Identification of leaf rust resistance genes in the new Russian varieties of common wheat

Background. Wheat leaf rust caused by Puccinia triticina Erikss. is a significant wheat disease in all regions of the Russian Federation. The genetic diversity of the cultivated wheat varieties regarding the type of resistance and genes that control it ensures reliable protection of this crop against the pathogen. The aim of this work was to characterize the diversity of new Russian varieties of winter and spring common wheat for leaf rust resistance genes (Lr-genes).Materials and Methods. The research material was represented by 43 varieties of winter and 25 of spring wheat included in the State Register of Selection Achievements of the Russian Federation in 2018-2020.Results. Using molecular markers, 18 Lr genes were identified: Lr1, Lr3, Lr9, Lr10, Lr19, Lr20, Lr21, Lr24, Lr25, Lr26, Lr28, Lr29, Lr34, Lr35, Lr37, Lr41 (39), Lr47 and Lr66. A phytopathological test was used to clarify the results of molecular analysis. Ninety-three percent of the studied wheat varieties were found to contain Lr genes, either separately or in combinations. These were the highly and partially effective genes Lr24, Lr9, and Lr19, adult plant resistance genes Lr34 and Lr37, and ineffective genes Lr1, Lr3, Lr10, Lr20, and Lr26. The Lr24 gene has been identified for the first time in Russian varieties. The spring variety ‘Leader 80’, harboring this gene, is recommended for cultivation in the West Siberian and East Siberian regions. An effective combination of Lr9 + Lr26 genes, individually overcome by the pathogen, was determined in the spring cultivar ‘Silach’, highly resistant to leaf rust. The Lr9 gene was found in the winter variety ‘Gerda’, which is recommended for cultivation in the North Caucasus region. Previously, the varieties with Lr9 were not grown in the North Caucasus. An increase in the number of leaf rust resistant accessions protected by the effective adult plant resistance gene Lr37 is noted among wheat varieties undergoing regional adaptation testing. Many of the identified Lr genes (Lr19, Lr24, Lr26, Lr34, Lr37) are linked with effective Sr genes (Sr25, Sr24, Sr31, Sr57, and Sr38), which additionally ensures stable genetic protection of wheat against stem rust.Conclusions. The obtained information about representation of Lr genes in wheat varieties should be used in regional breeding programs. A timely replacement of genetically protected varieties allows stabilizing the populational composition of the phytopathogen and reducing the likelihood of epiphytotics.

Evaluation of Wheat Germplasm for Resistance to Leaf Rust (Puccinia triticina) and Identification of the Sources of Lr Resistance Genes Using Molecular Markers

Leaf rust, caused by Puccinia triticina (Ptr), is a significant disease of spring wheat spread in Kazakhstan. The development of resistant cultivars importantly requires the effective use of leaf rust resistance genes. This study aims to: (i) determine variation in Ptr population using races from the East Kazakhstan, Akmola, and Almaty regions of Kazakhstan; (ii) examine resistance during seedling and adult plant stages; and (iii) identify the sources of Lr resistance genes among the spring wheat collection using molecular markers. Analysis of a mixed population of Ptr identified 25 distinct pathotypes. Analysis of these pathotypes using 16 Thatcher lines that are near-isogenic for leaf rust resistance genes (Lr) showed different virulence patterns, ranging from least virulent “CJF/B” and “JCL/G” to highly virulent “TKT/Q”. Most of the pathotypes were avirulent to Lr9, Lr19, Lr24, and Lr25 and virulent to Lr1, Lr2a, Lr3ka, Lr11, and Lr30. The Ptr population in Kazakhstan is diverse, as indicated by the range of virulence observed in five different races analyzed in this study. The number of genotypes showed high levels of seedling resistance to each of the five Ptr races, thus confirming genotypic diversity. Two genotypes, Stepnaya 62 and Omskaya 37, were highly resistant to almost all five tested Ptr pathotypes. Stepnaya 62, Omskaya 37, Avangard, Kazakhstanskaya rannespelaya, and Kazakhstanskaya 25 were identified as the most stable genotypes for seedling resistance. However, most of the varieties from Kazakhstan were susceptible in the seedling stage. Molecular screening of these genotypes showed contrasting differences in the genes frequencies. Among the 30 entries, 22 carried leaf rust resistance gene Lr1, and two had Lr9 and Lr68. Lr10 and Lr28 were found in three and four cultivars, respectively. Lr19 was detected in Omskaya 37. Two single cultivars separately carried Lr26 and Lr34, while Lr37 was not detected in any genotypes within this study. Field evaluation demonstrated that the most frequent Lr1 gene is ineffective. Kazakhstanskaya 19 and Omskaya 37 had the highest number of resistance genes: three and four Lr genes, respectively. Two gene combinations (Lr1, Lr68) were detected in Erythrospermum 35 and Astana. The result obtained may assist breeders in incorporating effective Lr genes into new cultivars and developing cultivars resistant to leaf rust.

Genotype groups of the wheat leaf rust fungus Puccinia triticina in the United States as determined by genotyping by sequencing

Wheat leaf rust caused by Puccinia triticina, is a widespread disease of wheat in the United States and worldwide. Populations of P. triticina are characterized by virulence phenotypes that change rapidly due to selection by wheat cultivars with leaf rust resistance genes. The objective of this study was to genotype collections of P. triticina from 2011-2018 in the United States, using restriction site associated genotyping by sequencing (GBS), to determine if recently identified new virulence phenotypes belong to established genotype groups or belong to groups previously not detected. A total of 158 isolates were phenotyped for virulence on 20 lines of Thatcher wheat that are isogenic for leaf rust resistance genes and were also genotyped for single nucleotide polymorphism. Eight distinct groups of P. triticina genotypes from common wheat were described based on coancestry, nucleotide divergence, and principal coordinate plots. A separate genotype group had isolates with virulence to durum wheat. Isolates within groups had similar virulence phenotype, and the overall population had high level of heterozygosity and a high level of linkage disequilibria, which were all indicators of clonality. Two new genotype groups were described, raising the possibility of new introductions of P. triticina, although genotypes in these groups may have also originated from somatic nuclear exchange and recombination. A genome wide association study detected 19 SNPs that were highly associated with virulence to 11 resistance genes in the Thatcher near isogenic lines.

