CGIAR Initiative on Accelerated Breeding

Permanent URI for this collectionhttps://hdl.handle.net/10568/117883

Part of the CGIAR Action Area on Genetic Innovation

Primary CGIAR impact area: Nutrition, health and food security

https://www.cgiar.org/initiative/01-accelerated-breeding/

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Now showing 1 - 20 of 1469

TreeEyed: A QGIS plugin for tree monitoring in silvopastoral systems using state of the art AI models
(Journal Article, 2025-01-29) Ruiz-Hurtado, Andres Felipe; Bolaños, Juliana Perez; Arrechea-Castillo, Darwin Alexis; Cardoso, Juan Andres
Tree monitoring is a challenging task due to the labour-intensive and time-consuming data collection methods required. We present TreeEyed, a QGIS plugin designed to facilitate the monitoring of trees using remote sensing RGB imagery and artificial intelligence models. The plugin offers several tools including tree inference process for tree segmentation and detection. This tool was implemented to facilitate the manipulation and processing of Geographical Information System (GIS) data from different sources, allowing multi-resolution, variable extent, and generating results in a standard GIS format (georeferenced raster and vector). Additional options like postprocessing, dataset generation, and data validation are also incorporated.
Costing Report for CGIAR-NARES-SME - Southern Africa Maize Breeding Network Operations
(Report, 2024-12-30) Cairns, Jill; Chaingeni, Davison; Sinyinda, Lubasi; Yakaulani, Louis; Musundire, Lennin; Das, Biswanath
The report presents the findings from the costing analysis done for the Southern Africa maize breeding networks. It includes information about network members, market segments and associated areas, partner roles, estimated costs, and the network's Trait Product Profiles (TPP).
Costing Report for CGIAR-NARES-SME - East Africa Maize Breeding Network Operations
(Report, 2024-12-30) Das, Aparna; Teklewold, Adefris; Awalla, Boniface; Kwemoi, Daniel; Kyando, Aggrey; Biratu, Wakuma; Musundire, Lennin; Das, Biswanath
The report presents the findings from the costing analysis done for the East Africa maize breeding networks. It includes information about network members, market segments and associated areas, partner roles, estimated costs, and the network's Trait Product Profiles (TPP).
Private sector led multi-stakeholder platforms positively influence certified seed supply in Malawi
(Journal Article, 2024-08-24) Gondwe, Wanangwa; Phiri, Alexander; Birachi, Eliud; Magreta, Ruth; Larochelle, Catherine; Machira, Kennedy; Mutua, Mercy; Rubyogo, Jean Claude; Nkhata, Wilson
Common bean yields in Malawi remain low, primarily due to the use of low-yielding, recycled local seeds by most smallholder farmers. The low uptake of certified bean seed is attributed to limited incentives from the private sector. This study hypothesizes that the sustainable adoption of market-preferred varieties can be achieved by synchronizing and linking seed production to the grain market through committed value chain actors in a private sector-led multi-stakeholder platform. This paper examines the role of private sector-led multi-stakeholder platforms in the supply of certified common bean seed in Malawi. The research draws on both qualitative and quantitative primary data collected through a semi-structured questionnaire and interviews with key informants. Data were analyzed using an Ordinary Least Squares (OLS) regression model. The results indicate that several variables representing membership in multi-stakeholder platforms (MSPs) significantly affect the supply of certified common bean seed. Participation in MSPs, contractual arrangements, market structure, extension services, and seed demonstrations positively influenced seed supply. The findings underscore the need for a well-coordinated multi-stakeholder platform to enhance the supply of certified common bean seed, supported by effective policies and incentives from policymakers.
Interspecific urochloa breeding program: Technical report - A521
(Report, 2024-12) Mejia, Juan Camilo
The genetic gain of yield, seed yield, and nutritional quality in the interspecific Urochloa pipeline was estimated through an ERA trial conducted at the CIAT campus in Palmira, Colombia. Each trial included 150 genotypes from seven cycles of selection at different stages, along with genebank accessions and cultivars. The assessed traits were shoot dry weight (SDW), cover (calculated from drone images), seed gross yield (SGY), crude protein content (CP), neutral detergent fiber content (NDF), and acid detergent fiber content (ADF). For the genetic gain estimation, we used a two-stage approach, considering only the hybrids in stage 4, which were selected after multi-location trials in Latin America by the Papalotla Group company (PG). Genetic gain rates were positive for SGY, SDW, and CP. Conversely, NDF and ADF showed negative genetic gain values, as the objective of these traits is to reduce them by improving the percentage of protein content and enhancing nutritional quality of the crop.
