ILRI forage genebank:Team-wide outputs

Permanent URI for this collectionhttps://hdl.handle.net/10568/658

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Overview of ILRI Forage Genebank
(Presentation, 2024-05-15) Negawo, Alemayehu T.
Reverse Transcriptase Loop-Mediated Isothermal Amplification Assays (RTLAMP) for the Detection of Alfalfa Mosaic Virus from Forage Crops
(Journal Article, 2023-09-29) Dawit, Woubit; Mulatu, Fikerte; Eshete, Yesuf; Negawo, Alemayehu T.; Muchugi, Alice; Jones, Christopher S.
AMV is one of the most economically important plant viruses and has a very wide host range including forage crops. To make sure that only seeds of satisfactory phytosanitary status are distributed to recipients in geographically diverse areas, the ILRI genebank routinely monitors seed-borne diseases during seed multiplication and in the field genebank. Current detection techniques for AMV include a dot-blot assay and a two-step Reverse Transcription Polymerase Chain Reaction (RT-PCR), both of which are time consuming. In the present study we developed a one step Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) method for the sensitive and rapid detection of AMV from forage crops. For the assay, six different AMV specific primers were used, and a series of reactions were performed to identify optimal conditions. Amplicons were easily visualized by means of an in-tube colour indicator (SYBR Green I dye) with no requirement to run gel electrophoresis. The sensitivity of the RT-LAMP assay was assessed by comparing the optimized AMV RT-LAMP assay with the conventional RT-PCR. In RT-LAMP, an amplicon was generated up to 100 ag/μl dilutions in contrast to the conventional RT-PCR, where no amplification at 1 fg/μl and onwards, indicating that the detection limit of the AMV RT-LAMP assay is much lower than for the conventional RT-PCR. Finally, the optimized RT-LAMP assay was further validated on 40 field samples of different forage species and other important forage viruses. The developed RT-LAMP assay was specific and detected AMV from different forages with no cross reaction with other plant viruses (SBMV and potyvirus) tested in the ILRI-genebank seed multiplication/regeneration fields. The optimized RT-LAMP assay is an effective tool for the detection of AMV for field samples in diagnostic laboratories, and for quarantine applications.
Evaluation of in situ and ex situ forage germplasm collections reveals the first detection of Alfalfa Mosaic Virus (AMV) and Southern Bean Mosaic Virus (SBMV) in Urochloa spp.
(Poster, 2023-08-20) Dawit, Woubit; Mulatu, Fikerte; Eshete, Yesuf; Negawo, Alemayehu T.; Muchugi, Alice; Jones, Christopher S.
CGIAR germplasm health units apply a systems approach to germplasm seed health protection for conservation and safe international distribution
(Conference Paper, 2023-08-21) Kumar, Lava; Alakonya, Amos; Castellion, Martina; Cuervo, Maritza; Dawit, Woubit; Kreuze, Jan; Kumari, Safaa; Massart, S.; Beatriz Muller Cadenillas, Giovanna; Onaga, Geoffrey
Germplasm seed exchange from CGIAR genebanks and breeding is important to global agricultural research and development programs. Seed as a pathway for pest spread is an inherent risk for international seed exchanges. Phytosanitary controls have been established in accordance with the International Plant Protection Convention (IPPC) to protect global plant health from transboundary pest invasion. This presentation summarizes pest risks to international germplasm distribution; CGIAR Germplasm Health Units (GHUs) procedures to ensure the production and distribution of pest-free germplasm; bottlenecks to germplasm distribution, including the inadequacy of phytosanitary regulations guided by the International Standards for Phytosanitary Measures (ISPMs) of IPPC; and consequences of delayed germplasm access on crop improvement programs. It also presents the ‘CGIAR Greenpass Phytosanitary Protocol (CGPP)’ concept as a comprehensive phytosanitary compliance assurance procedure. Based on a systems approach of pest risk identification and pest risk mitigation in the germplasm seed production pipeline and the rigorous implementation of phytosanitary controls in collaboration with national plant protection organizations, the CGPP is expected to fast-track pest-free germplasm distribution to the global community.
