Joost van Heerwaarden

Key message: Our scalable two-step method estimates genotypic performance and genetic parameters from ranking data, producing reliable results comparable to quantitative analyses, enabling the integration of ranking data into breeding pipelines. Plant breeding research has chiefly relied on on-station experiments to evaluate varietal performance. Nevertheless, these trials often fail to represent on-farm growing conditions and farmers’ preferences, potentially leading to poorly defined breeding targets. Recent work has demonstrated the potential of using on-farm verification trials combined with ranking data to support farmers in evaluating varieties while providing information that is representative of farmers’ needs. Despite this potential, scalable methods for quantifying genetic differences and assessing the strength of the genetic signal in such trials remain limited. Here, we present a two-step procedure for analyzing trials based on ranking data, allowing the estimation of genetic parameters. The approach follows a common strategy in quantitative genetics, in which parameters are estimated from tables of genotypic means and their variances. In our framework, these estimates are obtained from Thurstonian and/or Plackett-Luce models, which treat rankings as observations of an underlying continuous trait associated with genotypic performance. Using simulated data, we showed that genotypic mean estimates derived from ranking analyses are linearly related to those obtained from quantitative trait analyses and that their variances adequately capture estimation uncertainty. We further demonstrated that incorporating these estimates and their variances into a second-step mixed-effects model yields accurate estimates of variance components. Analyses of groundnut, maize, and sweetpotato datasets confirmed the applicability of the approach and showed that ranking data can provide reliable estimates of genetic parameters. We argue that this framework can be scaled to obtain genotypic performance estimates from multi-trial on-farm data.

Societal Impact Statement: Amid global challenges of food insecurity, poor nutrition, and climate change, neglected crops like amaranth are gaining renewed attention. We studied farmers' preferences for amaranth varieties across diverse geographical contexts to guide targeted breeding. Our results revealed significant variation in farmer preferences, emphasizing the need for context‐specific breeding strategies. These findings can support the development of improved amaranth varieties that meet local needs, expand economic opportunities—especially for women—promote healthier diets, and boost biodiversity. This work also offers a model for participatory research on opportunity crops, informing inclusive agricultural policies and sustainable development strategies across Africa and beyond.Summary: Opportunity crops, also known as neglected and underutilized species (NUS), offer benefits to diversify food systems with nutritious and climate‐resilient foods. A major limitation to incorporating these crops in farming systems is the lack of improved varieties, which impedes farmers from accessing quality planting materials of these crops. The study explored how citizen science methods can support demand‐driven breeding and seed production of NUS using leafy amaranth – a nutritious and hardy vegetable ‐ as a case study. The study identified farmer preferences and market segments, with particular attention to gender and social differentiation. We used the tricot approach to conduct participatory on‐farm trials of 14 varieties with 2,063 farmers from Benin, Mali, and Tanzania. We then analyzed farmer traits and varietal preferences in aggregate and among segments of farmers, using cluster analysis. Farmers' overall preferences for amaranth varieties were driven principally by plant survival, yield, leaf size, taste, and marketability. Distinct farmer segments (older women generalists, young women specialists, older men generalists, and young men specialists) preferred different varieties depending on gender and business orientation. The identified farmer segments, along with their unique variety preferences, provide valuable information for breeders and seed enterprises, and support demand‐driven amaranth breeding and seed system development. The methods used and lessons learned from our citizen science exercise can be applied to enhance breeding and seed supply of other opportunity crops that are underutilized in Africa and elsewhere.

More than 40% of the total oil palm area in Indonesia is owned and managed by smallholders. For large plantations, guidelines are available on so-called ‘best management practices’, which should give superior yields at acceptable costs when followed carefully. We tested a subset of such practices in a sample of smallholder plantations, aiming to increase yields and profitability. We implemented improved practices (weeding, pruning, harvesting, and fertiliser application) in 14 smallholder plantations of 13–15 years after planting in Jambi province (Sumatra) and in West-Kalimantan province (Kalimantan) for a duration of 3 to 3.5 years. During this period, we recorded yields, measured palm leaf parameters and analysed leaf nutrient contents. Yield recording then continued for an additional two years. In the treatment plots, the yields did not increase significantly, but the size of the bunches and the size of the palm leaves increased significantly and substantially. The tissue nutrient concentrations also increased significantly, although after three years, the potassium concentrations in the rachis were still below the critical value. Because of the absence of yield increase and the additional costs for fertiliser inputs, the net profit of implementing better management practices was negative, and ‘business as usual’ was justified financially. Some practices, such as harvesting at 10-day intervals and the weeding of circles and paths, were received positively by those farmers who could implement them autonomously, and were applied beyond the experiment. It is challenging to find and implement intensification options that are both sustainable and profitable, that have a substantial impact on yield, and that fit in the smallholders’ realities. On-farm experimentation and data collection are essential for achieving sustainable intensification in smallholder oil palm plantations.

