Genome-wide association analysis unveils novel QTLs for seminal root system architecture traits in Ethiopian durum wheat.

BACKGROUND: Genetic improvement of root system architecture is essential to improve water and nutrient use efficiency of crops or to boost their productivity under stress or non-optimal soil conditions. One hundred ninety-two Ethiopian durum wheat accessions comprising 167 historical landraces and 25 modern cultivars were assembled for GWAS analysis to identify QTLs for root system architecture (RSA) traits and genotyped with a high-density 90 K wheat SNP array by Illumina. RESULTS: Using a non-roll, paper-based root phenotyping platform, a total of 2880 seedlings and 14,947 seminal roots were measured at the three-leaf stage to collect data for total root length (TRL), total root number (TRN), root growth angle (RGA), average root length (ARL), bulk root dry weight (RDW), individual root dry weight (IRW), bulk shoot dry weight (SDW), presence of six seminal roots per seedling (RT6) and root shoot ratio (RSR). Analysis of variance revealed highly significant differences between accessions for all RSA traits. Four major (- log10P ≥ 4) and 34 nominal (- log10P ≥ 3) QTLs were identified and grouped in 16 RSA QTL clusters across chromosomes. A higher number of significant RSA QTL were identified on chromosome 4B particularly for root vigor traits (root length, number and/or weight). CONCLUSIONS: After projecting the identified QTLs on to a high-density tetraploid consensus map along with previously reported RSA QTL in both durum and bread wheat, fourteen nominal QTLs were found to be novel and could potentially be used to tailor RSA in elite lines. The major RGA QTLs on chromosome 6AL detected in the current study and reported in previous studies is a good candidate for cloning the causative underlining sequence and identifying the beneficial haplotypes able to positively affect yield under water- or nutrient-limited conditions.

Genetic diversity and population structure analysis based on the high density SNP markers in Ethiopian durum wheat (Triticum turgidum ssp. durum).

BACKGROUND: Ethiopia has been considered as a center of diversity and the second possible center of domestication of durum wheat. Genetic diversity and population structure analysis in the existing Ethiopian durum wheat germplasm have enormous importance in enhancing breeding effort and for sustainable conservation. Hence, 192 Ethiopian durum wheat accessions comprising 167 landraces collected from major wheat-growing areas of the country and 25 improved varieties released from Debre Zeit and Sinana Agricultural Research Centers, Ethiopia in different years (1994-2010) were assembled for the current study. RESULTS: The panel was genotyped with a High-density 90 K wheat SNP array by Illumina and generated 15,338 polymorphic SNPs that were used to analyze the genetic diversity and to estimate the population structure. Varied values of genetic diversity indices were scored across chromosomes and genomes. Genome-wide mean values of Nei's gene diversity (0.246) and polymorphism information content (0.203) were recorded signifying the presence of high genetic diversity within this collection. Minor allele frequency of the genome varied with a range of 0.005 to 0.5 scoring a mean value of 0.175. Improved varieties clustered separately to landraces in population structure analysis resulted from STRUCTURE, PCA and neighbor joining tree. Landraces clustering was irrespective of their geographical origin signifying the presence of higher admixture that could arise due to the existence of historical exchanges of seeds through informal seed system involving regional and countrywide farming communities in Ethiopia. CONCLUSIONS: Sustainable utilization and conservation of this rich Ethiopian durum wheat genetic resource is an irreplaceable means to cope up from the recurrent climate changes and biotic stresses happening widely and thereby able to keep meeting the demand of durum productivity for the ever-growing human population.

MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens.

BACKGROUND: Effective disease management depends on timely and accurate diagnosis to guide control measures. The capacity to distinguish between individuals in a pathogen population with specific properties such as fungicide resistance, toxin production and virulence profiles is often essential to inform disease management approaches. The genomics revolution has led to technologies that can rapidly produce high-resolution genotypic information to define individual variants of a pathogen species. However, their application to complex fungal pathogens has remained limited due to the frequent inability to culture these pathogens in the absence of their host and their large genome sizes. RESULTS: Here, we describe the development of Mobile And Real-time PLant disEase (MARPLE) diagnostics, a portable, genomics-based, point-of-care approach specifically tailored to identify individual strains of complex fungal plant pathogens. We used targeted sequencing to overcome limitations associated with the size of fungal genomes and their often obligately biotrophic nature. Focusing on the wheat yellow rust pathogen, Puccinia striiformis f.sp. tritici (Pst), we demonstrate that our approach can be used to rapidly define individual strains, assign strains to distinct genetic lineages that have been shown to correlate tightly with their virulence profiles and monitor genes of importance. CONCLUSIONS: MARPLE diagnostics enables rapid identification of individual pathogen strains and has the potential to monitor those with specific properties such as fungicide resistance directly from field-collected infected plant tissue in situ. Generating results within 48 h of field sampling, this new strategy has far-reaching implications for tracking plant health threats.

