Reference genome-assisted identification of stem rust resistance gene Sr62 encoding a tandem kinase

The wild relatives and progenitors of wheat have been widely used as sources of disease resistance (R) genes. Molecular identification and characterization of these R genes facilitates their manipulation and tracking in breeding programmes. We developed a reference-quality genome assembly of the wild diploid wheat relative Aegilops sharonensis and used positional mapping, mutagenesis, RNA-Seq and transgenesis to identify the stem rust resistance gene Sr62, which was also transferred to common wheat. This gene encodes a tandem kinase, homologues of which exist across multiple taxa in the plant kingdom. Stable Sr62 transgenic wheat lines showed high levels of resistance against diverse isolates of the stem rust pathogen, highlighting the utility of Sr62 for deployment as part of a polygenic stack to maximize the durability of stem rust resistance.

Adult Plant Stem Rust Resistance in Durum Wheat Glossy Huguenot – Mapping, Marker Development and Validation

An F3 population from a Glossy Huguenot (GH)/Bansi cross used in a previous Australian study was advanced to F6 for molecular mapping of adult plant stem rust resistance. Maturity differences among F6 lines confounded assessments of stem rust response. GH was crossed with a stem rust susceptible F6 recombinant inbred line (RIL), GHB14 (M14), with similar maturity and an F6:7 population was developed through single seed descent method. F7 and F8 RILs were tested along with the parents at different locations. The F6 individual plants and both parents were genotyped using the 90K single nucleotide polymorphism (SNP) wheat array. Stem rust resistance QTL on the long arms of chromosomes 1B (QSrGH.cs-1BL) and 2A (QSrGH.cs-2AL) were detected. QSrGH.cs-1BL and QSrGH.cs-2AL were both contributed by GH and explained 22% and 18% adult plant stem rust response variation, respectively, among GH/M14 RIL population. RILs carrying combinations of these QTL reduced more than 14% stem rust severity compared to those that possessed QSrGH.cs-1BL and QSrGH.cs-2AL individually. QSrGH.cs1BL was demonstrated to be the same as Sr58/Lr46/Yr29/Pm39 through marker genotyping. Lines lacking QSrGH.cs-1BL were used to Mendelise QSrGH.cs-2AL. Based on genomic locations of previously catalogued stem rust resistance genes and the QSrGH.cs-2AL map, it appeared to represent a new APR locus and was permanently named Sr63. SNP markers associated with Sr63 were converted to kompetetive allele specific PCR (KASP) assays and were validated on a set of durum cultivars.

A prebreeding study of introgression spring bread wheat lines carrying combinations of stem rust resistance genes, Sr22+Sr25 and Sr35+Sr25

The Sr22, Sr35, and Sr25 genes attract the attention of bread wheat breeders with their effectiveness against Puccinia graminis f. sp. tritici race Ug99 and its biotypes. The effectiveness and impact of Sr22+Sr25 and Sr35+Sr25 gene combinations on agronomic traits have not yet been studied. In the present article, these traits were studied using the spring bread wheat lines L503/W3534//L503, L503/Sr35//L503/3/L503 carrying the Sr22+Sr25 and Sr35+Sr25 genes during 2016–2020. These lines were assessed for resistance to P. graminis f. sp. tritici under natural epiphytotics and to the Saratov, Lysogorsk and Omsk populations of the pathogen and to the PgtZ1 (TKSTF) and PgtF18.6 fungus isolates in laboratory conditions (TKSTF + Sr33). The presence of the studied Sr-genes was confirmed by using molecular markers. Prebreeding studies were conducted during 2018–2020 vegetation periods. Under the natural epiphytotics of the pathogen and in the laboratory conditions, the Sr22+Sr25 combination was highly effective, while Sr35+Sr25 was ineffective. For grain yield, the lines with the Sr22+Sr25 and Sr35+Sr25 genes were superior to the recipient cultivar L503 in one year (Sr22+Sr25 in 2019; Sr35+Sr25 in 2018), with a decrease in 2020, but in general there were no differences. For the period 2018–2020, both combinations showed a decrease in 1000 grains weight and an increase in the germination-earing period. The line with Sr22+Sr25 genes showed insignificant effects on gluten and dough tenacity, but the ratio of dough tenacity to extensibility was higher, and flour strength, porosity and bread volume were lower; in the line with Sr35+Sr25 genes, the gluten content was lower, but the strength, tenacity of the dough and the ratio of dough tenacity to extensibility were higher, flour strength and the porosity of the bread were at the recipient level, but the volume of bread was lower.

