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"Germplasm"
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Assessing Genetic Distinctness and Redundancy of Plant Germplasm Conserved Ex Situ Based on Published Genomic SNP Data
Assessing genetic distinctness and redundancy is an important part of plant germplasm characterization. Over the last decade, such assessment has become more feasible and informative, thanks to the advances in genomic analysis. An attempt was made here to search for genebank germplasm with published genomic data and to assess their genetic distinctness and redundancy based on average pairwise dissimilarity (APD). The effort acquired 12 published genomic data sets from CIMMYT, IPK, USDA-ARS, IRRI, and ICRISAT genebanks. The characterized collections consisted of 661 to 55,879 accessions with up to 2.4 million genome-wide SNPs. The assessment generated an APD estimate for each sample. As a higher or lower APD is indicative of more genetic distinctness or redundance for an accession, respectively, these APD estimates helped to identify the most genetically distinct and redundant groups of 100 accessions each and a genetic outlier group with APD estimates larger than five standard deviations in each data set. An APD-based grouping of the conserved germplasm in each data set revealed among-group variances ranging from 1.5 to 53.4% across all data sets. Additional analyses showed that these APD estimations were more sensitive to SNP number, minor allele frequency, and missing data. Generally, 5000 to 10,000 genome-wide SNPs were required for an effective APD analysis. These findings together are encouraging and useful for germplasm management, utilization, and conservation, particularly in the genetic categorization of conserved germplasm.
Journal Article
Heirloom seeds and their keepers : marginality and memory in the conservation of biological diversity
Farmers and gardeners have long appreciated a wide variety of plants and have nurtured them for meals, medicine, and exchange. But diversity too often has been surrendered to monocultures of fields and spirits, predisposing much of modern agriculture to uniformity and, consequently, vulnerability. Today it is primarily at the individual level - such as growing and saving a strange old bean variety or a curious-looking gourd - that any lasting conservation actually takes place. Heirloom Seeds and Their Keepers offers a much-needed, scientifically researched perspective on the contribution of seedsaving that illustrates its critical significance to the preservation of both cultural knowledge and crop diversity around the world. It opens new conversations between anthropology and biology, and between researchers and practitioners, as it honors conservation as a way of life.
Book
Reap the crop wild relatives for breeding future crops
Crop wild relatives (CWRs) have provided breeders with several 'game-changing' traits or genes that have boosted crop resilience and global agricultural production. Advances in breeding and genomics have accelerated the identification of valuable CWRs for use in crop improvement. The enhanced genetic diversity of breeding pools carrying optimum combinations of favorable alleles for targeted crop-growing regions is crucial to sustain genetic gain. In parallel, growing sequence information on wild genomes in combination with precise gene-editing tools provide a fast-track route to transform CWRs into ideal future crops. Data-informed germplasm collection and management strategies together with adequate policy support will be equally important to improve access to CWRs and their sustainable use to meet food and nutrition security targets.
Exotic genetic libraries in different crops are valuable genetic resources for genetic dissection of complex quantitative traits.An informed choice of crop wild relatives (CWRs) for genetic studies and breeding can be made by taking account of the environmental variables of the collection sites.New breeding tools such as genomic selection and optimum contribution selection help to achieve the optimal combinations of beneficial alleles in exotic × elite crosses.Precise gene-editing tools open new avenues to broaden the array of current food crops by domesticating wild species de novo.Regulating the known crossover suppressors through mutagenesis and ploidy-level change has great potential to disrupt linkage drag.Systematic analysis of genebank collections would guide future germplasm collection strategies by prioritizing both target species and global sites.
