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The Ethiopian plateau hosts thousands of durum wheat landraces cultivated in low input agriculture conducted by an estimated 70 million smallholder farmers. Having thoroughly characterized the phenotypic and molecular uniqueness of Ethiopian durum wheat landraces, we produced a large nested association mapping (NAM) population harnessing their mostly untapped diversity in a set of recombinant inbred lines (RIL). The NAM founders are 50 landraces providing valuable traits such as drought tolerance and resistance to pests, and maximizing molecular diversity. Each selected landrace was crossed to a durum wheat line with an international background (Asassa), establishing independent interconnected bi-parental families, for a total of 6,280 RILs currently in F8. The Ethiopian NAM is at once i) a powerful QTL mapping tool that will side the increasing availability of genomic tools in wheat towards high-throughput candidate genes identification, and ii) a large pre-breeding panel closing the gap between local and international materials. Here we discuss the molecular and phenotypic characterization of twelve NAM families, represented by 100 RILs each. The 1,200 NAM RIL showed elevated allelic variation and a genetic structure reminiscent of the breeding design followed. The NAM RILs were phenotyped for ten agronomic and five disease traits in multiple locations in the Ethiopian highlands. A quantitative method eliciting smallholder farmers traditional knowledge was used to record local farmers appreciation of NAM RILs in all phenotyping locations. We report that the superior genetic properties of the NAM can be used to map QTL for both agronomic and farmer traits with unprecedented precision. The most promising NAM RILs can be identified combining farmers appreciation and agronomic measures, and prioritized for introgression of Ethiopian landraces traits in breeding pipelines aiming at higher uptake and productivity in local agriculture.
Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a significant disease limiting wheat yield in Ethiopia. Wheat varieties such as 'Digalu' with single major-effect stem rust resistance genes have not exhibited durable resistance in Ethiopia. Identifying wheat lines with adult plant resistance (APR) has been proposed as a strategy to select for durable resistance. Our objective was to test the hypothesis that APR to stem rust is non-race-specific. We selected 31 wheat lines (including 10 durum and 21 bread wheat lines) that were susceptible as seedlings to Pgt races TTKSK, TKTTF, and TRTTF. These 31 wheat lines and Digalu were evaluated in 2014 and 2015 at the Kulumsa Agricultural Research Center, Ethiopia. The lines were planted in 1 m rows and replicated twice in separate single-race-inoculated nurseries. The three single-race nurseries inoculated with Pgt races TTKSK, TKTTF, and TRTTF were separated by at least 100 m and included selective spreaders. Plot yield, thousand kernel weight (TKW), and visual disease responses were measured for each plot. We used a least-squared means test to detect differences in coefficient of infection and TKW of each line across paired race comparisons. Lines 'Park', 'CI11469', and 'CI12818' displayed significantly different coefficient of infections between races TTKSK and TRTTF. For CI11469 and CI12818, this difference was validated by significant differences in TKW. Significant differences in TKW were also detected between various race comparisons for 'ETHBW019', 'CI14798', 'CI15159', 'CI14618', and 'CI14094'. Our data demonstrated that APR in the selected germplasm was largely non-race-specific, but there were exceptions where race-specificity of APR was detected. These results have implications for resistance breeding and monitoring: testing of breeding material against prevalent Pgt races in target environments, not relying only on hotspot screening locations, and careful monitoring of deployed APR varieties are all warranted.
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.
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.
