Gene Banks Challenges for the Future

Total Page:16

File Type:pdf, Size:1020Kb

Gene Banks Challenges for the Future Gene banks Challenges for the future Susan McCouch Dept. Plant Breeding & Genetic Cornell University Grand Challenges • Population & income growth • Land & water resources • Climate change • Nutrition, Health, Biosafety • Sustainability Gene Banks • Gene banks exist to conserve the genetic diversity of wild and domesticated organisms that humans depend on for food, fiber, medicine & energy. • Over 7 million plant germplasm accessions are housed in ~1,750 national and international gene banks. • Most accessions are poorly characterized; few are ever used. • Gene banks manage both genetic resources and information about those resources. • Diverse genetic resources are essential to improving the productivity, nutritional quality and sustainability of agricultural systems. • Rapid scientific/ technological developments have changed the way scientists explore and understand natural variation. • Gene bank managers must stay abreast of scientific developments to fulfill their responsibilities to the public. We are standing at the threshold of a genomics revolution within our gene banks…. • Genomics impacts every aspect of gene bank activities: – Collection and conservation – Documentation, characterization, evaluation – Distribution and dissemination • The creation of “Digital Gene Banks” based on DNA fingerprints will help gene banks become more efficient, cost‐effective, & informative as collectors, conservers, and providers of germplasm and information DNA fingerprints – Provide a unique genetic “bar‐code” for each accession – Facilitate tracking of accessions in & out of the gene bank – Assess genetic similarity within and between accessions – Identify potential duplicates within and across collections – Evaluate population structure – Classify types of admixture and introgression – Find novel alleles and genome‐wide archetypes – Understand genotype ‐ phenotype relationships – Create databases for cross‐species comparisons – Develop new querying tools and on‐line ordering system A FEW EXAMPLES FROM MY OWN WORK Basmati rice is genetically more closely related to Chinese japonica than to Indian indica indica Basmati has long tropical japonica slender grain Morphologically, it looks more like indica than its closer japonica relatives. In the scientific temperate literature and in aus japonica legend, it is referred to as indica rice Basmati Garris et al. (2005) Genetics The Silk Road is key to understanding the genetics Sub‐population structure of O. glaberrima • Single domestication from African O. barthii ancestor •3 cryptic domesticated groups plus admixture with O. sativa •Groups not defined geographically (no “isolation by distance”) •Genetic groups associated with ecology (Portères, 1970) • floating • non‐floating • upland Nigeria sativa O. ‐ Semon et al. (2005) The population structure of African cultivated rice Oryza glaberrima. Genetics 169:1639‐1647 New insights into how to utilize hidden variation • It has irrevocably altered our understanding of the genetic potential of wild & exotic germplasm in plant improvement O. glaberrima NERICA O. sativa 6.3% O. glaberrima (93.7% O. sativa) Genomics is changing the face of plant breeding using genomics & information technology QUESTIONS FOR GENE BANK MANAGERS HOW SHOULD WE MANAGE SPECIALIZED GENETIC STOCKS? • Mapping populations, mutants and diversity panels are widely used for quantitative genetic analysis, gene discovery, and germplasm characterization; all require careful management, tracking and dissemination to maintain their utility. • Should gene banks extend their activities by collaborating with the research community and participating in this process? • Should “genetic stocks” be be put into short‐medium term storage, while other gene bank accessions are of long‐term interest? Use of gene bank holdings • How will the availability of whole genome sequence change the way recommendations are made or accessions are selected by gene bank managers? • How will users interact with the progressive accumulation of genomic information about the genetic resources housed in ex situ collections? • Will the growing body of genomic information impact the type of germplasm to be maintained in gene banks in the future? • Will it ultimately expand the utilization of gene bank holdings? How will users interact with the data? • Databases are needed to track, store, analyze and distribute genotypic and phenotypic data connected to genetic resources • Common standards must be adopted for acquiring, indexing, defining, organizing, and sharing genotypic and phenotypic data across laboratories and disciplines • A coordinated, distributed network of statisticians, computational biologists, population geneticists, and computer programmers must be added to the team of gene bank scientists to help analyze and interpret genomic data Conserving and utilizing diversity • Gene banks conserve living samples that bridge the past and the future • They complement investments in in situ conservation => conserve complex communities of locally adapted organisms living in dynamic ecological equilibrium • Genomics, if used wisely, can help us make better use of gene bank collections as we seed to address the grand challenges of the future.
