scholarly journals Genebank Phenomics: A Strategic Approach to Enhance Value and Utilization of Crop Germplasm

Plants ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 817 ◽  
Author(s):  
Giao N. Nguyen ◽  
Sally L. Norton
Keyword(s):  
High Throughput ◽  
Cost Effective ◽  
Screening Tools ◽  
Ex Situ ◽  
Phenotypic Data ◽  
Germplasm Collections ◽  
Digital Phenotyping ◽  
Seed Regeneration ◽  
Novel Alleles ◽  
Crop Germplasm

Genetically diverse plant germplasm stored in ex-situ genebanks are excellent resources for breeding new high yielding and sustainable crop varieties to ensure future food security. Novel alleles have been discovered through routine genebank activities such as seed regeneration and characterization, with subsequent utilization providing significant genetic gains and improvements for the selection of favorable traits, including yield, biotic, and abiotic resistance. Although some genebanks have implemented cost-effective genotyping technologies through advances in DNA technology, the adoption of modern phenotyping is lagging. The introduction of advanced phenotyping technologies in recent decades has provided genebank scientists with time and cost-effective screening tools to obtain valuable phenotypic data for more traits on large germplasm collections during routine activities. The utilization of these phenotyping tools, coupled with high-throughput genotyping, will accelerate the use of genetic resources and fast-track the development of more resilient food crops for the future. In this review, we highlight current digital phenotyping methods that can capture traits during annual seed regeneration to enrich genebank phenotypic datasets. Next, we describe strategies for the collection and use of phenotypic data of specific traits for downstream research using high-throughput phenotyping technology. Finally, we examine the challenges and future perspectives of genebank phenomics.

scholarly journals Unbalanced historical phenotypic data from seed regeneration of a barley ex situ collection

2018 ◽  
Vol 5 (1) ◽  
Author(s):  
Maria Y. Gonzalez ◽  
Stephan Weise ◽  
Yusheng Zhao ◽  
Norman Philipp ◽  
Daniel Arend ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Phenotypic Diversity ◽  
Spring Barley ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Model Organism ◽  
Ex Situ ◽  
Phenotypic Characterization ◽  
Phenotypic Data ◽  
Seed Regeneration

Abstract The scarce knowledge on phenotypic characterization restricts the usage of genetic diversity of plant genetic resources in research and breeding. We describe original and ready-to-use processed data for approximately 60% of ~22,000 barley accessions hosted at the Federal ex situ Genebank for Agricultural and Horticultural Plant Species. The dataset gathers records for three traits with agronomic relevance: flowering time, plant height and thousand grain weight. This information was collected for seven decades for winter and spring barley during the seed regeneration routine. The curated data represent a source for research on genetics and genomics of adaptive and yield related traits in cereals due to the importance of barley as model organism. This data could be used to predict the performance of non-phenotyped individuals in other collections through genomic prediction. Moreover, the dataset empowers the utilization of phenotypic diversity of genetic resources for crop improvement.

scholarly journals Historical phenotypic data from seven decades of seed regeneration in a wheat ex situ collection

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Norman Philipp ◽  
Stephan Weise ◽  
Markus Oppermann ◽  
Andreas Börner ◽  
Jens Keilwagen ◽  
...  
Keyword(s):  
Ex Situ ◽  
Phenotypic Data ◽  
Seed Regeneration ◽  
Ex Situ Collection

Innovative Field Screening Tools for a Reliable and Cost-effective Site Characterization

2004 ◽  
Vol 12 (2) ◽  
pp. 115-125
Author(s):  
Katrin Batereau ◽  
Martin Müller ◽  
Norbert Klaas ◽  
Baldur Barczewski
Keyword(s):  
Cost Effective ◽  
Site Characterization ◽  
Screening Tools ◽  
Field Screening ◽  
Effective Site

scholarly journals Evaluation of the effects of acetylcholinesterase inhibitors in the zebrafish touch-evoked response: quantitative vs. qualitative assessment

2020 ◽  
Vol 32 (1) ◽  
Author(s):  
Laura Guzman ◽  
Gisela Besa ◽  
Daniela Linares ◽  
Lara González ◽  
Caterina Pont ◽  
...  
Keyword(s):  
Neurological Diseases ◽  
Acetylcholinesterase Inhibitors ◽  
Cost Effective ◽  
Evoked Response ◽  
New Drugs ◽  
Screening Tools ◽  
Qualitative Assessment ◽  
Toxicity Screening ◽  
Novel Treatments ◽  
Ache Inhibitors

Abstract Background The difficulty of finding new treatments for neurological diseases with great impact in our society like Alzheimer’s disease can be ascribed in part to the complexity of the nervous system and the lack of quick and cost-effective screening tools. Such tools could not only help to identify potential novel treatments, but could also be used to test environmental contaminants for their potential to cause neurotoxicity. It has been estimated that 5–10% of the anthropogenic chemicals are developmental neurotoxic (DNT) and exposure to DNT compounds has been linked to several neurological diseases. Within this study we were testing the applicability of a quick and cost-effective behavioural test using zebrafish embryos: the touch-evoked response assay, in this case, an assay evaluating the swimming response to a tap in the tail. Two acetylcholinesterase (AChE) inhibitors positive controls (paraoxon and huprine Y), as well as 10 huprine-derivative compounds were tested and the results were evaluated using 2 different methods, a quantitative and a qualitative one. Results We could show that the methodology presented is able to detect behavioural effects of AChE inhibitors. A good correlation between the results obtained with the quantitative and the qualitative method was obtained (R2 = 0.84). Conclusions Our proposed method enables combination of screening for new drugs with toxicity screening in a whole embryo model alternative to animal experimentation, thereby merging 2 drug development steps into one.

