Sources Of Adult Plant Resistance Research Articles

Harnessing adult-plant resistance genes to deploy durable disease resistance in crops.

Adult-plant resistance (APR) is a type of genetic resistance in cereals that is effective during the later growth stages and can protect plants from a range of disease-causing pathogens. Our understanding of the functions of APR-associated genes stems from the well-studied wheat-rust pathosystem. Genes conferring APR can offer pathogen-specific resistance or multi-pathogen resistance, whereby resistance is activated following a molecular recognition event. The breeding community prefers APR to other types of resistance because it offers broad-spectrum protection that has proven to be more durable. In practice, however, deployment of new cultivars incorporating APR is challenging because there is a lack of well-characterised APRs in elite germplasm and multiple loci must be combined to achieve high levels of resistance. Genebanks provide an excellent source of genetic diversity that can be used to diversify resistance factors, but introgression of novel alleles into elite germplasm is a lengthy and challenging process. To overcome this bottleneck, new tools in breeding for resistance must be integrated to fast-track the discovery, introgression and pyramiding of APR genes. This review highlights recent advances in understanding the functions of APR genes in the well-studied wheat-rust pathosystem, the opportunities to adopt APR genes in other crops and the technology that can speed up the utilisation of new sources of APR in genebank accessions.

A reference-anchored oat linkage map reveals quantitative trait loci conferring adult plant resistance to crown rust (Puccinia coronata f. sp. avenae).

We mapped three adult plant resistance (APR) loci on oat chromosomes 4D and 6C and developed flanking KASP/PACE markers for marker-assisted selection and gene pyramiding. Using sequence orthology search and the available oat genomic and transcriptomic data, we surveyed these genomic regions for genes that may control disease resistance. Sources of durable disease resistance are needed to minimize yield losses in cultivated oat caused by crown rust (Puccinia coronata f. sp. avenae). In this study, we developed five oat recombinant inbred line mapping populations to identify sources of adult plant resistance from crosses between five APR donors and Otana, a susceptible variety. The preliminary bulk segregant mapping based on allele frequencies showed two regions in linkage group Mrg21 (Chr4D) that are associated with the APR phenotype in all five populations. Six markers from these regions in Chr4D were converted to high-throughput allele specific PCR assays and were used to genotype all individuals in each population. Simple interval mapping showed two peaks in Chr4D, named QPc.APR-4D.1 and QPc.APR-4D.2, which were detected in the OtanaA/CI4706-2 and OtanaA/CI9416-2 and in the Otana/PI189733, OtanaD/PI260616, and OtanaA/CI8000-4 populations, respectively. These results were validated by mapping two entire populations, Otana/PI189733 and OtanaA/CI9416, genotyped using Illumina HiSeq, in which polymorphisms were called against the OT3098 oat reference genome. Composite interval mapping results confirmed the presence of the two quantitative trait loci (QTL) located on oat chromosome 4D and an additional QTL with a smaller effect located on chromosome 6C. This mapping approach also narrowed down the physical intervals to between 5 and 19Mb, and indicated that QPc.APR-4D.1, QPc.APR-4D.2, and QPc.APR-6C explained 43.4%, 38.5%, and 21.5% of the phenotypic variation, respectively. In a survey of the gene content of each QTL, several clusters of disease resistance genes that may contribute to APR were found. The allele specific PCR markers developed for these QTL regions would be beneficial for marker-assisted breeding, gene pyramiding, and future cloning of resistance genes from oat.

Pathogenicity and microsatellite characterization of Puccinia hordei in South Africa

Cultivated barley (Hordeum vulgare) is an important winter cereal in South Africa (SA), ranked second after wheat. Leaf rust, caused by Puccinia hordei Otth. (Ph), is one of the most common diseases affecting grain yield and quality of barley. In this study, isolates of Ph were pathotyped using differential cultivars and lines with designated Rph-resistance genes, as well as a set of Bowman introgression lines (BW) containing resistance genes Rph1 to Rph15. Single pustule isolates derived from recently collected field isolates, typed as Ph race UVPh7235, showed increased virulence to Rph3 when compared with previously described races from SA. Discrepancies in phenotypic responses were recorded between standard differential lines carrying Rph2, Rph6 and Rph9 and the corresponding BW lines. Results for barley cultivars with designated sources of adult plant resistance revealed low seedling infection types (ITs) for Baronesse (Rph20 + Rph24) to all Ph isolates and for Lenka (Rph20 + Rph23 + Rph24) to isolates of Ph races UVPh3231 and UVPh7231. The barley cultivars Agulhas and Cristalia showed low seedling ITs and moderate to high levels of adult plant resistance under field and greenhouse conditions, respectively. Genotyping of 48 Ph isolates with 20 microsatellite markers revealed five closely related genetic lineages with low gene diversity and allelic richness levels. While STRUCTURE analysis revealed three clusters, no clear division of the isolates into the clusters was evident, as the isolates were admixed for all three. Linkage disequilibrium analysis, as well as higher HO versus HE values, supported the hypothesis that the South African Ph population is clonal, consisting of a single genetic lineage.

