CGIAR Initiative on Breeding Resources

Permanent URI for this collectionhttps://hdl.handle.net/10568/117899

Part of the CGIAR Action Area on Genetic Innovation.

Primary CGIAR impact area: Poverty reduction, livelihoods and jobs

https://www.cgiar.org/initiative/04-enabling-tools-technology-and-services-for-genetic-gains/

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    Directives techniques pour les transferts sécurisés de matériel génétique de cacaoyer. Révision des directives techniques FAO/IPGRI No. 20 (Cinquième édition, 2024)
    (Book, 2024-10-10) End, Michelle J.; Daymond, Andrew J.; Hadley, Paul
    Les directives techniques de CacaoNet pour les transferts sécurisés de matériel génétique de cacaoyer fournissent des informations actualisées sur les précautions et les mesures de quarantaine qui peuvent être prises pour minimiser le risque de propagation des parasites et des maladies lorsque les ressources génétiques du cacao sont déplacées pour la recherche, l'amélioration des cultures, la sélection végétale, l'exploration ou la conservation. Ces directives sont basées sur celles publiées pour la dernière fois par la FAO/IPGRI en 1999, mais ont été révisées et élargies par un groupe d'experts mis en place au sein de CacaoNet (le Réseau mondial des ressources génétiques du cacao coordonné par Bioversity International), afin de tenir compte des nouvelles connaissances sur les ravageurs et les maladies, y compris leur distribution actuelle, et des progrès des techniques de détection. Ces directives techniques de CacaoNet ont été publiées en ligne pour la première fois en 2012, mais ont été révisées en 2014, en 2017 et maintenant en 2021 pour tenir compte des nouvelles informations reçues. Le document comprend des conseils généraux concernant les procédures sûres à utiliser lors du transfert de matériel génétique de cacao, qu'il s'agisse de graines, de matériel végétatif ou de tissus, ainsi que des informations résumées sur la propagation géographique et les risques posés par les principaux ravageurs et maladies du cacao. En outre, des experts ont contribué à des sections donnant des informations détaillées sur les points suivants : Les maladies virales (virus de la nécrose du cacao, Virus de l’œdème des pousses du cacaoyer : genre Badnavirus (CSSV), virus de la mosaïque jaune du cacao), les maladies fongiques (balai de sorcière, pourriture des cabosses par Moniliophthora, pourriture des cabosses par Phytophthora, dépérissement des stries vasculaires, flétrissement par Verticillium, flétrissement par Ceratocystis, pourriture des racines par Rosellinia), les insectes nuisibles (foreur des cabosses du cacao, mirides/capsides, punaise des moustiques, autres insectes nuisibles) et les nématodes. Chaque section contient des informations sur les symptômes physiques, la distribution géographique, la biologie du ravageur ou de la maladie et les mesures de quarantaine recommandées. La publication de ces directives a été soutenue par des contributions financières et en nature de Bioversity International, du Programme de recherche du CGIAR sur les forêts, les arbres et l'agroforesterie, de la Cocoa Research Association Ltd, UK (CRA Ltd, une organisation basée au Royaume-Uni qui gère la recherche scientifique sur le cacao au nom de Mars Mondelēz International et du London Cocoa Trade (ICE Fuitures Europe) et de l'Université de Reading. CacaoNet a reçu un soutien financier supplémentaire de Mars, du service de recherche agricole du ministère américain de l'agriculture (USDA/ARS) et de la World Cocoa Foundation (WCF).
