Genetic Characterization and Genome-Wide Association Mapping for Stem Rust Resistance in Spring Bread Wheat

Abstract Background Emerging wheat stem rust races has become a major threat to global wheat production. Finding additional loci responsible for resistance to these races and incorporating them into currently cultivated varieties is the most economical and environmentally sound strategy to combat this problem. Thus, this study aimed to characterize the genetic diversity of wheat and to identify the genetic loci conferring resistance to stem rust of wheat. To accomplish this study, 245 elite lines introduced from the International Center for Agricultural Research in the Dry Areas (ICARDA) were tested under natural stem rust pressure in the field at the Debre Zeit Agricultural Research Center, Ethiopia. The SNP marker data was retrieved from a 15K SNP wheat array. Association analysis was undertaken between SNP markers and best linear unbiased prediction (BLUP) value of the stem rust coefficient of infection (CI) using a mixed linear model. Results Phenotypic analysis revealed 46% of lines had a coefficient of infection (CI) between 0 to 19. An average 0.38 in Nei’s gene diversity, 0.20 in polymorphism information content, and 0.71 in major allele frequency of the whole genome were identified.A total of 46 marker-trait associations (MTAs) that were encompassed within 13 quantitative trait loci (QTL) on chromosomes 1B, 3A, 3B, 4A, 4B, and 5A were found for CI. Four major QTLs with –log10 (p) ≥ 3 (EWYP1B.1, EWYP1B.3, EWYP1B.4, and EWYP1B.5) were identified on chromosome 1B. Conclusions This study contributes several novel markers associated with stem rust resistance. These can be further facilitating durable rust resistance development through marker-assisted selection. The resistant wheat genotypes identified in this study are recommended to be used in the national wheat breeding programs to improve stem rust resistance. Key words: markers; Puccinia graminis f. sp. tritici; QTL

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

Phytopathology ◽

10.1094/phyto-04-16-0165-r ◽

2016 ◽

Vol 106 (11) ◽

pp. 1352-1358 ◽

Cited By ~ 14

Author(s):

Jayaveeramuthu Nirmala ◽

Shiaoman Chao ◽

Pablo Olivera ◽

Ebrahiem M. Babiker ◽

Bekele Abeyo ◽

...

Keyword(s):

Stem Rust ◽

Rust Resistance ◽

Genetic Resistance ◽

Wheat Breeding ◽

Snp Markers ◽

Stem Rust Resistance ◽

Puccinia Graminis ◽

Wheat Stem Rust ◽

Wheat Varieties ◽

Breeding Lines

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.

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Stem Rust Resistance in A-Genome Diploid Relatives of Wheat

Plant Disease ◽

10.1094/pdis-04-10-0260 ◽

2011 ◽

Vol 95 (8) ◽

pp. 941-944 ◽

Cited By ~ 39

Author(s):

M. N. Rouse ◽

Y. Jin

Keyword(s):

Resistance Genes ◽

Stem Rust ◽

Rust Resistance ◽

Infection Type ◽

Genetic Resistance ◽

Wheat Breeding ◽

Stem Rust Resistance ◽

Wheat Stem Rust ◽

A Genome ◽

Stem Rust Resistance Genes

Wheat stem rust, caused by Puccinia graminis f. sp. tritici, has been effectively controlled through the use of genetic resistance. P. graminis f. sp. tritici race TTKSK (Ug99) possesses virulence to many resistance genes that have been used in wheat breeding worldwide. One strategy to aid breeders in developing resistant cultivars is to utilize resistance genes transferred from wild relatives to wheat. Stem rust resistance genes have previously been introgressed from Triticum monococcum to wheat. In order to identify additional resistance genes, we screened 1,061 accessions of T. monococcum and 205 accessions of T. urartu against race TTKSK and four additional P. graminis f. sp. tritici races: TTTTF, TRTTF, QFCSC, and MCCFC. A high frequency of the accessions (78.7% of T. monococcum and 93.0% of T. urartu) were resistant to P. graminis f. sp. tritici race TTKSK, with infection types ranging from 0 to 2+. Among these resistant accessions, 55 T. monococcum accessions (6.4% of the total) were also resistant to the other four races. Associations of resistance in T. monococcum germplasm to different races indicated the presence of genes conferring resistance to multiple races. Comparing the observed infection type patterns to the expected patterns of known genes indicated that previously uncharacterized genes for resistance to race TTKSK exist in both T. monococcum and T. urartu.

