Application of machine learning and genomics for orphan crop improvement

Orphan crops are important sources of nutrition in developing regions and many are tolerant to biotic and abiotic stressors; however, modern crop improvement technologies have not been widely applied to orphan crops due to the lack of resources available. There are orphan crop representatives across major crop types and the conservation of genes between these related species can be used in crop improvement. Machine learning (ML) has emerged as a promising tool for crop improvement. Transferring knowledge from major crops to orphan crops and using machine learning to improve accuracy and efficiency can be used to improve orphan crops.

Establishing the linkage between eba's instrumental and sensory descriptive profiles and their correlation with consumer preferences: implications for cassava breeding

BACKGROUND

Gari and eba, forms of cassava semolina, are mainly consumed in Nigeria and other West African countries. This study aimed to define the critical quality traits of gari and eba, to measure their heritability, to define medium and high throughput instrumental methods for use by breeders, and to link the traits with consumer preferences. The definition of a food product's profiles, including its biophysical, sensory, and textural qualities, and the identification of the characteristics that determine its acceptability, are important if new genotypes are to be adopted successfully.

RESULTS

Eighty cassava genotypes and varieties (three different sets) from the International Institute of Tropical Agriculture (IITA) research farm were used for the study. Participatory processing and consumer testing data on different types of gari and eba products were integrated to prioritize the traits preferred by processors and consumers. The color, sensory, and instrumental textural properties of these products were determined using standard analytical methods, and standard operating protocols (SOPs) developed by the RTBfoods project (Breeding Roots, Tubers, and Banana Products for End-user Preferences, https://rtbfoods.cirad.fr). There were significant (P < 0.05) correlations between instrumental hardness and sensory hardness and between adhesiveness and sensory moldability. Principal component analysis showed broad discrimination amongst the cassava genotypes and the association of the genotypes concerning the color and textural properties.

CONCLUSIONS

The color properties of gari and eba, together with instrumental measures of hardness and cohesiveness, are important quantitative discriminants of cassava genotypes. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Combined use of sensory methods for the selection of root, tuber and banana varieties acceptable to end-users

BACKGROUND

The assessment of user acceptability in relation to crop quality traits should be a full part of breeding selection programs. Our methodology is based on a combination of sensory approaches aiming to evaluate the sensory characteristics and user acceptability of root, tuber and banana (RTB) varieties.

RESULTS

The four-stepped approach links sensory characteristics to physicochemical properties and end-user acceptance. It starts with the development of key quality traits using qualitative approaches (surveys and ranking) and it applies a range of sensory tests such as Quantitative Descriptive Analysis with a trained panel, Check-All-That-apply, nine-point hedonic scale and Just-About-Right with consumers. Results obtained on the same samples from the consumer acceptance, sensory testing and physicochemical testing are combined to explore correlations and develop acceptability thresholds.

CONCLUSION

A combined qualitative and quantitative approach involving different sensory techniques is necessary to capture sensory acceptance of products from new RTB clones. Some sensory traits can be correlated with physicochemical characteristics and could be evaluated using laboratory instruments (e.g. texture). Other traits (e.g. aroma and mealiness) are more difficult to predict, and the use of a sensory panel is still necessary. For these latter traits, more advanced physicochemical methods that could accelerate the breeding selection through high throughput phenotyping are still to be developed. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Decision tree scoring system to guide selection for consumer preference in sweetpotato breeding trials

BACKGROUND

Previously, a lexicon and protocol for quantitative descriptive analysis (QDA) was established for the Uganda sweetpotato breeding program. The implication of QDA scores for priority sensory attributes on consumer preference should be determined to interpret results efficiently and make decisions effectively. The present study aimed to develop a gender-responsive decision tree to obtain an overall sweetpotato eating quality score to facilitate demand-led targeted breeding selection. It focused on Kamuli and Hoima districts (Uganda) and uses pre-lease advanced clones ('NKB3', 'NKB105', 'NKB135', 'D11' and 'D20'), released varieties ('NASPOT 8' and 'NAROSPOT 1') and landraces ('Muwulu-Aduduma', 'Umbrella').

RESULTS

Including boiled sweetpotato sensory characteristics, namely mealy, sweet taste, sweetpotato smell, firm and not fibrous, in breeding design would benefit end-users, especially women given their role in varietal selection, food preparation and marketing. 'D20', 'NASPOT 8' and 'NAROSPOT 1' were most liked in both districts. 'NKB3' and 'D11' were the least liked in Hoima, whereas 'Muwulu-Aduduma' was the least liked in Kamuli. There was a positive correlation between color and overall liking (r2 = 0.8) and consumers liked the color (average rating ≥ 6 on a nine-point hedonic scale) of all genotypes. Threshold values (average rating on 11-point scales) for consumer acceptability were identified (sweet taste = 6, sweetpotato aroma and flavor = 6, firmness = 3, and mealiness = 4). A regression decision tree tool was created to calculate an eating quality selection index when screening lines in breeding programs using the values.