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    Directrices técnicas para el movimiento seguro del germoplasma de cacao. Versión revisada de las Directrices técnicas de FAO/IPGRI No. 20 (Quinta actualización, 2024)
    (Book, 2024-10-10) End, Michelle J.; Daymond, Andrew J.; Hadley, Paul
    Las Directrices Técnicas de CacaoNet para el Movimiento Seguro del Germoplasma de Cacao ofrecen información actualizada sobre las precauciones y las medidas de cuarentena que pueden adoptarse para minimizar el riesgo de propagación de plagas y enfermedades cuando los recursos genéticos del cacao se trasladan para la investigación, la mejora de los cultivos, el fitomejoramiento, la exploración o la conservación. Estas directrices se basan en las publicadas por última vez por la FAO/IPGRI en 1999, pero han sido revisadas y ampliadas por un grupo de expertos creado en el seno de CacaoNet (la Red Mundial de Recursos Genéticos del Cacao coordinada por Bioversity International), para tener en cuenta los nuevos conocimientos sobre plagas y enfermedades, incluida su distribución actual, y los avances en las técnicas de detección. Estas directrices técnicas de CacaoNet se publicaron por primera vez en línea en 2012, pero se revisaron en 2014, 2017 y ahora en 2021 para tener en cuenta la nueva información recibida. El documento incluye consejos generales sobre los procedimientos seguros que deben emplearse al transferir germoplasma de cacao, ya sean semillas, material vegetativo o tejidos, así como información resumida sobre la propagación geográfica y los riesgos que plantean las principales plagas y enfermedades del cacao. Además, los expertos han aportado secciones con información detallada sobre Enfermedades víricas (virus de la necrosis del cacao, virus del edema de los brotes del cacao : (CSSV), el virus del mosaico amarillo del cacao), enfermedades fúngicas (escoba de bruja, podredumbre de la vaina por Moniliophthora, podredumbre de la vaina por Phytophthora, podredumbre de la raya vascular, Verticillium wilt, Ceratocystis wilt, Rosellinia root rot), plagas de insectos (barrenador de la vaina del cacao, miriñaques/cápsulas, mosquitos, otras plagas de insectos) y nematodos. Cada sección contiene información sobre los síntomas físicos, la distribución geográfica, la biología de la plaga o enfermedad y las medidas de cuarentena recomendadas. La publicación de estas directrices ha contado con el apoyo financiero y en especie de Bioversity International, el Programa de Investigación sobre Bosques, Árboles y Agroforestería del CGIAR, la Cocoa Research Association Ltd, UK (CRA Ltd, una organización con sede en el Reino Unido que gestiona la investigación científica sobre el cacao en nombre de Mars, Mondelēz International y la London Cocoa Trade (ICE Futures Europe) y la Universidad de Reading. CacaoNet ha recibido apoyo financiero adicional de Mars, el Servicio de Investigación Agrícola del Departamento de Agricultura de Estados Unidos (USDA/ARS) y la World Cocoa Foundation (WCF).
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    Stacking beneficial haplotypes from the Vavilov wheat collection to accelerate breeding for multiple disease resistance
    (Journal Article, 2024) Jingyang Tong; Tarekegn, Zerihun T.; Jambuthenne, Dilani; Alahmad, Samir; Periyannan, Sambasivam; Lee T. Hickey; Dinglasan, Eric; Hayes, Ben
    Wheat production is threatened by numerous fungal diseases, but the potential to breed for multiple disease resistance (MDR) mechanisms is yet to be explored. Here, significant global genetic correlations and underlying local genomic regions were identified in the Vavilov wheat diversity panel for six major fungal diseases, including biotrophic leaf rust (LR), yellow rust (YR), stem rust (SR), hemibiotrophic crown rot (CR), and necrotrophic tan spot (TS) and Septoria nodorum blotch (SNB). By adopting haplotype-based local genomic estimated breeding values, derived from an integrated set of 34,899 SNP and DArT markers, we established a novel haplotype catalogue for resistance to the six diseases in over 20 field experiments across Australia and Ethiopia. Haploblocks with high variances of haplotype effects in all environments were identified for three rusts, and pleiotropic haploblocks were identified for at least two diseases, with four haploblocks affecting all six diseases. Through simulation, we demonstrated that stacking optimal haplotypes for one disease could improve resistance substantially, but indirectly affected resistance for other five diseases, which varied depending on the genetic correlation with the non-target disease trait. On the other hand, our simulation results combining beneficial haplotypes for all diseases increased resistance to LR, YR, SR, CR, TS, and SNB, by up to 48.1%, 35.2%, 29.1%, 12.8%, 18.8%, and 32.8%, respectively. Overall, our results highlight the genetic potential to improve MDR in wheat. The haploblock-based catalogue with novel forms of resistance provides a useful resource to guide desirable haplotype stacking for breeding future wheat cultivars with MDR.
