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Negawo AT, Akinmade HO, Muktar MS, Habte E, Assefa Y, Muchugi A, Sartie AM, Jones CS. Genetic Diversity, Population Structure and Subset Development in a Sesbania sesban Collection. PLANTS (BASEL, SWITZERLAND) 2022; 12:13. [PMID: 36616142 PMCID: PMC9823922 DOI: 10.3390/plants12010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Sesbania sesban (L.) Merr. is a multipurpose legume tree grown primarily for fodder and forage in the tropical and subtropical world. In this study, the Sesbania sesban collection maintained in the International Livestock Research Institute (ILRI) forage Genebank was studied using genome-wide markers generated on the DArTseq platform. Genotyping produced 84,673 and 60,626 SNP and SilicoDArT markers with a mean polymorphic information content of 0.153 and 0.123, respectively. From the generated markers, 7587 and 15,031 highly informative SNP and SilicoDArT markers, respectively, were filtered and used for genetic diversity analysis and subset development. Analysis of molecular variance (AMOVA) revealed higher variability 'within' (52.73% for SNP markers and 67.36% for SilicoDArT markers) than 'between' accessions. Hierarchical cluster analysis showed the presence of four main clusters in the collection. Mantel correlation analysis showed a lack of relationship between genetic variation of the germplasm and their geographical origin. A representative subset of 34 accessions containing germplasm from diverse origins and agro-ecologies was developed using SNP markers. The genetic diversity information generated in this study could be used for marker-assisted screening for stress tolerance, gap analysis and identification and acquisition of new distinct genotype(s) to broaden the genetic basis of the collection for future improvement programs to develop high-yielding, stress-tolerant varieties for enhancing food and environmental security in crop-livestock-based production systems.
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Affiliation(s)
- Alemayehu Teressa Negawo
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia
| | - Habib Olumide Akinmade
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia
- Forage Breeding and Genetics, Agronomy Department, University of Florida, Gainesville, FL 32611, USA
| | - Meki S. Muktar
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia
| | - Ermias Habte
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia
| | - Yilikal Assefa
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia
| | - Alice Muchugi
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia
| | - Alieu M. Sartie
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia
- The Pacific Community (SPC), Private Mail Bag, Suva, Fiji
| | - Chris S. Jones
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia
- Feed and Forage Development, International Livestock Research Institute, Nairobi 00100, Kenya
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Negawo AT, Muktar MS, Assefa Y, Hanson J, Sartie AM, Habte E, Jones CS. Genetic Diversity and Population Structure of a Rhodes Grass ( Chloris gayana) Collection. Genes (Basel) 2021; 12:1233. [PMID: 34440407 PMCID: PMC8394257 DOI: 10.3390/genes12081233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/23/2021] [Accepted: 08/05/2021] [Indexed: 11/30/2022] Open
Abstract
Rhodes grass (Chloris gayana Kunth) is one of the most important forage grasses used throughout the tropical and subtropical regions of the world. Enhancing the conservation and use of genetic resources requires the development of knowledge and understanding about the existing global diversity of the species. In this study, 104 Rhodes grass accessions, held in trust in the ILRI forage genebank, were characterized using DArTSeq markers to evaluate the genetic diversity and population structure, and to develop representative subsets, of the collection. The genotyping produced 193,988 SNP and 142,522 SilicoDArT markers with an average polymorphic information content of 0.18 and 0.26, respectively. Hierarchical clustering using selected informative markers showed the presence of two and three main clusters using SNP and SilicoDArT markers, respectively, with a cophenetic correction coefficient of 82%. Bayesian population structure analysis also showed the presence of two main subpopulations using both marker types indicating the existence of significant genetic variation in the collection. A representative subset, containing 21 accessions from diverse origins, was developed using the SNP markers. In general, the results revealed substantial genetic diversity in the Rhodes grass collection, and the generated molecular information, together with the developed subset, should help enhance the management, use and improvement of Rhodes grass germplasm in the future.
