Association Mapping Reveals Novel Stem Rust Resistance Loci in Durum Wheat at the Seedling Stage

Wheat stem rust rapidly evolves new virulence to resistance genes. Recently emerged races in East Africa, such as TTKSK (or Ug99), possess broad virulence to durum cultivars, and only a limited number of genes provide resistance. An association mapping (AM) study conducted on 183 durum wheat accessions has allowed us to identify 41 quantitative trait loci (QTLs; determination coefficient [R2] values from 1.1 to 23.1%) for seedling resistance to one or more of four highly virulent stem rust races: TRTTF, TTTTF, TTKSK (Ug99), and JRCQC, two of which (TRTTF and JRCQC) were isolated from Ethiopia. Among these loci, 24 are novel, while the remaining 17 overlapped with loci previously shown to provide field resistance in Ethiopia and/or chromosome regions known to harbor designated stem rust resistance designated loci (Sr). The identified loci were either effective against multiple races or race specific, particularly for race JRCQC. Our results highlight that stem rust resistance in durum wheat is governed in part by loci for resistance across multiple races, and in part by race-specific ones (23 and 18, respectively). Collectively, these results provide useful information to improve the effectiveness of marker-assisted selection towards the release of durum wheat cultivars with durable stem rust resistance

Sources of Stem Rust Resistance in Ethiopian Tetraploid Wheat Accessions

Stem or black rust of wheat caused by the fungus Puccinia graminis f. sp. tritici Ericks and Henn (Pgt) is an important disease on wheat worldwide. Pgt is an obligate biotroph, heteroceous in its life cycle and heterothallic in mating type. Seedlings of 41 emmer ( Triticum dicoccum ), 56 durum (T. durum) wheat accessions were tested for their response to stem rust (Puccinia graminis f. sp. trictici) infection under greenhouse condition at Kulumsa Agricultural Research Center, Ethiopia. The test included screening of accessions and multipatotype testing to postulate sr genes. Vigorous screening of accessions was conducted using ten stem rust races, namely TKM/J, SKM/J, TTM/J, STM/J, TTL/K, TKR/J, TKM/J, TTM/H, SKM/J and JKM/G and, 33 stem rust differential lines. Flor's gene-for-gene theory was applied to postulate Sr genes in the tested accessions. Eighteen emmer and 6 durum accessions were found to be good sources of resistance to stem rust infection. In addition, the presence of Sr 7b, 8b, 9a, 9b, 10, 14, 24, 27, 28, 29, 30, 31, 32 and Tt-3 + 10 genes was postulated in 16 selected emmer and 5 durum wheat accessions. Hence, efforts to exploit these valuable Sr genes in Ethiopian cultivated tetraploid wheats could be rewarding to get stem rust resistant varieties and boost wheat production.La tige ou la rouille noire du blé causée par la moisissure Puccinia graminis f. sp. tritici Eriks et Henn (Pgt) est une maladie sérieuse universelle du blé. Le Pgt est une biotrophe, un hétérocious obligatoire dans le cycle de sa vie et un hétérothalique dans l'accomplissement de son espèce. Les jeunes plantes de 41 emmer ( Triticum dicoccum ), 56 durum (T. durum) nouvellement acquises étaient examinées en fonction de l'infection de la tige par l'infection de la rouille (Puccinia graminis f.sp. trictici) sous la condition de serre au Centre de Recherche Agronomique de Kalunsa en Ethiopie. L'expérience comprenait la sélection du blé nouvellement acquis et le test multipatotype pour postuler les gènes Sr. Une sélection rigoureuse de nouvelles acquisitions était entreprise en utilisant 10 races de tiges rouillées:TKM/J, SKM/J, TTM/J, STM/J, TTL/K, TKR/J, TKM/J, TTM/H, SKM/J et JKM/G et 33 tiges rouillées de traits différentiels. La théorie de Flor's gène-pour-gène était d'application pour postuler les gènes Sr pour l'examen des acquisitions nouvelles. Dix-huit emmer et six acquisitions nouvelles de durum étaient estimées comme source de résistance contre la contamination de la tige rouillée. En plus, la présence du Sr 7b, 8b, 9a, 9b, 10, 14, 24, 27, 28, 29, 30, 31, 32 et Tt-3+10 gènes étaient postulés dans 16 emmer sélectionnées et 5 durum du blé nouvellement acquis. Dès lors, des efforts pouvant permettre l'exploitation de ces Sr gènes Sr précieux des tétraploïdes éthiopiens cultivables pouvaient être considérés comme un don en tant que variétés résistant à la rouille des tiges et à la multiplication de la production du blé

