scholarly journals Bulked segregant analysis RNA-seq (BSR-Seq) validated a stem resistance locus in Aegilops umbellulata, a wild relative of wheat

2019 ◽  
Author(s):  
Erena A. Edae ◽  
Matthew N. Rouse
Keyword(s):  
Resistance Genes ◽  
Stem Rust ◽  
Bulk Segregant Analysis ◽  
Bulked Segregant Analysis ◽  
Analysis Approach ◽  
Resistance Locus ◽  
Potential Candidate ◽  
Chromosome Location ◽  
Sources Of Resistance ◽  
Stem Resistance

AbstractMany disease resistance genes that have been transferred from wild relatives to cultivated wheat have played a significant role in wheat production worldwide. Ae. umbellulata is one of the species within the genus Aegilops that have been successfully used as sources of resistance genes to leaf rust, stem rust and powdery mildew. The objectives of the current work was to validate the map position of a major QTL that confers resistance to the stem rust pathogen races Ug99 (TTKSK) and TTTTF with an independent bi-parental mapping population and to refine the QTL region with a bulk segregant analysis approach. Two F2 bi-parental mapping populations were developed from stem rust resistant Ae. umbellulata accessions (PI 298905 and PI 5422375) and stem rust susceptible accessions (PI 542369 and PI 554395). Firstly, one of the two populations was used to map the chromosome location of the resistance gene. Later on, the 2nd population was used to validate the chromosome location in combination with a bulk segregant analysis approach. For the bulk segregant analysis, RNA was extracted from a bulk of leaf tissues of 12 homozygous resistant F3 families, and a separate bulk of 11 susceptible homozygous F3 families derived from the PI 5422375 and PI 554395 cross. The RNA samples of the two bulks and the two parents were sequenced for SNPs identification. Stem rust resistance QTL was validated on chromosome 2U of Ae. umbellulata in the same region in both populations. With bulk segregant analysis, the QTL position was delimited within 3.2 Mbp. Although there were a large number of genes in the orthologous region of the detected QTL on chromosome 2D of Ae. tauschii, we detected only two Ae. umbellulata NLR genes which can be considered as a potential candidate genes.

scholarly journals Genetic Characterization of Resistance to Wheat Stem Rust Race TTKSK in Landrace and Wild Barley Accessions Identifies the rpg4/Rpg5 Locus

2015 ◽  
Vol 105 (1) ◽  
pp. 99-109 ◽  
Author(s):  
Bullo Erena Mamo ◽  
Kevin P. Smith ◽  
Robert S. Brueggeman ◽  
Brian J. Steffenson
Keyword(s):  
Stem Rust ◽  
Incubation Temperature ◽  
Wild Barley ◽  
Bulked Segregant Analysis ◽  
Single Gene ◽  
Temperature Sensitive ◽  
Resistance Locus ◽  
Sources Of Resistance ◽  
Wheat Stem Rust ◽  
Barley Landraces