Characterization of Ethiopian Wheat Germplasm for Resistance to Four Puccinia graminis f. sp. tritici Races Facilitated by Single-Race Nurseries.

In Ethiopia, breeding rust resistant wheat cultivars is a priority for wheat production. A stem rust epidemic during 2013 to 2014 on previously resistant cultivar Digalu highlighted the need to determine the effectiveness of wheat lines to multiple races of Puccinia graminis f. sp. tritici in Ethiopia. During 2014 and 2015, we evaluated a total of 97 bread wheat and 14 durum wheat genotypes against four P. graminis f. sp. tritici races at the seedling stage and in single-race field nurseries. Resistance genes were postulated using molecular marker assays. Bread wheat lines were resistant to race JRCQC, the race most virulent to durum wheat. Lines with stem rust resistance gene Sr24 possessed the most effective resistance to the four races. Only three lines with adult plant resistance possessed resistance effective to the four races comparable with cultivars with Sr24. Although responses of the wheat lines across races were positively correlated, wheat lines were identified that possessed adult plant resistance to race TTKSK but were relatively susceptible to race TKTTF. This study demonstrated the importance of testing wheat lines for response to multiple races of the stem rust pathogen to determine if lines possessed non-race-specific resistance. Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Markers Linked to Wheat Stem Rust Resistance Gene Sr11 Effective to Puccinia graminis f. sp. tritici Race TKTTF.

Wheat stem rust, caused by Puccinia graminis f. sp. tritici, can cause severe yield losses on susceptible wheat varieties and cultivars. Although stem rust can be controlled by the use of genetic resistance, population dynamics of P. graminis f. sp. tritici can frequently lead to defeat of wheat stem rust resistance genes. P. graminis f. sp. tritici race TKTTF caused a severe epidemic in Ethiopia on Ug99-resistant 'Digalu' in 2013 and 2014. The gene Sr11 confers resistance to race TKTTF and is present in 'Gabo 56'. We identified seven single-nucleotide polymorphism (SNP) markers linked to Sr11 from a cross between Gabo 56 and 'Chinese Spring' exploiting a 90K Infinium iSelect Custom beadchip. Five SNP markers were validated on a 'Berkut'/'Scalavatis' population that segregated for Sr11, using KBioscience competitive allele-specific polymerase chain reaction (KASP) assays. Two of the SNP markers, KASP_6BL_IWB10724 and KASP_6BL_IWB72471, were predictive of Sr11 among wheat genetic stocks, cultivars, and breeding lines from North America, Ethiopia, and Pakistan. These markers can be utilized to select for Sr11 in wheat breeding and to detect the presence of Sr11 in uncharacterized germplasm.

Pathways to wheat self-sufficiency in Africa.

A growing urban population and dietary changes increased wheat import bills in Africa to 9% per year. Though wheat production in the continent has been increasing over the past decades, to varying degrees depending on regions, this has not been commensurate with the rapidly increasing demand for wheat. Analyses of wheat yield gaps show that there is ample opportunity to increase wheat production in Africa through improved genetics and agronomic practices. Doing so would reduce import dependency and increase wheat self-sufficiency at national level in many African countries. In view of the uncertainties revealed by the global COVID-19 pandemic, extreme weather events, and world security issues, national policies in Africa should re-consider the value of self-sufficiency in production of staple food crops, specifically wheat. This is particularly so for areas where water-limited wheat yield gaps can be narrowed through intensification on existing cropland and judicious expansion of rainfed and irrigated wheat areas. Increasing the production of other sources of calories (and proteins) should also be considered to reduce dependency on wheat imports.

Evaluation of buffalograss genotypes and full-sibs for chinch bug resistance.