Recommended publications
  • Does Overdraft Affect Loan Application
    Does Overdraft Affect Loan Application Sequent Vladamir still chanced: steepled and co-ordinal Garfinkel disguise quite humbly but ankyloses her cascabel despitefully. Indusial Forrest sometimes disrates his subjunctive blamed and rerouted so tough! Tamer Karl unbonnets medicinally. We pay instead of overdraft line of overdraft affect a uk mortgage underwriters look at the interest, at the event would bring a real customer Is exempt some ingenious way I can have these foundation of transactions accepted without reason an overdraft fee charged? FAQs Overdraft Services Chasecom. Our mission is none provide readers with beige and unbiased information, too. We believe grace and be the standard. But here's sound good place even though overdraft fees might hamper your sample they do not way affect your credit score for's nothing. Could an overdraft affect future credit applications. When mortgage lenders assess your application they'll value how exactly you standing on your overdraft If you constantly use overdraft. Should you overdraw your loan affect the limits to the website run a mortgage applicant qualifications are not. We will notify bank could i speak to borrow money in such as a fee is there is a minor actions can only and toggle through? Canstar provides a student loan programs typically, withdrawals are using real estate taxes and even more flexibility you have not responsible for using. Is an institution requiredto provide new alternatives to automated overdraft payment programs? You overdraft affect overdrafts up on applicant qualifications are. Which actually let you overdraft the most? Steve at RFB was very attentive and reliable in getting from Business Mortgage.
    [Show full text]
  • Crop Genetic Resources Bulletin Number 2 an Economic Appraisal May 2005 Kelly Day Rubenstein, Paul Heisey, Robbin Shoemaker, John Sullivan, and George Frisvold
    A Report from the Economic Research Service United States Department www.ers.usda.gov of Agriculture Economic Information Crop Genetic Resources Bulletin Number 2 An Economic Appraisal May 2005 Kelly Day Rubenstein, Paul Heisey, Robbin Shoemaker, John Sullivan, and George Frisvold Abstract: Crop genetic resources are the basis of agricultural production, and significant economic benefits have resulted from their conservation and use. However, crop genetic resources are largely public goods, so private incentives for genetic resource conservation may fall short of achieving public objectives. Within the U.S. germplasm system, certain crop collec- tions lack sufficient diversity to reduce vulnerability to pests and diseases. Many such genetic resources lie outside the United States. This report examines the role of genetic resources, genetic diversity, and efforts to value genetic resources. The report also evaluates economic and institutional fac- tors influencing the flow of genetic resources, including international agree- ments, and their significance for agricultural research and development in the United States. Keywords: Genetic resources, genetic diversity, germplasm, R&D, interna- tional transfer of genetic resources, in situ conservation, ex situ conserva- tion, gene banks, intellectual property. Acknowledgments: The authors wish to thank Allan Stoner, Henry Shands, and Peter Bretting for their thoughtful reviews and their valuable comments. Thanks for reviews above and beyond the call of duty belong to June Blalock, whose patience and insight were critical to the production of this report. We also thank Joe Cooper who reviewed portions of the manuscripts. Keith Wiebe provided helpful guidance in the development of the final draft. We thank Dale Simms for his excellent editorial work and Susan DeGeorge for her help with graphics and layout.