Mining the Vavilov wheat diversity panel for new sources of adult plant resistance to stripe rust

Key messageMulti-year evaluation of the Vavilov wheat diversity panel identified new sources of adult plant resistance to stripe rust. Genome-wide association studies revealed the key genomic regions influencing resistance, including seven novel loci.Wheat stripe rust (YR) caused by Puccinia striiformis f. sp. tritici (Pst) poses a significant threat to global food security. Resistance genes commonly found in many wheat varieties have been rendered ineffective due to the rapid evolution of the pathogen. To identify novel sources of adult plant resistance (APR), 292 accessions from the N.I. Vavilov Institute of Plant Genetic Resources, Saint Petersburg, Russia, were screened for known APR genes (i.e. Yr18, Yr29, Yr46, Yr33, Yr39 and Yr59) using linked polymerase chain reaction (PCR) molecular markers. Accessions were evaluated against Pst (pathotype 134 E16 A + Yr17 + Yr27) at seedling and adult plant stages across multiple years (2014, 2015 and 2016) in Australia. Phenotypic analyses identified 132 lines that potentially carry novel sources of APR to YR. Genome-wide association studies (GWAS) identified 68 significant marker–trait associations (P < 0.001) for YR resistance, representing 47 independent quantitative trait loci (QTL) regions. Fourteen genomic regions overlapped with previously reported Yr genes, including Yr29, Yr56, Yr5, Yr43, Yr57, Yr30, Yr46, Yr47, Yr35, Yr36, Yrxy1, Yr59, Yr52 and YrYL. In total, seven QTL (positioned on chromosomes 1D, 2A, 3A, 3D, 5D, 7B and 7D) did not collocate with previously reported genes or QTL, indicating the presence of promising novel resistance factors. Overall, the Vavilov diversity panel provides a rich source of new alleles which could be used to broaden the genetic bases of YR resistance in modern wheat varieties.

Mining Vavilov's Treasure Chest of Wheat Diversity for Adult Plant Resistance to Puccinia triticina.

Leaf rust (LR) caused by Puccinia triticina, is among the most important diseases of wheat (Triticum aestivum L.) crops globally. Deployment of cultivars incorporating genetic resistance, such as adult plant resistance (APR) or all-stage resistance, is considered the most sustainable control method. APR is preferred for durability because it places lower selection pressure on the pathogen and is often polygenic. In the search for new sources of APR, here we explored a diversity panel sourced from the N. I. Vavilov Institute of Plant Genetic Resources. Based on DNA marker screening, 83 of the 300 lines were deemed to carry known APR genes; namely, Lr34, Lr46, and Lr67. Interestingly, lines carrying Lr67 were mostly landraces from India and Pakistan, reconfirming the likely origin of the gene. Rapid phenotypic screening using a method that integrates assessment at both seedling and adult growth stages under accelerated growth conditions (i.e., constant light and controlled temperature) identified 50 lines carrying APR. Levels of APR corresponded well with phenotypes obtained in a field nursery inoculated using the same pathotype (R2 = 0.82). The second year of field testing, using a mixture of pathotypes with additional virulence for race-specific APR genes (Lr13 and Lr37), identified a subset of 13 lines that consistently displayed high levels of APR across years and pathotypes. These lines provide useful sources of resistance for future research. A strategy combining rapid generation advance coupled with phenotyping under controlled conditions could accelerate introgression of these potentially novel alleles into adapted genetic backgrounds.

Leaf rust of cultivated barley: pathology and control.

Leaf rust of barley is caused by the macrocyclic, heteroecious rust pathogen Puccinia hordei, with aecia reported from selected species of the genera Ornithogalum, Leopoldia, and Dipcadi, and uredinia and telia occurring on Hordeum vulgare, H. vulgare ssp. spontaneum, Hordeum bulbosum, and Hordeum murinum, on which distinct parasitic specialization occurs. Although Puccinia hordei is sporadic in its occurrence, it is probably the most common and widely distributed rust disease of barley. Leaf rust has increased in importance in recent decades in temperate barley-growing regions, presumably because of more intensive agricultural practices. Although total crop loss does not occur, under epidemic conditions yield reductions of up to 62% have been reported in susceptible varieties. Leaf rust is primarily controlled by the use of resistant cultivars, and, to date, 21 seedling resistance genes and two adult plant resistance (APR) genes have been identified. Virulence has been detected for most seedling resistance genes but is unknown for the APR genes Rph20 and Rph23. Other potentially new sources of APR have been reported, and additivity has been described for some of these resistances. Approaches to achieving durable resistance to leaf rust in barley are discussed.

