Transcriptome-wide association study identifies putative elicitors/suppressor of Puccinia graminis f. sp. tritici that modulate barley rpg4-mediated stem rust resistance

Abstract Background Stem rust is an economically important disease of wheat and barley. However, studies to gain insight into the molecular basis of these host-pathogen interactions have primarily focused on wheat because of its importance in human sustenance. This is the first extensive study utilizing a transcriptome-wide association mapping approach to identify candidate Puccinia graminis f. sp. tritici (Pgt) effectors/suppressors that elicit or suppress barley stem rust resistance genes. Here we focus on identifying Pgt elicitors that interact with the rpg4-mediated resistance locus (RMRL), the only effective source of Pgt race TTKSK resistance in barley. Results Thirty-seven Pgt isolates showing differential responses on RMRL were genotyped using Restriction Site Associated DNA-Genotyping by Sequencing (RAD-GBS), identifying 24 diverse isolates that were used for transcript analysis during the infection process. In planta RNAseq was conducted with the 24 diverse isolates on the susceptible barley variety Harrington, 5 days post inoculation. The transcripts were mapped to the Pgt race SCCL reference genome identifying 114 K variants in predicted genes that would result in nonsynonymous amino acid substitutions. Transcriptome wide association analysis identified 33 variants across 28 genes that were associated with dominant RMRL virulence, thus, representing candidate suppressors of resistance. Comparative transcriptomics between the 9 RMRL virulent -vs- the 15 RMRL avirulent Pgt isolates identified 44 differentially expressed genes encoding candidate secreted effector proteins (CSEPs), among which 38 were expressed at lower levels in virulent isolates suggesting that they may represent RMRL avirulence genes. Barley transcript analysis after colonization with 9 RMRL virulent and 15 RMRL avirulent isolates inoculated on the susceptible line Harrington showed significantly lower expression of host biotic stress responses specific to RMRL virulent isolates suggesting virulent isolates harbor effectors that suppress resistance responses. Conclusions This transcriptomic study provided novel findings that help fill knowledge gaps in the understanding of stem rust virulence/avirulence and host resistance in barley. The pathogen transcriptome analysis suggested RMRL virulence might depend on the lack of avirulence genes, but evidence from pathogen association mapping analysis and host transcriptional analysis also suggested the alternate hypothesis that RMRL virulence may be due to the presence of suppressors of defense responses.

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Seedling Stage Resistance of Iranian Bread Wheat Germplasm to Race Ug99 of Puccinia graminis f. sp. tritici

Plant Disease ◽

10.1094/pdis-02-12-0138-re ◽

2013 ◽

Vol 97 (3) ◽

pp. 387-392 ◽

Cited By ~ 2

Author(s):

Mohsen Mohammadi ◽

Davoud Torkamaneh ◽

Mehran Patpour

Keyword(s):

Resistance Genes ◽

Stem Rust ◽

Rust Resistance ◽

Stem Rust Resistance ◽

Puccinia Graminis ◽

Wheat Cultivars ◽

Breeding Lines ◽

Wheat Germplasm ◽

Stem Rust Resistance Genes ◽

Rust Resistance Genes

Following emergence of Ug99, the new virulent race of Puccinia graminis f. sp. tritici in Africa, a global effort for identification and utilization of new sources of Ug99-resistant germplasm has been undertaken. In this study, we conducted replicated experiments to evaluate the resistance of Iranian wheat germplasm to the TTKSK lineage of the Ug99 race of P. graminis f. sp. tritici. We also evaluated for presence of stem rust resistance genes (i.e., Sr2, Sr24, Sr26, Sr38, Sr39, Sr31, and Sr1RSAmigo) in wheat cultivars and breeding lines widely cultivated in Iran. Our phenotyping data revealed high levels of susceptibility to Ug99 in Iranian bread wheat germplasm. Our genotyping data revealed that Iranian cultivars do not carry Sr24, Sr26, or Sr1RSAmigo. Only a few salt-tolerant cultivars and breeding lines tested positively for Sr2, Sr31, Sr38, or Sr39 markers. In conclusion, the genetic basis for resistance to Ug99 in Iranian wheat cultivars was found to be vulnerable. Acquiring knowledge about existing resistance genes and haplotypes in wheat cultivars and breeding lines will help breeders, cereal pathologists, and policy makers to select and pyramid effective stem rust resistance genes.