Key descriptors for forage grasses
(Book, 2023) Muchugi, Alice; Hanson, Jean; González-Guzmán, J.J; Habte, Ermias; Sime, Yonas; Alercia, Adriana Raquel; Cerutti, Ana Laura; López, Francisco
The key descriptors for forage grasses consist of an initial minimum set of characterization and evaluation descriptors for some species of the family Poaceae. Grasses belong to the plant family Poaceae and many of the important forage grass genera have similar morphology, making it possible to suggest a common set of descriptors that can be used for describing diversity within multiple species. Despite similarities, grasses show diversity in morphology, productivity, feed quality and their response to drought and cold, even within the same species. These general forage grass descriptors are limited to tropical species with specific examples from Andropogon gayanus, Bothriochloa pertusa, Cenchrus ciliaris, Cenchrus clandestinus, Cenchrus purpureus, Chloris gayana, Cynodon dactylon, Cynodon nlemfuensis, Digitaria eriantha, Megathrysus maximus, Melinis minutiflora, Panicum coloratum, Paspalum dilatatum, Paspalum plicatulum, Setaria sphacelata, Sorghum x almum, Tripsacum laxum, Urochloa brizantha, Urochloa decumbens and Urochloa ruziziensis. These are all grasses that are already being adopted by smallholder farmers worldwide.
Overcoming dormancy in Desmanthus virgatu seeds for improved viability monitoring protocols of genebank accessions
(Journal Article, 2023-10-16) Olbana, Tamiru; Muchugi, Alice; Woldemariam, Yeshi; Hay, Fiona R.; Ndiwa, Nicholas; Jones, Christopher S.
Desmanthus virgatus is a perennial forage legume used as a livestock feed source. Seeds of this species are physically dormant and thus, propagation is difficult. The dormancy also impacts the routine viability monitoring of genebank accessions. The present study investigated different methods to break dormancy in seeds collected from various locations at different times. The result showed that most pre-treatments significantly increased germination percentage. Accessions treated with concentrated sulphuric acid (25 or 30 minutes) followed by sandpaper scarification showed the highest proportion of normal seedlings (94.6 and 96%). Boiling water (2.3 or 3 minutes) was also effective in all accessions except for accession 331. However, accessions treated with hot water (3, 5 or 8 minutes) had a considerable proportion of hard seeds. The proportion of dead/abnormal seedlings was high in seeds treated with a hot wire in all accessions, ranging from 27.5 (accession 15489) to 75.5% (accession 16). The untreated seeds remained hard at the final germination count. We conclude that it is important to use concentrated sulphuric acid and mechanical scarification with sandpaper to break the dormancy for the species to enhance germination, obtain uniform field stands and make wise decisions during storage.
Assessment of duplicates in a perennial soybean (Neonotonia wightii) collection
(Poster, 2023-09-20) Negawo, Alemayehu T.; Demeke, Alemayehu; Gashaw, Michael; Muktar, Meki S.; Muchugi, Alice; Sartie, Alieu; Jones, Christopher S.
The potential of tropical forage species maintained in the ILRI-forage genebank for sustainable agriculture and food-security
(Poster, 2023-09-20) Muktar, Meki S.; Negawo, Alemayehu T.; Muchugi, Alice; Jones, Christopher S.
Assessing the impact of continued regeneration on accession’s genetic integrity
(Poster, 2023-09-20) Negawo, Alemayehu T.; Muktar, Meki S.; Jones, Christopher S.; Muchugi, Alice
Analysis of global Napier grass (Cenchrus purpureus) collections reveals high genetic diversity among genotypes with some redundancy between collections
(Journal Article, 2023) Muktar, Meki S.; Bizuneh, T.; Anderson, W.; Assefa, Yilikal; Negawo, Alemayehu T.; Teshome, Abel; Habte, Ermias; Muchugi, Alice; Feyissa, T.; Jones, Christopher S.
Genetic diversity amongst genotypes of several Napier grass collections was analyzed and compared with the diversity in a set of open pollinated progeny plants. A total of 114,881 SNP and 46,293 SilicoDArT genome-wide markers were generated on 574 Napier grass genotypes. Of these, 86% of the SNP and 66% of the SilicoDArT markers were mapped onto the fourteen chromosomes of the Napier grass genome. For genetic diversity analysis, a subset of highly polymorphic and informative SNP markers was filtered using genomic position information, a maximum of 10% missing values, a minimum minor allele frequency of 5%, and a maximum linkage-disequilibrium value of 0.5. Extensive genetic variation, with an average Nei’s genetic distance value of 0.23, was identified in the material. The genotypes clustered into three major and eleven sub-clusters with high levels of genetic variation contained both within (54%) and between (46%) clusters. However, we found that there was low to moderate genetic differentiation among the collections and that some overlap and redundancy occurred between collections. The progeny plants were genetically diverse and divergent from the germplasm collections, with an average FST value of 0.08. We also reported QTL regions associated with forage biomass yield based on field phenotype data measured on a subset of the Napier grass collections. The findings of this study offer useful information for Napier grass breeding strategies, enhancement of genetic diversity, and provide a guide for the management and conservation of the collections.