Gendered value chains, market segmentation, and customer profiling for breeding programs
(Book Chapter, 2024-01-01) Katungi, Enid; Tufan, Hale Ann; Isoto, Rosemary
Unleashing strategies to mitigate methane emissions in rice fields and livestock system
(Journal Article, 2024-12-02) Joseph-Fernando, Ezhilmathi Angela; Selvaraj, Michael; Arango, Jacobo
Participatory plant breeding to develop biofortified upland rice for marginal environments
(Journal Article, 2024-10-29) Castro-Pacheco, Sergio Antonio; Rabekijana, Ravo; Andriamiarana, Mahevanirina; Raveloson, Harinjaka; Rakotomalala, Joël; Ramanantsoanirina, Alain; Garin, Vincent; Grenier, Cecile; vom Brocke, Kirsten
Abstract In the Highlands of Madagascar, where rice is the main staple food, explosive demographic growth has driven the need for the development of upland rice. In that context, a Participatory Plant Breeding (PPB) program conducted by the FOFIFA-Cirad partnership, aims to develop upland rice varieties adapted to farmers’ needs, with superior agronomic performances, and with high grain zinc concentration. In the area, where ferralitic soils with N and P deficiencies prevail, limited fertilizer usage persists due to elevated costs, and upland rice varieties must adapt to these low fertility environments. Thus, this paper aims to identify the adequate selection conditions and methods that allow combining the above-mentioned criteria for selection. So, 56 rice breeding lines, including high-zinc genotypes, were evaluated in field trials with contrasting fertility conditions. A relative selection efficiency analysis demonstrated that selection for yield should be done in moderate fertility environments, while selection for grain zinc concentration could be done across a diverse range of conditions. Through participatory evaluations, we identified that, for this case, grain appreciation was the most important character for deciding whether to select a line, followed by productivity and earliness. We also noted that farmers were more willing to accept a variety if it had higher grain zinc concentration. Finally, we proposed a selection index that combines agronomic, farmers’ and nutritional criteria, with the purpose of selecting lines that fulfill the expectations on these areas. Overall, this paper proposes an adapted methodology for the combination of PPB and biofortification in marginal environments.
Salt tolerance in mungbean is associated with controlling Na and Cl transport across roots, regulating Na and Cl accumulation in chloroplasts and maintaining high K in root and leaf mesophyll cells
(Journal Article, 2024-09) Iqbal, Md Shahin; Clode, Peta L.; Malik, Al Imran; Erskine, William; Kotula, Lukasz
Salinity tolerance requires coordinated responses encompassing salt exclusion in roots and tissue/cellular compartmentation of salt in leaves. We investigated the possible control points for salt ions transport in roots and tissue tolerance to Na
Assessing the relevance of 2022-2024 variety releases deriving from CGIAR Breeding Pipelines and Networks – an internal MELIA study
(Report, 2024-12-31) Bänziger, Marianne; Lenaerts, Bert; Gitonga, Agnes; Coaldrake, Peter; Demont, Matty; Quinn, Michael
This study analyzes known CGIAR-related variety releases, that have taken place between 2022 and 2024, in the context of newly available market segment information and associated development indicators. The analysis is made possible by systematically collecting critical information across CGIAR breeding networks, in particular market segment, target product profile, breeding pipeline, known variety releases, and the scaling partners involved in those variety releases. In close collaboration with national partners, CGIAR breeding and market intelligence teams have defined (so far) 651 subregional market segments, thereby characterizing 390 million of the total 644 million crop area estimated by FAO to be annually harvested in countries targeted by CGIAR-collaborative breeding networks. Between 2022-2024, 179 partner organizations in 66 countries registered a total of 939 varieties for commercialization or not-for profit dissemination. Combining their breeding pipeline origin with the market segment information indicates that, when scaled, they could cover 16-26% of the crop area in target countries, and more specifically market segments where 50-100 million low-income people live. The range or uncertainty is due to the level of data incompleteness. This is the first time that an estimate at such a scale (cross-CGIAR) and at the granularity of market segments has been made possible. The analysis confirms the impressive and highly relevant reach of CGIAR-NARES collaborative breeding efforts while pointing to the need to further improve market segment area estimates. Also, market segmentation puts a new perspective on the number of scalable variety releases required to meet needs, more than often estimated given that different users voice different needs for the same crop and country. Close to two-thirds of the organizations registering the varieties were public, 34% were private and 4% from the not-for-profit sector. Knowing the 179 scaling partners involved allows to track successes and bottlenecks of variety uptake, gain insight and address issues as they relate to the existence or absence, respectively, of seed sector capacity, user-demanded variety characteristics, market opportunities, or government investments.