Race TTKSK of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici) threatens the production of wheat and barley worldwide because of its broad-spectrum virulence on many widely grown cultivars. Sources of resistance against race TTKSK were recently identified in several barley landraces (Hordeum vulgare subsp. vulgare) and wild barley accessions (H. vulgare subsp. spontaneum). The objectives of this study were to characterize the inheritance of resistance to wheat stem rust race TTKSK in four barley landraces (Hv501, Hv545, Hv602, and Hv612) and two wild barley (WBDC213 and WBDC345) accessions, map the resistance genes, and determine the allelic relationships among the genes in these accessions and the previously described rpg4/Rpg5 locus. Resistant accessions were crossed with the susceptible cv. Steptoe and resulting F3 populations were evaluated for resistance to race TTKSK at the seedling stage. Segregation of F3 families in populations involving the resistance sources of Hv501, Hv545, Hv612, WBDC213, and WBDC345 fit a 1:2:1 ratio for homozygous resistant (HR)/segregating (SEG)/homozygous susceptible (HS) progenies (with χ2 = 2.27 to 5.87 and P = 0.053 to 0.321), indicating that a single gene confers resistance to race TTKSK. Segregation of F3 families in cross Steptoe/Hv602 did not fit a 1:2:1 ratio (HR/SEG/HS of 20:47:43 with χ2 = 11.95 and P = 0.003), indicating that more than one gene is involved in imparting resistance to race TTKSK. Bulked segregant analysis using >1,500 single-nucleotide polymorphism markers positioned a resistance locus in all six populations on chromosome 5HL in very close proximity to the known location of the rpg4/Rpg5 complex locus. Allelism tests were conducted by making crosses among resistant accessions Hv501, Hv545, and Hv612 and also Q21861 with the rpg4/Rpg5 complex. No segregation was observed in F2 families inoculated with race TTKSK, demonstrating that all Hv lines carry the same allele for resistance and that it resides at or very near the rpg4/Rpg5 locus. Phenotype evaluations of the six barley accessions with wheat stem rust race QCCJ revealed resistant infection types (ITs) at a low incubation temperature and susceptible ITs at a high incubation temperature, similar to Q21861, which carries the temperature-sensitive gene rpg4. The accessions also exhibited low ITs against the rye stem rust isolate 92-MN-90, suggesting that they also carry Rpg5. This result was confirmed through molecular analysis, which revealed that all six barley accessions contain the serine threonine protein kinase domain that confers Rpg5 resistance. These results indicate that cultivated barley is extremely vulnerable to African stem rust races such as TTKSK because even these diverse selections of landrace and wild barley accessions carry only one locus for resistance.

DANGEROUS NEW RACES OF OAT STEM RUST AND SOURCES OF RESISTANCE TO THEM

1964 ◽  
Vol 44 (5) ◽  
pp. 418-426 ◽  
Author(s):  
G. J. Green ◽  
R. I. H. McKenzie
Keyword(s):  
Resistance Genes ◽  
Stem Rust ◽  
Seedling Stage ◽  
Adult Plant ◽  
Santa Fe ◽  
Sources Of Resistance ◽  
Adult Plant Stage ◽  
Plant Stage ◽  
New Races ◽  
Moderately Resistant

New races of oat stem rust that can attack varieties carrying all identified resistance genes were found in Canada between 1957 and 1963. Varieties moderately resistant to some of these races have been found, but they are susceptible to other less-prevalent races. Some of the sources of resistance are: Ukraine, C.I. 3259; Ark. 674(2)-39-F, C.I. 4529; C.I. 4673; C.I. 5109; Santa Fe Selection, C.I. 5844; C.I. 6792; Silva No. 1729-49-1, C.I. 6849; and Rosen’s Mutant. White Russian (gene D) and Sevnothree (gene E) were resistant in the adult plant stage to one culture of race 6AF, although susceptible in the seedling stage.

scholarly journals Sources of Stem Rust Resistance in Wheat-Alien Introgression Lines

Plant Disease ◽  
2016 ◽  
Vol 100 (6) ◽  
pp. 1101-1109 ◽  
Author(s):  
Mahbubjon Rahmatov ◽  
Matthew N. Rouse ◽  
Brian J. Steffenson ◽  
Staffan C. Andersson ◽  
Ruth Wanyera ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Resistance Genes ◽  
Stem Rust ◽  
Rust Resistance ◽  
Stem Rust Resistance ◽  
Introgression Lines ◽  
Resistance Pattern ◽  
Sources Of Resistance ◽  
Alien Introgression ◽  
New Genes

