GM technology can help reduce the amount of time required for breeding, but decades may still be required for consumer and regulatory acceptance. Both MAS and genome editing require the initial discovery of markers, which is complicated by the fact that alleles for traits of interest often co-segregate with millions of other alleles in wild germplasm. Yet, the potential benefit of accessing unique and desirable traits in wild germplasm could revolutionize perennial crop improvement.

      Unfortunately, the discovery of useful markers using GWAS and linkage mapping may still require decades to yield results. Thus, it is essential the collection and characterization of wild relatives begin immediately, while genomic and phenomic tools suited to diverse germplasm continue to improve. The continued vegetative propagation of domesticated perennial cultivars affords pathogens the opportunity to become increasingly effective while robbing both growers and consumers of the unique and desirable traits present in wild germplasm.

      After decades, or even millennia, of growing the same perennial cultivars frozen in genetic time, the decreasing costs of sequencing can finally allow us to harvest the potential of wild relatives through genomics-assisted breeding. We have only begun to enjoy the benefits of wild relatives in perennial crop improvement, and continued technological advances will surely result in the more efficient development of tastier food that requires less chemical input to grow.

      How to collect wild trees and capture the pot (Arjun tree)

      All authors listed have made substantial, direct, and intellectual contribution to the work, and have approved it for publication. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. We would like to acknowledge Mark O. Johnston, Christophe M. Herbinger, Robert G. Beiko, Robert G. Latta, and Michel S. McElroy for helpful discussion. Al-Amery, M. Crop Improv.

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      Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [ Picea abies L. It seems that you're in Germany. We have a dedicated site for Germany. Wild crop relatives are now playing a significant part in the elucidation and improvement of the genomes of their cultivated counterparts. This work includes comprehensive examinations of the status, origin, distribution, morphology, cytology, genetic diversity and available genetic and genomic resources of numerous wild crop relatives, as well as of their evolution and phylogenetic relationship.

      Further topics include their role as model plants, genetic erosion and conservation efforts, and their domestication for the purposes of bioenergy, phytomedicines, nutraceuticals and phytoremediation. It contains chapters written by nearly well-known authors from about 40 countries. JavaScript is currently disabled, this site works much better if you enable JavaScript in your browser. Life Sciences Plant Sciences. Free Preview.