Wheat rusts can be controlled by host resistance or chemicals. Ethiopian farmers are not widely experienced with chemicals. Sixty seven (49 bread wheat (BW) and 18 durum (DW)) non-replicated varieties were planted on 0.4 m2 plots at 22 rust hotspot locations in 2014. Kubsa and Digalu were used as susceptible checks for YR and SR, respectively. Rust severities were scored according to the modified Cobb scale. Ten YR and 12 SR hotspot locations with mean rust severities of ≥40% were used in data analyses. Kubsa had a mean 59% YR severity and Digalu, a 73% SR severity. Rust severity levels were divided into three categories, viz. low (≤35%), moderate (36-40%) and high (>40%), across locations for both diseases. The frequency of varieties with low YR severities in the BW group was 26.5%, medium 18.4% and high 55.1% compared to DW varieties at 61%, 28% and 11%, respectively. In the case of SR, both BW and DW had large proportions of entries in the high severity category at 69.4% and 72.2%, respectively. The medium and low SR severity groups were represented by 20.4% and 10.2% for BW, and 11.1% and 16.7% for DW, respectively. In summary, the top 10 widely cultivated BW and a few DW varieties categorised in the medium and high severity groups for both YR and SR, would definitely require fungicides in rust-prone areas for optimum disease control. Many cultivars released after 1974 are still cultivated indicating that susceptible varieties are only slowly replaced. Hence, development and distribution of resistant cultivars, replacement of susceptible cultivars, and training industry workers and farmers on effective field scouting and fungicide use will be paramount for sustainable wheat production in Ethiopia.
Berberis holstii, native to the highlands of East Africa, is susceptible to Puccinia graminis and P. striiformis in artificial inoculations. However, it is not known whether these pathogens complete their sexual cycles in the region. In an attempt to understand the role of B. holstii in pathogen variation and epidemiology of wheat stem rust and stripe rust, we investigated the functionality of B. holstii as an alternate host. Natural aecial infections on B. holstii were observed and sampled in August at Mt. Kenya and Narok (Kenya), and June to December at North Shewa (Ethiopia) from 2008. Aeciospores from the collections were inoculated to a panel of cereal species, including Line E and ‘Morocco’ wheat, 'Hiproly’ barley, 'Prolific' rye, and ‘Marvelous’ oat. For the majority of aecial samples, aeciospore viability was lost during shipment and storage; thus inoculations were not successful. Inoculations using relatively fresh samples collected at North Shewa in 2012 and 2014, resulted in stem rust infections on Line E, Prolific, Hiproly, and Marvelous. DNA assays using real-time PCR confirmed the presence of P. graminis in these samples. While it is likely that the pathogen infecting Line E, Prolific and Hiproly is P. graminis f. sp. secalis (Pgs), the inoculation and DNA assays did not provide sufficient resolution to distinguish Pgs from Pgt. Stem rust infections on Marvelous were assumed to involve Pg f. sp. avenae. Experiments are in progress to characterize isolates derived from these samples, and to determine if other rust fungi are present in these samples. Based on these preliminary data, we conclude that P. graminis completes its sexual cycle in Ethiopia. The contribution of the sexual cycle to the observed variation within the Pgt population in the region remains unclear.
During the 2014/15 main crop season 831 wheat fields and experimental plots were assessed for diseases; 66.2% were in the Oromiya, 20.3% in Tigray and 13.4% in SNNP regions. The major diseases encountered include rusts, septoria leaf blotches, foot and root diseases, Fusarium head blight and smuts. The overall mean prevalence of stem rust was 61%, yellow rust 22%, leaf rust 18.8% and Septoria leaf blotches 52.9%. The incidence of the important diseases was highest in SNNP region. The mean incidence of yellow rust ranged from 5.7% in Oromiya to 39.2% in SNNP. The lowest incidence of stem rust, 15.9%, was noted in Tigray and the highest, 64.4%, in SNNP. The minimum mean Septoria incidence was 23% in Oromiya, and maximum was 66.7% in SNNP. Stem rust severities varied from 7 MR-MSS in Tigray to 36 MR-MSS in SNNP. Furthermore, the widely grown varieties Digelu and Danda’a were resistant to yellow rust, but susceptible to stem rust. Varieties Meda Wolbu, Hogona and Ogolcho were not affected by any of the rusts in Oromiya. Variety Hidase was susceptible in SNNP. Out of 115 Pgt cultures established from stem rust samples collected from the three regions, races TKTTF, RRTTF, TTKSK, TRTTF and JRCQC were identified. Stem rust samples were collected from varieties Digelu, Danda’a, Kakaba, and Hidase. Race TKTTF, virulent on Digalu and first identified in Oromiya region in 2013, is now present in all areas. Adapted varieties with durable stem rust resistance in Ethiopia remains an urgent requirement.
