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Stripe rust caused by Puccinia striiformis f.sp.tritici, is one of the major diseases of wheat in the world. Experiments were carried out at two sites in Ethiopia (Kulumsa and Meraro) during the 2015 cropping season to evaluate the response of 198 elite bread wheat genotypes and two checks to the prevailing races of stripe rust at adult plant and seedling stage. The genetic profile of these genotypes was assessed using 13006 SNP markers and an association mapping was explored to determine marker?trait association. About 72.5% and 42.5% of the lines exhibited resistance at Kulumsa and Meraro, respectively. Out of 198 genotypes tested in the greenhouse, 31% exhibited common resistance for Kubsa and mixed stripe rust isolate. Only 8966 of the SNPs were polymorphic, only these were used for association mapping analysis. These markers spanned an average density of 3.47 cM per marker, with the poorest density on the D genome. Almost half of these markers were on known chromosomes, but had no position on the consensus map of bread wheat. Analysis of population structure revealed the existence of three clusters and the estimated genomic wide Linkage Disequilibrium (LD) decay in this study ranged from 0 to 50 cM. 53 SNPs in ten genomic regions located on wheat chromosome 1AL, 2AL, 2BL, 2DL, 3BL, 4BL, 4DL, 5AS, 7AL and 7BL were identified. Thirty nine SNP markers in five genomic regions at Kulumsa and 14 SNP markers in six genomic regions at Meraro explained more than 25.5% and 35.1% of phenotypic variability respectively. For seedling stage, 21 markers in ten genomic regions located on wheat chromosomes 1B, 2A, 2B, 3A, 3B, 4B, 4D, 5A, 6B and 7B were associated with resistant. These loci may be useful for choosing parents and incorporating new resistance genes into locally adapted cultivars.
In Ethiopia, breeding resistant wheat varieties is a priority for wheat rust management although new virulent rust races have periodically resulted in losses of R-genes, epidemic outbreaks, and yield losses of up to 100%. During 2014 and 2015, 160 wheat varieties and lines including five checks and 12 differential lines with known resistance genes were evaluated against four stem rust pathogen races at both seedling and adult plant stages. In the field at Kulumsa, Ethiopia, the lines were evaluated in four separate nurseries in an augmented design where each nursery was inoculated with a different Puccinia graminis f. sp. tritici race: TTKSK, TKTTF, TRTTF, and JRCQC. Kingbird, a check variety, displayed low average Area Under the Disease Progress Curve (AUDPC) (67 to 238) and Average Coefficient of Infection (ACI) (1.1 to 9.7) in response to the four races. Effect of lines possessing Sr24+Sr36 and Sr31+Sr36 resistance genes on rust development was comparable to Kingbird or even better. Likewise, 48, 34, 19 and 28 varieties and lines had lower or comparable AUDPC for TTKSK, TKTTF, TRTTF and JRCQC compared to Kingbird. Commercial bread wheat varieties Shorima, Huluka, Hogana, and advanced lines CIMMYT 14, ETBW7058, ETBW7101 and ETBW7258 for which Sr24/Lr24 was postulated, possessed AUDPC and ACI lower than Kingbird. However, all these lines possessed susceptible or intermediate seedling reactions to Sr24-virulent race TTKTT from Kenya at the seedling stage. CIMMYT 18 showed susceptibility to 3 races at seedling stage, but lower AUDPC and ACI than the checks except Kingbird, indicating adult plant resistance. However, this adult plant resistance was marginal in effect to race TKTTF. Resistance genes Sr2, Sr57/Lr34, Sr24/Lr24, Sr25/Lr19, Sr38/Lr37 and SrTmp were postulated at various frequencies in this germplasm. Seedling and adult plant resistance sources identified can be used for rust resistance breeding in Ethiopia.