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The inheritance of stem rust resistance in Thatcher wheat

Canadian Journal of Plant Science ◽

10.4141/p99-016 ◽

2000 ◽

Vol 80 (1) ◽

pp. 53-63 ◽

Cited By ~ 10

Author(s):

D. R. Knott

Keyword(s):

Stem Rust ◽

Rust Resistance ◽

Triticum Aestivum L ◽

Stem Rust Resistance ◽

Puccinia Graminis ◽

Single Seed Descent ◽

Good Resistance ◽

Canadian Prairies ◽

Single Seed ◽

Inheritance Of Rust Resistance

Thatcher was the predominant wheat (Triticum aestivum L.) cultivar on the Canadian prairies in the 1950s. Until race 15B (TMH) of stem rust (Puccinia graminis pers. f. sp. tritici Eriks. & Henn.) became widespread, Thatcher had good resistance to stem rust, but was susceptible to leaf rust (P. recondita f. sp. tritici Rob. ex Desm.). Although genes for stem rust resistance have been identified in Thatcher, the inheritance of its resistance has never been fully understood. The objective of this research was to attempt to elucidate the inheritance of the resistance of Thatcher and to determine why it had a reputation as a poor parent for rust resistance. Over a period of 40 yr, crosses and backcrosses to a susceptible genotype and two sets of single seed descent (SSD) lines were studied. The second set of SSD lines was tested with isolates of six races of stem rust to which Thatcher is resistant. The data showed that Thatcher is a very heterogenous cultivar with individual plants differing widely in the genes for stem rust resistance that they carry. The inheritance of rust resistance varied greatly from race to race and was often quite complex. Either complementary genes or a gene plus a suppressor appeared to condition resistance to one race. Most genes gave resistance to only one race. The presence of Sr5, which Thatcher is known to have obtained from Kanred, was confirmed. Most of its many additional genes probably came from Iumillo durum wheat. Key words: Stem rust, Thatcher wheat, single seed descent

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Association mapping and gene–gene interaction for stem rust resistance in CIMMYT spring wheat germplasm

Theoretical and Applied Genetics ◽

10.1007/s00122-011-1664-y ◽

2011 ◽

Vol 123 (8) ◽

pp. 1257-1268 ◽

Cited By ~ 91

Author(s):

Long-Xi Yu ◽

Aaron Lorenz ◽

Jessica Rutkoski ◽

Ravi P. Singh ◽

Sridhar Bhavani ◽

...

Keyword(s):

Association Mapping ◽

Spring Wheat ◽

Stem Rust ◽

Rust Resistance ◽

Gene Interaction ◽

Stem Rust Resistance ◽

Wheat Germplasm

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Genome-Wide Association Mapping of Stem Rust Resistance inHordeum vulgaresubsp.spontaneum

G3 Genes|Genome|Genetics ◽

10.1534/g3.117.300222 ◽

2017 ◽

Vol 7 (10) ◽

pp. 3491-3507 ◽

Cited By ~ 13

Author(s):

Ahmad H. Sallam ◽

Priyanka Tyagi ◽

Gina Brown-Guedira ◽

Gary J. Muehlbauer ◽

Alex Hulse ◽

...

Keyword(s):

Association Mapping ◽

Stem Rust ◽

Rust Resistance ◽

Stem Rust Resistance ◽

Genome Wide Association ◽

Genome Wide

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Inheritance of leaf rust and stem rust resistances in wheat cultivars Agent and Agatha

Australian Journal of Agricultural Research ◽

10.1071/ar9770037 ◽

1977 ◽

Vol 28 (1) ◽

pp. 37 ◽

Cited By ~ 56

Author(s):

RA McIntosh ◽

PL Dyck ◽

GJ Green

Keyword(s):

Leaf Rust ◽

Stem Rust ◽

Rust Resistance ◽

Wheat Chromosome ◽

Wheat Breeding ◽

Stem Rust Resistance ◽

Puccinia Graminis ◽

Wheat Cultivars ◽

Agropyron Elongatum ◽

Adult Plants

The wheat cultivars Agent and Agatha each possess closely linked genes for resistance to Puccinia graminis tritici and P. recondita derived from Agropyron elongatum. The genes in Agent, located in chromosome 3D, were designated Sr24 and Lr24. The gene in Agatha for resistance to P. graminis tritici was designated Sr25 and is linked with Lr19 in chromosome 7D. Both Agent and Agatha possess additional genes for resistance to certain cultures of P. graminis tritici. Sr24 is considered a valuable source of resistance for wheat-breeding purposes, but Sr25 conferred an inadequate level of resistance to adult plants. A translocation from an A. elongatum chromosome to wheat chromosome 6A, present in Australian cultivars Eagle, Kite and Jabiru, carries a third gene, Sr26, for stem rust resistance.

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Virulence Characterization of Puccinia graminis f. sp. avenae and Resistance of Oat Cultivars in China

Plant Disease ◽

10.1094/pdis-06-21-1239-re ◽

2021 ◽

Author(s):

Tianya Li ◽

Yiwei Xu ◽

Xue Zhang ◽

Xian Xin Wu ◽

Yazhao Zhang ◽

...