Molecular Identification of Triticale Introgression Lines Carrying Leaf Rust Resistance Genes Transferred From Aegilops Kotschyi Boiss. and Ae. Tauschii Coss.

Triticale (×Triticosecale Wittmack) is a commercial hybrid harboring wheat (Triticum sp.) and rye (Secale cereale L.) genomes. The limited genetic diversity of this crop resulted in the collapse of fungal disease resistance. Leaf rust disease, caused by Puccinia triticina Eriks. is reported to reduce the triticale yield significantly (more than 30%). There is a need to enlarge the genetic variability of this crop including leaf resistance genes. The main aim of this research was to transfer Lr39 and Lr54 leaf rust resistance genes into triticale from Aegilops tauschii and Ae. kotschyi, respectively. A reaction of seedlings of 200 plants of two triticale-Aegilops translocation lines (Bogo-2Dt.2R and Sekundo-2Sk.2R) was compared after inoculation with a natural mixture of P. triticina races, specific to triticale. Before inoculation, each plant was screened using molecular cytogenetics and molecular markers linked to leaf rust resistance genes. Presence of Aegilops chromosome segments was confirmed using genomic in situ hybridization (GISH). Lr39 and Lr54 leaf rust resistance genes were identified using Xgdm35 and S14 molecular markers, respectively. After inoculation, a significant improvement of resistance severity was observed in Sekundo-2Sk.2R in comparison with triticale cv. Sekundo plants. The resistance level of Bogo-2Dt.2R did not differ compared to triticale cv. Bogo plants. It was shown, that Lr39 gene did not increase the leaf rust resistance level of triticale cv. Bogo.

The use of molecular-genetic and phytopathological methods to identify genes for effective leaf rust resistance in Aegilops accessions

Background. Identification of effective genes for disease resistance in resistant plant samples is the most important step toward recommending them for breeding. There are three main methods for such identification: hybridological analysis, phytopathological test, and DNA marking. The method of PCR markers is widely used in Russia to identify resistance genes in wheat relatives, including the genus Aegi lops L. for resistance to leaf rust. From a theoretical viewpoint, the presence of a certain amplification fragment can hardly be interpreted as a definite proof of the presence of a resistance gene: during the species evolution, recombinations and mutations could occur, resulting in disturbance of the fragment’s presence and phenotypic expression of its connection with resistance. The purpose of this work was a comparison between molecular-genetic and phytopathological methods to identify leaf rust resistance genes Lr9 and Lr41 in three Aegilops species.Materials and methods. We identified leaf rust resistance genes Lr9 and Lr41 in forty Aegilops accessions using PCR with J13 and GDM35 primers, respectively. In the phytopathological test, the seedlings were infected with the pathogen population (avirulent to Lr9 and Lr41 genes) and the fungus clones virulent to the wheat line with the Lr9 gene.Results and conclusions. According to the data of molecular marking, the Lr41 gene was present in twelve Ae. tauschii Coss. accessions; Lr9 in four Ae umbellulata Zhuk. accessions and four of Ae. biuncialis Vis. All accessions of Ae. tauschii, two of Ae. umbellulata, and three of Ae. biuncialis, possessing effective resistance genes according to the molecular testing, were susceptible to the pathogen population. For three Ae. umbellulata accessions resistant to the population, where DNA marking failed to identify an Lr9 gene, the presence of this gene was shown by a phytopathological test. Thus, there were significant differences in the postulation of effective Lr9 and Lr41 leaf rust resistance genes in Aegilops accessions after a phytopatological test and the use of DNA markers.

Race and Virulence Analysis of Puccinia triticina in China in 2014 and 2015

Wheat leaf rust, caused by Puccinia triticina, is an important fungal disease of wheat in China. To study races of the pathogen in China, leaf rust samples were collected from 14 provinces in 2014 and 15 provinces in 2015. From the samples, 494 single-uredinial isolates were derived from the 2014 collection and 649 from the 2015 collection. These isolates were tested on 40 near-isogenic lines of Thatcher carrying single leaf rust resistance genes. From the isolates, 84 races were identified in 2014 and 65 races in 2015. Races THTT (22.1%), THTS (19.6%), THJT (8.7%), PHTT (4.9%), and PHJT (3.6%) were the most common races in 2014, and THTT (28.4%), THTS (12.8%), THJT (11.6%), THJS (9.9%), and PHTT (9.7%) were the most frequent in 2015. All of these races were avirulent to resistance genes Lr9 and Lr24. THTT and THTS, the most frequent races in both years, were widely distributed throughout the country. The frequencies of isolates with virulence to Lr1, Lr2a, Lr2c, Lr3, Lr16, Lr26, Lr11, Lr17, LrB, Lr10, Lr14a, Lr2b, Lr3bg, Lr14b, Lr32, Lr33, and Lr50 were over 80%, whereas the frequencies of virulence to Lr9, Lr19, Lr25, Lr28, Lr29, and Lr47 were less than 3.5%. In the present study, all isolates were avirulent to Lr24 and Lr38. The race analysis and individual virulence frequencies provide guidance to breeders in choosing leaf rust resistance genes for use in breeding programs.