CONCLUSION

Decision trees that include consumer needs and gender considerations would facilitate demand-led breeding and make varietal selection in sweetpotato breeding programs more effective. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Q&A: Methods for estimating genetic gain in sub-Saharan Africa and achieving improved gains

Regular measurement of realized genetic gain allows plant breeders to assess and review the effectiveness of their strategies, allocate resources efficiently, and make informed decisions throughout the breeding process. Realized genetic gain estimation requires separating genetic trends from nongenetic trends using the linear mixed model (LMM) on historical multi-environment trial data. The LMM, accounting for the year effect, experimental designs, and heterogeneous residual variances, estimates best linear unbiased estimators of genotypes and regresses them on their years of origin. An illustrative example of estimating realized genetic gain was provided by analyzing historical data on fresh cassava (Manihot esculenta Crantz) yield in West Africa (https://github.com/Biometrics-IITA/Estimating-Realized-Genetic-Gain). This approach can serve as a model applicable to other crops and regions. Modernization of breeding programs is necessary to maximize the rate of genetic gain. This can be achieved by adopting genomics to enable faster breeding, accurate selection, and improved traits through genomic selection and gene editing. Tracking operational costs, establishing robust, digitalized data management and analytics systems, and developing effective varietal selection processes based on customer insights are also crucial for success. Capacity building and collaboration of breeding programs and institutions also play a significant role in accelerating genetic gains.

Drivers of consumer acceptability of cassava gari-eba food products across cultural and environmental settings using the triadic comparison of technologies approach (tricot)

BACKGROUND

Nigeria and Cameroon are multi-ethnic countries with diverse preferences for food characteristics. The present study aimed to inform cassava breeders on consumer-prioritized eba quality traits. Consumer testing was carried out using the triadic comparison of technologies (tricot). Diverse consumers in villages, towns and cities evaluated the overall acceptability of eba made from different cassava genotypes. Data from both countries were combined and linked to laboratory analyses of eba and the gari used to make it.

RESULTS

There is a strong preference for eba with higher cohesiveness and eba from gari with higher brightness and especially in Cameroon, with lower redness and yellowness. Relatively higher eba hardness and springiness values are preferred in the Nigerian locations, whereas lower values are preferred in Cameroon. Trends for solubility and swelling power of the gari differ between the two countries. The study also reveals that the older improved cassava genotype TMS30572 is a benchmark genotype with superior eba characteristics across different regions in Nigeria, whereas the recently released variety Game changer performs very well in Cameroon. In both locations, the recently released genotypes Obansanjo-2 and improved variety TM14F1278P0003 have good stability and overall acceptability for eba characteristics.

CONCLUSION

The wide acceptance of a single genotype across diverse geographical and cultural conditions in Nigeria, as well as three acceptable new improved varieties in both locations, indicates that consumers' preferences are surprisingly homogeneous for eba. This would enhance breeding efforts to develop varieties with wider acceptability and expand potential target areas for released varieties. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Gender mainstreaming in sweetpotato breeding and dissemination in Ghana and Malawi

Gender responsiveness in breeding programs to meet client and end user preferences for crops is essential. This case study analyzes the implementation experience of gender-responsive breeding and variety dissemination in Malawi and Ghana, focusing on good practices and challenges encountered. In Malawi, a training-of-trainers approach was employed to share knowledge among trained farmers. In Ghana, a research study was conducted to identify gender-based preferences for sweetpotato to define breeding objectives. The participation of social scientists, food scientists, and sweetpotato breeders in the GREAT (Gender Researchers Equipped for Agricultural Transformation) team provided a multidisciplinary perspective, addressing questions and responses in the field. Research efforts were strengthened by focusing on food quality through the establishment of an analytical laboratory for rapid evaluation of nutrition and food quality, including sugars. This helped develop sensory analytical capacity to better understand quality attributes and market segments, guiding breeding and improving market opportunities for women. Breeding outcomes resulting from gender inclusion led to the release of some sweetpotato varieties meeting end user and consumer preferences, as well as adoption of OFSP varieties by men and women. Other good practices for gender inclusion and responsiveness include providing funds for gender-based research and activities, engaging gender specialists and social scientists in trans-disciplinary teams, designing program activities with gender considerations, and incorporating traits in seed multiplication and dissemination decisions. Application of these gender inclusion practices resulted in adoption and development of acceptable sweetpotato varieties.