Stem rust is one of the most devastating diseases of wheat. Widely virulent races of the pathogen in the Ug99 lineage (e.g., TTKSK) are threatening wheat production worldwide; therefore, there is an urgent need to enhance the diversity of resistance genes in the crop. The objectives of this study were to identify new sources of resistance in wheat-alien introgression derivatives from Secale cereale, Leymus mollis, L. racemosus, and Thinopyrum junceiforme, postulate genes conferring the resistance, and verify the postulated genes by use of molecular markers. From seedling tests conducted in the greenhouse, the presence of seven known stem rust resistance genes (Sr7b, Sr8a, Sr9d, Sr10, Sr31, Sr36, and SrSatu) was postulated in the wheat-alien introgression lines. More lines possessed a high level of resistance in the field compared with the number of lines that were resistant at the seedling stage. Three 2R (2D) wheat-rye substitution lines (SLU210, SLU238, and SLU239) seemed likely to possess new genes for resistance to stem rust based on their resistance pattern to 13 different stem rust races but the genes responsible could not be identified. Wheat-rye, wheat-L. racemosus, and wheat-L. mollis substitutions or translocations with single and multiple interchanges of chromosomes, in particular of the B and D chromosomes of wheat, were verified by a combination of genomic in situ hybridization and molecular markers. Thus, the present study identified novel resistance genes originating from different alien introgressions into the wheat genome of the evaluated lines. Such genes may prove useful in enhancing the diversity of stem rust resistance in wheat against widely virulent pathogen races such as those in the Ug99 lineage.

scholarly journals Fine mapping of Ur-3, a historically important rust resistance locus in common bean

2016 ◽  
Author(s):  
O.P. Hurtado-Gonzales ◽  
G. Valentini ◽  
T.A.S Gilio ◽  
A.M. Martins ◽  
Q. Song ◽  
...  
Keyword(s):  
Common Bean ◽  
Resistance Genes ◽  
Fine Mapping ◽  
Rust Resistance ◽  
Bulked Segregant Analysis ◽  
Snp Markers ◽  
Resistance Locus ◽  
Bean Rust ◽  
Rust Pathogen ◽  
Rust Resistance Genes

AbstractBean rust is a devastating disease of common bean in the Americas and Africa. The historically important Ur-3 gene confers resistance to many races of the highly variable bean rust pathogen that overcome all known rust resistance genes. Existing molecular markers tagging Ur-3 for use in marker assisted selection produce false results. We described here the fine mapping of Ur-3 for the development of highly accurate markers linked to this gene. An F2 population from Pinto 114 × Aurora was evaluated for its reaction to four different races of the bean rust pathogen. A bulked segregant analysis using the SNP chip BARCBEAN6K_3 positioned the approximate location of the Ur-3 locus to the lower arm of chromosome Pv11. Specific SSR and SNP markers and haplotype analysis of 18 sequenced bean lines led to position the Ur-3 locus to a 46.5 Kb genomic region. We discovered a KASP marker, SS68 that was tightly linked to the Ur-3 locus. Validation of SS68 on a panel of 130 diverse common bean lines and varieties containing all known rust resistance genes revealed that it was highly accurate producing no false results. The SS68 marker will be of great value to pyramid Ur-3 with other rust resistance genes. It will also reduce significantly time and labor associated with the current phenotypic detection of Ur-3. This is the first utilization of fine mapping to discover markers linked to a rust resistance in common bean.

Wheat Rusts

1995 ◽  
Author(s):  
RA McIntosh ◽  
CR Wellings ◽  
RF Park
Keyword(s):  
Stripe Rust ◽  
Resistance Genes ◽  
Stem Rust ◽  
Chromosome Location ◽  
Resistant Cultivars ◽  
Rust Diseases ◽  
Pathogen Variation ◽  
The World ◽  
Wheat Rust ◽  
Wheat Rusts

Although stem rust has been controlled by means of resistant cultivars, leaf and stripe rust continue as problems for many growing areas of the world. Wheat Rusts: An Atlas of Resistance Genes has been prepared by specialists from one of the leading international laboratories, and illustrates with colour photographs typical resistance phenotypes associated with most known genes for resistance to the three rust diseases of wheat. Relevant details for each gene include chromosome location, aspects of genetics and pathogen variation, the effects of environment on expression, origin, availability in genetic and breeding stocks, and use in agriculture. This atlas includes an introduction to host:pathogen genetics, methodologies for wheat rust research and breeding for resistance.

scholarly journals Sources of Resistance to Stem Rust Race Ug99 in Spring Wheat Germplasm