In Ethiopia, quality seed of improved varieties is the least expensive and most critical input for the sustainable production of wheat, a strategic food security crop grown by some 4.7 million households on 1.7 million hectares. Because wheat is self-pollinated, farmers can save and replant seed from their harvests for several years, without the variety losing its genetic identity. At the same time, recommended seed rates for wheat (150 to 200 kilograms per hectare) are significantly higher than those for tef (15 kg/ha) or maize (25 kg/ha), so some 255,000 tons of seed is required to sow Ethiopia's entire wheat area each year. Most of this still comes from informal seed systems; only four seed enterprises (ESE, ASE, OSE and SNNPSE) currently produce certified seed of various crops and they lack the capacity to supply enough high quality seed for the nation's approximately 20 million households. In collaboration with the Ethiopian Institute of Agricultural Research (EIAR) and through the USAID-funded project "Seed multiplication and delivery of high-yielding rust resistant bread and durum wheat varieties to Ethiopian farmers," the International Maize and Wheat Improvement Center (CIMMYT) is working to increase wheat farmers access to affordable, certified seed of improved varieties that are high-yielding and also feature durable resistance to the rust diseases. Approaches pursued include the fast-track evaluation and release of improved varieties, the pre-release or accelerated seed multiplication of released wheat varieties through formal and informal seed systems, and demonstrations and scaling up of improved wheat varieties. This paper describes best practices to address seed shortages faced by wheat farmers in 53 woredas.
Septoria tritici blotch (STB) is a devastating fungal disease affecting durum and bread wheat cultivation worldwide. The search for resistance sources in untapped genetic resources may speed up breeding for STB resistance. Ethiopian durum wheat landraces represent a valuable source of allelic diversity for several traits, including disease resistance. In this study, we measure STB phenotypes under natural infection on two interconnected populations: i) a diversity panel comprising 318 Ethiopian durum wheat lines, mostly farmer varieties, and ii) a nested association mapping (NAM) population developed from a subset of the diversity panel. Phenology, yield and yield component traits were concurrently measured in the populations. We evaluated the distribution of STB resistance in Ethiopian genetic materials and the relationship existing between STB resistance and agronomic traits. STB resistance sources were found in landraces as well as in NAM lines. The genetic material was genotyped with more than 13 thousand genome-wide SNP markers to describe the linkage disequilibrium and genetic structure existing within the panels. The genotyping information was combined with phenotypes to identify marker-trait associations and loci involved in STB resistance. We identified several loci, each explaining up to 10% of the phenotypic variance for disease resistance. We developed KASP markers tagging the most interesting loci to allow the uptake of our results in a breeding perspective. Our results showed that the Ethiopian untapped allelic diversity bears a great value for studying the molecular basis of STB resistance and for breeding for resistance in local and international material.
Stem rust caused by Puccinia graminis f. sp. tritici (Pgt) is a major production constraint in most wheat growing areas of Ethiopia. The stem rust pathogen is capable of rapidly developing new virulence to resistance genes. The highlands of Ethiopia are considered a hot spot for Pgt diversity. The present study was conducted to investigate the virulence diversity and spatial distribution of races of Pgt in the major wheat growing areas of Ethiopia. The physiologic races of Pgt were determined on seedlings of the standard wheat stem rust differentials following the international system of nomenclature. Stem rust race analyses were carried out both at Ambo Plant Protection Center and the Cereal Disease Laboratory in Minnesota. 426 stem rust samples were collected from major wheat growing of the country in the 2016 cropping season and 185 viable samples were analyzed. Stem rust races TKTTF, TTKSK, TTTTF, JRCQC and RRTTF were identified. Among the identified races, TKTTTF was dominant at a frequency of 78.7% followed by TTKSK (10.6%). Race TTTTF was found for the first time in Ethiopia in 2016. Only one resistance gene in the differential set, Sr24, was effective against all isolates. Stem rust resistance gene Sr31 was found to confer resistance to most of the races prevalent in Ethiopia with the exception of Ug99. Sr24 could be used in combination with other resistance genes in breeding for resistance to stem rust in Ethiopia.