Fifteen buffalograss, Buchloe dactyloides (Nutt.) Engelm, genotypes and 94 diploid full-sib progeny were evaluated for western chinch bug, Blissus occiduus Barber (Hemiptera: Lygaeidae), resistance in two separate studies. The experimental design for each study was a completely randomized design. Adult chinch bugs were introduced onto caged single clone genotypes and progeny in the greenhouse. Chinch bug damage was assessed using a 1-5 visual damage rating scale with 1 = < or = 10%; 2 = 11-30%; 3 = 31-50%; 4 = 51-70%; and 5 = > or = 70% of the buffalograss leaf area with severe discoloration, or dead tissue. Highly significant differences were found among the genotypes and progeny for chinch bug damage. Among the genotypes, Legacy, Prestige, 184, 196, Bowie, NE 3297, NE 2769, and NE 2768 were moderately resistant with damage ratings of > 1, but < 3, while NE 2990, NE 2838, and 1-57-19 were moderately susceptible with damage ratings of > or = 3, but < 4. Among the progeny, one progeny (MP45) was highly resistant with a chinch bug damage rating of 1.0, 78 progeny (83%) had moderate resistance, with damage ratings of > 1.0 and < 3.0, 13 progeny (14%) were moderately susceptible with damage ratings ranging from 3.0 to 3.9, while only two were highly susceptible with damage ratings of > or = 4.0. The significant variability among genotypes and progeny for chinch bug resistance indicates the ability to improve buffalograss resistance to chinch bugs through selection or hybridization of selected genotypes.

Genome-Wide Association Study Reveals Novel Genetic Loci for Quantitative Resistance to Septoria Tritici Blotch in Wheat (Triticum aestivum L.).

Septoria tritici blotch, caused by the fungus Zymoseptoria titici, poses serious and persistent challenges to wheat cultivation in Ethiopia and worldwide. Deploying resistant cultivars is a major component of controlling septoria tritici blotch (STB). Thus, the objective of this study was to elucidate the genomic architecture of STB resistance in an association panel of 178 bread wheat genotypes. The association panel was phenotyped for STB resistance, phenology, yield, and yield-related traits in three locations for 2 years. The panel was also genotyped for single nucleotide polymorphism (SNP) markers using the genotyping-by-sequencing (GBS) method, and a total of 7,776 polymorphic SNPs were used in the subsequent analyses. Marker-trait associations were also computed using a genome association and prediction integrated tool (GAPIT). The study then found that the broad-sense heritability for STB resistance ranged from 0.58 to 0.97 and 0.72 to 0.81 at the individual and across-environment levels, respectively, indicating the presence of STB resistance alleles in the association panel. Population structure and principal component analyses detected two sub-groups with greater degrees of admixture. A linkage disequilibrium (LD) analysis in 338,125 marker pairs also detected the existence of significant (p ≤ 0.01) linkage in 27.6% of the marker pairs. Specifically, in all chromosomes, the LD between SNPs declined within 2.26-105.62 Mbp, with an overall mean of 31.44 Mbp. Furthermore, the association analysis identified 53 loci that were significantly (false discovery rate, FDR, <0.05) associated with STB resistance, further pointing to 33 putative quantitative trait loci (QTLs). Most of these shared similar chromosomes with already published Septoria resistance genes, which were distributed across chromosomes 1B, 1D, 2A, 2B, 2D, 3A,3 B, 3D, 4A, 5A, 5B, 6A, 7A, 7B, and 7D. However, five of the putative QTLs identified on chromosomes 1A, 5D, and 6B appeared to be novel. Dissecting the detected loci on IWGSC RefSeq Annotation v2.1 revealed the existence of disease resistance-associated genes in the identified QTL regions that are involved in plant defense responses. These putative QTLs explained 2.7-13.2% of the total phenotypic variation. Seven of the QTLs (R 2 = 2.7-10.8%) for STB resistance also co-localized with marker-trait associations (MTAs) for agronomic traits. Overall, this analysis reported on putative QTLs for adult plant resistance to STB and some important agronomic traits. The reported and novel QTLs have been identified previously, indicating the potential to improve STB resistance by pyramiding QTLs by marker-assisted selection.

Genome-wide association mapping of seedling and adult plant response to stem rust in a durum wheat panel.

Many of the major stem rust resistance genes deployed in commercial wheat (Triticum spp.) cultivars and breeding lines become ineffective over time because of the continuous emergence of virulent races. A genome-wide association study (GWAS) was conducted using 26,439 single nucleotide polymorphism (SNP) markers and 280 durum wheat [Triticum turgidum L. subsp. Durum (Desf.) Husnot] lines from CIMMYT to identify genomic regions associated with seedling resistance to races TTKSK, TKTTF, JRCQC, and TTRTF and field resistance to TKTTF and JRCQC. The phenotypic data analysis across environments revealed 61-91 and 59-77% of phenotypic variation was explained by the genotypic component for seedling and adult plant response of lines, respectively. For seedling resistance, mixed linear model (MLM) identified eight novel and nine previously reported quantitative trait loci (QTL) while a fixed and random model circulating probability unification (FarmCPU) detected 12 novel and eight previously reported QTL. For field resistance, MLM identified 12 novel and seven previously reported loci while FarmCPU identified seven novel and nine previously reported loci. The regions of Sr7a, Sr8155B1, Sr11, alleles of Sr13, Sr17, Sr22/Sr25, and Sr49 were identified. Novel loci on chromosomes 3B, 4A, 6A, 6B, 7A, and 7B could be used as sources of resistance to the races virulent on durum wheat. Two large-effect markers on chromosome 6A could potentially be used to differentiate resistant haplotypes of Sr13 (R1 and R3). Allelism tests for Sr13, breaking the deleterious effect associated with Sr22/Sr25 and retaining the resistance allele at the Sr49 locus, are needed to protect future varieties from emerging races.

