- Wild Crop Relatives: Genomic and Breeding Resources: Cereals
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They have the added benefit of being discrete and approachable genetic resources for breeders. Other types of introgression lines are useful for isolating the effect of a single gene from a wild species in a crop background. For example, tomato breeders at the World Vegetable Centre AVRDC annually distribute hundreds of introgression lines with genes from wild tomatoes to breeders in national agricultural research institutes, who then develop and release varieties suited to local conditions P.
Hanson, personal communication, Desired recombinants can be produced in early generations given a large enough population. For example, marker-assisted backcrossing MABC has been used in lowland rice to introduce an important QTL into a new background in just two rounds of backcrossing Iftekharuddaula et al. With genomic tools, it is also becoming increasingly possible to directly assess the contribution of CWR in modern varieties Baute et al. Genome scans can also reveal candidate domestication and improvement loci, as well as postdomestication introgression with wild relatives Lin et al.
This is sometimes preferred as an alternative to the use of transgenic technologies associated with high regulatory costs and widespread consumer concern. However, transgenic approaches continue to prove useful as an experimental method in understanding the function of candidate alleles from CWR. Once the function of an allele is confirmed, MAS can be used to incorporate allele s without incurring the regulatory costs associated with genetically modified organisms.
Transgenic technologies are mostly employed by the private sector Brummer et al. Genomics has revolutionized the rate of marker development and deployment. Clarke et al.http://managewebsite.com/cache/2019-06-16/2648.php
Wild Crop Relatives: Genomic and Breeding Resources: Cereals
Hulse-Kemp et al. Livaja et al. Crops lacking SNP genotyping platforms, or in cases where new, diverse material is being used such as CWR , high-throughput sequencing offers a cheap and rapid way to deploy thousands to millions of markers for mapping studies Kilian and Graner, The marker density offered by these technologies allows for rapid fine mapping and can saturate mapping populations in terms of detecting all of the recombination events. For association panels, which contain a great deal more recombination events than biparental populations, ultra-dense markers may be especially important.
Although much of the early sequencing efforts focused primarily on cultivated material, largescale CWR genomic re sequencing efforts are now well underway The Tomato Genome Sequencing Consortium et al. Rice, for example, has a relatively small genome at Mbp, and several wild genomes have been resequenced using WGS Xu et al.
Many complete germplasm collections are already being genotyped or even sequenced, including maize Romay et al. Landscape genomics and environmental association analysis are also ways to detect putatively valuable alleles in CWR Anderson et al. Genomics may thus be able to support the collecting and conservation of CWR, as well as their use. Unlike collection data such as environment or local ecology, genomics data can be generated for every single plant.
Sequence data truly represent the diversity in accessions and could be used as a common currency with which to compare accessions. It must be noted, however, that the development and application of genomics resources is still not a priority for all crop communities. For example, experts from the pea Pisum sativum L. The advent of genome editing is predicted to revolutionize plant breeding Voytas ; Bortesi and Fischer, ; Khatodia et al. These technologies enable scientists to alter the genome of an organism with unprecedented precision and without the introduction of DNA from another organism.
Although these methods are still in their infancy, their increased precision will likely result in substantial efficiency gains in crop improvement processes Hu et al. However, as the regulatory landscape continues to evolve, it remains to be seen whether they will prove a viable alternative to transgenic and traditional breeding approaches EFSA Panel on Genetically Modified Organisms, ; Araki and Ishii, In any case, genome editing relies on a thorough understanding of the genetic basis of a given trait that is still often lacking for the majority of traits of interest, which are commonly complex and quantitative.
However, alterations of larger pieces of sequence information and of different genes simultaneously e. Genome-editing tools may well provide a further boost to the use of CWR in the near term. Crop wild relatives and the sequence information contained within them may serve as a reference library for all kinds of allelic diversity. Information on allelic diversity and its phenotypic effects is an essential requirement for many of the genome-editing techniques that are now emerging. Approximately 7 million crop accessions are currently stored ex situ in genebanks, of which an estimated 2 million are biologically unique Commission on Genetic Resources for Food and Agriculture, Much critical information is lacking for a lot of this material.