The CIMMYT wheat breeding strategies and its relevance to Ethiopia

Wheat is the most important food security crop globally. Recent world wheat production stand at 766 million tons on 216 million hectares though wheat production is challenged by various biotic, abiotic, and other factors. As a global leader in wheat research, CIMMYT’s primary goal is to develop broadly adapted germplasm with high and stable yield, durable disease resistance, stress tolerance and acceptable end-use quality strategically addressing the different mega-environments such as irrigated regions, high-rainfall areas, acid soils, semiarid zones, tropical areas, and winter wheat zones. CIMMYT’s Global wheat program is one of the most important public sources of high yielding, nutritious, disease resistant and climate-resilient wheat varieties for Africa, Asia, and Latin America. The program works with the International Center for Agriculture Research in the Dry Areas (ICARDA), the CGIAR Research Program on Wheat, and NARS. The CIMMYT wheat breeding program is supported by multidisciplinary team of experts with breeders strategically and internationally located at key regional offices to facilitate germplasm and information exchange as well as technically support NARS. The primary focus of the breeding program is on core (must have) traits with some emphasis on additional traits for specific environments. The center is crossing, selecting, developing, and distributing stable, and high yielding advanced lines which includes some Zn and Fe enriched germplasm, with durable pest resistance, stress tolerance and superior quality using the different strategies, and methods, highlighted. In addition, CIMMYT collaboration with Ethiopian NARS in some areas will also be briefed

Management of wheat rust diseases, challenges and the way forward

Wheat is the most important food security crop globally. Recent world wheat production stand at 766 million tons on 216 million hectares though wheat production is challenged by various biotic, abiotic, and other factors. As a global leader in wheat research, CIMMYT’s primary goal is to develop broadly adapted germplasm with high and stable yield, durable disease resistance, stress tolerance and acceptable end-use quality strategically addressing the different mega-environments such as irrigated regions, high-rainfall areas, acid soils, semiarid zones, tropical areas, and winter wheat zones. CIMMYT’s Global wheat program is one of the most important public sources of high yielding, nutritious, disease resistant and climate-resilient wheat varieties for Africa, Asia, and Latin America. The program works with the International Center for Agriculture Research in the Dry Areas (ICARDA), the CGIAR Research Program on Wheat, and NARS. The CIMMYT wheat breeding program is supported by multidisciplinary team of experts with breeders strategically and internationally located at key regional offices to facilitate germplasm and information exchange as well as technically support NARS. The primary focus of the breeding program is on core (must have) traits with some emphasis on additional traits for specific environments. The center is crossing, selecting, developing, and distributing stable, and high yielding advanced lines which includes some Zn and Fe enriched germplasm, with durable pest resistance, stress tolerance and superior quality using the different strategies, and methods, highlighted. In addition, CIMMYT collaboration with Ethiopian NARS in some areas will also be briefed

Pathogenic Variability of Wheat Stem Rust Pathogen (Puccinia graminis f. sp. tritici) in Hararghe Highlands, Ethiopia

Wheat is one of the important major crops of Hararghe Highlands. It is third in land coverage and total production after sorghum and maize. However, the wheat stem rust disease is threatening production of wheat in this region. So, this research was conducted with the following objective: to determine the population of Puccinia graminis f. sp. tritici in Hararghe Highlands. A total of 200 fields were surveyed and stem rust samples were collected and transported to Kulumsa Agricultural Research Center for race analysis. Inoculation of differentials carrying resistance genes Sr24 and Sr-Tmp indicated typical low infection types on all isolates. Isolates EH5, EH8, and EH3 from East Hararghe and WH2, WH1, and WH3 from West Hararghe showed high virulence of infection in all differential lines. Ten (10) races were identified by using Puccinia graminis tritici code system: TTGSK, PTJQK, TTSSK, TTKSK, TRSSK, and TTJQK from East Hararghe and TTTSK and TTSQK from West Hararghe zones. Race TTSSK was most frequent (25%) followed by TTKSK (25%) in East Hararghe. Race TTSSK showed 50% frequency of occurrence in West Hararghe zones. The low frequency of occurrences indicated high variability of the races in the survey areas. Therefore, monitoring of populations of pathogens is important for the national and regional research centers. Detection of pathogen virulence evolution and of currently effective resistance genes is necessary and must be applied within a system of resistance gene management

