Pre-breeding of tef [Eragrostic tef (Zucc.) trotter] for tolerance to aluminium toxicity.

Doctor of Philosophy in Plant Breeding. University of KwaZulu-Natal, Pietermaritzburg 2015.Tef [Eragrostis tef (Zucc.) Trotter] is the most widely grown cereal crop in Ethiopia. Its grain is used for human consumption and the straw is an important and highly valued livestock feed. Soil acidity and Al toxicity are among the major production constraints affecting tef in Ethiopia. Utilization of lime and other non-genetic acid soil management options is constrained by various socio-economic factors. Development of cultivars with tolerance to Al-toxicity is a complementary approach to liming in the production of globally important crops such as wheat, rice, maize, barley, sorghum and rye. However, no breeding for tolerance to Al toxicity in tef had been undertaken previously. Hence, this research project was initiated in order to address the following objectives: 1. To assess the perceptions, challenges and coping mechanisms of farmers dealing with soil acidity and Al-toxicity in problem areas of north western Ethiopia; 2. To characterize the reactions of released tef varieties to soil acidity and the associated Al-toxicity; 3. To determine the extent of genetic diversity among tef germplasm collected from areas of Ethiopia with acid soil; 4. To isolate and characterize EMS-induced mutants of tef for tolerance to Al-toxicity and other important agronomic traits; 5. To evaluate the use of hydroponics system as a phenotyping platform to screen for Al-tolerance in tef, using root measurement and haematoxylin assay methods. There is no information on breeding for Al-tolerance in tef. Therefore, relational background literature was collated on other cereals on their mechanisms of Al-toxicity, tolerance mechanisms, genetic control, screening methods and marker assisted breeding. The information obtained from such sources was used to develop and undertake the subsequent breeding activities on tef. In order to meet the set objectives, several laboratory, greenhouse, and field experiments were conducted at the Amhara Regional Agricultural Research Institute (ARARI), Ethiopia, from December 2012 to June 2015. A Participatory Rural Appraisal (PRA) study was conducted in three Districts of north western Ethiopia that are affected by acid soils, in order to assess the state of soil acidity, and to determine its perceived causes and indicators, and to document the coping strategies of the farmers. Semi-structured interviews, group discussions and soil analyses were the main techniques used to generate data in this background study. Farmers’ perceived the causes of soil acidity to include: soil erosion; poor nutrient recycling; the abandoning of traditional fertility management practices; the unbalanced and/or minimal use of external inputs; and the exclusive use of acid-forming, inorganic fertilizers. Soil erosion, soil acidity, the high cost of mineral fertilizers and lime, cash shortages, and a lack of acid tolerant crop varieties were ranked as the top constraints. Species tolerance to soil acidity was found to be one of the major factors that influenced crop choice by farmers. A decline in genetic diversity and the rapid expansions of newly introduced, acid tolerant crops such as oat and triticale were noticed. The pH (H2O) of most of the soils in the study sites was in a strongly acidic range (4.6–5.5). Gashena Akayita of Banja District was the most acidic of all and had high levels of exchangeable Al. The limitations of the current coping strategies suggested the need to introduce compatible technologies that would ensure the sustainable management of the soils in the region, by the small-scale farmers there. Thirty three Released Varieties and selected accessions of tef were evaluated for their tolerance to soil acidity in pot trials. Twenty eight of these were then evaluated under field conditions. The results revealed the presence of significant genetic variability within the test genotypes. Nearly all the test genotypes were highly sensitive to soil acidity and Al-toxicity. However, a local landrace that is widely grown in Banja, a District severely affect by soil acidity, consistently outperformed the other genotypes both under pot and field conditions. There were changes in the ranking of the tef genotypes tested under pot and field conditions, which suggested the need to consider other edaphic and climatic factors when breeding for Al-tolerance. Overall, the grain yield of the test genotypes and the tolerant local landrace were less than the national mean yield of tef, identifying the need to develop varieties with better tolerance of acid soils and the associated Al-toxicity, aiming for superior agronomic performances in acid soils. Twenty-seven tef accessions collected from three regions of Ethiopia that are affected by acid soils were evaluated, together with released breeders’ varieties, and selected breeding materials for genetic diversity, using 16 selected and highly polymorphic SSR markers. Analysis of molecular variance (AMOVA) showed highly significant differences (P<0.001) among and within populations. Despite the wide geographical separation of the collection sites, 88.5% of the accessions from acid soils were grouped into two clusters (Clusters II and III) while 90% of the breeding materials and the Released Varieties were grouped into Cluster I. A significant degree of genetic differentiation was observed among the populations. Accessions from the north western Ethiopia exhibited a significant level of variation for most of the genetic diversity parameters. The number of private alleles was significantly higher for tef plants from acid soils than the Released Varieties and the breeding materials the Pair-wise estimates of genetic identity and gene flow showed higher values existed between the Released Varieties and breeding materials. About 15,000 M2 seeds were screened under acid soil conditions along with the M0 mutagenized seeds of the parent variety Tsedey and an Al-tolerant local landrace, Dabo banja. Twenty one M2 plants with root lengths of greater than the mean plus standard deviation of the tolerant check were selected and their M3 progenies were characterized for Al-tolerance and morpho-agronomic traits under greenhouse and field conditions, respectively. There were highly significant differences for Al-tolerance between the M3 mutant lines and the parent (P<0.001); and between the M3 mutant lines and the sensitive check (P<0.001). However, there was no significant difference between the M3 mutant lines and the tolerant check. The result of the morpho-agronomic characterization revealed the presence of significant differences between the M3 mutants for 16 of the 20 quantitative traits measured. Five levels of AlK(SO4)2.12H2O were evaluated (0, 150, 250,350, 450, 550 μM) in order to select the optimal concentration of Al that can most efficiently discriminate between sensitive and tolerant tef genotypes, using a hydroponic growing facility and measuring root lengths. The haematoxylin staining method was also assessed as a tool for the visual evaluation of tef varieties for Al-tolerance using selected test genotypes. There were highly significant differences (P<0.001) between the treatments, both for dose of Al and for genotype sensitivity to Al. The maximum differences in relative root length (RRL) (%) and root length (RL) (mm) between the sensitive and the tolerant genotypes were observed at the Al level of 150 μM Al. This concentration efficiently discriminated between 28 test genotypes with different levels of sensitivity to Al-toxicity. A visual assessment of the reactions of two sensitive and two tolerant genotypes to haematoxylin staining using 0, 150 and 250 μM of AlK(SO4)2.12H2O showed differential staining reactions in their roots that were consistent with their prior root growth measurements

