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

Alemu, Sisay; Badebo, Ayele; Tesfaye, Kassahun; Uauy, Cristóbal

doi:10.35248/2157-7471.19.10.483

Cited by 7 publications

(8 citation statements)

References 43 publications

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“…In agreement to this, biotic and abiotic resistance/tolerance genes or genomic regions were identified in Ethiopian durum wheat landraces, e.g. resistance to biotic factors such as stripe rust resistance [ 75 ], adult plant resistance to leaf rust and stem rust [ 46 , 76 , 77 ], abiotic stress resistance such as aluminum tolerance [ 78 ] and terminal drought tolerance [ 23 ]. Therefore, Ethiopian durum wheat landraces may increase the rate of genetic gain if strategically included in wheat breeding programs.…”

Section: Discussionmentioning

confidence: 81%

Genetic diversity of Ethiopian durum wheat landraces

et al. 2021

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Genetic diversity and population structure assessment in crops is essential for marker trait association, marker assisted breeding and crop germplasm conservation. We analyzed a set of 285 durum wheat accessions comprising 215 Ethiopian durum wheat landraces, 10 released durum wheat varieties, 10 advanced durum wheat lines from Ethiopia, and 50 durum wheat lines from CIMMYT. We investigated the genetic diversity and population structure for the complete panel as well as for the 215 landraces, separately based on 11,919 SNP markers with known physical positions. The whole panel was clustered into two populations representing on the one hand mainly the landraces, and on the other hand mainly released, advanced and CIMMYT lines. Further population structure analysis of the landraces uncovered 4 subgroups emphasizing the high degree of genetic diversity within Ethiopian durum landraces. Population structure based AMOVA for both sets unveiled significant (P < 0.001) variation between populations and within populations. Total variation within population accessions (81%, 76%) was higher than total variation between populations (19%, 24%) for both sets. Population structure analysis based genetic differentiation (FST) and gene flow (Nm) for the whole set and the Ethiopian landraces were 0.19 and 0.24, 1.04, and 0.81, respectively indicating high genetic differentiation and limited gene flow. Diversity indices verify that the landrace panel was more diverse with (I = 0.7, He = 0.46, uHe = 0.46) than the advanced lines (I = 0.6, He = 0.42, uHe = 0.42). Similarly, differences within the landrace clusters were observed. In summary a high genetic diversity within Ethiopian durum wheat landraces was detected, which may be a target for national and international wheat improvement programs to exploit valuable traits for biotic and abiotic stresses.

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Section: Discussionmentioning

confidence: 81%

Genetic diversity of Ethiopian durum wheat landraces

et al. 2021

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“…As a follow-up investigation, the associated SNPs can be validated for their diagnostic values in an independent germplasm. Ethiopian durum landraces have been suggested as a good source of resistance to wheat rusts [44][45]. This has been supported by association studies on relatively small sized Ethiopian durum panels in limited study environments [17].…”

Section: Introductionmentioning

confidence: 91%

“…Ethiopian durum landraces have been suggested as a good source of resistance to wheat rusts [44–45]. This has been supported by association studies on relatively small sized Ethiopian durum panels in limited study environments [17].…”

Section: Introductionmentioning

confidence: 94%

“…Two additional SNPs were identified on chromosome 1A while the other two came from chromosome 2B and chromosome 7B. Several yellow rust QTLs and Yr genes are mapped on these chromosomes including Yr5 on chromosome 2B [80] which could be amongst the few that are effective against Ethiopian Pst races [45,81].…”

Section: Analysis Of the Major Resistance Locus Identified On Chromosmentioning

confidence: 99%

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Genome-wide association mapping identifies Yellow Rust resistance locus in Ethiopian Durum Wheat germplasm

Alemu

Huluka

Tesfaye

et al. 2020

Preprint

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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 to 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 in an alpha lattice design (10 × 30) in two replications at Meraro, Kulumsa and Chefe-Donsa in the 2015 and 2016 main growing seasons. Disease Scoring was carried out using a modified Cobb scale and then converted to Coefficient of Infection (CI). Analysis of the 35K Axiom Array genotyping data 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. We identified twelve SNPs significantly associated with yellow rust resistance across four chromosomes (1A, 1B, 2B, and 7B). Six of the SNPs (AX-95171339, AX-94436448, AX-95238778, AX-95096041, AX-94730403 & AX-94427201), were consistently identified on chromosome 1B at the three field locations and combined across the six environments. The phenotypic variation (R2) explained by all six SNPs on chromosome 1B ranged from 63.7 – 65.4%. Locus-based analysis of phenotypic values between resistant and susceptible allele resulted in a significant difference at (p < 0.001). Further investigation across the genomic interval encompassing the identified loci indicated the presence of disease resistance protein (NBS-LRR class) family and RPM1 in the vicinity of the loci. This study provides SNPs for tracking the QTL associated with yellow rust resistance in durum wheat improvement programs.

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“…Many studies have been done on stripe rust resistance using GWAS and identi ed many QTLs controlling the resistance distributing across the whole genome [29][30][31]. In addition, many simple sequence repeats (SSR), sequence-Tagged site (STS), sequence-characterized ampli ed region (SCAR), diversity arrays technology (DArT), and Kompetitive allele-speci c PCR (KASP) markers have been reported as good markers for MAS for stripe rust resistance genes in wheat [32][33][34][35]. Furthermore, Maccaferri et al, (2015) reported association mapping of the resistance to the American race of P. striiformis using a world-wide collection of spring wheat genotyped by DArT markers.…”

Section: Introductionmentioning

confidence: 99%

Genomic regions associated with stripe rust resistance against the Egyptian race revealed by genome-wide association study

Mohamed

Mourad

2020

Preprint

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Background: Wheat stripe rust (caused by Puccinia striiformis f. sp. Tritici), is a major disease that causes huge yield damage. New pathogen races appeared in the last few years and caused a broke down in the resistant genotypes. In Egypt, some of the resistant genotypes began to be susceptible to stripe rust in recent years. This situation increases the need to produce new genotypes with durable resistance. Besides, looking for a new resistant source from the available wheat genotypes all over the world help in enhancing the breeding programs. Results: In the recent study, a set of 103-spring wheat genotypes from different fourteen countries were evaluated to their field resistant to stripe rust for two years. These genotypes included 17 Egyptian genotypes from the old and new cultivars. The 103-spring wheat genotypes were reported to be well adapted to the Egyptian environmental conditions. Out of the tested genotypes, eight genotypes from four different countries were found to be resistant in both years. Genotyping was carried out using genotyping-by-sequencing and a set of 26,703 SNPs were used in the genome-wide association study. Five SNP markers, located on chromosomes 2A and 4A, were found to be significantly associated with the resistance in both years. Three gene models associated with disease resistance and underlying these significant SNPs were identified. One immune Iranian genotype, with the highest number of different alleles from the most resistant Egyptian genotypes, was detected. Conclusion: the high variation among the tested genotypes in their resistance to the Egyptian stripe rust race confirming the possible improvement of stripe rust resistance in the Egyptian wheat genotypes. The identified five SNP markers are stable and could be used in marker-assisted selection after validation in different genetic backgrounds. Crossing between the immune Iranian genotype and the Egyptian genotypes will improve stripe rust resistance in Egypt.

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

Cited by 7 publications

References 43 publications

Genetic diversity of Ethiopian durum wheat landraces

Genetic diversity of Ethiopian durum wheat landraces

Genome-wide association mapping identifies Yellow Rust resistance locus in Ethiopian Durum Wheat germplasm

Genomic regions associated with stripe rust resistance against the Egyptian race revealed by genome-wide association study

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