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Affiliation(s)
- Alemayehu Teressa Negawo
- Feed and Forage Development Program, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia; (A.T.N.); (M.S.M.); (Y.A.); (J.H.); (A.M.S.); (E.H.)
| | - Meki S. Muktar
- Feed and Forage Development Program, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia; (A.T.N.); (M.S.M.); (Y.A.); (J.H.); (A.M.S.); (E.H.)
| | - Yilikal Assefa
- Feed and Forage Development Program, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia; (A.T.N.); (M.S.M.); (Y.A.); (J.H.); (A.M.S.); (E.H.)
| | - Jean Hanson
- Feed and Forage Development Program, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia; (A.T.N.); (M.S.M.); (Y.A.); (J.H.); (A.M.S.); (E.H.)
| | - Alieu M. Sartie
- Feed and Forage Development Program, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia; (A.T.N.); (M.S.M.); (Y.A.); (J.H.); (A.M.S.); (E.H.)
- The Pacific Community (SPC), Private Mail Bag, Suva, Fiji
| | - Ermias Habte
- Feed and Forage Development Program, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia; (A.T.N.); (M.S.M.); (Y.A.); (J.H.); (A.M.S.); (E.H.)
| | - Chris S. Jones
- Feed and Forage Development Program, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia; (A.T.N.); (M.S.M.); (Y.A.); (J.H.); (A.M.S.); (E.H.)
- Feed and Forage Development Program, International Livestock Research Institute, Nairobi 00100, Kenya
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Andersen JC, Havill NP, Caccone A, Elkinton JS. Four times out of Europe: Serial invasions of the winter moth, Operophtera brumata, to North America. Mol Ecol 2021; 30:3439-3452. [PMID: 34033202 DOI: 10.1111/mec.15983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 11/30/2022]
Abstract
Reconstructing the geographic origins of non-native species is important for studying the factors that influence invasion success, however; these analyses can be constrained by the amount of diversity present in the native and invaded regions, and by changes in the genetic background of the invading population following bottlenecks and/or hybridization events. Here we explore the geographical origins of the invasive winter moth (Operopthera brumata L.) that has caused widespread defoliation to forests, orchards, and crops in Nova Scotia, British Columbia, Oregon, and the northeastern United States. It is not known whether these represent independent introductions to North America, or a "stepping stone" spread among regions. Using a combination of Bayesian assignment and approximate Bayesian computation methods, we analysed a population genetic data set of 24 microsatellite loci. We estimate that winter moth was introduced to North America on at least four occasions, with the Nova Scotian and British Columbian populations probably being introduced from France and Sweden, respectively; the Oregonian population probably being introduced from either the British Isles or northern Fennoscandia; and the population in the northeastern United States probably being introduced from somewhere in Central Europe. We discuss the impact of genetic bottlenecks on analyses meant to determine region of origin.
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Affiliation(s)
- Jeremy C Andersen
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
| | - Nathan P Havill
- Northern Research Station, USDA Forest Service, Hamden, CT, USA
| | - Adalgisa Caccone
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Joseph S Elkinton
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
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Halewood M, Jamora N, Noriega IL, Anglin NL, Wenzl P, Payne T, Ndjiondjop MN, Guarino L, Kumar PL, Yazbek M, Muchugi A, Azevedo V, Tchamba M, Jones CS, Venuprasad R, Roux N, Rojas E, Lusty C. Germplasm Acquisition and Distribution by CGIAR Genebanks. PLANTS 2020; 9:plants9101296. [PMID: 33019539 PMCID: PMC7601315 DOI: 10.3390/plants9101296] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/03/2020] [Accepted: 09/10/2020] [Indexed: 12/22/2022]
Abstract
The international collections of plant genetic resources for food and agriculture (PGRFA) hosted by 11 CGIAR Centers are important components of the United Nations Food and Agriculture Organization's global system of conservation and use of PGRFA. They also play an important supportive role in realizing Target 2.5 of the Sustainable Development Goals. This paper analyzes CGIAR genebanks' trends in acquiring and distributing PGRFA over the last 35 years, with a particular focus on the last decade. The paper highlights a number of factors influencing the Centers' acquisition of new PGRFA to include in the international collections, including increased capacity to analyze gaps in those collections and precisely target new collecting missions, availability of financial resources, and the state of international and national access and benefit-sharing laws and phytosanitary regulations. Factors contributing to Centers' distributions of PGRFA included the extent of accession-level information, users' capacity to identify the materials they want, and policies. The genebanks' rates of both acquisition and distribution increased over the last decade. The paper ends on a cautionary note concerning the potential of unresolved tensions regarding access and benefit sharing and digital genomic sequence information to undermine international cooperation to conserve and use PGRFA.
