SummaryDurum wheat (Triticum turgidum subsp. durum) is a key crop worldwide, and yet, its improvement and adaptation to emerging environmental threats is made difficult by the limited amount of allelic variation included in its elite pool. New allelic diversity may provide novel loci to international crop breeding through quantitative trait loci (QTL) mapping in unexplored material. Here, we report the extensive molecular and phenotypic characterization of hundreds of Ethiopian durum wheat landraces and several Ethiopian improved lines. We test 81 587 markers scoring 30 155 single nucleotide polymorphisms and use them to survey the diversity, structure, and genome‐specific variation in the panel. We show the uniqueness of Ethiopian germplasm using a siding collection of Mediterranean durum wheat accessions. We phenotype the Ethiopian panel for ten agronomic traits in two highly diversified Ethiopian environments for two consecutive years and use this information to conduct a genome‐wide association study. We identify several loci underpinning agronomic traits of interest, both confirming loci already reported and describing new promising genomic regions. These loci may be efficiently targeted with molecular markers already available to conduct marker‐assisted selection in Ethiopian and international wheat. We show that Ethiopian durum wheat represents an important and mostly unexplored source of durum wheat diversity. The panel analysed in this study allows the accumulation of QTL mapping experiments, providing the initial step for a quantitative, methodical exploitation of untapped diversity in producing a better wheat.

Crop adaptation to climate change requires accelerated crop variety introduction accompanied by recommendations to help farmers match the best variety with their field contexts. Existing approaches to generate these recommendations lack scalability and predictivity in marginal production environments. We tested if crowdsourced citizen science can address this challenge, producing empirical data across geographic space that, in aggregate, can characterize varietal climatic responses. We present the results of 12,409 farmer-managed experimental plots of common bean (Phaseolus vulgarisL.) in Nicaragua, durum wheat (Triticum durumDesf.) in Ethiopia, and bread wheat (Triticum aestivumL.) in India. Farmers collaborated as citizen scientists, each ranking the performance of three varieties randomly assigned from a larger set. We show that the approach can register known specific effects of climate variation on varietal performance. The prediction of variety performance from seasonal climatic variables was generalizable across growing seasons. We show that these analyses can improve variety recommendations in four aspects: reduction of climate bias, incorporation of seasonal climate forecasts, risk analysis, and geographic extrapolation. Variety recommendations derived from the citizen science trials led to important differences with previous recommendations.

SUMMARYRapid climatic and socio-economic changes challenge current agricultural R&D capacity. The necessary quantum leap in knowledge generation should build on the innovation capacity of farmers themselves. A novel citizen science methodology, triadic comparisons of technologies or tricot, was implemented in pilot studies in India, East Africa, and Central America. The methodology involves distributing a pool of agricultural technologies in different combinations of three to individual farmers who observe these technologies under farm conditions and compare their performance. Since the combinations of three technologies overlap, statistical methods can piece together the overall performance ranking of the complete pool of technologies. The tricot approach affords wide scaling, as the distribution of trial packages and instruction sessions is relatively easy to execute, farmers do not need to be organized in collaborative groups, and feedback is easy to collect, even by phone. The tricot approach provides interpretable, meaningful results and was widely accepted by farmers. The methodology underwent improvement in data input formats. A number of methodological issues remain: integrating environmental analysis, capturing gender-specific differences, stimulating farmers' motivation, and supporting implementation with an integrated digital platform. Future studies should apply the tricot approach to a wider range of technologies, quantify its potential contribution to climate adaptation, and embed the approach in appropriate institutions and business models, empowering participants and democratizing science.

Smallholder farming communities face highly variable climatic conditions that threaten locally adapted, low-input agriculture. The benefits of modern crop breeding may fail to reach their fields when broadly adapted genetic materials do not address local requirements. To date, participatory methods only scratched the surface of the exploitability of farmers’ traditional knowledge in breeding. In this study, 30 smallholder farmers in each of two locations in Ethiopia provided quantitative evaluations of earliness, spike morphology, tillering capacity and overall quality on 400 wheat genotypes, mostly traditional varieties, yielding altogether 192,000 data points. Metric measurements of ten agronomic traits were simultaneously collected, allowing to systematically break down farmers’ preferences on quantitative phenotypes. Results showed that the relative importance of wheat traits differed by gender and location. Farmer traits were variously contributed by metric traits, and could only partially be explained by them. Eventually, farmer trait values were used to produce a ranking of the 400 wheat varieties identifying the trait combinations most desired by farmers. The study scale and methods lead to a better understanding of the quantitative basis of Ethiopian smallholder farmer preference in wheat, broadening the discussion for the future of local, sustainable breeding efforts accommodating farmers’ knowledge.