CONTEXT Opportunity crops, also known as neglected and underutilized species (NUS), offer benefits to diversify food systems with nutritious and climate-resilient foods. A major limitation to incorporate these crops in farming systems is the lack of improved varieties impedes farmers accessing quality planting material of these crops. OBJECTIVES The study explored how citizen science methods can support demand-driven breeding and seed production of opportunity crops using leafy amaranth – a nutritious and hardy vegetable- as a case study. The study identified farmer preferences and market segments, with particular attention to gender and social differentiation. METHODS We used the tricot approach to conduct participatory on-farm trials of 14 varieties with 2,063 farmers from Benin, Mali, and Tanzania. We then analyzed farmer trait and varietal preferences in aggregate and among segments of farmers, generated using cluster analysis. RESULTS Farmers’ overall preferences for amaranth varieties was driven principally by plant survival, yield, leaf size, taste, and marketability. Distinct farmer segments (older women generalists, young women specialists, older men generalists, and young men specialists) preferred different varieties depending on gender, business-orientation. DISCUSSION AND CONCLUSION The farmer segments identified here, along with their unique variety preferences provide valuable information for breeders and seed enterprises, and support demand-driven amaranth breeding and seed system development. We specifically noted the need for breeding programs to understand the preferences of young amaranth specialists, both men and women, and to explore organoleptic and market-related properties of amaranth. SIGNIFICANCE Our findings on differentiated producer preferences will support scaling seed supply of amaranth in Africa to diversify farming systems with a climate-resilient and nutritious crop. The methods used and lessons learned from our citizen science exercise can be applied to enhance breeding and seed supply of other opportunity crops that are underutilized in Africa or other continents. Highlights Farmer citizen science methods reveal seed market insights for opportunity crops Amaranth variety preferences vary widely across gender, age, and countries Young amaranth producers focus on market and sensory traits compared to old producers Large-scale farmer feedback guides opportunity crop breeding for diverse segments

Poor and variable crop responses to fertilizer applications constitute a production risk and may pose a barrier to fertilizer adoption in sub-Saharan Africa (SSA). Attempts to measure response variability and quantify the prevalence of non-response empirically are complicated by the fact that data from on-farm fertilizer trials generally include diverse nutrients and do not include on-site replications. The first aspect limits the extent to which different studies can be combined and compared, while the second does not allow to distinguish actual field-level response variability from experimental error and other residual variations. In this study, we assembled datasets from 41 on-farm fertilizer response trials on cereals and legumes across 11 countries, representing different nutrient applications, to assess response variability and quantify the frequency of occurrence of non-response to fertilizers. Using two approaches to account for residual variation, we estimated non-response, defined here as a zero agronomic response to fertilizer in a given year, to be relatively rare, affecting 0–1 and 7–16% of fields on average for cereals and legumes respectively. The magnitude of response could not be explained by climatic and selected topsoil variables, suggesting that much of the observed variation may relate to unpredictable seasonal and/or local conditions. This implies that, despite demonstrable spatial bias in our sample of trials, the estimated proportion of non-response may be representative for other agro-ecologies across SSA. Under the latter assumption, we estimated that roughly 260,000 ha of cereals and 3,240,000 ha of legumes could be expected to be non-responsive in any particular year.

Chickpea (Cicer arietinum L.) used to be considered a restrictive host that nodulated and fixed nitrogen only with Mesorhizobium ciceri and M. mediterraneum. Recent analysis revealed that chickpea can also establish effective symbioses with strains of several other Mesorhizobium species such as M. loti, M. haukuii, M. amorphae, M. muleiense, etc. These strains vary in their nitrogen fixation potential inviting further exploration. We characterized newly collected mesorhizobial strains isolated from various locations in Ethiopia to evaluate genetic diversity, biogeographic structure and symbiotic effectiveness. Symbiotic effectiveness was evaluated in Leonard Jars using a locally released chickpea cultivar “Nattoli”. Most of the new isolates belonged to a clade related to M. plurifarium, with very few sequence differences, while the total collection of strains contained three additional mesorhizobial genospecies associated with M. ciceri, M. abyssinicae and an unidentified Mesorhizobium species isolated from a wild host in Eritrea. The four genospecies identified represented a subset of the eight major Mesorhizobium clades recently reported for Ethiopia based on metagenomic data. All Ethiopian strains had nearly identical symbiotic genes that grouped them in a single cluster with M. ciceri, M. mediterraneum and M. muleiense, but not with M. plurifarium. Some phylogeographic structure was observed, with elevation and geography explaining some of the genetic differences among strains, but the relation between genetic identity and symbiotic effectiveness was observed to be weak.

The existence of genotype-by-strain (G _L × G _R ) interaction has implications for the expected stability of performance of legume inoculants and could represent both challenges and opportunities for improvement of nitrogen fixation. We find that significant genotype-by-strain interaction exists in common bean ( Phaseolus vulgaris L.) but that the strength and direction of this interaction depends on the growing environment used to evaluate biomass. Strong genotype and strain main effects, combined with a lack of predictable patterns in G _L × G _R , suggests that at best individual bean genotypes and strains can be selected for superior additive performance. The observation that the screening environment may affect experimental outcome of G _L × G _R means that identified patterns should be corroborated under more realistic conditions.