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Mapping and Characterization of a Wheat Stem Rust Resistance Gene in Durum Wheat “Kronos”

Frontiers in Plant Science ◽

10.3389/fpls.2021.751398 ◽

2021 ◽

Vol 12 ◽

Author(s):

Hongna Li ◽

Lei Hua ◽

Matthew N. Rouse ◽

Tianya Li ◽

Shuyong Pang ◽

...

Keyword(s):

Durum Wheat ◽

Resistance Genes ◽

Stem Rust ◽

Rust Resistance ◽

Wheat Variety ◽

Wheat Breeding ◽

Stem Rust Resistance ◽

Wheat Stem Rust ◽

Seedling Resistance ◽

Or Gene

Wheat stem (or black) rust is one of the most devastating fungal diseases, threatening global wheat production. Identification, mapping, and deployment of effective resistance genes are critical to addressing this challenge. In this study, we mapped and characterized one stem rust resistance (Sr) gene from the tetraploid durum wheat variety Kronos (temporary designation SrKN). This gene was mapped on the long arm of chromosome 2B and confers resistance to multiple virulent Pgt races, such as TRTTF and BCCBC. Using a large mapping population (3,366 gametes), we mapped SrKN within a 0.29 cM region flanked by the sequenced-based markers pku4856F2R2 and pku4917F3R3, which corresponds to 5.6- and 7.2-Mb regions in the Svevo and Chinese Spring reference genomes, respectively. Both regions include a cluster of nucleotide binding leucine-repeat (NLR) genes that likely includes the candidate gene. An allelism test failed to detect recombination between SrKN and the previously mapped Sr9e gene. This result, together with the similar seedling resistance responses and resistance profiles, suggested that SrKN and Sr9e may represent the same gene. We introgressed SrKN into common wheat and developed completely linked markers to accelerate its deployment in the wheat breeding programs. SrKN can be a valuable component of transgenic cassettes or gene pyramids that includes multiple resistance genes to control this devastating disease.

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Mapping of SrTm4, a Recessive Stem Rust Resistance Gene from Diploid Wheat Effective to Ug99

Phytopathology ◽

10.1094/phyto-12-14-0382-r ◽

2015 ◽

Vol 105 (10) ◽

pp. 1347-1354 ◽

Cited By ~ 8

Author(s):

Jordan Briggs ◽

Shisheng Chen ◽

Wenjun Zhang ◽

Sarah Nelson ◽

Jorge Dubcovsky ◽

...

Keyword(s):

Resistance Gene ◽

Stem Rust ◽

Rust Resistance ◽

Wheat Breeding ◽

Stem Rust Resistance ◽

Rust Resistance Gene ◽

Diploid Wheat ◽

Stem Rust Resistance Gene ◽

Wheat Stem Rust ◽

Stem Rust Resistance Genes

Race TTKSK (or Ug99) of Puccinia graminis f. sp. tritici, the causal agent of wheat stem rust, is a serious threat to wheat production worldwide. Diploid wheat, Triticum monococcum (genome Am), has been utilized previously for the introgression of stem rust resistance genes Sr21, Sr22, and Sr35. Multipathotype seedling tests of biparental populations demonstrated that T. monococcum accession PI 306540 collected in Romania contains a recessive resistance gene effective to all P. graminis f. sp. tritici races screened, including race TTKSK. We will refer to this gene as SrTm4, which is the fourth stem rust resistance gene characterized from T. monococcum. Using two mapping populations derived from crosses of PI 272557 × PI 306540 and G3116 × PI 306540, we mapped SrTm4 on chromosome arm 2AmL within a 2.1 cM interval flanked by sequence-tagged markers BQ461276 and DR732348, which corresponds to a 240-kb region in Brachypodium chromosome 5. The eight microsatellite and nine sequence-tagged markers linked to SrTm4 will facilitate the introgression and accelerate the deployment of SrTm4-mediated Ug99 resistance in wheat breeding programs.