Information about changes associated with advances in crop breeding is essential for understanding yield-limiting factors and developing new strategies for future breeding programmes. Thirty-six durum wheat varieties released since 1966 were evaluated in three replications of the Randomized Complete Design at Debre Zeit and Akaki, Ethiopia during the 2016 cropping season to estimate the amount of genetic gain made over time in grain yield potential, yield-associated traits and in protein content. Analysis of variance revealed significant differences among varieties for all 16 quantitative traits, protein content and protein harvest in Kg ha-1 at each of the locations. Grain yield varied between 1.66t ha-1 for Arendato released in 1966 to 3.90t ha-1 for Megenagna released in 2012 with mean of 2.952t ha-1 at Debre Zeit. At Akaki yield range was between 2.45 and 5.04t ha-1 with mean of 3.992t ha-1. 25 varieties surpassed Arendato (3.754t ha-1) at this location. In the combined ANOVA significant difference between the varieties was observed only for spike length, spikelets spike-1, grains spikelet, grains spike-1, plant height, days to flowering, thousand grain weight and hectoliter weight. Varieties specifically adapted to only one of the locations, widely adapted varieties and varieties not adapted to any of the locations were identified. Regression analysis revealed that grain yield has increased by 22kg ha-1 year-1 since 1966; an increase of 40.6% over yield in 1966. This was accompanied with a significant decline of 11.4% in spike length, 6.7% in spikelets spike-1, 17.9% in protein content and 31.2% in protein yield ha-1 and a significant increase of 41.1% in grains spikelet-1, 32.9% in number of grains spike-1, 22.3% in thousand grain weight, 17.8% in grain filling period, 23.9% in seed growth rate, 40.1% in grain yield production rate, 7.9% in harvest index.
Puccinia graminis f. sp. tritici (Pgt) is the major wheat production constraint in Ethiopia causing recurrent epidemics that resulted in the withdrawal of widely grown wheat cultivars from production. Among the current Pgt races detected in Ethiopia, TKTTF is the most frequent and has caused a severe epidemic in the south wheat growing regions (Bale and Arsi) after its first detection in 2012. Therefore, to avert the current situation, identifying sources of resistance to race TKTTF in breeding germplasm is a top priority to the National Wheat Breeding Program. Hence, 82 promising bread wheat lines including five check cultivars were evaluated in Debre Zeit in a TKTTF single race nursery for three consecutive seasons, 2014-2016. Ethiopian bread wheat cultivar Digalu was used as a spreader row and was inoculated using a single isolate of race TKTTF at different growth stages. The nursery was bounded by oat to reduce interference with any other stem rust race. The 82 lines were tested in the greenhouse at Cereal Disease Laboratory and were also tested with known diagnostic molecular markers. Twenty-nine lines displayed low levels of terminal stem rust severity in the field and low coefficient of infections. Fourty-one lines were resistant to race TKTTF at the seedling stage. Bread wheat lines resistant to TKTTF are valuable sources of resistance that can be deployed in wheat growing regions of Ethiopia prone to stem rust.
Wheat stem rust is one of the major wheat yield limiting factors in Ethiopia. A stem rust epidemic occurred in the wheat belts of Arsi and Bale zones in the 2013-2014 crop season caused by Pgt race TKTTF that is virulent to the widely grown Ug99-resistant variety Digelu. This epidemic highlighted the need for wheat varieties with resistance to multiple Pgt races. This study was therefore, carried out to evaluate the reaction of the major Ethiopian varieties and advanced breeding lines against the dominant Pgt races in Ethiopia. Races TKTTF, TTKSK, TRTTF and JRCQC were isolated from field samples and multiplied on the susceptible cultivar McNair starting in May 2014. Four wheat stem rust nurseries, each inoculated with a single Pgt race, were established at Kulumsa and monitored from July through October, 2014. Each nursery included 34 entries in two replicates and 137 entries in a single replicate, augmented with six sets of five repeating checks. An additional nursery established at Debre Zeit, containing 551 entries in an augmented design, was evaluated with the epidemic Pgt race TKTTF. These entries included the most relevant Ethiopian bread and durum wheat breeding lines and cultivars, and 34 seedling-susceptible lines to evaluate the race-specificity of adult plant resistance. Stem rust severities for the four races ranged from trace to 80 %. Out of all entries evaluated, 10 were resistant to all four Pgt races, while 11 entries were effective to three of the four races. At Debre Zeit, 31.4% of the entries were resistant to Pgt race TKTTF. This study showed that rapid isolation and increase of Pgt races in Ethiopia is possible to facilitate field screening of breeding lines to select for candidate cultivars with resistance to multiple virulent races of Pgt.