    [Show full text]
  • Screening of Different Contaminated Environments For
    Biologia, Bratislava, 62/6: 650—656, 2007 Section Cellular and Molecular Biology DOI: 10.2478/s11756-007-0144-y Screening of different contaminated environments for polyhydroxyalkanoates-producing bacterial strains Shafiq ur Rehman,NaziaJamil* & Shahida Husnain Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore 54590, Pakistan; e-mail: jamil [email protected] Abstract: Total sixteen bacterial strains were isolated and purified from the samples collected from sugarcane molasses soil, sewage water and long-chain-hydrocarbon-contaminated area of the Punjab University, Lahore, Pakistan. Tolerance to different antibiotics was studied and strains showed multiple antibiotic resistance. All strains were characterized for Gram stain, biochemical reactions and polyhydroxyalkanoate (PHA) production. Total fourteen strains were Gram negative and two were Gram positive, while biochemically nine PHA producers showed affiliation to Pseudomonas, Enterobacter, Citrobacter, Bacillus and Escherichia. Screening for PHA production was done by Sudan black staining and nine out of sixteen strains exhibited PHA producing ability. PHA production was optimized for different growth parameters, like nitrogen concentration, pH and temperature. PHA extraction was done by solvent extraction method. Bacterial strains US1 and M1 accumulated up to 30% PHA of their cell dry weight on PHA extraction by solvent extraction method. Bacterial strain US1 was identified by 16S rRNA gene analysis as P. aeruginosa (DQ455691). PHA production was confirmed by PCR amplification of 500 bp fragment from PHA polymerase (Pha C) gene; five strains from nine PHA producers gave positive results on PCR. Pha C gene fragment of US1 was sequenced and submitted to Gene Bank under the accession number DQ455690. The amino acid sequence showed homology using the protein BLAST at 129–132 sites with different PHA synthases of the Pseudomonas sp.
    [Show full text]
  • Gene Bank Curators Towards Implementation of the International Treaty on Plant Genetic Resources for Food and Agriculture by the Indian National Gene Bank
    Chapter 14 Gene Bank Curators Towards Implementation of the International Treaty on Plant Genetic Resources for Food and Agriculture by the Indian National Gene Bank Shyam Kumar Sharma and Pratibha Brahmi Introduction: PGRFA diversity in India The Indian subcontinent is very rich in biological diversity, harbouring around 49,000 species of plants, including about 17,500 species of higher plants. The Indian gene centre holds a prominent position among the 12 mega-gene centres of the world. It is also one of the Vavilovian centres of origin and diversity of crop plants. Two out of the 25 global hotspots of biodiversity, namely the Indo-Burma and Western Ghats are located here. India possesses about 12 per cent of world flora with 5725 endemic species of higher plants belonging to about 141 endemic genera and over 47 families. About 166 species of crops including 25 major and minor crops have originated and/or developed diversity in this part of the world. Further, 320 species of wild relatives of crop plants are also known to occur here. Presently, the Indian diversity is composed of rich genetic wealth of native as well as introduced types. India is a primary as well as a secondary centre of diversity for several crops, and also has rich regional diversity for several South/ Southeast Asian crops such as rice, black gram, moth bean, pigeon pea, cucur- bits (like smooth gourd, ridged gourd and pointed gourd), tree cotton, capsularis jute, jackfruit, banana, mango, Syzygium cumini/jamun, large cardamom, black pepper and several minor millets and medicinal plants like Rauvolfia serpentina and Saussurea costus.
    [Show full text]
  • Isolation and Molecular Identi Cation of Microorganisms Isolated from Soils
    Isolation and molecular identication of microorganisms isolated from soils contaminated with heavy metals in Mosul city Sana Qasim ( [email protected] ) University of Mosul College of Environmental Sciences and Technology https://orcid.org/0000-0002- 1624-0717 Mazin N. Fadhel University of Mosul Mohammad I. Khalil University of Mosul Research Article Keywords: Posted Date: July 28th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-747759/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/11 Abstract This research is concerned with organisms isolated from soils contaminated with heavy metals in industrial and residential areas in the city of Mosul, the center of Nineveh Governorate, and the diagnosis of these organisms using molecular biology technique. Samples were collected from four locations in the city between the industrial area and residential neighborhoods. Soil samples were analyzed and dilutions were prepared, then the dilutions were grown on potato extract and dextrose (PDA) medium for the development of fungi and Nutrient agar for bacterial development. The dilutions were planted by casting method by three replications, then the process of purifying the fungal and bacterial colonies was carried out using the traditional methods. For the purpose of diagnosing these pure colonies using PCR technique, colonies of fungi were grown on the medium of PDA, and bacteria were grown on the medium of nutritious broth. As a result, nine fungal species were diagnosed, two of them are new undiagnosed genera that have been registered in the gene bank, four of them contain genetic mutations, and three of them are known and previously diagnosed fungi.
