Source Of Leaf Rust Resistance Research Articles

Identification of leaf rust resistance loci in a geographically diverse panel of wheat using genome-wide association analysis.

Leaf rust, caused by Puccinia triticina (Pt) is among the most devastating diseases posing a significant threat to global wheat production. The continuously evolving virulent Pt races in North America calls for exploring new sources of leaf rust resistance. A diversity panel of 365 bread wheat accessions selected from a worldwide population of landraces and cultivars was evaluated at the seedling stage against four Pt races (TDBJQ, TBBGS, MNPSD and, TNBJS). A wide distribution of seedling responses against the four Pt races was observed. Majority of the genotypes displayed a susceptible response with only 28 (9.8%), 59 (13.5%), 45 (12.5%), and 29 (8.1%) wheat accessions exhibiting a highly resistant response to TDBJQ, TBBGS, MNPSD and, TNBJS, respectively. Further, we conducted a high-resolution multi-locus genome-wide association study (GWAS) using a set of 302,524 high-quality single nucleotide polymorphisms (SNPs). The GWAS analysis identified 27 marker-trait associations (MTAs) for leaf rust resistance on different wheat chromosomes of which 20 MTAs were found in the vicinity of known Lr genes, MTAs, or quantitative traits loci (QTLs) identified in previous studies. The remaining seven significant MTAs identified represent genomic regions that harbor potentially novel genes for leaf rust resistance. Furthermore, the candidate gene analysis for the significant MTAs identified various genes of interest that may be involved in disease resistance. The identified resistant lines and SNPs linked to the QTLs in this study will serve as valuable resources in wheat rust resistance breeding programs.

Discovery of Resistance Genes in Rye by Targeted Long-Read Sequencing and Association Genetics

The majority of released rye cultivars are susceptible to leaf rust because of a low level of resistance in the predominant hybrid rye-breeding gene pools Petkus and Carsten. To discover new sources of leaf rust resistance, we phenotyped a diverse panel of inbred lines from the less prevalent Gülzow germplasm using six distinct isolates of Puccinia recondita f. sp. secalis and found that 55 out of 92 lines were resistant to all isolates. By performing a genome-wide association study using 261,406 informative SNP markers, we identified five resistance-associated QTLs on chromosome arms 1RS, 1RL, 2RL, 5RL and 7RS. To identify candidate Puccinia recondita (Pr) resistance genes in these QTLs, we sequenced the rye nucleotide-binding leucine-rich repeat (NLR) intracellular immune receptor complement using a Triticeae NLR bait-library and PacBio® long-read single-molecule high-fidelity (HiFi) sequencing. Trait-genotype correlations across 10 resistant and 10 susceptible lines identified four candidate NLR-encoding Pr genes. One of these physically co-localized with molecular markers delimiting Pr3 on chromosome arm 1RS and the top-most resistance-associated QTL in the panel.

Lr80: A new and widely effective source of leaf rust resistance of wheat for enhancing diversity of resistance among modern cultivars.

A new leaf rust resistance gene Lr80 was identified and closely linked markers were developed for its successful pyramiding with other marker-tagged genes to achieve durable control of leaf rust. Common wheat landrace Hango-2, collected in 2006 from the Himalayan area of Hango, District Kinnaur, in Himachal Pradesh, exhibited a very low infection type (IT;) at the seedling stage to all Indian Puccinia triticina (Pt) pathotypes, except the pathotype 5R9-7 which produced IT 3+. Genetic analysis based on Agra Local/Hango-2-derived F3 families indicated monogenic control of leaf rust resistance, and the underlying locus was temporarily named LrH2. Bulked segregant analysis using 303 simple sequence repeat (SSR) markers located LrH2 in the short arm of chromosome 2D. An additional set of 10 chromosome 2DS-specific markers showed polymorphism between the parents and these weremapped on the entire Agra Local/Hango-2 F3 population. LrH2 was flanked by markers cau96 (distally) and barc124 (proximally). The 90K Infinium SNP array was used to identify SNP markers linked with LrH2. Markers KASP_17425 and KASP_17148 showed association with LrH2. Comparison of seedling leaf rust response data and marker locations across different maps demonstrated the uniqueness of LrH2 and it was formally named Lr80. The Lr80-linked markers KASP_17425, KASP_17148 and barc124 amplified alleles/products different to Hango-2 in 82 Australian cultivars indicating their robustness for marker-assisted selection of this gene in wheat breeding programs.