Pgt race TKTTF, virulent for the SrTmp gene present in Ethiopian cv. Digalu and first detected in 2012, caused significant yield losses in Digalu during the 2013 and 2014 seasons. No suitable replacement varieties with significant seed volume were available, and alternate solutions were sought. EIAR, with the support of the DRRW project through CIMMYT-Ethiopia, introduced 5 tonnes of adult plant, rust resistant wheat cv. Kingbird from Kenya. Kingbird was evaluated for agronomic performance at seven locations vs. three checks in 2014, and was also evaluated for stem rust reaction in single-race nurseries (TKTTF, TTKSK, TRTTF and JRCQC). With support from USAID/CIMMYT, seed was concurrently multiplied on 37 ha producing 80 tonnes of seed that was distributed to farmers in 2015. Mean grain yield over locations was 2.76 t ha-1. Mean performance of Kingbird was 3.00 t ha-1 compared to 2.79 t ha-1 for Ogolcho, 2.83 t ha-1 for Biqa and 2.42 t ha-1 for Kakaba. Thus Kingbird gave yield advantages of 5 to 22% over the check varieties. Stem rust severities on Kingbird in the single race nurseries ranged from Tr to 15% and reactions ranged from TMR to SMS. The check varieties rated up to 45% severity with S type reactions. Thus Kingbird was superior in terms of yield potential and stem rust resistance as measured in these trials vs. the check varieties. Stem rust resistance of Kingbird is based on Sr2 and Sr57 and is hypothesized to have at least three additional APR loci. Seedling reactions of Kingbird to races TKTTF and Ug99 are characterized as susceptible. Sr57 is pleiotropic and confers partial resistance to all three rusts, powdery mildew, spot blotch, and BYDV. Based on early maturity, yield performance, and stem rust resistance, Kingbird is recommended for low- to mid-altitude wheat-growing areas of Ethiopia.
Recurrent outbreaks of rusts debilitated mega wheat varieties in major production areas in Ethiopia. Projects to accelerate seed multiplication of rust resistant varieties funded by USAID, BMGF and others contributed to the replacement of the widely grown susceptible varieties Kubsa and Galama. In 2013/14, a new Pgt race (TKTTF) - unrelated to Ug99 - caused 100% yield losses on bread wheat variety Digalu. The continuing epidemic calls for fast replacement of the now susceptible varieties by accelerated seed multiplication to scale-up new varieties with durable rust resistance, and demonstrations to promote their adoption. In 2014, CIMMYT initiated a short term R4D project ‘Emergency Seed Support and Demonstration of Rust Resistant Wheat Varieties in Stem Rust Affected Areas of Ethiopia’. The project was financed by USAID and implemented in collaboration with EIAR, regional agricultural research institutes, and the Oromia Bureau of Agriculture. In collaboration with DRRW, CDL, and WSU, technical assistance was given to research centers to phenotype and genotype their breeding lines and commercial cultivars. A total of 352 Development Agents (15% female) were trained in rust identification, seed technology and crop management. Eight rust resistant varieties were demonstrated on 430 model farms in 16 districts in Oromia, Amhara and SNNPR. Awareness was created through field days organized by the Kulumsa and Sinana research centers in Arsi and Bale, respectively. Technical and financial support was given to four federal (Kulumsa, Werer, Debre Zeit, and Holetta) and three regional (Mekele, Sinana, and Adet) research centers for early generation seed multiplication. A total of 2,000 resource-poor farm households (10% female headed) selected on the basis of having suffered heavy losses to stem rust in the previous season, received technical assistance and 165 tonnes of seed of rust resistant varieties. Assisted farmers recorded above average zonal yields in 2014/15.