scholarly journals High-Throughput Phenotyping Methods for Breeding Drought-Tolerant Crops

2021 ◽  
Vol 22 (15) ◽  
pp. 8266
Author(s):  
Minsu Kim ◽  
Chaewon Lee ◽  
Subin Hong ◽  
Song Lim Kim ◽  
Jeong-Ho Baek ◽  
...  
Keyword(s):  
Drought Stress ◽  
High Throughput ◽  
Large Scale ◽  
Crop Yields ◽  
Plant Traits ◽  
Rapid Development ◽  
Plant Responses ◽  
Phenotypic Data ◽  
Agricultural Technologies ◽  
High Throughput Phenotyping

Drought is a main factor limiting crop yields. Modern agricultural technologies such as irrigation systems, ground mulching, and rainwater storage can prevent drought, but these are only temporary solutions. Understanding the physiological, biochemical, and molecular reactions of plants to drought stress is therefore urgent. The recent rapid development of genomics tools has led to an increasing interest in phenomics, i.e., the study of phenotypic plant traits. Among phenomic strategies, high-throughput phenotyping (HTP) is attracting increasing attention as a way to address the bottlenecks of genomic and phenomic studies. HTP provides researchers a non-destructive and non-invasive method yet accurate in analyzing large-scale phenotypic data. This review describes plant responses to drought stress and introduces HTP methods that can detect changes in plant phenotypes in response to drought.

scholarly journals 38 Using pooled data for single-step genomic prediction: Impact of within-pool variance and size

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 9-9
Author(s):  
Johnna L Baller ◽  
Stephen D Kachman ◽  
Larry A Kuehn ◽  
Matthew L Spangler
Keyword(s):  
Phenotypic Variation ◽  
Equal Opportunity ◽  
Cost Effective ◽  
Single Step ◽  
Pool Size ◽  
Individual Data ◽  
Phenotypic Data ◽  
Breeding Values ◽  
Mean Values ◽  
Genetic Evaluations

Abstract Economically relevant traits (ERT) are routinely collected within commercial segments of the beef industry but are rarely included in genetic evaluations because of unknown pedigrees. Individual relationships could be resurrected with genomics, which would be costly; pooling DNA and phenotypic data provides a cost-effective solution. A simulated beef cattle population consisting of 15 generations was genotyped with approximately 50k markers (841 quantitative trait loci were located across the genome) and phenotyped for a moderately heritable trait. Individuals from generation 15 were included in pools (observed genotype and phenotype were mean values of a group). Estimated breeding values (EBV) were generated from a single-step GBLUP model. The effects of pooling strategy (random and minimizing or uniformly maximizing phenotypic variation), pool size (1, 2, 10, 20, 50, 100, or no data from generation 15), and generational gaps of genotyping on EBV accuracy (correlation of EBV with true breeding values) were quantified. Greatest EBV accuracies of sires and dams were observed when no gap between genotyped parents and pooled offspring occurred. The EBV accuracies resulting from pools were greater than no data from generation 15 regardless of sire or dam genotyping. Minimizing phenotypic variation increased EBV accuracy by 8% and 9% over random pooling and uniformly maximizing phenotypic variation, respectively. Pool size of 2 was the only scenario that did not significantly decrease EBV accuracy compared to individual data when pools were formed randomly or by uniformly maximizing phenotypic variation (P > 0.05). Pool sizes of 2, 10, 20, or 50 did not generally lead to EBV accuracies that were statistically different than individual data when pools were constructed to minimize phenotypic variation (P > 0.05). Pooled genotyping to garner commercial-level phenotypes for genetic evaluations seems plausible, although differences exist depending on pool size and pool formation strategy. The USDA is an equal opportunity employer.

scholarly journals Cryopreservation of Woody Crops: The Avocado Case

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 934
Author(s):  
Chris O’Brien ◽  
Jayeni Hiti-Bandaralage ◽  
Raquel Folgado ◽  
Alice Hayward ◽  
Sean Lahmeyer ◽  
...  
Keyword(s):  
Tissue Culture ◽  
Ex Situ Conservation ◽  
Plant Genetic Resources ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Recalcitrant Seed ◽  
In Vitro Storage ◽  
Germplasm Collections ◽  
Seed Crops

Recent development and implementation of crop cryopreservation protocols has increased the capacity to maintain recalcitrant seeded germplasm collections via cryopreserved in vitro material. To preserve the greatest possible plant genetic resources globally for future food security and breeding programs, it is essential to integrate in situ and ex situ conservation methods into a cohesive conservation plan. In vitro storage using tissue culture and cryopreservation techniques offers promising complementary tools that can be used to promote this approach. These techniques can be employed for crops difficult or impossible to maintain in seed banks for long-term conservation. This includes woody perennial plants, recalcitrant seed crops or crops with no seeds at all and vegetatively or clonally propagated crops where seeds are not true-to-type. Many of the world’s most important crops for food, nutrition and livelihoods, are vegetatively propagated or have recalcitrant seeds. This review will look at ex situ conservation, namely field repositories and in vitro storage for some of these economically important crops, focusing on conservation strategies for avocado. To date, cultivar-specific multiplication protocols have been established for maintaining multiple avocado cultivars in tissue culture. Cryopreservation of avocado somatic embryos and somatic embryogenesis have been successful. In addition, a shoot-tip cryopreservation protocol has been developed for cryo-storage and regeneration of true-to-type clonal avocado plants.

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