    [Show full text]
  • Unit 5 Ex-Situ Conservation
    UNIT 2 EX-SITU CONSERVATION Structure 5.0 Introduction 5.1 Advantage of Ex-situ Conservation 5.2 Objectives 5.3 Ex-situ Conservation : Principles & Practices 5.4 Conventional methods of ex-situ conservation 5.4.1 Gene Bank 5.4.2 Community Seed Bank 5.4.3 Seed Bank 5.4.4 Botanical Garden 5.4.5 Field Gene Bank 5.5 Biotechnological methods of ex-situ conservation 5.4.1 In-vitro Conservation 5.4.2 In-vitro storage of germplasm and cryopreservation 5.4.3 Other method 5.4.4 Germplasm facilities in India 5.6 General Account of Important Institutions 5.4.1 BSI 5.4.2 NBPGR 5.4.3 IARI 5.4.4 SCIR 5.4.5 DBT 5.7 Let us sum up 5.8 Check your progress & the key 5.9 Assignments/ Activities 5.10 References/ Further Reading 44 5.0 INTRODUCTION For much of the time man lived in a hunter-gather society and thus depended entirely on biodiversity for sustenance. But, with the increased dependence on agriculture and industrialisation, the emphasis on biodiversity has decreased. Indeed, the biodiversity, in wild and domesticated forms, is the sources for most of humanity food, medicine, clothing and housing, much of the cultural diversity and most of the intellectual and spiritual inspiration. It is, without doubt, the very basis of life. Further that, a quarter of the earth‟s total biological diversity amounting to a million species, which might be useful to mankind in one way or other, is in serious risk of extinction over the next 2-3 decades.
    [Show full text]
  • Evaluation of Scab and Mildew Resistance in the Gene Bank Collection of Apples in Dresden-Pillnitz
    plants Article Evaluation of Scab and Mildew Resistance in the Gene Bank Collection of Apples in Dresden-Pillnitz Monika Höfer * , Henryk Flachowsky, Susan Schröpfer and Andreas Peil Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany; henryk.fl[email protected] (H.F.); [email protected] (S.S.); [email protected] (A.P.) * Correspondence: [email protected] Abstract: A set of 680 apple cultivars from the Fruit Gene bank in Dresden Pillnitz was evaluated for the incidence of powdery mildew and scab in two consecutive years. The incidence of both scab and powdery mildew increased significantly in the second year. Sixty and 43 cultivars with very low incidence in both years of scab and powdery mildew, respectively, were analysed with molecular markers linked to known resistance genes. Thirty-five cultivars were identified to express alleles or combinations of alleles linked to Rvi2, Rvi4, Rvi6, Rvi13, Rvi14, or Rvi17. Twenty of them, modern as well as a few traditional cultivars known before the introduction or Rvi6 from Malus floribunda 821, amplified the 159 bp fragment of marker CH_Vf1 that is linked to Rvi6. Alleles linked to Pl1, Pld, or Plm were expressed from five cultivars resistant to powdery mildew. Eleven cultivars were identified to have very low susceptibility to both powdery mildew and scab. The information on resistance/susceptibility of fruit genetic resources towards economically important diseases is important for breeding and for replanting traditional cultivars. Furthermore, our work provides a well-defined basis for the discovery of undescribed, new scab, and powdery mildew resistance.