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

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

Genomics-driven breeding for local adaptation of durum wheat is enhanced by farmers’ traditional knowledge

In the smallholder, low-input farming systems widespread in sub-Saharan Africa, farmers select and propagate crop varieties based on their traditional knowledge and experience. A data-driven integration of their knowledge into breeding pipelines may support the sustainable intensification of local farming. Here, we combine genomics with participatory research to tap into traditional knowledge in smallholder farming systems, using durum wheat (Triticum durum Desf.) in Ethiopia as a case study. We developed and genotyped a large multiparental population, called the Ethiopian NAM (EtNAM), that recombines an elite international breeding line with Ethiopian traditional varieties maintained by local farmers. A total of 1,200 EtNAM lines were evaluated for agronomic performance and farmers’ appreciation in three locations in Ethiopia, finding that women and men farmers could skillfully identify the worth of wheat genotypes and their potential for local adaptation. We then trained a genomic selection (GS) model using farmer appreciation scores and found that its prediction accuracy over grain yield (GY) was higher than that of a benchmark GS model trained on GY. Finally, we used forward genetics approaches to identify marker–trait associations for agronomic traits and farmer appreciation scores. We produced genetic maps for individual EtNAM families and used them to support the characterization of genomic loci of breeding relevance with pleiotropic effects on phenology, yield, and farmer preference. Our data show that farmers’ traditional knowledge can be integrated in genomics-driven breeding to support the selection of best allelic combinations for local adaptation

Technology generation to dissemination:lessons learned from the tef improvement project

Indigenous crops also known as orphan crops are key contributors to food security, which is becoming increasingly vulnerable with the current trend of population growth and climate change. They have the major advantage that they fit well into the general socio-economic and ecological context of developing world agriculture. However, most indigenous crops did not benefit from the Green Revolution, which dramatically increased the yield of major crops such as wheat and rice. Here, we describe the Tef Improvement Project, which employs both conventional- and molecular-breeding techniques to improve tef\u2014an orphan crop important to the food security in the Horn of Africa, a region of the world with recurring devastating famines. We have established an efficient pipeline to bring improved tef lines from the laboratory to the farmers of Ethiopia. Of critical importance to the long-term success of this project is the cooperation among participants in Ethiopia and Switzerland, including donors, policy makers, research institutions, and farmers. Together, European and African scientists have developed a pipeline using breeding and genomic tools to improve the orphan crop tef and bring new cultivars to the farmers in Ethiopia. We highlight a new variety, Tesfa, developed in this pipeline and possessing a novel and desirable combination of traits. Tesfa\u2019s recent approval for release illustrates the success of the project and marks a milestone as it is the first variety (of many in the pipeline) to be released