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    Modèle conceptuel de prévision du prix du bétail : Étude de cas du sénégal
    (Report, 2024-12-23) Edorh, Theophile; Thiaw, Moussa; Houessionon, Prosper; Worou, Nadine; Wane, Abdrahmane
    L'élevage est un pilier de l'économie sénégalaise, jouant un rôle essentiel dans la sécurité alimentaire, la réduction de la pauvreté et la résilience face aux crises climatiques et économiques. Cependant, les fluctuations des prix du bétail représentent un défi majeur pour les éleveurs, les commerçants et les décideurs. Ce rapport présente un modèle conceptuel de prévision des prix du bétail au Sénégal, en se focalisant sur les boeufs de plus de 6 ans. En utilisant la décomposition en ondelettes discrètes et le modèle ARIMA (WAV-ARIMA), les résultats montrent une amélioration significative de la précision des prévisions, en excluant la composante détaillée considérée comme du bruit. Cette méthodologie hybride, inspirée d'études précédentes, offre un outil efficace pour anticiper les tendances des prix et réduire l'incertitude. Les implications pour les éleveurs, les chercheurs et les décideurs incluent la mise en œuvre de stratégies adaptées, telles que l'alignement sur les pics saisonniers de demande, l'amélioration des infrastructures et l'intégration de données supplémentaires pour affiner les modèles. En vue d'une gestion optimale du secteur, des recommandations sont formulées pour renforcer les capacités des éleveurs, stabiliser les marchés et développer des prévisions hebdomadaires basées sur des données collectées régulièrement. Ce travail constitue une base pour des recherches futures sur l'adaptation aux changements climatiques et la résilience économique des filières d'élevage.
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    Genomic analysis of modern maize inbred lines reveals diversity and selective breeding effects
    (Journal Article, 2024) Kaijian Fan; Ali, Mohsin; Kunhui He; Yingwei Feng; Tingxi Yu; Hao Zhang; Tai An; Weiwei Zeng; Junjie Fu; Ying Zhou; Yanfang Heng; Fei Gu; Jiankang Wang; Changling Huang; Liang Li; Huihui Li
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    Technical Guidelines for the Safe Movement of Cacao Germplasm. Revised from the FAO/IPGRI Technical Guidelines No. 20 (Fifth Update 2024)
    (Book, 2024-10-10) End, Michelle J.; Daymond, Andrew J.; Hadley, Paul
    The CacaoNet Technical Guidelines for the Safe Movement of Cacao Germplasm provide updated information on the precautions and quarantine measures that can be taken to minimise the risk of spread of pests and diseases when cacao genetic resources are being moved for research, crop improvement, plant breeding, exploration or conservation. These Guidelines are based on those last published by FAO/IPGRI in 1999 but have been revised and expanded by a group of experts set up within CacaoNet (the Global Cacao Genetic Resources Network coordinated by Bioversity International), to take account of new knowledge of the pests and diseases, including their current distribution, and advances in detection techniques. These CacaoNet Guidelines were first published on-line in 2012 but have been revised in 2014, 2017, 2021 and now 2024 to take account of new information received. The document includes general advice regarding safe procedures to use when moving cacao germplasm, whether as seed, vegetative and tissue cultured materials, and summarised information on the geographical spread and risks posed by significant pests and diseases of cacao. In addition, experts have contributed sections giving detailed information on the following: Virus diseases (Cacao necrosis virus, Cacao swollen shoot virus (CSSV) and other Badna viruses, Cacao Yellow mosaic virus), Fungal diseases (Witches’ broom disease, Moniliophthora pod rot, Phytophthora pod rot, Vascular streak die-back, Verticillium wilt, Ceratocystis wilt, Rosellinia root rot), Insect pests (Cocoa pod borer, mirids/capsids, mosquito bug, other insect pests) and nematodes. Each section contains information on physical symptoms, geographical distribution, biology of the pest or disease and recommended quarantine measures. The publication of these Guidelines has been supported by financial and in-kind contributions from Bioversity International, the CGIAR Research Programme on Forests, Trees and Agroforestry, the Cocoa Research Association Ltd., UK (CRA Ltd., a UK-based organization managing scientific cocoa research on behalf of Mars Mondelēz International and the London Cocoa Trade (ICE Futures Europe) and the University of Reading. CacaoNet has received additional financial support from Mars, the U.S. Department of Agriculture, Agricultural Research Service (USDA/ARS) and the World Cocoa Foundation (WCF).