Key descriptors for fodder trees
(Book, 2023-06-20) Muchugi, Alice; Hanson, Jean; Habte, Ermias; Sime, Yonas; Alemayehu, Arega; Alercia, Adriana Raquel; Cerutti, Ana Laura; López, Francisco
The Key descriptors for fodder trees consist of an initial minimum set of characterization and evaluation descriptors for some species of the family Fabaceae (Leguminosae). This strategic set aims at facilitating access to and utilization of these species and it does not exclude the addition of other descriptors later. This work has been done jointly with the International Livestock Research Institute (ILRI) and the FAO International Treaty on Plant Genetic Resources for Food and Agriculture. The list was based on a preliminary set of descriptors developed by ILRI. In addition, internet searches were carried out looking for the most updated information on relevant characteristics and traits. The original list was subsequently integrated with evaluation traits. Special attention was given to the inclusion of descriptors relevant to germplasm utilization and abiotic stresses of particular importance in the context of emerging adverse weather events, which are expected to intensify under current and future climate challenges. The key set of access and utilization descriptors was defined through an online survey, in which 24 experts from 14 different organizations and universities from 13 countries participated. Survey results were subsequently validated in consultation with a Core Advisory Group (see “Contributors”) led by Alice Muchugi and Jean Hanson from ILRI. The strategic set of data standards is designed to facilitate access to and utilization of plant genetic resources for food and agriculture. Together with passport information (Alercia et al. 2015, 2018), descriptors are critical to the effective sharing of characterization and evaluation data and to the efficient use of plant genetic resources for food and agriculture.
Methods and practices for the evaluation of forage legumes, grasses and fodder trees for use as livestock feeds
(Manual, 2023-04-15) Teshome, Abel; Habte, Ermias; Negawo, Alemayehu T.; Muktar, Meki S.; Assefa, Yilikal; Jones, Christopher S.
Key descriptors for forage legumes
(Book, 2023-03-09) Muchugi, Alice; Hanson, Jean; Habte, Ermias; Sime, Yonas; Alemayehu, Arega; Alercia, Adriana Raquel; Cerutti, Ana Laura; López, Francisco
Report of the global online survey to identify key knowledge and capacity gaps on diagnostics and surveillance of pests & diseases in targeted countries
(Report, 2022-12-23) Carvajal-Yepes, Mónica; Cuervo, Maritza; Kreuze, Jan F.; Alakonya, Amos; Kumar, P. Lava; Onaga, Geoffrey; Dawit, Woubit; Castillon, Martina; Kumari, Safaa; Sharma, Rajan; Kawarazuka, Nozomi; Bui, Trang; Johnson, Vincent
An online survey was co-designed in collaboration with CGIAR Germplasm Health Units (GHUs) leaders and social scientists of the Plant Health Initiative (PHI), with the objective to identify and map the key knowledge and capacity gaps on lab/field detection, characterization, and surveillance of P&D of local and regional NPPOs in targeted countries. The questionnaire consisted of 43 open-ended, single and multiple-choice questions. It was divided into three parts: the first includes questions to collect general information (Institution, country, gender, age group, position, scientific level and role). The second part was aimed to learn and identify current capacities, major challenges, capacity building needs of National Plant Protection Organizations (NPPOs) for pest diagnostics and surveillance. The third part was related to specific questions for early- and mid-career scientists (below 45 years old) to inquire into challenges faced by young and women scientists to identify gender-based constraints. The questionnaire was translated into five different languages (English, Arabic, Spanish, French and Vietnamese), and distributed to NPPOs and national institutions across Latin America and the Caribbean (LAC), Africa, Asia and Central and West Asia and North Africa (CWANA). The report summarizes responses from 52 respondents from 35 institutions across 26 countries.
Genetic Diversity, Population Structure and Subset Development in a Sesbania sesban Collection
(Journal Article, 2022-12-20) Negawo, Alemayehu T.; Akinmade, Habib Olumide; Muktar, Meki S.; Habte, Ermias; Assefa, Yilikal; Muchugi, Alice; Sartie, Alieu; Jones, Christopher S.
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.