    [Show full text]
  • Gene Banks Pay Big Dividends to Agriculture, the Environment, and Human Welfare R
    Community Page Gene Banks Pay Big Dividends to Agriculture, the Environment, and Human Welfare R. C. Johnson early a century after the pioneering American Napple tree purveyor Johnny Appleseed traveled from town to town planting nurseries in the Midwestern United States, Frans Nicholas Meijer left his Netherlands home to pursue a similar vocation as an “agricultural explorer” for the US Department of Agriculture. Over the course of his career, Meijer, who changed his name to Frank Meyer after reaching the New World, helped introduce over 2,500 foreign plants from Europe, Russia, and China, including the lemon that would bear his name. Starting with his first expedition for Asian plants in 1905, Meyer would encounter isolation, physical discomfort, disease, robbers, and revolutionaries in his quest to collect useful plants. Although some of Meyer’s collections are still used today, only a few are conserved in their original doi:10.1371/journal.pbio.0060148.g001 form. They, along with countless other Figure 1. Collecting Accessions collections from the early 20th century, Walter Kaiser collects taper-tip onion (Allium acuminatum) along the Snake River in Idaho in 2005. disappeared because there was no long- Collections were made across a broad area of Western rangeland to strengthen the WRPIS Allium term system for conservation. To rectify collection and for research to determine taper-tip onion adaptation zones needed for successful revegetation. this problem, Congress established a system of repositories after World and maintain germplasm is ongoing genetic uniformity and dependence on War II to maintain and distribute and urgent. Since agriculture’s just a few crops.
    [Show full text]
  • 2PG 135 Abamectin 341 Acceptable Risk 172–3
    Index 2PG5 13 agricultural labour composition, Africa 457–8 Abamectin 341 agricultural markets, policy 513 acceptable risk 172–3 agricultural policies, India 432–4, 435 access and benefit sharing 40, 42, 43–4 and pest management 324–41 accessions 3–10, 11–12, 26–7, 37, 38, 39, 52–3, post-war 164–5 56, 57, 226, 227 agricultural regulation 162–79 acetylated starches 122 agricultural subsidies 269–70, 424–5, 452–4 active sensors 370 Africa 452–4 Aegilops tauschii 22, 26 China 424–5 aerobic methane oxidisers 283 agricultural sustainability, China 423 Afghanistan 454 agricultural technology, Africa 448–50 Africa, agricultural input markets 451–2 side effects 165 agricultural labour composition 457–8 Agricultural Technology Management Agency agricultural potential 446–59 (ATMA) 432 agricultural subsidies 452–4 agricultural transformation, in Asia 419–20 agricultural technology 448–50 agricultural universities, USA 149 agro-dealers 87, 450, 451–3 agriculture, China 411–26 climate change 458–9 India 429–42 fertiliser use 224, 258, 452, 453 technological innovation 164–5 Green Revolution 447–8, 449, 462–3 use of remote sensing 376–7 land markets 457 water management 352–64 land tenure security 457 agri-food industry, and RS 123–4 public investment 458 agri-ppps 399–400 rural input markets 451–2 agro-dealers, Africa 87, 450, 451–3 small holder famers 448 agronomic biofortification 68 staple crop processing zones 455–7 alfalfa 152 transformational policies 451–9 alleles for breeding 8 see also sub-Saharan Africa allelic diversity 4, 5, 6, 7, 8 Africa
    [Show full text]
  • Influence of Cathodic Water Invigoration on the Emergence And
    plants Article Influence of Cathodic Water Invigoration on the Emergence and Subsequent Growth of Controlled Deteriorated Pea and Pumpkin Seeds Kayode Fatokun 1,*, Richard P. Beckett 2,3, Boby Varghese 1, Jacques Cloete 4 and Norman W. Pammenter 1 1 School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban 4000, South Africa; [email protected] (B.V.); [email protected] (N.W.P.) 2 School of Life Sciences, University of KwaZulu-Natal Pietermaritzburg, Private Bag X01, Scottsville 3209, South Africa; [email protected] 3 Openlab “Biomarker”, Kazan Federal University, 420008 Kazan, Republic of Tatarstan, Russia 4 Department of Mathematical Sciences, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; [email protected] * Correspondence: [email protected] Received: 24 March 2020; Accepted: 2 June 2020; Published: 29 July 2020 Abstract: The quality of seeds in gene banks gradually deteriorates during long-term storage, which is probably, at least in part, a result of the progressive development of oxidative stress. Here, we report a greenhouse study that was carried out to test whether a novel approach of seed invigoration using priming with cathodic water (cathodic portion of an electrolysed calcium magnesium solution) could improve seedling emergence and growth in two deteriorated crop seeds. Fresh seeds of Pisum sativum and Cucurbita pepo were subjected to controlled deterioration to 50% viability at 14% seed moisture content (fresh weight basis), 40 ◦C and 100% relative humidity. The deteriorated seeds were thereafter primed with cathodic water, calcium magnesium solution and deionized water. In addition, to study the mechanism of the impacts of invigoration, the effects of such priming on the lipid peroxidation products malondialdehyde (MDA) and 4-hydroxynonenal (4-HNE) and on the reactive oxygen species (ROS) scavenging enzymes superoxide dismutase and catalase were also determined in the fresh and deteriorated seeds.