Journal Article
Genetic resources, justice, and reconciliation : Canada and global access and benefit sharing
\"When the oral history of a medicinal plant as a genetic resource is used to develop a blockbuster drug, how is the contribution of indigenous peoples recognized in research and commercialization? What other ethical, legal, and policy issues come into play? Is it accurate for countries to self-identify as users or providers of genetic resources? This edited collection, which focuses on Canada, is the result of research conducted in partnership with indigenous peoples in that country, where melting permafrost and new sea lanes have opened the region's biodiversity, underscoring Canada's status as a user and provider of genetic resources and associated indigenous knowledge\"-- Provided by publisher.
Book
Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection
Summary Years of selection for desirable fruit quality traits in dessert watermelon (Citrullus lanatus) has resulted in a narrow genetic base in modern cultivars. Development of novel genomic and genetic resources offers great potential to expand genetic diversity and improve important traits in watermelon. Here, we report a high‐quality genome sequence of watermelon cultivar ‘Charleston Gray’, a principal American dessert watermelon, to complement the existing reference genome from ‘97103’, an East Asian cultivar. Comparative analyses between genomes of ‘Charleston Gray’ and ‘97103’ revealed genomic variants that may underlie phenotypic differences between the two cultivars. We then genotyped 1365 watermelon plant introduction (PI) lines maintained at the U.S. National Plant Germplasm System using genotyping‐by‐sequencing (GBS). These PI lines were collected throughout the world and belong to three Citrullus species, C. lanatus, C. mucosospermus and C. amarus. Approximately 25 000 high‐quality single nucleotide polymorphisms (SNPs) were derived from the GBS data using the ‘Charleston Gray’ genome as the reference. Population genomic analyses using these SNPs discovered a close relationship between C. lanatus and C. mucosospermus and identified four major groups in these two species correlated to their geographic locations. Citrullus amarus was found to have a distinct genetic makeup compared to C. lanatus and C. mucosospermus. The SNPs also enabled identification of genomic regions associated with important fruit quality and disease resistance traits through genome‐wide association studies. The high‐quality ‘Charleston Gray’ genome and the genotyping data of this large collection of watermelon accessions provide valuable resources for facilitating watermelon research, breeding and improvement.
Journal Article
Intellectual property law and plant protection : challenges and developments in Asia
\"This book provides a detailed and critical account of the emergence, development and implementation of plant variety protection laws in Asian countries. Each chapter undertakes a critical socio-legal analysis of one or more legal frameworks to understand, evaluate, and explore: the concerns of diverse national stakeholders; the histories and dynamics of law-making; and the ways in which plant variety protection and seed certification laws interact with local agricultural systems. The book also assesses how Asian countries can capitalise on the 'unused policy space' in international agreements such as TRIPS and UPOV, as well as international obligations beyond this, such as those contained in the CBD and the Plant Treaty. It also highlights the many ways Asian experiences can offer new insights into how regimes that grant intellectual property rights in plants might be re-imagined in other regions, including Africa, Europe and the Americas. By adding an important new perspective to the ongoing debate on intellectual property and plants, this book will appeal to academics, practitioners and policymakers engaged in work surrounding intellectual property laws, agricultural biodiversity and plant breeding\"-- Provided by publisher.
Book
Construction Strategy of Core Collection Based on Leaf Phenotypic Traits of Tetracentron sinense / 基于水青树叶表型性状的核心种质资源库构建策略
[Objective] To construct the core collection bank of Tetracentron sinense.[Method] Taking 161 germplasm of T. sinense as samples, the genetic variation data of leaf phenotypic characters of T. sinense were studied. First, the methods of Euclidean distance and Wald were used to cluster all individuals step by step. Second, 10 sampling ratios (10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, and 55%) were set, and then their core collection were screened by random sampling strategy, deviation sampling strategy and allele preferred sampling strategy. The germplasm resource banks constructed under different sampling strategies were compared and then the optimum core collection was screened out.[Result] (1) Among the three sampling strategies, the allele preferred sampling strategy significantly increased the percentage of variance difference (VD), the variation rate of coefficient of variation(VR) and the coincidence rate of range difference (CR) in core collection. 45% is the most suitable sampling ratio to construc
Journal Article