Yellow Rust Resistance in Advanced Lines and Commercial Cultivars of Bread Wheat from Ethiopia

Bread wheat (Triticum aestivum L.) cultivars often succumb to yellow rust (Puccinia striiformis f.sp. tritici Westend.) soon after their release for commercial production, especially in the highlands of south-eastern Ethiopia. Variety diversification may buffer the ever evolving new races of the yellow rust pathogen. The objective of this study was to characterize seedling yellow rust resistance in 21 advanced bread wheat lines and 20 cultivars from Ethiopia. Yellow rust infection types (ITs) produced on test wheat lines and cultivars from nine yellow rust races were compared with ITs produced on standard differential lines that differed for specific yellow rust resistance genes. The experiment was conducted at seedling stage under greenhouse conditions in Goettingen, Germany during 2001. The result indicated that most of the advanced bread wheat lines possess different yellow rust resistance genes when compared to the commercial cultivars. Seedling genes Yr1, Yr2, Yr3V, Yr4, Yr6 and Yr17 with or without Yr9 were postulated to be present in 11 advanced lines. However, only Yr7 and Yr9 were postulated to be present in five of the commercial bread wheat cultivars. The newly identified resistance sources could be of great importance for enhancing the genetic base of resistance of bread wheat to yellow rust in Ethiopia

Identification of Stripe Rust Resistance in Ethiopian Durum Wheat by Phenotypic Screening and Kompetitive Allele Specific PCR (KASP) SNP Markers

Stripe (Yellow) rust caused by Puccinia striiformis f.sp. tritici (Pst) is one of the most devastating diseases of wheat in the highlands of Ethiopia. Improved cultivars often lose their resistance due to occurrence of new virulent races which overcome the genes and make the cultivars out of production. Therefore, identification of new sources of resistance genes helps in battling yellow rust and maximizes wheat production in Ethiopia. In this study, 300 durum wheat lines (landraces & cultivars) were screened with three virulent isolates (Pst_Is1, Pst_Is4 and Pst_Is8) for seedling resistance using Infection Type (IT) scoring method. The lines were also screened with 16 KASP-based SNP markers linked to 7 Yr genes already identified in various studies. Highly resistant infection type (IT: 0 -3) to Pst_Is1, Pst_Is4, and Pst_Is8 was exhibited by 59.3%; 67.3%; and 46.3% of the lines, respectively. 124 lines constantly exhibited high level of resistance to all three isolates. The majority (96.8%) of the resistant lines are landraces while four (3.2%) are commercial cultivars (Cocorit/71, Yerer, Obsa and Dire). In the molecular screening 12 of the markers gave clear amplifications in the controls and the tested lines. Yr7, Yr15 and YrSp were detected in 81.7%, 88.3% and 0.7% of the lines respectively while Yr1, Yr17 and Yr36 were not detected. Detection frequency was higher in landraces (58.7%) than in cultivars (32.8%). Gene combinations frequency was the highest (72.7%) for Yr7+Yr15 followed by Yr15+YrSp (0.3%). Overall, this study has resulted in detection of genes Yr15 and YrSp, which are potential candidates for marker assisted breeding for Pst resistance in wheat. Besides, it has shown that resistant source identification and detection of genes can be facilitated through combined application of phenotyping and molecular screening

Evaluation of nutritional, anti-nutritional and mineral content of amaranths species grown in Gamo and Konso zone, Southern Ethiopia