Qualitative report on: qualitative baseline investigation on the current practices and institutional arrangements in breeding by CGIAR – NARES- and private sector to define breeding objectives
(Report, 2025-01-15) Edosa, G.H.; Nchanji, E.; Webber, H.; Pede, V.; Polar, V.; Teeken, B.
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.
Multispectral and thermal infrared data, visual scores for severity of common rust symptoms, and genotypic single nucleotide polymorphism data of three F2-derived biparental doubled-haploid maize populations
(Journal Article, 2024-06) Loladze, Alexander; Rodrigues, Francelino; Petroli, Cesar; Muñoz-Zavala, Carlos; Naranjo, Sergio; San Vicente Garcia, Felix M.; Gerard, Bruno; Montesinos-Lopez, Osval A.; Crossa, Jose; Martini, Johannes W.R.
Three F2-derived biparental doubled haploid (DH) maize populations were generated for genetic mapping of resistance to common rust. Each of the three populations has the same susceptible parent, but a different resistance donor parent. Population 1 and 3 consist of 320 lines each, population 2 consists of 260 lines. The DH lines were evaluated for their susceptibility to common rust in two years and with two replications in each year. For phenotyping, a visual score (VS) for susceptibility was assigned. Additionally, unmanned aerial vehicle (UAV) derived multispectral and thermal infrared data was recorded and combined in different vegetation indices (“remote sensing”, RS). The DH lines were genotyped with the DarTseq method, to obtain data on single nucleotide polymorphisms (SNPs). After quality control, 9051 markers remained. Missing values were “imputed” by the empirical mean of the marker scores of the respective locus. We used the data for comparison of genome-wide association studies and genomic prediction when based on different phenotyping methods, that is either VS or RS data. The data may be interesting for reuse for instance for benchmarking genomic prediction models, for phytopathological studies addressing common rust, or for specifications of vegetation indices.
Inheritance of resistance to maize lethal necrosis in tropical maize inbred lines
(Journal Article, 2025-01-09) Kavai, Hilda M.; Makumbi, Dan; Nzuve, Felister M.; Woyengo, Vincent W.; Suresh, L. M.; Muiru, William M.; Gowda, Manje; Prasanna, Boddupalli
Maize (Zea mays L.) production in sub-Saharan Africa can be improved by using hybrids with genetic resistance to maize lethal necrosis (MLN). This study aimed to assess the general (GCA) and specific combining ability (SCA), reciprocal effects, and quantitative genetic basis of MLN resistance and agronomic traits in tropical maize inbred lines. A total of 182 hybrids from a 14-parent diallel, along with their parents, were evaluated under artificial MLN inoculation and rainfed conditions for 3 years in Kenya. Disease ratings at four time points, grain yield (GY), and other agronomic traits were analyzed using Griffing’s Method 3 and Hayman’s diallel models. Significant (P < 0.001) GCA and SCA mean squares were observed for all traits under disease conditions and most traits under rainfed conditions, highlighting the importance of both additive and non-additive genetic effects. However, additive gene action predominated for all traits. Narrow-sense heritability estimates for MLN resistance (h2 = 0.52–0.56) indicated a strong additive genetic component. Reciprocal effects were not significant for MLN resistance, suggesting minimal maternal or cytoplasmic inheritance. Four inbred lines showed significant negative GCA effects for MLN resistance and positive GCA effects for GY under artificial MLN inoculation. Inbred lines CKL181281 and CKL182037 (GCA effects for MLN4 = -0.45 and -0.24, respectively) contained the most recessive alleles for MLN resistance. The minimum number of groups of genes involved in MLN resistance was estimated to be three. Breeding strategies that emphasize GCA could effectively be used to improve MLN resistance in this germplasm.
