scholarly journals Mining and predictive characterization for resistance to leaf rust (Puccinia hordei Otth) using two subsets of barley genetic resources

2021 ◽  
Author(s):  
Mariam Amouzoune ◽  
Ahmed Amri ◽  
Rachid Benkirane ◽  
Zakaria Kehel ◽  
Muamer Al-Jaboobi ◽  
...  
Keyword(s):  
Machine Learning ◽  
Genetic Resources ◽  
Leaf Rust ◽  
Goodness Of Fit ◽  
Seedling Stage ◽  
Fine Tuning ◽  
Ex Situ ◽  
Puccinia Hordei ◽  
Adult Plant ◽  
Sources Of Resistance

Abstract Sustainable barley production will require access to diverse ex-situ conserved collections to develop varieties with high yields and capable of overcoming the challenges imposed by major abiotic and biotic stresses. This study aimed at searching efficient approaches for the identification of new sources of resistance to barley leaf rust (LR). Two subsets, Generation Challenge Program Reference set (GCP) with 190 accessions and leaf rust subset constructed using the filtering approach of the Focused Identification of Germplasm Strategy (FIGS) with 100 accessions, were evaluated for the seedling as well as the adult plant stage resistance (APR) using two LR isolates (ISO-SAT and ISO-MRC) and in four environments in Morocco, respectively. Both subsets yielded a high percent of accessions with a moderately resistant (MR) reaction to the two LR isolates at the seedling stage. For APR, more than 50% of the accessions showed resistant reactions in SAT2018 and GCH2018, while this rate was less than 20% in SAT2017 and SAT2019. Statistical analysis using chi-square test of independence revealed the dependency of LR reaction on subsets at the seedling (ISO-MRC), as well as at the APR (SAT2017 and SAT2018) stage. Furthermore, the test of goodness of fit showed that FIGS_LR yielded higher percentages of resistant accessions than GCP subset in case of ISO-MRC at the seedling stage, and in case of SAT2017 and SAT2018 at APR stage. Although some of the tested machine learning models had moderate to high accuracies, none of them was able to find a strong and significant relationship between the reaction to LR and the environmental conditions showing the needs for more fine tuning of approaches for efficient mining of genetic resources using machine learning.

scholarly journals Mining and predictive characterization of resistance to leaf rust (Puccinia hordei Otth) using two subsets of barley genetic resources

2021 ◽  
Author(s):  
Mariam Amouzoune ◽  
Ahmed Amri ◽  
Rachid Benkirane ◽  
Zakaria Kehel ◽  
Muamer Al-Jaboobi ◽  
...  
Keyword(s):  
Machine Learning ◽  
Genetic Resources ◽  
Leaf Rust ◽  
Goodness Of Fit ◽  
Seedling Stage ◽  
Fine Tuning ◽  
Ex Situ ◽  
Puccinia Hordei ◽  
Barley Leaf Rust ◽  
Barley Leaf

AbstractSustainable barley (Hordeum vulgare L.) production will require access to diverse ex-situ conserved collections to develop varieties with high yields and capable of overcoming the challenges imposed by major abiotic and biotic stresses. This study aimed at searching efficient approaches for the identification of new sources of resistance to barley leaf rust (Puccinia hordei Otth). Two subsets, Generation Challenge Program Reference set (GCP) with 188 accessions and leaf rust subset constructed using the filtering approach of the Focused Identification of Germplasm Strategy (FIGS) with 86 accessions, were evaluated for the seedling as well as the adult plant stage resistance (APR) using two barley leaf rust (LR) isolates (ISO-SAT and ISO-MRC) and in four environments in Morocco, respectively. Both subsets yielded a high percent of accessions with a moderately resistant (MR) reaction to the two LR isolates at the seedling stage. For APR, more than 50% of the accessions showed resistant reactions in SAT2018 and GCH2018, while this rate was less than 20% in SAT2017 and SAT2019. Statistical analysis using chi-square test of independence revealed the dependency of LR reaction on subsets at the seedling (ISO-MRC), as well as at the APR (SAT2017 and SAT2018) stage. At seedling stage, the test of goodness of fit showed that GCP subset yielded higher percentages of resistant accessions than FIGS-LR in case of ISO-MRC isolate but the two subsets did not differ for ISO-SAT. At APR, FIGS approach performed better than GCP in yielding higher percentages of accessions in case of SAT2017 and SAT2018. Although some of the tested machine learning models had moderate to high accuracies, none of them was able to find a strong and significant relationship between the reaction to LR and the environmental conditions showing the needs for more fine tuning of approaches for efficient mining of genetic resources using machine learning.