Without accurate passport, characterization, and evaluation data, both genebank curators and potential users of materials are left with unanswered questions regarding how much diversity is in each accession, how similar accessions are, how much duplication exists within and among collections, how to capture the most diversity across the genepool, and how to find alleles for specific traits. This limits the usefulness of collections, and experts from many crop communities warn against further collecting without first improving the existing system of managing collections and their associated data, both of CWR and derived genetic stocks.
Using standardized systems for identifying accessions and agreed taxonomies are essential measures for improving documentation and will facilitate the development of standardized protocols for managing collections. The reported lack of data on crop wild relatives could, in some cases, indicate actual gaps in collections with regards to physical CWR accessions. Genebank collections are often incomplete, and the diversity of the CWR for many crops is not captured to an adequate extent Commission on Genetic Resources for Food and Agriculture, Collection and conservation of this diversity is critical, because the future of materials that are still in the wild is precarious.
One strategy for targeting underrepresented diversity of the greatest potential value is to focus collection in areas of extreme climates to mine for specific, rare traits. Linking collection location information with genomic data to map allelic variation and predict the usefulness of specific wild populations, or even alleles, is a novel approach Thormann et al.
Data recorded at the time of collection is crucially important, but collection data should ideally move beyond just collection locality and associated environmental factors.
Soil type, disease presences, and the local ecology are all important factors in the evolutionary history of a particular CWR accession, and this information may turn out to be of key importance to someone interested in the potential usefulness of a particular accession. In our consultations, many crop communities highlighted the need for common information resources to be developed that make germplasm available together with all relevant information McCouch et al.
Comprehensive online databases exist for some crops already, but efforts have been insufficient for bridging the basic research and the applied breeding communities, and there is still little data available for breeding materials under development. Challenges to an increased use of crop wild relatives for a selected number of crops that were considered in the analysis. Identifying traits of interest is complicated by the difficulty in predicting how alleles from wild species will be expressed once transferred into crop backgrounds and grown in the field. Wild species can carry beneficial allelic variation for traits without expressing them directly.
It is difficult to predict potential yield gains from nondomesticated plants with small seeds and pods that shatter, for example, or to identify interesting alleles when their measured effects are masked by inferior wild background traits. Experts in wheat and banana emphasized how cryptic variation can result in significant, and often unexpected, superior performance of crosses between wilds and their domesticated crops.
Experts across the crop communities call for a more systematic evaluation and screening of trait variability within CWR ex situ collections. Potato, pea, and sorghum experts emphasized that existing accessions remain underexploited, that the screening of materials is far from exhaustive, and that funds are more appropriately concentrated on maintaining existing collections, rather than developing prebreeding materials or expanding collections.
These recommendations, however, are consistently qualified with warnings about genetic erosion of wild populations in situ and the continued importance of targeted collection based on gap analyses.
This is a real dilemma in many crop expert communities, given limited financial resources. Coordinated phenotypic evaluation of prebreeding material among researchers is recognized as a valuable means of assessing genotype—environment interaction.
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Common introgression lines developed from agreed sets of cultivated backgrounds could be exchanged and used to develop regionally adapted materials. However, phenotypic evaluations of CWR of clonal crops—especially those of long-lived perennials—can be challenging, due to resource limitations and practical considerations associated with their cultivation. Many of these materials carry beneficial traits introgressed from CWR, yet they are not appropriately maintained or made available for further use.
An additional hurdle that is often overlooked is inadequate human resource capacity to make use of wild accessions stored in genebanks. Several crop communities, including banana, wheat, and pea, reported an aging skill base and a decline in available expertise in botany, cytogenetics, taxonomy, and curation of genebank collections of wild material. Our capacity to employ methods to better maintain and use CWR is predicated on reestablishing this skill base and investing in strong breeding capacity.
Resource constraints underpin the majority of the challenges discussed here. Funding is identified as a limiting factor to accessing CWR diversity across all crop communities surveyed. Identifying, isolating, and transferring traits of interest from wild species into crop backgrounds, and then evaluating the resulting material, is a time-consuming and risky endeavor that requires significant funding and long-term commitment. However, since CWR are at the nexus between food security, climate change adaptation, and biodiversity conservation issues, donors can be presented with an opportunity to allocate resources in a way that contributes to all of these ends at once.