    [Show full text]
  • Biodiversity and Gene Patents
    United Nations Environment Programme UFRGSMUN | UFRGS Model United Nations Journal ISSN: 2318-3195 | v1, 2013| p.244-263 Biodiversity and Gene Patents Luciana Costa Brandão Júlia Paludo 1. Historical background We are noticing an increased consciousness of biodiversity importance in our daily lives, and how its changes (and mostly its losses) strongly aff ect not only our wealth, but also several domains, such as our economy, security, and culture. According to UNEP, “[t]he roles of biodiversity in the supply of ecosystem services can be categorized as provisioning, regulating, cultural and supporting [...], and biodiversity may play multiple roles in the supply of these types of services. For example, in agriculture, biodiversity is the basis for a provisioning service (food, fuel or fi ber is the end product), a supporting service (such as micro-organisms cycling nutrients and soil formation), a regulatory service (such as through pollination), and potentially, a cultural service in terms of spiritual or aesthetic benefi ts, or cultural identity” (Ash and Fazel 2007, 161). Th us besides satisfying human needs, biodiversity also plays a strong role in our culture, whose basis is the relationship between people and the environment, which is diff erent in each society. In this sense, biodiversity loss may imply also the loss of an important set of practices and values exclusive of some communities (Sala 2009). Given its historical importance to humanity, biodiversity was considered part of the “common heritage of humankind”, but this status began to change very recently. Under the former condition, biological elements were treated as a public good, free of claims by States or private companies, and available only for peaceful and scientifi c purposes.
    [Show full text]
  • Near East and North Africa Regional Synthesis for the State of the World’S Biodiversity for Food and Agriculture
    REGIONAL SYNTHESIS REPORTS NEAR EAST AND NORTH AFRICA REGIONAL SYNTHESIS FOR THE STATE OF THE WORLD’S BIODIVERSITY FOR FOOD AND AGRICULTURE NEAR EAST AND NORTH AFRICA REGIONAL SYNTHESIS FOR THE STATE OF THE WORLD’S BIODIVERSITY FOR FOOD AND AGRICULTURE FOOD AND AGRICULTURE ORGANIZATION OF THE UNITED NATIONS ROME, 2019 Required citation: FAO. 2019. Near East and North Africa Regional Synthesis for The State of the World’s Biodiversity for Food and Agriculture. Rome. The designations employed and the presentation of material in this information product do not imply the expression of any opinion whatsoever on the part of the Food and Agriculture Organization of the United Nations (FAO) concerning the legal or development status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. The mention of specific companies or products of manufacturers, whether or not these have been patented, does not imply that these have been endorsed or recommended by FAO in preference to others of a similar nature that are not mentioned. The views expressed in this information product are those of the author(s) and do not necessarily reflect the views or policies of FAO. ISBN 978-92-5-131823-2 © FAO, 2019 Some rights reserved. This work is made available under the Creative Commons Attribution-NonCommercial- ShareAlike 3.0 IGO licence (CC BY-NC-SA 3.0 IGO; https://creativecommons.org/licenses/by-nc-sa/3.0/igo/ legalcode/legalcode). Under the terms of this licence, this work may be copied, redistributed and adapted for non-commercial purposes, provided that the work is appropriately cited.
    [Show full text]