Septoria tritici blotch (STB) is a devastating fungal disease affecting durum and bread wheat cultivation worldwide. The identification, development, and employment of resistant wheat genetic material is the key to overcoming costs and limitations of fungicide treatments. The search for resistance sources in untapped genetic material may speed up the deployment of STB genetic resistance in the field. Ethiopian durum wheat landraces represent a valuable source of such diversity. In this study, 318 Ethiopian durum wheat genotypes, for the most part traditional landraces, were phenotyped for resistance to different aspects of STB infection. Phenology, yield and yield component traits were concurrently measured the collection. Here we describe the distribution of STB resistance traits in modern varieties and in landraces, and the relation existing between STB resistance and other agronomic traits. STB resistance sources were found in landraces as well as in modern varieties tested, suggesting the presence of alleles of breeding relevance. The genetic material was genotyped with more than 16 thousand genome-wide polymorphic markers to describe the linkage disequilibrium and genetic structure existing within the panel of genotypes, and a genome-wide association (GWA) study was run to allow the identification of genomic loci involved in STB resistance. High diversity and low genetic structure in the panel allowed high efficiency GWA. The GWA scan detected five major putative QTL for STB resistance, only partially overlapping those already reported in the wheat literature. We report four putative loci for Septoria resistance with no match in previous literature: two highly significant ones on Chr 3A and 5A, and two suggestive ones on Chr 4B and 5B. Markers underlying these QTL explained as much as 10% of the phenotypic variance for disease resistance. We found three cases in which putative QTL for agronomic traits overlapped marker trait association deriving from STB GWA. Our results show that the Ethiopian untapped allelic diversity bears a great value in studying the molecular basis of STB resistance and in breeding for resistance in local and international material.

Smallholder agriculture involves millions of farmers worldwide. A methodical utilization of their traditional knowledge in modern breeding efforts may help the production of locally adapted varieties better addressing their needs. In this study, a combination of participatory approaches, genomics, and quantitative genetics is used to trace the genetic basis of smallholder farmer preferences of durum wheat traits. Two smallholder communities evaluated 400 Ethiopian wheat varieties, mostly landraces, for traits of local interest in two locations in the Ethiopian highlands. For each wheat variety, farmers provided quantitative evaluations of their preference for flowering time, spike morphology, tillering capacity, and overall quality. Ten agronomic and phenology traits were simultaneously measured on the same varieties, providing the means to compare them with farmer traits. The analysis of farmer traits showed that they were partially influenced by gender and location but were repeatable and heritable, in some cases more than metric traits. The durum wheat varieties were genotyped for more than 80,000 SNP markers, and the resulting data was used in a genome wide association (GWA) study providing the molecular dissection of smallholder farmers' choice criteria. We found 124 putative quantitative trait loci (QTL) controlling farmer traits and 30 putative QTL controlling metric traits. Twenty of such QTL were jointly identified by farmer and metric traits. QTL derived from farmer traits were in some cases dependent on gender and location, but were consistent throughout. The results of the GWA study show that smallholder farmers' traditional knowledge can yield QTL eluding metric measurements of phenotypes. We discuss the potential of including farmer evaluations based on traditional knowledge in crop breeding, arguing for the utilization of this untapped resource to develop better adapted genetic materials for local agriculture.

Summary The Ethiopian plateau hosts thousands of durum wheat ( Triticum turgidum subsp. durum ) farmer varieties ( FV ) with high adaptability and breeding potential. To harness their unique allelic diversity, we produced a large nested association mapping ( NAM ) population intercrossing fifty Ethiopian FV s with an international elite durum wheat variety (Asassa). The Ethiopian NAM population (Et NAM ) is composed of fifty interconnected bi‐parental families, totalling 6280 recombinant inbred lines ( RIL s) that represent both a powerful quantitative trait loci ( QTL ) mapping tool, and a large pre‐breeding panel. Here, we discuss the molecular and phenotypic diversity of the Et NAM founder lines, then we use an array featuring 13 000 single nucleotide polymorphisms ( SNP s) to characterize a subset of 1200 Et NAM RIL s from 12 families. Finally, we test the usefulness of the population by mapping phenology traits and plant height using a genome wide association ( GWA ) approach. Et NAM RIL s showed high allelic variation and a genetic makeup combining genetic diversity from Ethiopian FV s with the international durum wheat allele pool. Et NAM SNP data were projected on the fully sequenced AB genome of wild emmer wheat, and were used to estimate pairwise linkage disequilibrium ( LD ) measures that reported an LD decay distance of 7.4 Mb on average, and balanced founder contributions across Et NAM families. GWA analyses identified 11 genomic loci individually affecting up to 3 days in flowering time and more than 1.6 cm in height. We argue that the Et NAM is a powerful tool to support the production of new durum wheat varieties targeting local and global agriculture.

The valorization of genetic diversities of major crops like wheat may help substantially to feed the world Population. Durum wheat genotypes consisting of 265 farmers' varieties (FVs), which have been cultivated for many centuries in Ethiopia, as well as 24 improved varieties (IMVs) have been recently evaluated in northern Ethiopia. The evaluation has been carried out at two different locations for 2 consecutive years to verify the inherited diversity in FVs for important phenological and agronomic traits; with the intention to provide refined information to breeders and genebank managers. As a result of a careful evaluation, a very significant variation was observed between the FVs and IMVs. A large number of the former have demonstrated superior performance to the latter in terms of mean values of the major traits within the stipulated years and locations. The best performing FV has shown a gain of 20% grain yield over the best IMV. Multivariate analyses revealed that FVs displayed larger genetic diversity than in those IMVs. FVs could therefore be used as donor of useful alleles in durum wheat breeding for improvement of yield per se and other traits of agronomic and phenological importance. The identified stable superior FVs include: 8208, 226834A, 238567, 222426, 226282 could be best candidates for farmers in marginal environments. Genotypes that have shown stable performance for spatial variation such as 204493A, 214357 and 238567; and temporal variation such as 8208, 208479, 214357 and 226834A could be the best candidates for exploitation in future breeding programs.