Genetic diversity in Ethiopian Durum wheat ( Triticum turgidum var durum ) inferred from phenotypic variations

The valorization of genetic diversities of major crops like wheat may help substantially to feed the world Population. Durum heat 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 perform- ing 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

Which wheat for smallholder Ethiopian farmers? Joining traditional knowledge with metric phenotypes

Africa hosts approximately 33 million smallholder farms, which account for 80% of the continent's farming system. Subsistence farming systems face highly variable climatic conditions that threaten locally-adapted, low-input agriculture. For the near future, they are among the most seriously affected by changing climatic conditions, posing additional risks to these systems. The benefits of modern breeding benefits may fail to reach small farming communities when broadly adapted material does not address specific local requirements. To date, participatory variety selection has only scratched the surface of the exploitability of farmers' knowledge in breeding. Yet, considering that over 80% of the farmers receive seeds from informal systems, making sure that well adapted material is available in production systems, seems to be a reasonable solution to quickly affect a large populations. Ethiopia is one of the most populous countries in Africa, with more than 96 million inhabitants, 80% of whom are engaged in small-scale agriculture, and often subsistence farming. We involved 60 smallholder farmers in two locations in Ethiopia to evaluate traits of their interest in 400 wheat accessions, producing 230,400 data points. We couple this information with metric measurements of 10 agronomic traits, breaking down farmers' preferences on quantitative phenotypes. We found that the relative importance of wheat traits is gender- and locality- dependent, and produced a ranking of the 400 varieties identifying the combination of traits most desired by farmers. The study scale and methods lead to a better understanding of smallholder farmer needs, broadening the discussion for the future of local, sustainable breeding efforts accommodating farmers' knowledge

A crowdsourcing approach to detect farmers’ preferences: evidences from Ethiopia for adapting to climate change

Climate change is severely affecting production systems all over Africa. Ethiopia will face an increase in temperature and changes in rainfall patterns. One solution for long term management of climate related risks is to introduce new traits into production systems. We present an approach to quickly deliver to farmers a selected number of preferred accessions of durum wheat using a crowdsourcing approach. After having completed a phenotypic and genotypic characterisation of 400 accessions of Ethiopian landraces and asked farmers to evaluate them, we distributed seeds of preferred varieties to a large number of farmers using a crowdsourcing approach. In two sites representing different agroecological zones, we distributed 20 superior varieties and one check, an improved variety very common in both areas to 200 farmers in 12 villages per site, covering an area of roughly 350 km 2. We repeated the experiment for 2 years. Each farmer was given 3 blind varieties and the check, each variety being equally represented in the sample. In addition, in each village we included 2 i-buttons, measuring temperature and humidity every 3 hours throughout the growing season. This allowed to analyse the data on critical climatic parameters. Results clearly indicate farmers’ preferences: a) Landraces were preferred over improved varieties for their multiple uses; b) By considering farmers as citizen scientists, we have a better understanding of the criteria farmers use to select their preferred varieties (in our case straw and grain yield, drought tolerance, uniformity, long and dense spikes). In conclusion: • This process has been very effective in quickly disseminating seeds that match farmers’ needs. After 2 years several hundred farmers can use better adapted material. • It shows the potential of landraces to provide immediate option for managing climate related risks and calls for broader use of material conserved in gene banks. • It indicates the need to strengthen local seed systems to better manage these resources. • It indicates how farmers can provide very valuable scientific information that can be translated into research as well as development potential in other areas of research

High-density molecular characterization and association mapping in Ethiopian durum wheat landraces reveals high diversity and potential for wheat breeding

Durum 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

Genome wide association study to identify the genetic base of smallholder farmer preferences of Durum wheat traits

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

Islet isolation assessment in man and large animals

Recent progress in islet isolation from the pancreas of large mammals including man, accentuated the need for the development of precise and reproducible techniques to assess islet yield. In this report both quantitative and qualitative criteria for islet isolation assessment were discussed, the main topics being the determination of number, volume, purity, morphologic integrity and in vitro and in vivo function tests of the final islet preparations. It has been recommended that dithizone should be used as a specific stain for immediate detection of islet tissue making it possible to estimate both the total number of islets (dividing them into classes of 50 μ diameter range increments) and the purity of the final preparation. Appropriate morphological assessment should include confirmation of islet identification, assessment of the morphological integrity and of the purity of the islet preparation. The use of fluorometric inclusion and exclusion dyes together have been suggested as a viability assay to simultaneously quantitate the proportion of cells that are intact or damaged. Perifusion of islets with glucose provides a dynamic profile of glucose-mediated insulin release and of the ability of the cells to down regulate insulin secretion after the glycemic challenge is interrupted. Although perifusion data provides a useful guide to islet viability the quantity and kinetics of insulin release do not necessarily predict islet performance after implantation. Therefore, the ultimate test of islet viability is their function after transplantation into a diabetic recipient. For this reason, in vivo models of transplantation of an aliquot of the final islet preparation into diabetic nude (athymic) rodents have been suggested. We hope that these general guidelines will be of assistance to standardize the assessment of islet isolations, making it possible to better interpret and compare procedures from different centers. © 1990 Casa Editrice il Ponte