Fruit Trees in agroforestry systems: complementing globally traded commodities with local nutritional benefits
(Book Chapter, 2022-04-21) Noordwijk, Meine van; Hendre, Prasad; Kindt, Roeland; McMullin, Stepha; Muchugi, Alice; Tchoundjeu, Zacharie; Tsobeng, Alain; Jamnadass, Ramni
Commodity tree crop planting material infrastructures in Africa
(Book Chapter, 2022) Muchugi, Alice; Kalinganire, Antoine; Chege, Christine Gacheri Kiria; Nyoka, Isaac
State of ex situ conservation of landrace groups of 25 major crops
(Journal Article, 2022-05) Ramírez Villegas, Julián Armando; Khoury, Colin K.; Achicanoy Estrella, Harold Armando; Díaz, Maria Victoria; Mendez Alzate, Andres Camilo; Sosa, Chrystian C.; Kehel, Zakaria; Guarino, Luigi; Abberton, Michael T.; Aunario, Jorrel; Al Awar, Bashir; Alarcón, Juan Carlos; Amri, Ahmed; Anglin, Noelle L.; Azevedo, Vania; Aziz, Khadija; Capilit, Grace Lee; Chavez, Oswaldo; Chebotarov, Dmytro; Costich, Denise E.; Debouck, Daniel G.; Ellis, David; Falalou, Hamidou; Fiu, Albert; Ghanem, Michel Edmond; Giovannini, Peter; Goungoulou, Alphonse J.; Gueye, Badara; El Hobyb, Amal Ibn; Jamnadass, Ramni; Jones, Christopher S.; Kpeki, Bienvenu; Lee, Jae-Sung; McNally, Kenneth L.; Muchugi, Alice; Ndjiondjop, Marie-Noelle; Oyatomi, Olaniyi; Payne, Thomas S.; Ramachandran, Senthil; Rossel, Genoveva; Roux, Nicolas Stephan M.; Ruas, Max; Sansaloni, Carolina P.; Sardos, Julie; Setiyono, Tri Deri; Tchamba, Marimagne; Houwe, Ines van den; Velazquez, J. Alejandro; Venuprasad, Ramaiah; Wenzl, Peter; Yazbek, Mariana; Zavala, Cristian
Crop landraces have unique local agroecological and societal functions and offer important genetic resources for plant breeding. Recognition of the value of landrace diversity and concern about its erosion on farms have led to sustained efforts to establish ex situ collections worldwide. The degree to which these efforts have succeeded in conserving landraces has not been comprehensively assessed. Here we modelled the potential distributions of eco-geographically distinguishable groups of landraces of 25 cereal, pulse and starchy root/tuber/fruit crops within their geographic regions of diversity. We then analysed the extent to which these landrace groups are represented in genebank collections, using geographic and ecological coverage metrics as a proxy for genetic diversity. We find that ex situ conservation of landrace groups is currently moderately comprehensive on average, with substantial variation among crops; a mean of 63% ± 12.6% of distributions is currently represented in genebanks. Breadfruit, bananas and plantains, lentils, common beans, chickpeas, barley and bread wheat landrace groups are among the most fully represented, whereas the largest conservation gaps persist for pearl millet, yams, finger millet, groundnut, potatoes and peas. Geographic regions prioritized for further collection of landrace groups for ex situ conservation include South Asia, the Mediterranean and West Asia, Mesoamerica, sub-Saharan Africa, the Andean mountains of South America and Central to East Asia. With further progress to fill these gaps, a high degree of representation of landrace group diversity in genebanks is feasible globally, thus fulfilling international targets for their ex situ conservation.
Chromosome evolution and the genetic basis of agronomically important traits in greater yam
(Journal Article, 2022-04-14) Bredeson, J.V.; Lyons, J.B.; Oniyinde, I.O.; Okereke, N.R.; Kolade, O.; Nnabue, I.; Nwadili, C.O.; Hřibová, E.; Parker, M.; Nwogha, J.; Shu, S.; Carlson, J.; Kariba, R.; Muthemba, S.; Knop, K.; Barton, G.J.; Sherwood, A.V.; López Montes, A.; Asiedu, R.; Jamnadass, Ramni; Muchugi, A.; Goodstein, D.; Egesi, Chiedozie N.; Featherston, J.; Asfaw, A.; Simpson, G.G.; Doležel, J.; Hendre, P.S.; Deynze, A. van; Kumar, P. Lava; Obidiegwu, J.E.; Bhattacharjee, Ranjana; Rokhsar, D.S.
The nutrient-rich tubers of the greater yam Dioscorea alata L. provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an “orphan crop.” Here we address this resource gap by presenting a highly-contiguous chromosome-scale genome assembly of greater yam combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient lineage-specific genome duplication, followed by extensive genome-wide reorganization. Using our new genomic tools we find quantitative trait loci for susceptibility to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments.
Key descriptors for Docynia indica (Wall.) Decne
(Report, 2021-12-21) Muchugi, Alice; Pham Huu Thuong; Alercia, Adriana; Hai Phi Hong; Hendre, P.; Jamnadass, Ramni; Cerutti, A.L.; Cognetti de Martiis, S.; López, F.

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