Keyword(s):

Stem Rust ◽

Rust Resistance ◽

Cost Effective ◽

Stem Rust Resistance ◽

Adult Plant ◽

Puccinia Graminis ◽

Resistant Cultivars ◽

Oat Cultivars ◽

First Time

Oat stem rust, caused by Puccinia graminis f. sp. avenae (Pga), is one of the most devastating diseases of oat. The most cost-effective and eco-friendly strategy to control this disease is the use of resistant cultivars. However, P. graminis f. sp. avenae can overcome the resistance of cultivars by rapidly changing its virulence. Thus, information on the virulence of P. graminis f. sp. avenae populations and resistance of cultivars is critical to control the disease. The current study was conducted to monitor the virulence composition and dynamics in the P. graminis f. sp. avenae population in China and to evaluate resistance of oat cultivars. Oat leaves naturally infected by P. graminis f. sp. avenae were collected during 2018 and 2019 and 159 isolates were derived from single uredinia. The isolates were tested on 12 international differential lines, and eight races, TJJ, TBD, TJB, TJD, TJL, TJN, TGD, and TKN, were identified for the first time in China. The predominant race was TJD, virulent against Pg1, Pg2, Pg3, Pg4, Pg8, Pg9, and Pg15, accounting for 35.8% and 37.8% in 2018 and 2019, respectively. The sub-predominant races were TJN (30.2% in 2018, 28.3% in 2019) and TKN (20.8% in 2018, 12.3% in 2019). All isolates were virulent to Pg1, Pg2, Pg3, and Pg4, and avirulent to Pg6 and Pg16. The three predominant races (TJD, TJN, and TKN) were used to evaluate resistance in 30 Chinese oat cultivars at the seedling and adult-plant stages. Five cultivars, Bayan 1, Baiyan 2, Baiyan 3, Baiyan 5, and Baiyan 9, were highly resistant to the three races at both seedling and adult-plant stages. The results of the virulences and frequencies of P. graminis f. sp. avenae races and the resistant cultivars will be useful in understanding the pathogen migration and evolution and for breeding oat cultivars with stem rust resistance.

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Resistance in U.S. Wheat to Recent Eastern African Isolates of Puccinia graminis f. sp. tritici with Virulence to Resistance Gene Sr31

Plant Disease ◽

10.1094/pd-90-0476 ◽

2006 ◽

Vol 90 (4) ◽

pp. 476-480 ◽

Cited By ~ 114

Author(s):

Y. Jin ◽

R. P. Singh

Keyword(s):

Winter Wheat ◽

Resistance Gene ◽

Stem Rust ◽

Rust Resistance ◽

Stem Rust Resistance ◽

Puccinia Graminis ◽

Breeding Lines ◽

Hard Red Winter Wheat ◽

Soft Winter Wheat ◽

Red Winter Wheat

The stem rust resistance gene Sr31 derived from rye has been used as an important source of stem rust resistance in many wheat cultivars worldwide. Isolates of Puccinia graminis f. sp. tritici with virulence to Sr31 were identified from Uganda in 1999. Stem rust susceptibility in wheat lines with Sr31 was observed in Kenya in 2003 and 2004. An isolate collected from Uganda in 1999 and an isolate collected from Kenya in 2004, identified to be race TTKS, were used in the rust evaluations. Selected cultivars and advanced breeding lines (450 in total) of wheat from the United States were tested against these two stem rust isolates. Resistance to race TTKS was detected in major classes of wheat with the following frequencies: 16% of hard red spring wheat, 48% of hard red winter wheat, and 27% of soft winter wheat. The genes that conferred resistance in the spring wheat have not been conclusively identified. Resistance in cultivar Ivan was likely due to Sr24. Resistance in hard red winter wheat was postulated to be primarily due to Sr24, and resistance in soft winter wheat was postulated to be primarily due to Sr36. The 1AL.1RS translocation present in many U.S. winter wheat cultivars and breeding lines appears to carry an effective resistance gene different from Sr31. The presence of resistance to race TTKS in the adapted germ plasm presents an opportunity to improve stem rust resistance in wheat.

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GENETICS OF STEM RUST RESISTANCE IN WHEAT CULTIVARS ROMANY, Es.P 518/9, BONNY AND TAMA

Canadian Journal of Genetics and Cytology ◽

10.1139/g75-082 ◽

1975 ◽

Vol 17 (4) ◽

pp. 667-674 ◽

Cited By ~ 2

Author(s):

P. L. Dyck ◽

G. J. Green

Keyword(s):

Triticum Aestivum ◽

Stem Rust ◽

Rust Resistance ◽

Triticum Aestivum L ◽

Stem Rust Resistance ◽

Puccinia Graminis ◽

Wheat Cultivars ◽

Genetics Of Resistance ◽

Seedling Resistance ◽

Moderate Resistance

The genetics of resistance to stem rust (Puccinia graminis tritici) was investigated in wheat (Triticum aestivum L.) cultivars Romany, Es.P 518/9, Bonny and Tama that are resistant to many races in both Canada and Kenya. Seedling resistance in the four cultivars to 12 Canadian races is controlled primarily by previously identified genes. The results indicate that the cultivars have the following genes: Romany — Sr5, Sr6, Sr7a, Sr9b and SrW; Es.P 518/9 — Sr5, Sr6, Sr7a, Sr8, Sr9b, SrW and possibly Sr17; Bonny — Sr6 and Sr11; and Tama — Sr6 and Sr8. Gene SrW confers moderate resistance and is also present in the cultivar Webster.

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