Table 1 summarizes the findings presented in this review. Significant advances have been made towards overcoming the challenges associated with using CWR in crop improvement. Ongoing basic and applied research will indubitably further facilitate their use in coming years. At the same time, the numerous challenges in the prebreeding process identified in this report need to be addressed for progress to be achieved.
In particular, strategies aimed at increasing coordination among actors along the prebreeding continuum will facilitate sharing of characterization and evaluation data, as well as raw genetic material stored in genebanks and more advanced materials under development. Important elements of a strategy for improving the prebreeding process are likely to include the selection of common parents to be used in introgression lines, the systematic and coordinated evaluation of prebreeding materials in multiple locations, the development of feedback mechanisms for screening data, and data management and sharing initiatives.
Many accessions of CWR currently held in genebanks lack important information, including where they were collected, what their basic characteristics are, what they may be useful for, and whether they are a unique sample or a duplicate of another. Extensive consultation with experts in 24 crop communities identified this lack of passport, characterization, and evaluation information on both wild germplasm and intermediary materials as the biggest constraint to increasing the use of CWR in breeding.
Lack of clarity surrounding the specific roles of actors along the prebreeding continuum and coordination among basic and applied research communities, along with funding and capacity limitations, have inhibited the systematic use of the breadth of wild species diversity that is available today. In conclusion, some key requirements for the more effective use of CWR in crop improvement include: Collection of underrepresented diversity, informed by gap analyses based on taxonomic designations and ecogeographic information, along with detailed passport data to both conserve the breadth of diversity available in the wild and facilitate predictive trait mining based on ecogeographic data;.
Coordinated evaluation and sharing of prebreeding products across environmental conditions to better understand genotype—environment interactions;. Improved information sharing and feedback, especially with regards to genotypic and phenotypic data—and the way they are linked—between genetic resource conservationists, pre-breeders, breeders, and end users; and. As the need to explore wild genetic diversity grows along with threats of climate change and the narrowing genetic base of crops, it is increasingly important that we understand how wild species are being used to improve crops and where efforts should best be concentrated to overcome constraints to use.
A closer look at the current state of CWR use reveals persisting challenges, as well as significant opportunities for harnessing their value. Our capacity to overcome these challenges and harness the adaptive capacity stored in CWR is predicated on increased coordination, information sharing, and investment in prebreeding programs and human capacity development.
Gains have already been made and momentum is building. With a clearer picture of where bottlenecks remain, the value of CWR for increasing the adaptive capacity of agricultural crops can be realized. Supplemental Material Available Supplemental material for this article is available online.
The project is managed by the Global Crop Diversity Trust with the Millennium Seed Bank of the Royal Botanic Gardens, Kew, and implemented in partnership with national and international genebanks and plant breeding institutes around the world. Editorial Board. Subscription Questions.
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Abstract Wild species related to agricultural crops crop wild relatives, or CWR can increase the adaptive capacity of agricultural systems around the world. In conclusion, some key requirements for the more effective use of CWR in crop improvement include: Collection of underrepresented diversity, informed by gap analyses based on taxonomic designations and ecogeographic information, along with detailed passport data to both conserve the breadth of diversity available in the wild and facilitate predictive trait mining based on ecogeographic data; Coordinated evaluation and sharing of prebreeding products across environmental conditions to better understand genotype—environment interactions; Improved information sharing and feedback, especially with regards to genotypic and phenotypic data—and the way they are linked—between genetic resource conservationists, pre-breeders, breeders, and end users; and Enhanced coordination between basic and applied research communities.
Conflict of Interest The authors declare there to be no conflict of interest. Bioversity International, Rome. Nucleic Acids Res. Environmental association analyses identify candidates for abiotic stress tolerance in glycine soja, the wild progenitor of cultivated soybeans. G3: Genes, Genomes, Genet. Gene flow between crops and their wild relatives. Towards social acceptance of plant breeding by genome editing.
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Wild Crop Relatives: Genomic and Breeding Resources: Cereals | NHBS Academic & Professional Books
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