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    Policy dimension for promoting inter and intra‑varietal diversity and evolutionary crop populations
    (Journal Article, 2024-09-09) Joshi, Bal Krishna; Neupane, Shree Prasad; Gauchan, Devendra; Ajaya, Karkee; Dipendra, Ayer Kumar; Mengistu, Dejene Kassahun
    The value of broad genetic base cultivars is often underestimated in the formal seed system, which primarily emphasizes uniform, monogenotyped varieties to ensure food security. To gather insights on the significance of farmer’s varieties, cultivar mixtures, and evolutionary populations, a comprehensive approach involving surveys, focus group discussions, interviews, field observation and literature reviews was undertaken. Current legal frameworks in seed systems and variety handling predominantly serve the interests of seed companies, breeders, and extension officials, with limited consideration for the needs and preferences of farmers. This results in farmer’s varieties, characterized by their high genetic variation, as well as cultivar mixtures and evolutionary populations, receiving limited support within the policy framework. These broad genetic base cultivars have been cultivated and preserved by farmers for generations and exhibit resilience to diverse environmental conditions. The formal seed system, which has gained prominence, has separated farmers from a crucial aspect of their agricultural heritage. It is now managed by government offices and private seed companies, necessitating financial contributions from farmers to participate in the seed system. To encourage the cultivation of site-specific varieties with substantial genetic diversity, there is a need to promote these varieties, whether registered or unregistered, through a legal framework that encompasses all agricultural produces, not solely seeds. Such a framework acknowledges the capacity of farmers to independently maintain and cultivate their seeds, contributing to the preservation of genetic diversity and sustainable agriculture.
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    Genetic innovation gender strategy
    (Brief, 2024) Ashby, Jacqueline A.; Polar, Vivian
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    CGIAR Research Initiative on Breeding Resources: Annual Technical Report 2023
    (Annual Report, 2024-04) CGIAR Initiative on Breeding Resources
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    Genetic innovation gender strategy
    (Report, 2024-04) Ashby, Jacqueline A.; Polar, Vivian; Bonaiuti, Enrico; Bikketti, E.; Belcher, B.
    The Gender Strategy developed by CGIAR aims to address gender inequality in the adoption and benefits of new crop varieties. Women are key producers, processors, and consumers of CGIAR's priority crops, yet their needs are often overlooked. The Strategy uses gender research to develop more attractive varieties that are adopted faster and have fair outcomes for both women and men. It outlines 6 priorities, including mapping gender differences, identifying gender-intentional varieties, and analyzing drivers of gender equality in seed access and use. The Strategy also emphasizes building partnerships and capacity to make CGIAR's breeding programs more gender-responsive, involving social scientists and engaging with gender-transformative organizations. The overarching goal is to ensure new varieties benefit increasing numbers of women and men, advancing gender equality.
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    Empowering breeding resources dynamic strategies for effective capacity building
    (Abstract, 2023) Garcia Oliveira, Ana Luisa; Musundire, Lennin; Eng Hwa Ng; Bohar, Rajaguru; Sneller, Clay; Das, Biswanath; Kehel, Zakaria; Alwee, Sharifah S. S.; Einarson, Stefan
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    Biofortification of tropical maize synthetics using markers
    (Abstract, 2023) Mengesha, Wende; Kebede, Dejene; Menkir, Abebe; Abe, Ayodeji; Garcia Oliveira, Ana Luisa; Gedil, Melaku
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    A mid-density single-nucleotide polymorphism panel for molecular applications in cowpea (Vigna unguiculata (L.) Walp)
    (Journal Article, 2024) Ongom, Patrick Obia; Fatokun, Christian; Togola, Abou; Garcia Oliveira, Ana Luisa; Eng Hwa Ng; Kilian, Andrzej; Lonardi, Stefano; Close, Timothy J.; Boukar, Ousmane
    Molecular markers are increasingly being deployed to accelerate genetic gain in crop plants. The objective of this study was to assess the potential of a mid-density genotyping panel for molecular applications in cowpea breeding. A core set of 2,602 targeted diversity array technology (DArTag) single-nucleotide polymorphisms (SNPs) was designed from an existing 51,128 Cowpea iSelect Consortium Array. The panel's usefulness was assessed using 376 genotypes from different populations of known genetic backgrounds. The panel was informative, with over 78% of SNPs exceeding a minor allele frequency of 0.20. The panel decoded three stratifications in the constituted population, as was expected. Linkage disequilibrium (LD) decay was correctly depicted as slower in a biparental subset than in other populations. A known flower and seed coat color gene region was located on chromosome Vu07, suggesting that the mid-density panel may be used to hypothesize genomic regions underlying target traits in cowpea. Unexpected heterozygosity was detected in some lines and highly among F-1 progenies, divulging the panel's potential application in germplasm purity and hybridity verification. The study unveils the potential of an excellent genomic resource that can be tapped to enhance the development of improved cowpea cultivars.