scholarly journals Assessment and modeling using machine learning of resistance to scald (Rhynchosporium commune) in two specific barley genetic resources subsets

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Houda Hiddar ◽  
Sajid Rehman ◽  
Berhane Lakew ◽  
Ramesh Pal Singh Verma ◽  
Muamar Al-Jaboobi ◽  
...  
Keyword(s):  
Machine Learning ◽  
Seedling Stage ◽  
Fine Tuning ◽  
Adult Plant ◽  
Growth Stages ◽  
Sources Of Resistance ◽  
Leaf Scald ◽  
Adult Plant Stage ◽  
Plant Stage ◽  
Filtering Approach

AbstractBarley production worldwide is limited by several abiotic and biotic stresses and breeding of highly productive and adapted varieties is key to overcome these challenges. Leaf scald, caused by Rhynchosporium commune is a major disease of barley that requires the identification of novel sources of resistance. In this study two subsets of genebank accessions were used: one extracted from the Reference set developed within the Generation Challenge Program (GCP) with 191 accessions, and the other with 101 accessions selected using the filtering approach of the Focused Identification of Germplasm Strategy (FIGS). These subsets were evaluated for resistance to scald at the seedling stage under controlled conditions using two Moroccan isolates, and at the adult plant stage in Ethiopia and Morocco. The results showed that both GCP and FIGS subsets were able to identify sources of resistance to leaf scald at both plant growth stages. In addition, the test of independence and goodness of fit showed that FIGS filtering approach was able to capture higher percentages of resistant accessions compared to GCP subset at the seedling stage against two Moroccan scald isolates, and at the adult plant stage against four field populations of Morocco and Ethiopia, with the exception of Holetta nursery 2017. Furthermore, four machine learning models were tuned on training sets to predict scald reactions on the test sets based on diverse metrics (accuracy, specificity, and Kappa). All models efficiently identified resistant accessions with specificities higher than 0.88 but showed different performances between isolates at the seedling and to field populations at the adult plant stage. The findings of our study will help in fine-tuning FIGS approach using machine learning for the selection of best-bet subsets for resistance to scald disease from the large number of genebank accessions.

scholarly journals Validating molecular markers for barley leaf rust resistance genes Rph20 and Rph24

2020 ◽  
Author(s):  
PM Dracatos ◽  
RF Park ◽  
D Singh
Keyword(s):  
Molecular Markers ◽  
Leaf Rust ◽  
Resistance Genes ◽  
Leaf Rust Resistance ◽  
Puccinia Hordei ◽  
Adult Plant ◽  
Barley Leaf Rust ◽  
Efficient Gene ◽  
Barley Leaf ◽  
Barley Germplasm

Improving resistance to barley leaf rust (caused by Puccinia hordei) is an important breeding objective in most barley growing regions worldwide. The development and subsequent utilisation of high-throughput PCR-based co-dominant molecular markers remains an effective approach to select genotypes with multiple effective resistance genes, permitting efficient gene deployment and stewardship. The genes Rph20 and Rph24 confer widely effective adult plant resistance (APR) to leaf rust, are common in European and Australian barley germplasm (often in combination), and act interactively to confer high levels of resistance (Dracatos et al. 2015; Zeims et al. 2017; Singh et al. 2018). Here we report on the development and validation of co-dominant insertion-deletion (indel) based PCR markers that are highly predictive for the Rph20 and Rph24 resistances.

ADULT PLANT RESISTANCE IN WHEAT TO PHYSIOLOGIC RACES OF PUCCINIA TRITICINA ERIKSS.