Identification of new sources of adult plant resistance to Puccinia hordei in international barley (Hordeum vulgare L.) germplasm

Barley leaf rust, caused by Puccinia hordei, is one of the most destructive foliar pathogens of cultivated barley, causing significant yield losses in many regions throughout the world. In this study, 521 seedling-susceptible barley germplasm obtained from diverse breeding material sourced from the Australian Winter Cereals Collection (AWCC), the University of Western Australia (UWA), and international collections from Australia, China, Germany, Spain, and Uruguay were assessed for adult plant resistance (APR) in field nurseries over multiple growing seasons. Lines (213) that consistently showed APR over multiple seasons were screened with PCR-based markers closely linked to Rph20 (bPb0837) and Rph23 (EBmac0603). About 93 % of the lines that were resistant in the field carried one or more uncharacterised APR genes with or without Rph20 and Rph23. There was high variability for APR within specific international germplasm collections. The presence of bPb0837 was strongly correlated with high APR (TR-MR) responses in the field, while lines that were positive for the EBmac0603 allele had intermediate resistance (MRMS). Both EBmac0603 and bPb0837 were present in three German lines (Lenka, Line 17 and Volla) and in the Australian variety Macquarie, all were thus were postulated to carry both Rph20 and Rph23 and had TR-20MR responses in the field. Molecular markers closely linked to Rph20 and Rph23 provide a valuable resource that can be used to assist the incorporation of these genes into new cultivars and identify uncharacterised APR.

Molecular mapping of an adult plant stem rust resistance gene Sr56 in winter wheat cultivar Arina.

This article covers detailed characterization and naming of QSr.sun - 5BL as Sr56 . Molecular markers linked with adult plant stem rust resistance gene Sr56 were identified and validated for marker-assisted selection. The identification of new sources of adult plant resistance (APR) and effective combinations of major and minor genes is well appreciated in breeding for durable rust resistance in wheat. A QTL, QSr.sun-5BL, contributed by winter wheat cultivar Arina providing 12-15% reduction in stem rust severity, was reported in an Arina/Forno recombinant inbred line (RIL) population. Following the demonstration of monogenic segregation for APR in the Arina/Yitpi RIL population, the resistance locus was formally named Sr56. Saturation mapping of the Sr56 region using STS (from EST and DArT clones), SNP (9K) and SSR markers from wheat chromosome survey sequences that were ordered based on synteny with Brachypodium distachyon genes in chromosome 1 resulted in the flanking of Sr56 by sun209 (SSR) and sun320 (STS) at 2.6 and 1.2cM on the proximal and distal ends, respectively. Investigation of conservation of gene order between the Sr56 region in wheat and B. distachyon showed that the syntenic region defined by SSR marker interval sun209-sun215 corresponded to approximately 192kb in B. distachyon, which contains five predicted genes. Conservation of gene order for the Sr56 region between wheat and Brachypodium, except for two inversions, provides a starting point for future map-based cloning of Sr56. The Arina/Forno RILs carrying both Sr56 and Sr57 exhibited low disease severity compared to those RILs carrying these genes singly. Markers linked with Sr56 would be useful for marker-assisted pyramiding of this gene with other major and APR genes for which closely linked markers are available.

Genetic Diversity for Adult Plant Resistance to Leaf Rust (Puccinia recondita) in Near‐Isogenic Lines and in Indian Wheats

AbstractVariation for adult plant resistance in near‐isogenic wheat lines carrying Lrl4b, Lrl4ab and Lr30 in a ‘Thatcher’ background indicated the possible presence of novel adult plant resistance genes effective against the Indian leaf rust population.Sixty‐one wheats released for cultivation in India were grown in isolated nurseries. Each nursery was separately inoculated with one of four leaf rust pathotypes which had been selected to aid identification of resistance effective only in the adult plant stage. Seven distinct response groups were recognised and a minimum of six sources of adult plant resistance were postulated. In a group of 14 wheats, resistance was explained on the basis of the seedling response genes that were identified. Similar results for two years with pathotype 77‐1 gave support to the reliability of field tests. Adult plant resistance (APR) sources were either race‐specific or effective against all pathotypes used. Seedlings of cultivars with APR showed susceptible reactions. The possible presence of Lr34 in Indian wheats and its role in durable leaf rust resistance are discussed.