Plant Disease ◽  
2011 ◽  
Vol 95 (6) ◽  
pp. 762-766 ◽  
Author(s):  
M. N. Rouse ◽  
R. Wanyera ◽  
P. Njau ◽  
Y. Jin
Keyword(s):  
Spring Wheat ◽  
Resistance Genes ◽  
North American ◽  
Stem Rust ◽  
Wheat Breeding ◽  
Field Resistance ◽  
Eastern Africa ◽  
Adult Plant ◽  
Sources Of Resistance ◽  
Wheat Stem Rust

Wheat stem rust (Puccinia graminis f. sp. tritici) race TTKSK (Ug99), with virulence to the majority of the world's wheat (Triticum aestivum) cultivars, has spread from Uganda throughout eastern Africa, Yemen, and Iran. The identification and spread of variants of race TTKSK with virulence to additional stem rust resistance genes has reminded breeders and pathologists of the danger of deploying major resistance genes alone. In order to protect wheat from this rapidly spreading and adapting pathogen, multiple resistance genes are needed, preferably from improved germplasm. Preliminary screening of over 700 spring wheat breeding lines and cultivars developed at least 20 years ago identified 88 accessions with field resistance to Ug99. We included these resistant accessions in the stem rust screening nursery in Njoro, Kenya for two additional seasons. The accessions were also screened with a bulk of North American isolates of P. graminis f. sp. tritici in the field in St. Paul, MN. In order to further characterize the resistance in these accessions, we obtained seedling phenotypes for 10 races of P. graminis f. sp. tritici, including two races from the race TTKSK complex. This phenotyping led to the identification of accessions with either adult-plant or all-stage resistance to race TTKSK, and often North American races of P. graminis f. sp. tritici as well. These Ug99 resistant accessions can be obtained by breeders and introgressed into current breeding germplasm.

PHYSIOLOGIC SPECIALIZATION IN OAT STEM RUST IN CANADA FROM 1944 TO 1959

1961 ◽  
Vol 41 (1) ◽  
pp. 153-165 ◽  
Author(s):  
G. J. Green ◽  
T. Johnson ◽  
J. N. Welsh
Keyword(s):  
Resistance Genes ◽  
Stem Rust ◽  
Physiologic Race ◽  
Sources Of Resistance ◽  
Physiologic Specialization ◽  
Economic Significance ◽  
Resistant Varieties ◽  
Eastern Ontario

Annual physiologic race surveys of oat stem rust have shown that races 1, 2, and 5 predominated in Canada from 1921 to 1944; races 8, 10, and 11 from 1945 to 1952; and races 3, 7, and 12 from 1953 to 1959. The increased prevalence of races 8, 10, and 11 led to increased rusting of the rust-resistant varieties produced in Canada between 1937 and 1941. The increased prevalence of races 3, 7, and 12 was of little economic significance because these varieties were resistant to this group of races. Race 7A, which differs from other cultures of race 7 in being virulent on Rodney, has increased slowly but steadily since its discovery in 1952. Races 6A, 8A, 11A, and 13A which are virulent on Garry as well as Rodney have been found in eastern Ontario and Quebec. The "A" signifies virulence on the variety Rodney which is resistant to earlier cultures of races 6, 7, 8, 11, and 13. Race 6A is virulent on varieties with any or all of the resistance genes A, BC, D, and E. These are the only genes for resistance to stem rust carried by present-day varieties that are grown commercially in Canada. Several sources of resistance to these new and dangerous races have been found. The variety C.I. 4023 appears to have outstanding resistance.

scholarly journals The rpg4/ Rpg5 stem rust resistance locus in barley; resistance genes and cytoskeleton dynamic

Cell Cycle ◽  
2009 ◽  
Vol 8 (7) ◽  
pp. 977-981 ◽  
Author(s):  
Robert Brueggeman ◽  
Brian J. Steffenson ◽  
Andris Kleinhofs
Keyword(s):  
Resistance Genes ◽  
Stem Rust ◽  
Rust Resistance ◽  
Stem Rust Resistance ◽  
Resistance Locus ◽  
Barley Resistance

scholarly journals Emergence of Virulence to Sr25 of Puccinia graminis f. sp. tritici on Wheat in India