Misidentification by farmers of the crop varieties they grow: Lessons from DNA fingerprinting of wheat in Ethiopia.

Accurate identification of crop varieties grown by farmers is crucial, among others, for crop management, food security and varietal development and dissemination purposes. One may expect varietal identification to be more challenging in the context of developing countries where literacy and education are limited and informal seed systems and seed recycling are common. This paper evaluates the extent to which smallholder farmers misidentify their wheat varieties in Ethiopia and explores the associated factors and their implications. The study uses data from a nationally representative wheat growing sample household survey and DNA fingerprinting of seed samples from 3,884 wheat plots in major wheat growing zones of Ethiopia. 28-34% of the farmers correctly identified their wheat varieties. Correct identification was positively associated with farmer education and seed purchases from trusted sources (cooperatives or known farmers) and negatively associated with seed recycling. Farmers' varietal identification thereby is problematic and leads to erroneous results in adoption and impact assessments. DNA fingerprinting can enhance varietal identification but remains mute in the identification of contextual and explanatory factors. Thus, combining household survey and DNA fingerprinting approaches is needed for reliable varietal adoption and impact assessments, and generate useful knowledge to inform policy recommendations related to varietal replacement and seed systems development.

Smallholders' coping mechanisms with wheat rust epidemics: Lessons from Ethiopia.

Crops are variously susceptible to biotic stresses-something expected to increase under climate change. In the case of staple crops, this potentially undermines household and national food security. We examine recent wheat rust epidemics and smallholders' coping mechanisms in Ethiopia as a case study. Wheat is a major food crop in Ethiopia widely grown by smallholders. In 2010/11 a yellow rust epidemic affected over one-third of the national wheat area. Two waves of nationally representative household level panel data collected for the preceding wheat season (2009/10) and three years after (2013/14) the occurrence of the epidemic allow us to analyze the different coping mechanisms farmers used in response. Apart from using fungicides as ex-post coping mechanism, increasing wheat area under yellow rust resistant varieties, increasing diversity of wheat varieties grown, or a combination of these strategies were the main ex-ante coping mechanisms farmers had taken in reducing the potential effects of rust re-occurrence. Large-scale dis-adoption of highly susceptible varieties and replacement with new, rust resistant varieties was observed subsequent to the 2010/11 epidemic. Multinomial logistic regression models were used to identify the key factors associated with smallholder ex-ante coping strategies. Household characteristics, level of specialization in wheat and access to improved wheat seed were the major factors that explained observed choices. There was 29-41% yield advantage in increasing wheat area to the new, resistant varieties even under normal seasons with minimum rust occurrence in the field. Continuous varietal development in responding to emerging new rust races and supporting the deployment of newly released resistant varieties could help smallholders in dealing with rust challenges and maintaining improved yields in the rust-prone environments of Ethiopia. Given the global importance of both wheat and yellow rust and climate change dynamics study findings have relevance to other regions.

Gender and agricultural innovation in Oromia region, Ethiopia: from innovator to tempered radical.

Tempered radicals are change agents who experience the dominant culture as a violation of the integrity and authenticity of their personal values and beliefs. They seek to move forward whilst challenging the status quo. Does the concept provide a useful analytic lens through which the strategies of women and men farmer innovators, who are 'doing things differently' in agriculture, can be interpreted? What are their strategies for turning ambivalence and tension to their advantage? The paper uses research data derived from two wheat-growing communities in Oromia Region, Ethiopia, an area characterized by generally restrictive gendered norms and a technology transfer extension system. The findings demonstrate that women and men innovators actively interrogate and contest gender norms and extension narratives. Whilst both women and men innovators face considerable challenges, women, in particular, are precariously located 'outsiders within,' negotiating carefully between norm and sanction. Although the findings are drawn from a small sample, they have implications for interventions aiming to support agricultural innovation processes which support women's, as well as men's, innovatory practice. The framework facilitates a useful understanding of how farmer innovators operate and in particular, significant differences in how women and men interrogate, negotiate and align themselves with competing narratives.