1943 ◽  
Vol 21c (1) ◽  
pp. 10-17 ◽  
Author(s):  
Margaret Newton ◽  
T. Johnson
Keyword(s):  
Leaf Rust ◽  
Plant Resistance ◽  
Adult Plant Resistance ◽  
Puccinia Triticina ◽  
Seedling Stage ◽  
Adult Plant ◽  
Wheat Varieties ◽  
Physiologic Races ◽  
Two Stages ◽  
Derivatives Of

Nine wheat varieties were studied in two stages of growth, the seedling stage and the heading stage, for their reaction to a number of physiologic races of leaf rust of wheat, Puccinia triticina Erikss. Several varieties susceptible to certain physiologic races in the seedling stage were found to acquire, as they grew to maturity, a resistance to these races. In the adult plant, the resistance was greatest in the uppermost leaves but diminished progressively on lower leaves. The varieties tested fell into three groups on the basis of their rust reaction. (1) Renown and Regent, which developed adult plant resistance to all of the 19 races to which they were tested. In these two varieties, and possibly in other derivatives of H-44 and Hope, adult plant resistance to physiologic races of leaf rust may be a generalized phenomenon comparable to the resistance such varieties show towards stem rust. (2) Thatcher, Apex, Marquis, Reward, and Kenya R.L. 1373, which showed adult plant resistance only to certain physiologic races, a condition not hitherto encountered in other cereal rusts. (3) McMurachy and Warden × Hybrid, each of which reacted somewhat similarly in the seedling and heading stages, the former being susceptible and the latter resistant in both stages.

scholarly journals Validating molecular markers for barley leaf rust resistance genes Rph20 and Rph24

Plant Disease ◽  
2020 ◽  
Author(s):  
P. M. Dracatos ◽  
Robert F Park ◽  
Davinder Singh
Keyword(s):  
Molecular Markers ◽  
Leaf Rust ◽  
Resistance Genes ◽  
Leaf Rust Resistance ◽  
Puccinia Hordei ◽  
Adult Plant ◽  
Barley Leaf Rust ◽  
Efficient Gene ◽  
Barley Leaf ◽  
Barley Germplasm

Improving resistance to barley leaf rust (caused by Puccinia hordei) is an important breeding objective in most barley growing regions worldwide. The development and subsequent utilization of high-throughput polymerase chain reaction (PCR) based co-dominant molecular markers remains an effective approach to select genotypes with multiple effective resistance genes, permitting efficient gene deployment and stewardship. The genes Rph20 and Rph24, which confer widely effective adult plant resistance (APR) to leaf rust, are common in European and Australian barley germplasm (often in combination), and act interactively to confer high levels of resistance. Here we report on the development and validation of co-dominant insertion-deletion (indel) based PCR markers that are highly predictive for the resistance alleles Rph20.ai and Rph24.an (both referred to as Rph20 and Rph24).

DANGEROUS NEW RACES OF OAT STEM RUST AND SOURCES OF RESISTANCE TO THEM

1964 ◽  
Vol 44 (5) ◽  
pp. 418-426 ◽  
Author(s):  
G. J. Green ◽  
R. I. H. McKenzie
Keyword(s):  
Resistance Genes ◽  
Stem Rust ◽  
Seedling Stage ◽  
Adult Plant ◽  
Santa Fe ◽  
Sources Of Resistance ◽  
Adult Plant Stage ◽  
Plant Stage ◽  
New Races ◽  
Moderately Resistant

New races of oat stem rust that can attack varieties carrying all identified resistance genes were found in Canada between 1957 and 1963. Varieties moderately resistant to some of these races have been found, but they are susceptible to other less-prevalent races. Some of the sources of resistance are: Ukraine, C.I. 3259; Ark. 674(2)-39-F, C.I. 4529; C.I. 4673; C.I. 5109; Santa Fe Selection, C.I. 5844; C.I. 6792; Silva No. 1729-49-1, C.I. 6849; and Rosen’s Mutant. White Russian (gene D) and Sevnothree (gene E) were resistant in the adult plant stage to one culture of race 6AF, although susceptible in the seedling stage.