Assessment of Genetic Diversity for Stem Rust and Stripe Rust Resistance in an International Wheat Nursery Using Phenotypic and Molecular Technologies

The objective of this study was to assess diversity for stem rust and stripe rust resistance in an international wheat screening nursery under greenhouse conditions using pathotypes with known avirulence/ virulence profiles. A set of 95 entries of an international wheat screening nursery collected from material generated by staff of the International Maize and Wheat Improvement Centre (CIMMYT) was tested against seven Australian Pgt and five Pst pathotypes through artificial inoculation under the greenhouse conditions using standard procedures. Ten all-stage stem rust resistance genes (Sr8a, Sr8b, Sr9b, Sr12, Sr17, Sr23, Sr24, Sr30, Sr31 and Sr38) and seven all-stage stripe rust resistance genes (Yr3, Yr4, Yr6, Yr9, Yr17, Yr27 and Yr34) were postulated either singly or in combinations based on seedling responses of test entries against pathotypes differing in virulence for commonly deployed genes. Sr30 and Sr38 were the most common stem rust resistance genes in this nursery. The Sr38-linked stripe rust resistance gene Yr17 was present in high proportion. The presence of rust resistance genes Sr24, Sr31/Yr9, Sr38/Yr17 and Yr4 were confirmed using the closely linked molecular markers. The adult plant resistance (APR) genes Sr2 and Lr34/Yr18/Sr57 were detected using linked molecular markers csSr2 and csLV34, respectively. Genotypes carrying combinations of stem rust and stripe rust resistance were identified for use as donor sources in breeding programs.

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

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.

Identification and Validation of High LD Hotspot Genomic Regions Harboring Stem Rust Resistant Genes on 1B, 2A (Sr38), and 7B Chromosomes in Wheat

Stem rust caused by Puccinia graminis f. sp. tritici Eriks. is an important disease of common wheat globally. The production and cultivation of genetically resistant cultivars are one of the most successful and environmentally friendly ways to protect wheat against fungal pathogens. Seedling screening and genome-wide association study (GWAS) were used to determine the genetic diversity of wheat genotypes obtained on stem rust resistance loci. At the seedling stage, the reaction of the common stem rust race QFCSC in Nebraska was measured in a set of 212 genotypes from F3:6 lines. The results indicated that 184 genotypes (86.8%) had different degrees of resistance to this common race. While 28 genotypes (13.2%) were susceptible to stem rust. A set of 11,911 single-nucleotide polymorphism (SNP) markers was used to perform GWAS which detected 84 significant marker-trait associations (MTAs) with SNPs located on chromosomes 1B, 2A, 2B, 7B and an unknown chromosome. Promising high linkage disequilibrium (LD) genomic regions were found in all chromosomes except 2B which suggested they include candidate genes controlling stem rust resistance. Highly significant LD was found among these 59 significant SNPs on chromosome 2A and 12 significant SNPs with an unknown chromosomal position. The LD analysis between SNPs located on 2A and Sr38 gene reveal high significant LD genomic regions which was previously reported. To select the most promising stem rust resistant genotypes, a new approach was suggested based on four criteria including, phenotypic selection, number of resistant allele(s), the genetic distance among the selected parents, and number of the different resistant allele(s) in the candidate crosses. As a result, 23 genotypes were considered as the most suitable parents for crossing to produce highly resistant stem rust genotypes against the QFCSC.

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

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.