Unlocking the power of gene banks: diversity in base growth temperature provides opportunities for climate-smart agriculture
(Journal Article, 2025-01) Gambart, C.; Van Wesemael, J.; Swennen, R.; Tardieu, F.; Carpentier, S.
Implementation of context-specific solutions, including cultivation of varieties adapted to current and future climatic conditions, have been found to be effective in establishing resilient, climate-smart agricultural systems. Gene banks play a pivotal role in this. However, a large fraction of the collections remains neither genotyped nor phenotyped. Hypothesizing that significant genotypic diversity in Musa temperature responses exists, this study aimed to assess the diversity in the world's largest banana gene bank in terms of base temperature (Tbase) and to evaluate its impact on plant performance in the East African highlands during a projected climate scenario. One hundred and sixteen gene bank accessions were evaluated in the BananaTainer, a tailor-made high throughput phenotyping installation. Plant growth was quantified in response to temperature and genotype-specific Tbase were modelled. Growth responses of two genotypes were validated under greenhouse conditions, and gas exchange capacity measurements were made. The model confirmed genotype-specific Tbase, with 30% of the accessions showing a Tbase below the reference of 14°C. The Mutika/Lujugira subgroup, endemic to the East African highlands, appeared to display a low Tbase, although within subgroup diversity was revealed. Greenhouse validation further showed low temperature sensitivity/tolerance to be related to the photosynthetic capacity. This study, therefore, significantly advances the debate of within species diversity in temperature growth responses, while at the same time unlocking the power of gene banks. Moreover, with this case study on banana, we provide a high throughput method to reveal the existing genotypic diversity in temperature responses, paving the way for future research to establish climate-smart varieties.
Unlocking market potential: CRI Breeding Program's targeted market segments for sustainable maize production
(Poster, 2024-10) Ribeiro, F. P.; Muungani, D.; Oppong, A.; Yeboah, S.; Baffoe, E.; Frimpong-Manso, E.; Acquah, E.; Yeboah, R.
The Crop Research Institute (CRI) Breeding Program aims to develop high-yielding, nutritious and climate smart maize varieties for diverse market segments. Until recently, the breeding programe had the opportunity to review market segments, refine market segments for national needs and define target product profiles for each market segment. The review was done by diverse group of stakeholders (farmers, processors, youth and gender, aggregator etc). This poster highlights our program's targeted market segments, including: (food); Smallholder farmers seeking improved yields and drought tolerance, commercial farmers requiring high-yielding, disease-resistant varieties, (animal feed); livestock and poultry industries demanding high-energy maize, (Brewery); food processors seeking specialized maize for value-added products. Our breeding program focuses on developing maize varieties with desirable traits for each segment, ensuring the following: increased productivity and food security, improved livelihoods for smallholder farmers, enhanced competitiveness for commercial farmers, sustainable maize production for industry stakeholders. A comprehensive scoring system assessed operations of the breeding program across key performance indicators. The program scored averagely good for its operational efficiency
Developing impactful, in-demand, gender-intentional, and feasible target product profiles (TPPs)
(Poster, 2024-10) Muungani, Dean; Banda, Vishnuvardhan Reddy; Coaldrake, Peter; Connor, Melanie; Najjar, Dina; Yadav, Shailesh; Taleon, Victor; Newby, Jonathan; Mendes, Thiago; Dufour, Dominique; Dermont, Matty; Polar, Vivian; Banzinger, Marianne
The uptake of new crop varieties in low to medium-income countries remains low partly due to a mismatch between breeder and farmer trait priorities. Breeders often focus on agronomic traits like drought and pest resistance, overlooking traits important to farmers, such as processing and sensory qualities. This can particularly affect women farmers, who represent a large proportion of the farming population. Addressing these needs is crucial for new varieties to succeed. The CGIAR Initiatives on Market Intelligence and Accelerated Breeding addresses this challenge through a standardized Target Product Profile (TPP), which identifies traits important to different market segments. The TPP standard classifies traits as essential or “nice-to-have”. Essential traits are necessary for a variety’s success and can either be “improved” or “maintained” deliberately through breeding. Nice-to-have traits are optional. However, balancing multiple traits in a TPP is challenging. Too many traits can hinder breeding progress, making it critical for TPP design teams to make trade-offs. A high-quality TPP must be impactful, in-demand, gender-intentional, and feasible. Impactful means the TPP should focus on 1 – 3 key value propositions that deliver the greatest benefit to farmers. In-demand means that farmers and seed companies must recognize the benefits of improved traits and be motivated to adopt the new varieties. Feasibility means that improvements in key traits must be achievable within 10 – 15 years. Gender intentional means evaluating specific traits that affect men, women, and youth, ensuring that their needs and impacts are considered in the breeding process.