Plant Disease ◽  
2009 ◽  
Vol 93 (8) ◽  
pp. 840-840 ◽  
Author(s):  
S. K. Jain ◽  
M. Prashar ◽  
S. C. Bhardwaj ◽  
S. B. Singh ◽  
Y. P. Sharma
Keyword(s):  
Resistance Genes ◽  
Stem Rust ◽  
Infection Type ◽  
Adult Plant ◽  
Puccinia Graminis ◽  
Wheat Cultivars ◽  
Sources Of Resistance ◽  
Seedling Resistance ◽  
Additional Gene ◽  
Adult Plants

Stem (black) rust, caused by Puccinia graminis Pers. f. sp. tritici Eriks. & Henn., is one of the most destructive diseases of wheat. It could be controlled through introgression of race-specific resistance genes. However, such kind of resistance is mostly short lived due to emergence of new virulences. For example, resistance genes Sr11, Sr24, Sr30, and Sr31 are no longer effective (2,4). Detection of new virulences has remained vital in the evaluation and identification of new sources of resistance. We report here the detection of virulence to Sr25, a gene from Thinopyrum elongatum (4), which had been effective or partially effective against stem rust worldwide, including race Ug99 (TTKSK) (4). A stem rust isolate collected in 2006 from Karnataka (southern India) produced susceptible reactions (infection type [IT] 3+ to 4) on the primary leaves of differential genotype ‘Agatha’ carrying Sr25 and susceptible check ‘Agra Local’ at 22 ± 2°C. To verify virulence to Sr25, single-pustule isolates from this sample were inoculated onto seedlings of ‘Agrus’, ‘Agatha’, ‘RL6040’ (‘Thatcher’ + Sr25), ‘Superseri#1’, ‘Wheatear’, and ‘Morocco’ + Sr25 (obtained from CIMMYT), which all carry Sr25. All these accessions were found susceptible (IT 3+ to 4) to this isolate, except Wheatear which expressed resistance (IT ;1), indicating the presence of additional gene(s). These genotypes are resistant (ITs ;1 to 2+) to Sr25-avirulent pathotypes. The new pathotype is avirulent to Sr11, 13, 14, 21, 22, 23, 24, 26, 27, 29, 31, 32, 33, 35, 37, 38, 39, 40, 43, and Tmp and virulent to Sr5, 6, 7a, 7b, 8a, 9a, 9b, 9d, 9e, 9f, 9g, 10, 12, 15, 16, 17, 18, 19, 20, 25, 28, 30, 34, 36, 42, Wld-1, and Gt at 22 ± 2°C. This pathotype has been designated as 58G13-3 and PKTSC according to the Indian nomenclature (1) and the North American system (3), respectively. It represents race 40 based on Stakman's differentials. It may have arisen from race 40 through mutation. The type culture of the pathotype has been added to the culture collection at Flowerdale, Shimla. Interestingly, ‘Festiguay’ (Sr30) was found resistant to this pathotype, indicating the presence of additional gene(s), whereas ‘Webster’ (Sr30) was susceptible. Adult plants of Agrus, Agatha, RL6040, Superseri#1, and Morocco+Sr25 also were susceptible, producing 20S to 60S responses. Sr25-avirulent pathotype 62G29 produced a TR (flecking in traces) response on these lines except Morocco + Sr25 that showed 20 to 40MR (moderately resistant) responses. In the same study however, adult plants of Thatcher showed a resistant reaction (10R to MR) at low (16 ± 2°C) and susceptible (20S) at high (22 ± 2°C) temperatures. Agatha and RL6040, having Thatcher as one of the parents, had similar responses. The detection of Sr25 virulence is significant since Sr25 is an important gene to be targeted for breeding wheat cultivars resistant to Ug99. We should use either adult plant resistance and/or pyramiding two or more genes for seedling resistance to enhance the field life of wheat cultivars. References: (1) P. Bahadur et al. Proc. Indian Acad. Sci. 95:29, 1985. (2) S. C. Bhardwaj et al. J. Wheat Res. 1:51, 2007. (3) Y. Jin et al. Plant Dis. 92:923, 2008. (4) R. P. Singh et al. CAB Rev. No. 054:1, 2006.

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