Amaranth (Amaranthus sp.) is an underutilized pseudo-cereal with excellent nutritional and functional properties. The nutritional compositions, anti-nutritional and mineral content of two Amaranth species were evaluated by using standard procedures. Completely Randomized Design (CRD) was used for nutritional, anti-nutritional and mineral content with two treatments and five replications. The nutritional compositions of Amaranthus cruentus and Amaranthus hypochondriacus were shown a significant difference (p<0.05) in mean scores excepting moisture content. Phytate and oxalate content of A. cruentus and A. hypochondriacus were shown a significant difference (p<0.05), but tannin content did not show a significant difference (p<0.05). The calcium, iron and zinc content of A. cruentus and A. hypochondriacus were shown a significant difference (p<0.05) in mean, scores. The Amaranth grain species were rich in crude protein, fat and fiber as compared to common cereal grains (maize, sorghum, rice, teff and wheat). A. cruentus and A. hypochondriacus can contribute minerals such as calcium, iron and zinc, which are very important for human nutrition. The results of the current study indicate that A. cruentus and A. hypochondriacus can provide better nutritional values and mineral content with a minimum value of anti-nutrients that are very important to minimize binds and block the absorption of certain minerals, such as iron, zinc and calcium. Using A. cruentus and A. hypochondriacus alone and with other cereals should be encouraged and recommended for consumption to increase the nutritional composition of diets and decrease food security problem in a study areas

Genome-wide association mapping identifies yellow rust resistance loci in Ethiopian durum wheat germplasm.

Durum wheat is an important cereal grown in Ethiopia, a country which is also its center for genetic diversity. Yellow (stripe) rust caused by Puccinia striiformis fsp tritici is one of the most devastating diseases threatening Ethiopian wheat production. To identify sources of genetic resistance and combat this pathogen, we conducted a genome wide association study of yellow rust resistance on 300 durum wheat accessions comprising 261 landraces and 39 cultivars. The accessions were evaluated for their field resistance using a modified Cobb scale at Meraro, Kulumsa and Chefe Donsa in the 2015 and 2016 main growing seasons. Analysis of the 35K Axiom Array genotyping data of the panel resulted in a total of 8,797 polymorphic SNPs of which 7,093 were used in subsequent analyses. Population structure analysis suggested two groups in which the cultivars clearly stood out separately from the landraces. Eleven SNPs significantly associated with yellow rust resistance were identified on four chromosomes (1A, 1B, 2B, and 5A) which defined at least five genomic loci. Six of the SNPs were consistently identified on chromosome 1B singly at each and combined overall environments which explained 62.6-64.0% of the phenotypic variation (R2). Resistant allele frequency ranged from 14.0-71.0%; Zooming in to the identified resistance loci revealed the presence of disease resistance related genes involved in the plant defense system such as the ABC transporter gene family, disease resistance protein RPM1 (NBS-LRR class), Receptor kinases and Protein kinases. This study has provided SNPs for tracking the loci associated with yellow rust resistance and a diversity panel which can be used for association study of other agriculturally important traits in durum wheat

Searching for novel sources of field resistance to Ug99 and Ethiopian stem rust races in durum wheat via association mapping

Puccinia graminis f. sp. tritici, the causative agent of stem rust in wheat, is a devastating disease of durum wheat. While more than 50 stem rust resistance (Sr) loci have been identified in wheat, only a few of them have remained effective against Ug99 (TTKSK race) and other durum-specific Ethiopian races. An association mapping (AM) approach based on 183 diverse durum wheat accessions was utilized to identify resistance loci for stem rust response in Ethiopia over four field-evaluation seasons and artificial inoculation with Ug99 and a mixture of durum-specific races. The panel was profiled with simple sequence repeat, Diversity Arrays Technology and sequence-tagged site markers (1,253 in total). The resistance turned out to be oligogenic, with twelve QTL-tagging markers that were significant (P < 0.05) across three or four seasons. R (2) values ranged from 1.1 to 11.3 %.Twenty-four additional single-marker/QTL regions were found to be significant over two seasons. The AM results confirmed the role of Sr13, previously described in bi-parental mapping studies, and the role of chromosome regions putatively harbouring Sr9, Sr14, Sr17 and Sr28. Three minor QTLs were coincident with those reported in hexaploid wheat and five overlapped with those recently reported in the Sebatel 7 Kristal durum mapping population. Thirteen single-marker/QTL regions were located in chromosome regions where no Sr genes/QTLs have been previously reported. The allelic variation identified in this study is readily available and can be exploited for marker-assisted selection, thus providing additional opportunities for a more durable stem rust resistance under field conditions