CIMMYT wheat germplasm flow to Ethiopia started in the late 1960s. Over 90 bread wheat varieties were released over the decades. Of these, about 77% had CIMMYT origins or were derived from CIMMYT materials. Wheat is a traditional rainfed crop grown by 5 million small-scale farmers on 1.6 ha more or less. Yields have increased from 1.0 t/ha in the 1960s to 2.54 t/ha in 2014 mainly due to high yielding semi-dwarf bread wheat varieties and modern agronomic practices. Using such technologies, better farmers often get 5-6 t/ha. The rusts are the most important production constraints. For example, the 2010 yellow rust epidemic debilitated the mega varieties Kubsa and Galama in the highlands. In 2013/14, stem rust caused up to 100% yield losses in the widely adopted bread wheat variety Digalu in Arsi and Bale. This epidemic was caused by Pgt race TKTTF, which is virulent to the gene SrTmp that is present in Digalu, but is avirulent to Sr31, which is overcome by race Ug99 (TTKSK) and derivatives. To avert the increasing threat of rusts, CIMMYT developed a shuttle breeding program where germplasm moves back and forth between Mexico and Kenya and has increased nursery testing sites (Holetta, Kulumsa, Debre Zeit, Sinana, Adet, and Melkassa) in Ethiopia from two to six. The germplasm passes through rigorous tests against major diseases during both the main- and off-seasons. To obtain high yielding rust resistant germplasm, many hundreds of genotypes were introduced and tested over the last two years. In 2014/15, 266 (25%) lines with multiple disease resistances and high yield were promoted to national trials. CIMMYT continues to be an important source of germplasm. Fast tracked variety testing and release, accelerated seed multiplication, demonstration and popularization of new varieties with high yield, multiple disease resistance, and acceptable quality will continue.
Stem rust (SR) resistance is required for CIMMYT durum germplasm to keep relevance in Ethiopia, where Ug99 and other Pgt races are a major yield-limiting constraint, and in countries along the possible dissemination paths of these races. Resistance to Ug99 is widespread in most durum germplasm groups when tested in Kenya, but resistance is lost when exposed to Ethiopian races; hence selection at the Debre Zeit site in Ethiopia is essential for durum wheat. Due to difficulties with shuttling segregating populations between Mexico and Ethiopia, we have adopted a strategy involving the identification of resistant/moderately resistant lines at Debre- Zeit, and inter-crossing in Mexico followed by selection for resistance to leaf rust and agronomic type and finally screening for SR reaction in the resulting F6 lines at Debre-Zeit at the same time as they are tested for yield and quality in preliminary yield trials in Mexico. This has generated a significant increase in the proportion of resistant and moderately resistant genotypes within outgoing CIMMYT germplasm, from less than 3% at the onset of the initiative in 2008 to 16% in 2011, and 38% in 2013. SR-resistant germplasm was characterized by similar frequency distributions to other traits in the overall germplasm such as yield potential, drought tolerance and industrial quality parameters. Advances have also been realized using marker-assisted selection (MAS) to introgress Sr22 from bread wheat and to combine it with Sr25, producing advanced lines with 2-gene stacks with confirmed outstanding resistance and superior quality attributes. Since the two genes are closely linked but from different sources bringing them together required a very rare recombination event finally detected via MAS among thousands of plants. They are now essentially inherited together with a very low likelihood of generating recombinant individuals with either gene. The yield potential and stability of these lines are under evaluation in Ethiopia and the best lines are being used in a second round of breeding.