Origin of leaf rust adult plant resistance gene Rph20 in barley

Genome ◽  
2012 ◽  
Vol 55 (5) ◽  
pp. 396-399 ◽  
Author(s):  
Lee T. Hickey ◽  
Wendy Lawson ◽  
Greg J. Platz ◽  
Mark Dieters ◽  
Jerome Franckowiak
Keyword(s):  
Hordeum Vulgare ◽  
Leaf Rust ◽  
Plant Resistance ◽  
Dna Analysis ◽  
Adult Plant Resistance ◽  
Puccinia Hordei ◽  
Adult Plant ◽  
Hordeum Vulgare L ◽  
Barley Cultivars ◽  
Alternative Sources

Rph20 is the only reported, simply inherited gene conferring moderate to high levels of adult plant resistance (APR) to leaf rust ( Puccinia hordei Otth) in barley ( Hordeum vulgare L.). Key parental genotypes were examined to determine the origin of Rph20 in two-rowed barley. The Dutch cultivar ‘Vada’ (released in the 1950s) and parents, ‘Hordeum laevigatum’ and ‘Gull’ (‘Gold’), along with the related cultivar ‘Emir’ (a derivative of ‘Delta’), were assessed for APR to P. hordei in a disease screening nursery. The marker bPb-0837-PCR, co-located with Rph20 on the short arm of chromosome 5H (5HS), was used to screen genotypes for the resistance allele, Rph20.ai. Results from phenotypic assessment and DNA analysis confirmed that Rph20 originated from the landrace ‘H. laevigatum’ (i.e., Hordeum vulgare subsp. vulgare). Tracing back this gene through the pedigrees of two-rowed barley cultivars, indicated that Rph20 has contributed APR to P. hordei for more than 60 years. Although there have been no reports of an Rph20-virulent pathotype, the search for alternative sources of APR should continue to avoid widespread reliance upon a single resistance factor.

scholarly journals Characterization of Rph24: A Gene Conferring Adult Plant Resistance to Puccinia hordei in Barley

2017 ◽  
Vol 107 (7) ◽  
pp. 834-841 ◽  
Author(s):  
Laura A. Ziems ◽  
Lee T. Hickey ◽  
Gregory J. Platz ◽  
Jerome D. Franckowiak ◽  
Peter M. Dracatos ◽  
...  
Keyword(s):  
Leaf Rust ◽  
Plant Resistance ◽  
Adult Plant Resistance ◽  
Genotyping By Sequencing ◽  
Puccinia Hordei ◽  
Adult Plant ◽  
Hordeum Vulgare L ◽  
Barley Cultivars ◽  
Trait Locus ◽  
Marker Frequency

We identified Rph24 as a locus in barley (Hordeum vulgare L.) controlling adult plant resistance (APR) to leaf rust, caused by Puccinia hordei. The locus was previously reported as a quantitative trait locus in barley line ND24260-1 and named qRphND. We crossed ND24260-1 to the leaf-rust-susceptible standard Gus and determined inheritance patterns in the progeny. For the comparative marker frequency analysis (MFA), resistant and susceptible tails of the F2 were genotyped with Diversity Arrays Technology genotyping-by-sequencing (DArT-Seq) markers. The Rph24 locus was positioned at 55.5 centimorgans on chromosome 6H on the DArT-Seq consensus map. Evaluation of F2:3 families confirmed that a single locus from ND24260-1 conferred partial resistance. The haploblock strongly associated with the Rph24 locus was used to estimate the allele frequency in a collection of 282 international barley cultivars. Rph24 was frequently paired with APR locus Rph20 in cultivars displaying high levels of APR to leaf rust. The markers identified in this study for Rph24 should be useful for marker-assisted selection.

Identification of Resistant Germplasm and Detection of Genes for Resistance to Powdery Mildew and Leaf Rust from 2,978 Wheat Accessions

Plant Disease ◽  
2021 ◽  
Author(s):  
Yuli Jin ◽  
Fengyu Shi ◽  
Weihua Liu ◽  
Xiaoyi Fu ◽  
Tiantian Gu ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Leaf Rust ◽  
Puccinia Triticina ◽  
Wheat Breeding ◽  
Seedling Stage ◽  
Adult Plant ◽  
Breeding Lines ◽  
Adult Plant Stage ◽  
Lr Genes ◽  
Plant Stage