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Affiliation(s)
- Michael Halewood
- Alliance of Bioversity International and the International Center for Tropical Agriculture (Alliance of Bioversity and CIAT), Via dei Tre Denari 472/a, 00057 Maccarese (Fiumicino) Rome, Italy; (I.L.N.); (P.W.); (N.R.)
- Correspondence:
| | - Nelissa Jamora
- Global Crop Diversity Trust (Crop Trust), Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (N.J.); (L.G.); (C.L.)
| | - Isabel Lopez Noriega
- Alliance of Bioversity International and the International Center for Tropical Agriculture (Alliance of Bioversity and CIAT), Via dei Tre Denari 472/a, 00057 Maccarese (Fiumicino) Rome, Italy; (I.L.N.); (P.W.); (N.R.)
| | - Noelle L. Anglin
- International Potato Center (CIP), Av. La Molina 1895, La Molina Apartado 1558, Lima 12, Peru; (N.L.A.); (E.R.)
| | - Peter Wenzl
- Alliance of Bioversity International and the International Center for Tropical Agriculture (Alliance of Bioversity and CIAT), Via dei Tre Denari 472/a, 00057 Maccarese (Fiumicino) Rome, Italy; (I.L.N.); (P.W.); (N.R.)
| | - Thomas Payne
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600 Mexico, D.F., Mexico;
| | | | - Luigi Guarino
- Global Crop Diversity Trust (Crop Trust), Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (N.J.); (L.G.); (C.L.)
| | - P. Lava Kumar
- International Institute for Tropical Agriculture (IITA), PMB 5320, Ibadan 200001, Oyo State, Nigeria; (P.L.K.); (M.T.)
| | - Mariana Yazbek
- International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 114/5055, Beirut, Lebanon;
| | - Alice Muchugi
- World Agroforestry (ICRAF), Box 30677, Nairobi 00100, Kenya;
| | - Vania Azevedo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana State, India;
| | - Marimagne Tchamba
- International Institute for Tropical Agriculture (IITA), PMB 5320, Ibadan 200001, Oyo State, Nigeria; (P.L.K.); (M.T.)
| | - Chris S. Jones
- International Livestock Research Institute (ILRI), Box 30709, Nairobi 00100, Kenya;
| | - Ramaiah Venuprasad
- International Rice Research Institute (IRRI), Los Baños 4030, Laguna, Philippines;
| | - Nicolas Roux
- Alliance of Bioversity International and the International Center for Tropical Agriculture (Alliance of Bioversity and CIAT), Via dei Tre Denari 472/a, 00057 Maccarese (Fiumicino) Rome, Italy; (I.L.N.); (P.W.); (N.R.)
| | - Edwin Rojas
- International Potato Center (CIP), Av. La Molina 1895, La Molina Apartado 1558, Lima 12, Peru; (N.L.A.); (E.R.)
| | - Charlotte Lusty
- Global Crop Diversity Trust (Crop Trust), Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (N.J.); (L.G.); (C.L.)
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