Quantitative Trait Loci Conferring Leaf Rust Resistance in Hexaploid Wheat.

Leaf rust, caused by the fungal pathogen Puccinia triticina, is a major threat to wheat production in many wheat-growing regions of the world. The introduction of leaf rust resistance genes into elite wheat germplasm is the preferred method of disease control, being environmentally friendly and crucial to sustained wheat production. Consequently, there is considerable value in identifying and characterizing new sources of leaf rust resistance. While many major, qualitative leaf rust resistance genes have been identified in wheat, a growing number of valuable sources of quantitative resistance have been reported. Here we review the progress made in the genetic identification of quantitative trait loci (QTL) for leaf rust resistance detected primarily in field analyses, i.e., adult plant resistance. Over the past 50 years, leaf rust resistance loci have been assigned to genomic locations through chromosome analyses and genetic mapping in biparental mapping populations, studies that represent 79 different wheat leaf rust resistance donor lines. In addition, seven association mapping studies have identified adult plant and seedling leaf rust resistance marker trait associations in over 4,000 wheat genotypes. Adult plant leaf rust resistance QTL have been found on all 21 chromosomes of hexaploid wheat, with the B genome carrying the greatest number of QTL. The group 2 chromosomes are also particularly rich in leaf rust resistance QTL. The A genome has the lowest number of QTL for leaf rust resistance. Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Molecular and Genetic Analysis of Leaf Rust Resistance Genes in Two New Egyptian Wheat Cultivars

Leaf rust caused by Puccinia triticina f. sp. tritici is the most common and wide-spread rust disease attacking many wheat cultivars in Egypt. Three main methods were used to identify leaf rust resistance genes; gene postulation, genetic analysis and molecular markers. The two resistant wheat cultivars i.e., Giza-171 and Sids-14, as well as the ten monogenic lines for leaf rust resistance; Lr9, Lr19, Lr21, Lr24, Lr25, Lr28, Lr29, Lr34, Lr46 and Lr47, were selected to carry out the present study. Out of the three methods used, genetic analysis and molecular markers were the best to identify the resistance genes in the two studied cultivars. Ten specific primers were used for the identification of 10 resistance genes in the two new Egyptian wheat cultivars i.e., Giza-171 and Sids-14. Six leaf rust resistance genes, Lr9, Lr25, Lr28, Lr29, Lr46 and Lr47 were identified in Giza-171, but only three genes, Lr29, Lr46 and Lr47, were detected in Sids-14. Each of these two new wheat cultivars proved to have an adequate and high level of genetic resistance to leaf rust. The tested wheat cultivars should be used as a good source of leaf rust resistance in breeding programs for rust resistance. Knowledge of the leaf rust resistance genes which has not been designated yet, will help to narrow the gap and throw light on the future objectives for the researchers interested in the full utilization of these genes in breeding materials.

Prediction and analysis of three gene families related to leaf rust (Puccinia triticina) resistance in wheat (Triticum aestivum L.)