Soil acidity under multiple land-uses: assessment of perceived causes and indicators, and nutrient dynamics in small-holders’ mixed-farming system of northwest Ethiopia

Knowledge on farmers’ perspectives is of paramount importance in order to design appropriate agricultural research and development interventions attuned to local farming systems. A participatory rural appraisal was conducted in order to understand perceived causes and indicators of soil acidity under multiple land-uses in three Districts of northwest Ethiopia. Soil samples were also collected from five dominant land-uses. The samples were analysed for soil pH, exchangeable acidity and other physico-chemical properties. The result indicated that the pH(H2O) of most of the soils in the study sites were in a strongly acidic range (4.6–5.5). Gashena Akayita of the Banja District was the most acidic of all. Among the land-uses, eucalyptus fields were the most acidic followed by crop outfields and grazing lands in that order. At all the study sites, exchangeable Al was detected in soils having a pH of less than 5.0. Overall, the nutrient dynamics showed variation across land-uses and study sites. Farmers’ perceived causes of soil acidity included: soil erosion; contending use of fertility replenishing local resources; abandoning traditional fertility management practices and minimal use of external inputs. The farmers attributed the exclusive use of acid-forming inorganic fertilizers to exhaustion of the soil. Various land and soil characteristics, plant growth attributes, changes in genetic diversity were mentioned as indicators of soil acidity. Particularly, the farmers used prevalence of acidophilic weed species on crop fields and grazing lands as marker of strongly acidic soil. Farmers’ perceived causes and indicators were in agreement with scientific facts and can be utilized as input in designing sustainable acid soil management strategies. Decline in genetic diversity of the once widespread crop species and land races, and expansion of newly introduced soil acidity tolerant species, suggests the need to undertake rescue collections in these areas

Genetic diversity of Eragrostis tef accessions collected from acid soil-affected areas and cross-amplification of SSR markers linked to Al-toxicity tolerance in cereals

The aim of this study was to assess the extent of genetic diversity among and within tef populations collected from acid-affected soils in Ethiopia, and to test the cross-amplification of markers linked to Al-toxicity tolerance in other cereals. Forty-two tef genotypes were studied using 33 highly polymorphic SSRs. About 55% of the amplified putative alleles were effective in discriminating the genotypes. The mean PIC value was 0.66, suggesting that the majority of the markers had high discriminatory power. The population structure analysis revealed the presence of two genetically distinct populations and clearly distinguished landraces from the rest. A significant difference in genetic diversity parameters was observed between the two inferred populations. The landraces consistently had higher values for all of the diversity parameters and had contrastingly a higher value of private alleles. The AMOVA showed highly significant (P = 0.001) genetic variation among tef populations and among genotypes, with variance contribution of 17% and 67%, respectively. Eighty-two percent of the Al-toxicity tolerance markers amplified 84 alleles. This finding suggests the possibility of in-situ preservation of rare alleles that may confer acid tolerance through the improvement of available landraces in acid affected soils. Thus, urgent efforts are needed to collect accessions from areas with acid-affected soils

Assessment of the severity and incidence of Septoria tritici blotch (Zymoseptoria tritici) of wheat in Northwestern Ethiopia

Wheat is a global staple crop, which contributes 20% of the total dietary proteins and calories. Despite its importance, wheat production and productivity are affected by various biotic and abiotic stresses. Septoria leaf blotch is one of the biotic stresses that decreases production and grain quality. A field survey was conducted in twenty-four districts of Northwestern Ethiopia to figure out its distribution, inci dence, severity, and association with agronomic practices and agroecological factors. Logistic regression models were used to figure out associations of the disease intensity with independent variables. The highest mean disease incidence and severity were 90.7 and 46.67%. High severity and inci dence were associated with early planting, milk growth stage, and vertisol soil type. This shows that Septoria leaf blotch is a major biotic constraint for the study area. Therefore, effective, and suitable disease management options should be developed to improve the productivity of the crop in Northwestern Ethiopia