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    RNAseq of diverse spring wheat cultivars released during last 110 years
    (Journal Article, 2023) Maqbool, Saman; Naseer, Samar; Zahra, Nageen; Rasool, Fatima; Qayyum, Humaira; Majeed, Khawar; Jahanzaib, Muhammad; Sajjad, Muhammad; Fayyaz, Muhammad; Kashif Naeem, Muhammad; Ramzan Khan, Muhammad; Zhang, Hao; Rasheed, Awais; Li, Huihui
    Here, we performed RNA-seq based expression analysis of root and leaf tissues of a set of 24 historical spring wheat cultivars representing 110 years of temporal genetic variations. This huge 130 tissues RNAseq dataset was initially used to study expression pattern of 97 genes regulating root growth and development in wheat. Root system architecture (RSA) is an important target for breeding stress-resilient and high-yielding wheat cultivars under climatic fluctuations. However, root transcriptome analysis is usually obscured due to challenges in root research due to their below ground presence. We also validated the dataset by performing correlation analysis between expression of RSA related genes in roots and leaves with 25 root traits analyzed under varying moisture conditions and 10 yield-related traits. The Pearson’s correlation coefficients between root phenotypes and expression of root-specific genes varied from −0.72 to 0.78, and strong correlations with genes such as DRO1, TaMOR, ARF4, PIN1 was observed. The presented datasets have multiple uses such as a) studying the change in expression pattern of genes during time, b) differential expression of genes in two very important tissues of wheat i.e., leaf and roots, and c) studying customized expression of genes associated with important phenotypes in diverse wheat cultivars. The initial findings presented here provided key insights into understanding the transcriptomic basis of phenotypic variability of RSA in wheat cultivars.
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    CGIAR Initiative on Breeding Resources: Plan of Results and Budget 2024 (PORB)
    (Internal Document, 2024-02-05) CGIAR System Organization
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    Capacity building of National Agricultural Research System (NARES) partners on common bean breeding
    (Blog Post, 2023-07-18) Assefa, Teshale; Beebe, Steve; Amongi, Winnyfred; Odama, Roy; Nchanji, Eileen; Yao, Nasser; Mukankusi, Clare; Rubyogo, Jean Claude
    As part of Alliance/PABRA’s initiative to modernize bean breeding, technicians and scientist from the Pan African Bean Research Alliance (PABRA) targeted countries in Africa, were invited for a training on bean breeding with a gender lens. The main purpose of the training was to strengthen the capacity of 54 field technicians and scientists across 30 sub-Saharan countries for four days from May 15 to 18, 2023, in Arusha, Tanzania. The training was specially designed for PABRA member country technicians and scientists of the National Bean and Legume Breeding programs. Participants were trained on the importance of beans in the diet, genetic resources, Mendelian and quantitative segregation basics, how to combine traits in successful crosses, breeding methods, how genealogies are constructed, and the potential of interspecific crosses. Participants were also trained on Demand Led Breeding and Gender integration with respect to bean varietal improvement within the social and economic context.
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    Genomic selection project: Kukidhi mahitaji ya wakulima wa baadaye kwa aina ya maharagwe
    (Brochure, 2023-11-02) Mamo, Teshale Assefa; Nchanji, Eileen; Birachi, Eliud
    Ni kwa jinsi gani njia hii inayotumia maarifa ya genomic inaweza kuongeza uzalishaji wa mazao kwenye mashamba yanayomilikiwa na wanawake, wanaume, na yanayomilikiwa kwa pamoja katika mazingira tofauti?
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    New Drought-Tolerant Crops for Resilient Dryland Livelihoods
    (Blog Post, 2023-03-15) International Center for Agricultural Research in the Dry Areas
    An international collaboration of world-leading scientists led by ICARDA Morocco has delivered six ground-breaking new durum wheat and barley varieties tolerant to increasingly severe droughts ravaging the region.