BackgroundThe resistance to leaf rust (Lr) caused by Puccinia triticina in wheat (Triticum aestivum L.) has been well studied over the past decades with over 70 Lr genes being mapped on different chromosomes and numerous QTLs (quantitative trait loci) being detected or mapped using DNA markers. Such resistance is often divided into race-specific and race-nonspecific resistance. The race-nonspecific resistance can be further divided into resistance to most or all races of the same pathogen and resistance to multiple pathogens. At the molecular level, these three types of resistance may cover across the whole spectrum of pathogen specificities that are controlled by genes encoding different protein families in wheat. The objective of this study is to predict and analyze genes in three such families: NBS-LRR (nucleotide-binding sites and leucine-rich repeats or NLR), START (Steroidogenic Acute Regulatory protein [STaR] related lipid-transfer) and ABC (ATP-Binding Cassette) transporter. The focus of the analysis is on the patterns of relationships between these protein-coding genes within the gene families and QTLs detected for leaf rust resistance.ResultsWe predicted 526 ABC, 1117 NLR and 144 START genes in the hexaploid wheat genome through a domain analysis of wheat proteome. Of the 1809 SNPs from leaf rust resistance QTLs in seedling and adult stages of wheat, 126 SNPs were found within coding regions of these genes or their neighborhood (5 Kb upstream from transcription start site [TSS] or downstream from transcription termination site [TTS] of the genes). Forty-three of these SNPs for adult resistance and 18 SNPs for seedling resistance reside within coding or neighboring regions of the ABC genes whereas 14 SNPs for adult resistance and 29 SNPs for seedling resistance reside within coding or neighboring regions of the NLR gene. Moreover, we found 17 nonsynonymous SNPs for adult resistance and five SNPs for seedling resistance in the ABC genes, and five nonsynonymous SNPs for adult resistance and six SNPs for seedling resistance in the NLR genes. Most of these coding SNPs were predicted to alter encoded amino acids and such information may serve as a starting point towards more thorough molecular and functional characterization of the designated Lr genes. Using the primer sequences of 99 known non-SNP markers from leaf rust resistance QTLs, we found candidate genes closely linked to these markers, including Lr34 with distances to its two gene-specific markers being 1212 bases (to cssfr1) and 2189 bases (to cssfr2).ConclusionThis study represents a comprehensive analysis of ABC, NLR and START genes in the hexaploid wheat genome and their physical relationships with QTLs for leaf rust resistance at seedling and adult stages. Our analysis suggests that the ABC (and START) genes are more likely to be co-located with QTLs for race-nonspecific, adult resistance whereas the NLR genes are more likely to be co-located with QTLs for race-specific resistance that would be often expressed at the seedling stage. Though our analysis was hampered by inaccurate or unknown physical positions of numerous QTLs due to the incomplete assembly of the complex hexaploid wheat genome that is currently available, the observed associations between (i) QTLs for race-specific resistance and NLR genes and (ii) QTLs for nonspecific resistance and ABC genes will help discover SNP variants for leaf rust resistance at seedling and adult stages. The genes containing nonsynonymous SNPs are promising candidates that can be investigated in future studies as potential new sources of leaf rust resistance in wheat breeding.

Genetics of Leaf Rust Resistance in the Hard Red Winter Wheat Cultivars Santa Fe and Duster

Leaf rust, caused by Puccinia triticina, is a common and important disease of hard red winter wheat (Triticum aeistivum L.) in the Great Plains of the United States. The hard red winter wheat cultivars ‘Santa Fe’ and ‘Duster’ have had effective leaf rust resistance since their release in 2003 and 2006, respectively. The objective of this research was to determine the identity of the leaf rust resistance genes in these cultivars. Both cultivars were vernalized and crossed with the susceptible spring wheat ‘Thatcher’, F1 plants were backcrossed to Thatcher, and 90 backcross (BC) F1 plants from each cross were grown out to develop BC1F2 families. Seedlings of the Thatcher*2/Santa Fe BC1F2 families segregated for two genes. The seedling resistance was correlated with the presence of the 2AS/2NS translocation from Aegilops ventricosa Tausch, which indicated one of the genes was Lr37. In field plots, the families segregated for a single gene that was independent of the seedling resistance and the 2NS translocation. Seedlings of the Thatcher*2/Duster BC1F2 families segregated for two genes. In field plots, the families segregated for two genes that were independent of the seedling resistance genes. Santa Fe has Lr37 on the 2NS translocation, an additional adult plant resistance gene, and was postulated to have Lr3a. A previous postulation of Lr17a in Santa Fe was determined to be incorrect. Duster was postulated to have Lr3a and Lr11 for seedling resistance and, based on a molecular marker, Lr34 plus another adult plant resistance gene for field resistance. Lines with the additional adult plant resistance gene in both crosses had leaf rust severity of 10 to 30% with a resistance response of small to large uredinia with chlorosis and necrosis. Santa Fe and Duster are valuable sources of leaf rust resistance for the southern Great Plains region.

Novel Sources of Leaf Rust Resistance in Winter Wheat

Leaf rust is one of the most widespread diseases of wheat (Titicum aestivum L.), causing significant yield losses. More than 70 leaf rust resistance genes have been identified, but most of them have lost their effectiveness in the southern Great Plains of the United States. The objectives of this study were to evaluate leaf rust resistance of newly released wheat breeding lines and to identify novel resistance sources from a worldwide collection of landraces and historical cultivars. Results showed that only 4 out of 183 cultivars and breeding lines recently developed in the United States were highly resistant in the seedling stage to Pt2013, a bulk of Puccinia triticina Eriks. (Pt) races collected from multiple fields in Oklahoma in 2013, indicating the urgency of finding new resistance genes. We screened a set of 2171 accessions using Pt2013 and identified 26 landraces and 61 historical cultivars exhibiting high resistance. In addition, 159 landraces and 309 historical cultivars showed moderate resistance to Pt2013. These highly or moderately resistant accessions were further evaluated for their responses to another two Pt races predominant in Oklahoma in 2015, Pt52‐2 and Pt54‐1, and 25 of them showed high resistance to these two races and to the race composite. Another 66 and 53 accessions showed high resistance to one and two Pt races, respectively. Genetic diversity analysis using 5011 single‐nucleotide polymorphism markers identified genetically diverse resistance sources. The resistance sources identified in this study may be valuable for breeding leaf rust resistance.