Farmers’ heterogeneous preferences for traits of improved varieties: Informing demand-oriented crop breeding in Tanzania
(Poster, 2024-10) Regassa, Mekdim D.; Miriti, Philip K.; Melesse, Mequanint B.
This study uses choice experiment data from a random sample of 1299 Tanzanian farmers to analyze preferences for traits of groundnut varieties, trade-offs in the valuation of attributes, and heterogeneity in preferences. Groundnut farmers have strong preferences for varieties that are high-yielding, tolerant to environmental stresses, early-maturing, red-colored, and fetching high sale prices in grain markets. Farmers are willing to pay the highest premium for high-yielding and tolerance attributes. Further, a latent class analysis identifies considerable heterogeneity in farmers’ trait preferences. A specific distinction is between consumption-oriented and market-oriented farmer classes. The results have important implications for demand-driven variety development and targeted dissemination of improved varieties. Breeding programs need to consider the heterogeneity in farmers’ preferences and weigh the potential market size before scarce resources are committed to improving an attribute. The results highlight that trait-based promotion and marketing of varieties may offer an effective strategy to promote improved varieties.
Sweetpotato targeted product profiles alignment to market knowledge by NARS programs in Southern Africa
(Poster, 2024-10) Makunde, Godwill; Musundire, Lennin; Taula, Antonio; Mtonga, Andrew; Serenje, Gerald; Philime, Memory; Lindqvist-Kreuze, Hannele
To enhance the efficiency and impact of sweetpotato breeding teams in Southern Africa the development and alignment of targetted product profiles to market segments was top priority in Mozambique, Malawi, Zambia and Zimbabwe. Multidisciplinary product development teams were constituted in each country to develop targetted product profiles, prioritize key traits that lead to adoption and increase performance of new varieties. The key results were each country developed two targetted product profiles which addressed the market requirements of the white flesh, drought, heat and salinity prone environments and orange flesh, drought, heat and salinity prone environments of southern Africa. The teams defined sweetpotato market segments in terms of size and dominant varieties per segment (release dates, market share, key strengths and weaknesses) for each country. NARS program assessment was carried out and improvement plans developed and documented for partner. One of cross cutting recommendations was strengthening collaboration with third parties to establish regular germplasm exchange with other NARES targeting similar target product profiles. Pathways to improve collaborations across countries were laid down, and one outcome was sharing of elite clones from International Potato Center breeding program in Mozambique to all countries for further testing and release by national partners.
Enhancing market segmentation with GloMIP's Impact Opportunities Portal
(Poster, 2024-10) Lenaerts, Bert; Paguirigan, Neale Marvin; Demont, Matty
The GloMIP Impact Opportunities Portal helps analyse over 200 development and crop production indicators across the five CGIAR Impact Areas, three scaling levels (national, national-crop, and market segment), 46 crops (including 20 CGIAR crops), 170 countries, and 23 grouping levels. Market segmentation can benefit from evidence generated at scale through the tool in three main ways. First, the portal allows prioritizing market segments based on selected indicators, either individually or combined in an index. Second, the portal calculates the split between segmented and unsegmented opportunities, showing what portion of regional impact opportunities the market segments cover. This can help ensure that market segmentation aligns with global needs and identify any missing market segments. Third, the portal aids in market segmentation by providing national cropping area, yield, and price data from FAO, which can act as building blocks for new market segments.

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