Multivariate analysis in the dissection of phenotypic variation of Ethiopian cultivated barley (Hordeum vulgare ssp Vulgare L.) genotypes

Efficient conservation and subsequent utilization of genetic resources are primarily dependent on the strength in the assessment of variation among geno-types. An experiment was carried out aiming at determining the extent of pheno-typic variability present in a panel of 320 barley genotypes and identifying candidate lines for further evaluation in improvement programs and successive utilization. It was conducted at two locations in Ethiopia, Aris Negelle and Holetta in the 2017/18 and 2018/19 cropping seasons. Among the best 30 lines for grain yield across all the environments, lines from farmers’ varieties constitute 73% and lines that mature in less than 85 days were identified. Based on the spike row number, the best-performing lines combined across all the environments were six-rowed types. Based on the two years’ data at Arsi Negelle the two-rowed spike type dominates, and at Holetta the six-rowed type. After principal component analysis, the first three PCs with an eigenvalue greater than one explained 70% of the variation. The correlation coefficient between grain and biomass yield was signifi-cant and though low (r = 0.38***). Significant, high, and negative correlation coef-ficient (−0.72***) was observed between 1000 kernel weight and the number of seeds per spike. A positive correlation between biomass and grain yield attracts farmers as a feed and food crop as it has also been signified in the current research. Having the improved barley gene pool largely from international sources, combining the improved materials with farmers’ varieties may minimize the existing gap between the local and improved barley gene pool

Data-driven, participatory characterization of farmer varieties discloses teff breeding potential under current and future climates

In smallholder farming systems, traditional farmer varieties of neglected and underutilized species (NUS) support the livelihoods of millions of growers and consumers. NUS combine cultural and agronomic value with local adaptation, and transdisciplinary methods are needed to fully evaluate their breeding potential. Here, we assembled and characterized the genetic diversity of a representative collection of 366 Ethiopian teff (Eragrostis tef) farmer varieties and breeding materials, describing their phylogenetic relations and local adaptation on the Ethiopian landscape. We phenotyped the collection for its agronomic performance, involving local teff farmers in a participatory variety evaluation. Our analyses revealed environmental patterns of teff genetic diversity and allowed us to identify 10 genetic clusters associated with climate variation and with uneven spatial distribution. A genome-wide association study was used to identify loci and candidate genes related to phenology, yield, local adaptation, and farmers' appreciation. The estimated teff genomic offset under climate change scenarios highlighted an area around lake Tana where teff cropping may be most vulnerable to climate change. Our results show that transdisciplinary approaches may efficiently propel untapped NUS farmer varieties into modern breeding to foster more resilient and sustainable cropping systems

Increasing cell culture density during a developmental window prevents fated rod precursors derailment toward hybrid rod-glia cells

: In proliferating multipotent retinal progenitors, transcription factors dynamics set the fate of postmitotic daughter cells, but postmitotic cell fate plasticity driven by extrinsic factors remains controversial. Transcriptome analysis reveals the concurrent expression by postmitotic rod precursors of genes critical for the Müller glia cell fate, which are rarely generated from terminally-dividing progenitors as a pair with rod precursors. By combining gene expression and functional characterisation in single cultured rod precursors, we identified a time-restricted window where increasing cell culture density switches off the expression of genes critical for Müller glial cells. Intriguingly, rod precursors in low cell culture density maintain the expression of genes of rod and glial cell fate and develop a mixed rod/Muller glial cells electrophysiological fingerprint, revealing rods derailment toward a hybrid rod-glial phenotype. The notion of cell culture density as an extrinsic factor critical for preventing rod-fated cells diversion toward a hybrid cell state may explain the occurrence of hybrid rod/MG cells in the adult retina and provide a strategy to improve engraftment yield in regenerative approaches to retinal degenerative disease by stabilising the fate of grafted rod precursors

Data-driven decentralized breeding increases prediction accuracy in a challenging crop production environment

Crop breeding must embrace the broad diversity of smallholder agricultural systems to ensure food security to the hundreds of millions of people living in challenging production environments. This need can be addressed by combining genomics, farmers’ knowledge, and environmental analysis into a data-driven decentralized approach (3D-breeding). We tested this idea as a proof-of-concept by comparing a durum wheat (Triticum durum Desf.) decentralized trial distributed as incomplete blocks in 1,165 farmer-managed fields across the Ethiopian highlands with a benchmark representing genomic prediction applied to conventional breeding. We found that 3D-breeding could double the prediction accuracy of the benchmark. 3D-breeding could identify genotypes with enhanced local adaptation providing superior productive performance across seasons. We propose this decentralized approach to leverage the diversity in farmer fields and complement conventional plant breeding to enhance local adaptation in challenging crop production environments.publishedVersio