‘CPAN 1842’: a new source of adult plant leaf rust resistance in bread wheat

AbstractThere is worldwide interest in adult plant resistance (APR) because of greater durability of APR to the cereal rusts. Peruvian bread wheat genotype ‘CPAN (Coordinated Project Accession Number) 1842’ (LM 50–53) has shown leaf rust resistance in disease screening nurseries since its introduction in 1977. However, it is susceptible at the seedling stage to several Puccinia triticina (Pt) pathotypes including the widely prevalent 77‐5 (121R63‐1) that infects bread wheat. Inheritance studies showed that CPAN 1842 carried a dominant gene for APR to pathotype 77‐5, which was different from Lr12, Lr13, Lr22a, Lr34, Lr35, Lr37, Lr46, Lr48, Lr49 and Lr68, based on the tests of allelism; and from Lr67, based on genotyping with the closely linked SSR marker cfd71. This gene should also be different from Lr22b as the latter is totally ineffective against pathotype 77‐5. CPAN 1842 therefore appears to be a new promising source of leaf rust resistance. Also having resistance to stem rust and stripe rust, this line can contribute to breeding for multiple rust resistances in wheat.

Inheritance and molecular mapping of leaf rust resistance inTriticum turgidumvar.durumcv. Trinakria

Leaf rust of wheat, caused by Puccinia triticina Eriks. is the most regularly occurring rust disease that can cause severe yield losses. Due to relatively lower economic value of durum wheat compared to the common wheat, genetic analysis of leaf rust resistance in durum wheat has been carried out only to a limited extent. Durum wheat genotype Trinakria showed high level and broad spectrum seedling resistance to 18 Indian leaf rust pathotypes. Genetic analysis at seedling stage in F2 and BC1 populations using leaf rust pathotype 77-5 showed a single dominant gene for resistance. The leaf rust resistance gene was mapped to the short arm of 5B chromosome and Xgwm234 was the closest marker at a distance of 6.3cM. The leaf rust resistance gene present in Trinakria is tentatively named as LrTrk. In durum wheat very few Lr genes have been documented, and hence Trinakria could be a promising source of leaf rust resistance for wheat breeders. The Xgwm234 marker linked to leaf rust resistance can be used for transfer of leaf rust resistance from Trinakria to other wheat cultivars through marker assisted selection.

Evaluation and reduction of Lr19-149, a recombined form of the Lr19 translocation of wheat

The Lr19 translocation was introgressed from Thinopyrum ponticum in 1966. It has not been used in wheat breeding in many countries despite it being an excellent source of leaf rust resistance as it carries an undesirable gene(s) coding for yellow endosperm pigmentation. A shortened form, Lr19-149, was since produced and lacks the yellow pigment genes. A yield trial with near isogenic lines of both the original and shortened translocations suggested that Lr19 may cause a small reduction in kernel size and anincrease in loaf volume, effects which are not associated with Lr19-149. In Lr19-149 heterozygotes the translocation generally showed reduced pollen transmission whereas its transmission through egg cells was mostly normal. An attempt to shorten Lr19-149 through allosyndetic recombination in the absence of Ph1b produced four recombinants which were characterized by means of RFLP and AFLP polymorphisms and physically mapped with a set of 27 deletion lines. In three recombinants (252, 299 and 462) Thinopyrum chromatin proximally to Lr19 was exchanged for wheat chromatin. In one recombinant (478) chromatin distally from Lr19 was replaced. Based on physical map distance estimates it appears that the Lr19 translocation in the shortest recombinant (299) may have been reduced to about one third or less of its original size. It may now be possible to obtain a further, albeit relatively small, decrease in the size of the translocation through homologous crossover between recombinants 299 and 478. Similar to Lr19-149, the new recombinants show self elimination in heterozygotes and they have apparently retained the Sd2 locus.