Farmer preference for macadamia varieties and constraints to production in Malawi

Macadamia nuts constitute a vital component of both nutrition and livelihoods for smallholder producers in Malawi. We conducted a comprehensive mixed-methods study, combining qualitative and quantitative analyses, to explore varietal preferences and production challenges among these farmers. Leveraging cross-sectional data from 144 members of the Highlands Macadamia Cooperative Union Limited, our study underscores several significant findings. Our findings reveal that the majority of smallholder macadamia farmers (62%) are aged over 50, with farming as their primary occupation. Varied preferences are driven by yield-related traits, including high yield potential (38%), nut quality (29%), and extended flowering patterns (15%). Among the macadamia varieties, the top five choices, grown by over half of the farmers, include HAES 660 (18%), 800 (10%), 791 (9%), 816 (8%), and 246 (7%). Additionally, our study identifies five primary constraints faced by smallholder macadamia farmers: insect pests (81%), diseases (34%), limited market access (33%), wind damage (25%), and inadequate agricultural advisory services (17%). Based on these findings, we propose two policy recommendations to enhance smallholder macadamia production and productivity in Malawi and other regions. Specifically, we advocate for informed breeding programs that align with farmer preferences to promote greater adoption of macadamia varieties. Additionally, we emphasize the crucial role of the Malawian government in the macadamia value chain, suggesting active participation in providing extension services and marketing support, akin to its support for other cash crops.

The tricot approach: an agile framework for decentralized on-farm testing supported by citizen science. A retrospective

Matching crop varieties to their target use context and user preferences is a challenge faced by many plant breeding programs serving smallholder agriculture. Numerous participatory approaches proposed by CGIAR and other research teams over the last four decades have attempted to capture farmers' priorities/preferences and crop variety field performance in representative growing environments through experimental trials with higher external validity. Yet none have overcome the challenges of scalability, data validity and reliability, and difficulties in capturing socio-economic and environmental heterogeneity. Building on the strengths of these attempts, we developed a new data-generation approach, called triadic comparison of technology options (tricot). Tricot is a decentralized experimental approach supported by crowdsourced citizen science. In this article, we review the development, validation, and evolution of the tricot approach, through our own research results and reviewing the literature in which tricot approaches have been successfully applied. The first results indicated that tricot-aggregated farmer-led assessments contained information with adequate validity and that reliability could be achieved with a large sample. Costs were lower than current participatory approaches. Scaling the tricot approach into a large on-farm testing network successfully registered specific climatic effects of crop variety performance in representative growing environments. Tricot's recent application in plant breeding networks in relation to decision-making has (i) advanced plant breeding lines recognizing socio-economic heterogeneity, and (ii) identified consumers' preferences and market demands, generating alternative breeding design priorities. We review lessons learned from tricot applications that have enabled a large scaling effort, which should lead to stronger decision-making in crop improvement and increased use of improved varieties in smallholder agriculture.

Potato and sweetpotato breeding at the international potato center: approaches, outcomes and the way forward

Root and tuber crop breeding is at the front and center of CIP's science program, which seeks to develop and disseminate sustainable agri-food technologies, information and practices to serve objectives including poverty alleviation, income generation, food security and the sustainable use of natural resources. CIP was established in 1971 in Peru, which is part of potato's center of origin and diversity, with an initial mandate on potato and expanding to include sweetpotato in 1986. Potato and sweetpotato are among the top 10 most consumed food staples globally and provide some of the most affordable sources of energy and vital nutrients. Sweetpotato plays a key role in securing food for many households in Africa and South Asia, while potato is important worldwide. Both crops grow in a range of conditions with relatively few inputs and simple agronomic techniques. Potato is adapted to the cooler environments, while sweetpotato grows well in hot climates, and hence, the two crops complement each other. Germplasm enhancement (pre-breeding), the development of new varieties and building capacity for breeding and variety testing in changing climates with emphasis on adaptation, resistance, nutritional quality and resource-use efficiency are CIP's central activities with significant benefits to the poor. Investments in potato and sweetpotato breeding and allied disciplines at CIP have resulted in the release of many varieties some of which have had documented impact in the release countries. Partnership with diverse types of organizations has been key to the centers way of working toward improving livelihoods through crop production in the global South.

Gender mainstreaming in sweetpotato breeding in Uganda: a case study

Purpose

In Uganda, sweetpotato [Ipomoea batatas (L.) Lam] is typically a "woman's crop," grown, processed, stored and also mainly consumed by smallholder farmers for food and income. Farmers value sweetpotato for its early maturity, resilience to stresses, and minimal input requirements. However, productivity remains low despite the effort of breeding programs to introduce new varieties. Low uptake of new varieties is partly attributed to previous focus by breeders on agronomic traits and much less on quality traits and the diverse preferences of men and women in sweetpotato value chains.