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THE INHERITANCE OF PATHOGENICITY IN RACES 111 AND 29 OF WHEAT STEM RUST

Canadian Journal of Genetics and Cytology ◽

10.1139/g69-033 ◽

1969 ◽

Vol 11 (2) ◽

pp. 266-274 ◽

Cited By ~ 4

Author(s):

K. N. Kao ◽

D. R. Knott

Keyword(s):

Stem Rust ◽

Rust Resistance ◽

Single Gene ◽

Stem Rust Resistance ◽

Wheat Stem Rust ◽

Complementary Genes

The inheritance of pathogenicity in wheat stem rust was studied in selfed cultures of races 29 and 111, F1 and F2 cultures of a cross between the two races and cultures from a backcross to race 29. The various cultures were tested on Marquis and Prelude and on a series of lines of these varieties carrying single genes for stem rust resistance. Virulence on Sr 5, Sr 6, Sr 8, Sr 9a, Sr 14 and a gene in Marquis was recessive and in each case there was a single gene for virulence corresponding to each gene for resistance. Virulence on Sr 1 was possibly controlled by two dominant complementary genes. There appeared to be two alleles for virulence on Prelude, one dominant and one recessive.

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Identification and characterization of Sr22b , a new allele of the wheat stem rust resistance gene Sr22 effective against the Ug99 race group

Plant Biotechnology Journal ◽

10.1111/pbi.13737 ◽

2021 ◽

Author(s):

Jing Luo ◽

Matthew N. Rouse ◽

Lei Hua ◽

Hongna Li ◽

Boshu Li ◽

...

Keyword(s):

Resistance Gene ◽

Stem Rust ◽

Rust Resistance ◽

Stem Rust Resistance ◽

Rust Resistance Gene ◽

Stem Rust Resistance Gene ◽

Wheat Stem Rust ◽

Identification And Characterization

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Mapping and characterization of wheat stem rust resistance genes SrTm5 and Sr60 from Triticum monococcum

Theoretical and Applied Genetics ◽

10.1007/s00122-017-3024-z ◽

2017 ◽

Vol 131 (3) ◽

pp. 625-635 ◽

Cited By ~ 10

Author(s):

Shisheng Chen ◽

Yan Guo ◽

Jordan Briggs ◽

Felix Dubach ◽

Shiaoman Chao ◽

...

Keyword(s):

Resistance Genes ◽

Stem Rust ◽

Rust Resistance ◽

Stem Rust Resistance ◽

Triticum Monococcum ◽

Wheat Stem Rust ◽

Stem Rust Resistance Genes ◽

Rust Resistance Genes

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Identification of stem rust resistance genes in wheat cultivars in China using molecular markers

PeerJ ◽

10.7717/peerj.4882 ◽

2018 ◽

Vol 6 ◽

pp. e4882 ◽

Cited By ~ 7

Author(s):

Xiaofeng Xu ◽

Depeng Yuan ◽

Dandan Li ◽

Yue Gao ◽

Ziyuan Wang ◽

...

Keyword(s):

Molecular Markers ◽

Resistance Genes ◽

Stem Rust ◽

Rust Resistance ◽

Genetic Material ◽

Stem Rust Resistance ◽

Wheat Cultivars ◽

Wheat Stem Rust ◽

Stem Rust Resistance Genes ◽

Rust Resistance Genes

Wheat stem rust caused by Puccinia graminis f. sp. tritici Eriks. & E. Henn. (Pgt), is a major disease that has been effectively controlled using resistance genes. The appearance and spread of Pgt races such as Ug99, TKTTF, and TTTTF, which are virulent to most stem rust-resistant genes currently deployed in wheat breeding programs, renewed the interest in breeding cultivars resistant to wheat stem rust. It is therefore important to investigate the levels of resistance or vulnerability of wheat cultivars to Pgt races. Resistance to Pgt races 21C3CTHQM, 34MKGQM, and 34C3RTGQM was evaluated in 136 Chinese wheat cultivars at the seedling stage. A total of 124 cultivars (91.2%) were resistant to the three races. Resistance genes Sr2, Sr24, Sr25, Sr26, Sr31, and Sr38 were analyzed using molecular markers closely linked to them, and 63 of the 136 wheat cultivars carried at least one of these genes: 21, 25, and 28 wheat cultivars likely carried Sr2, Sr31, and Sr38, respectively. Cultivars “Kehan 3” and “Jimai 22” likely carried Sr25. None of the cultivars carried Sr24 or Sr26. These cultivars with known stem rust resistance genes provide valuable genetic material for breeding resistant wheat cultivars.

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