Genes Governing Resistance to Puccinia hordei in Thirteen Spring Barley Accessions

ABSTRACT Leaf rust, caused by Puccinia hordei, is an important disease of barley in many parts of the world. In the eastern United States, this disease was effectively controlled for over 20 years through the deployment of cultivars carrying the resistance gene Rph7. Isolates of P. hordei with virulence for Rph7 appeared in this region in the early 1990s rendering barley cultivars with this gene vulnerable to leaf rust infection. From a preliminary evaluation test, 13 accessions from diverse geographic locations possessed resistance to P. hordei isolate VA90-34, which has virulence for genes Rph1, 2, 4, 6, 7, 8, and 11. Each of these 13 accessions was crossed with susceptible cvs. Moore or Larker to characterize gene number and gene action for resistance to P. hordei. Additionally, the 13 accessions were intercrossed and crossed to host differential lines possessing genes Rph3, Rph5, and Rph9 to determine allelic relationships of resistance genes. Seedlings of F(1), F(2), and BC(1)F(1) populations were evaluated in the greenhouse for their reaction to P. hordei isolate VA90-34. Leaf rust resistance in six of the accessions including Collo sib, CR270.3.2, Deir Alla 105, Giza 119, Gloria, and Lenka is governed by a single dominant gene located at or near the Rph3 locus. All accessions for which the gene Rph3 was postulated to govern leaf rust resistance, except for Deir Alla 105, likely possess an allele different than Rph3.c found in Estate based on the differential reaction to isolates of P. hordei. The resistance gene in Grit and Donan is located at or near the Rph9 locus. Alleles at both the Rph3 and Rph9 loci confer resistance in Femina and Dorina. In addition to Rph3, Caroline and CR366.13.2 likely possess a second unknown recessive gene for leaf rust resistance. Resistance in Carre 180 is governed by a recessive gene that is different from all other genes considered in this study. Identification of both known and unique genes conferring leaf rust resistance in the barley germplasm included in this study provides breeding programs with the knowledge and opportunity to assess currently used sources of leaf rust resistance and to incorporate new sources of resistance into their programs.

First report of leaf rust pathotypes virulent to highly effective Lr‐genes transferred from Agropyron species to bread wheat

AbstractThe gene pool of effective sources of leaf rust resistance used in the breeding of wheat (Triticum aestivum L.) includes several species of the genus Agropyron. The genes deriving therefrom (Lr 19, 19d, 29, Agi1, Agi2, 38) are highly effective to pathotypes of Puccinia recondita Rob. ex Desm. In the Saratov and Orenbhurg districts of Russia, however, pathotypes virulent to these genes have been discovered. These pathotypes are virulent to Saratov‐bred cultivars carrying Lr 19, to ‘Indis’ (Lr 19d) and RL 6097 (Lr 38). The distribution of virulence on the ‘Thatcher’ near‐isogenic lines with different Lr genes shows that most of the Lr genes tested are susceptible to these new pathotypes of P. recondita, but the Lr genes Lr 9, 23, 24, 26 were exceptions. The inoculation of Mexican bread wheat cultivars, which carry widespread Lr gene combinations, by these pathotypes disclosed different infection types. Out of 10 Lr‐gene combinations, four were highly effective; namely the combinations Lr 13 + 26, Lr 26 +?, Lr 23+26 and Lr 23+26+34.

Evaluation of cultivated and wild barley for resistance to pathotypes ofPuccinia hordei with wide virulence

An isolate ofPuccinia hordei (ND89-3) originally collected in Morocco is virulent on most barley genotypes reported to possess resistance, except cultivar Estate (CI 3410), which possesses theRph3 gene and exhibits a low to intermediate level of resistance (infection type 12). Isolate ND89-3 possesses one of the widest virulence spectrums reported forP. hordei. Accessions ofHordeum vulgare (1,997 in total) andH. spontaneum (885 in total), mostly originating from the Mediterranean region and parts of North Africa, were evaluated with isolate ND89-3 at the seedling stage to identify new sources of leaf rust resistance. Fifty-eight accessions ofH. vulgare, and 222 accessions ofH. spontaneum exhibited low infection types to this isolate. Further evaluations of these resistant accessions with isolates ofP. hordei virulent forRph3,Rph7, andRph12 suggested that most of the resistantH. vulgare accessions possess theRph3 gene. Data suggested additional sources of effective resistance inH. vulgare are rather limited. FiveH. vulgare accessions and 167H. spontaneum accessions were identified as possible sources of new genes for leaf rust resistance. These accessions likely possess resistance genes that are different fromRph1 toRph12, or gene combinations thereof based on their reaction to four leaf rust isolates. Utilization of these accessions in barley breeding will broaden the germplasm resources available for genetic control ofP. hordei.