Powdery mildew and leaf rust, caused by Blumeria graminis f. sp. tritici (Bgt) and Puccinia triticina (Pt), respectively, are widespread diseases of wheat worldwide. Utilizing resistant cultivars is considered as the most economical, environmental-friendly, and effective method to control these diseases. In the present study, a collection of 2,978 wheat accessions consisting of 1,394 advanced breeding lines, 1,078 Chinese cultivars, 291 introduced cultivars, 132 lines containing alien chromosomes, and 83 landraces was tested for reactions to powdery mildew and leaf rust. The results indicated that 659 (22.1%) wheat accessions were highly resistant to a widely prevalent Bgt isolate, E09, at the seedling stage, and 390 were consistently resistant to the mixture of Bgt isolates at the adult-plant stage. Meanwhile, 63 (2.1%) accessions were highly resistant to leaf rust at the adult-plant stage, of which 54 were resistant to a predominant and highly virulent Pt race, THTT, at the seedling stage. Notably, 17 accessions were resistant to both powdery mildew and leaf rust. To detect known genes for resistance to powdery mildew and leaf rust, these accessions were tested with gene-specific or tightly linked markers for seven Pm genes (Pm2, Pm4, Pm5, Pm6, Pm8, Pm21, and Pm24) and ten Lr genes (Lr1, Lr9, Lr10, Lr19, Lr20, Lr24, Lr26, Lr34, Lr37, and Lr46). Of the 659 powdery mildew-resistant accessions, 328 might carry single Pm genes and 191 carry combined Pm genes. Pm2 was detected at the highest frequency of 59.6%, followed by Pm8, Pm6, Pm21, Pm4, and Pm5, while Pm24 was not detected. Besides, 139 accessions might contain unknown Pm genes different from those tested in this study. In the 63 accessions resistant leaf rust, four Lr genes (Lr1, Lr10, Lr26, and Lr34) were detected in 41 accessions either singly or in combination, while six genes (Lr9, Lr19, Lr20, Lr24, Lr37, and Lr46) were not detected. Twenty-two accessions might contain unknown Lr genes different from those tested in this study. This study not only provided important information for rationally distributing resistance genes in wheat breeding programs, but also identified resistant germplasm that might have novel genes to enrich the diversity of resistance sources.

scholarly journals Relative Ratio of Mature Pustules: A Simple Method to Assess Partial Resistance of Barley to Puccinia hordei

Plant Disease ◽  
2007 ◽  
Vol 91 (3) ◽  
pp. 301-307 ◽  
Author(s):  
Guo-Liang Jiang ◽  
Thierry C. Marcel ◽  
Fernando Martínez ◽  
Rients E. Niks
Keyword(s):  
Partial Resistance ◽  
Recombinant Inbred Lines ◽  
Seedling Stage ◽  
Puccinia Hordei ◽  
Optimal Time ◽  
Adult Plant ◽  
Simple Method ◽  
Adult Plant Stage ◽  
Relative Ratio ◽  
Plant Stage

In plant breeding and germplasm evaluation, large-scale assessment of quantitative resistance is desirable, but feasible only if a simple and accurate measure is available. In several plant-pathogen systems, latent period (LP) is a parameter that is well correlated with the level of partial resistance observed in field trials. However, measuring LP or relative LP (RLP), i.e., relative to the reference accessions, is laborious. We investigated the value of relative ratio of mature pustules (RRMP, relative to the susceptible control) as a simple and rapid alternative to replace LP estimation in barley to barley leaf rust (Puccinia hordei). A set of 103 F9 recombinant inbred lines (RILs) derived from a cross L94 × Vada was sown in a greenhouse compartment, and was inoculated at the seedling stage with isolate Uppsala or 24, and at the adult plant stage with isolate 24. In demarcated sections of leaves, the number of mature pustules was counted several times after inoculation. The ratio of mature pustules (RMP) and LP50 were calculated to assess RRMP and RLP, respectively, and to identify the quantitative trait loci (QTLs) contributing to the genetic variation. The contrasts in RRMP among accessions were highest when the susceptible reference line had developed 70 to 90% mature orange pustules, the immature infection sites being visible as pale flecks. At this optimal time of observation, the correlation between RRMP and RLP in both the seedling stage and the adult plant stage was highly significant (r = -0.82 ~-0.98). Compared with RLP, RRMP was much easier and simpler to measure and still showed good correspondence with RLP in the identification of QTLs for partial resistance. In another experiment at the seedling stage with 25 barley cultivars and lines inoculated with isolate 1.2.1, the coefficient of correlation between RRMP and RLP was -0.98. Therefore, we conclude that RRMP should have great application potential in breeding programs and germplasm screening and could be used in fundamental studies as well.

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