Method

To address this gap, breeders, food scientists, and social scientists (including gender specialists) systematically mainstreamed gender into the breeding program. This multidisciplinary approach, grounded in examining gender roles and their relationship with varietal and trait preferences, integrated important traits into product profiles.

Results

Building on earlier efforts of participatory plant breeding and participatory varietal selection, new interventions showed subtle but important gender differences in preferences. For instance, in a study for the RTBFoods project, women prioritized mealiness, sweetness, firmness and non-fibrous boiled roots. These were further subjected to a rigorous gender analysis using the G+ product profile query tool. The breeding pipelines then incorporated these gender-responsive priority quality traits, prompting the development of standard operating procedures to phenotype these traits.

Conclusion

Following an all-inclusive approach coupled with training of multidisciplinary teams involving food scientists, breeders, biochemists, gender specialists and social scientists, integration into participatory variety selection in Uganda enabled accentuation of women and men's trait preferences, contributing to clearer breeding targets. The research has positioned sweetpotato breeding to better respond to the varying needs and preferences of the users.

Innovative approaches to integrating gender into conventional maize breeding: lessons from the Seed Production Technology for Africa project

The integration of gender concerns in crop breeding programs aims to improve the suitability and appeal of new varieties to both women and men, in response to concerns about unequal adoption of improved seed. However, few conventional breeding programs have sought to center social inclusion concerns. This community case study documents efforts to integrate gender into the maize-focused Seed Production Technology for Africa (SPTA) project using innovation history analysis drawing on project documents and the authors' experiences. These efforts included deliberate exploration of potential gendered impacts of project technologies and innovations in the project's approach to variety evaluation, culminating in the use of decentralized on-farm trials using the tricot approach. Through this case study, we illustrate the power of active and respectful collaborations between breeders and social scientists, spurred by donor mandates to address gender and social inclusion. Gender integration in this case was further facilitated by open-minded project leaders and allocation of funding for gender research. SPTA proved to be fertile ground for experimentation and interdisciplinary collaboration around gender and maize breeding, and has provided proof of concept for larger breeding projects seeking to integrate gender considerations.

gosset: An R package for analysis and synthesis of ranking data in agricultural experimentation

To derive insights from data, researchers working on agricultural experiments need appropriate data management and analysis tools. To ensure that workflows are reproducible and can be applied on a routine basis, programmatic tools are needed. Such tools are increasingly necessary for rank-based data, a type of data that is generated in on-farm experimentation and data synthesis exercises, among others. To address this need, we developed the R package gosset, which provides functionality for rank-based data and models. The gosset package facilitates data preparation, modeling and results presentation stages. It introduces novel functions not available in existing R packages for analyzing ranking data. This paper demonstrates the package functionality using the case study of a decentralized on-farm trial of common bean (Phaseolus vulgaris L.) varieties in Nicaragua.

Sensory guided selection criteria for breeding consumer-preferred sweetpotatos in Uganda

Prioritizing sensory attributes and consumer evaluation early in breeding trials to screen for end-user preferred traits could improve adoption rates of released genotypes. In this study, a lexicon and protocol for descriptive sensory analysis (DSA) was established for sweetpotato and used to validate an instrumental texture method for which critical values for consumer preference were set. The study comprised several phases: lexicon development during a 4-day workshop; 3-day intensive panel training; follow-up virtual training, evaluation of 12 advanced genotypes and 101 additional samples from two trials in 2021 by DSA and instrumental texture analysis using TPA double compression; and DSA, instrumental texture analysis and consumer acceptability tests on 7 genotypes in on-farm trials. The established sweetpotato lexicon comprising 27 sensory attributes enabled characterization and differentiation of genotypes by sensory profiles. Significant correlation was found between sensory firmness by hand and mouth with TPA peak positive force (r = 0.695 and r = 0.648, respectively) and positive area (r = 0.748, r = 0.715, respectively). D20, NAROSPOT 1, NASPOT 8, and Umbrella were the most liked genotypes in on-farm trials (overall liking = 7). An average peak positive force of 3700 gf was proposed as a minimum texture value for screening sweetpotato genotypes, since it corresponded with at least 46 % of consumers perceiving sweetpotatoes as just-about-right in firmness and a minimum overall liking of 6 on average. Combining DSA with instrumental texture analysis facilitates efficient screening of genotypes in sweetpotato breeding programs.