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

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.

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

10.21203/rs.3.rs-394214/v1 ◽

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.

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Variation in partial resistance to barley leaf rust (Puccinia hordei) and agronomic characters of Ethiopian landrace lines

Euphytica ◽

10.1007/s10681-007-9438-y ◽

2007 ◽

Vol 158 (1-2) ◽

pp. 139-151 ◽

Cited By ~ 9

Author(s):

Getaneh Woldeab ◽

Chemeda Fininsa ◽

Harjit Singh ◽

Jonathan Yuen ◽

Jose Crossa

Keyword(s):

Leaf Rust ◽

Partial Resistance ◽

Puccinia Hordei ◽

Agronomic Characters ◽

Barley Leaf Rust ◽

Barley Leaf

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

10.1101/2020.07.12.199075 ◽

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.

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

Plant Disease ◽

10.1094/pdis-08-20-1735-sc ◽

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).

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Changes in Frequency of Plants Resistant to Barley Leaf Rust Caused by Puccinia hordei Otth. in a Barley Composite Cross Population

Plant Breeding ◽

10.1111/j.1439-0523.1993.tb00566.x ◽

1993 ◽

Vol 110 (1) ◽

pp. 35-40 ◽

Cited By ~ 3

Author(s):

M. Reinhold ◽

M. E. Bjarko ◽

D. C. Sands ◽

H. E. Bockelman

Keyword(s):

Leaf Rust ◽

Puccinia Hordei ◽

Barley Leaf Rust ◽

Barley Leaf

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Development of barley leaf rust, Puccinia hordei, infections in barley. I. Effect of partial resistance and plant stage

Euphytica ◽

10.1007/bf00028605 ◽

1986 ◽

Vol 35 (3) ◽

pp. 953-959 ◽

Cited By ~ 24

Author(s):

J. E. Parlevliet ◽

C. Kievit

Keyword(s):

Leaf Rust ◽

Partial Resistance ◽

Puccinia Hordei ◽

Barley Leaf Rust ◽

Plant Stage ◽

Barley Leaf

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Isolation and characterization of microsatellite markers for the causal agent of barley leaf rust, Puccinia hordei

Australasian Plant Pathology ◽

10.1007/s13313-013-0244-9 ◽

2013 ◽

Vol 43 (1) ◽

pp. 47-52 ◽

Cited By ~ 5

Author(s):

H. Karaoglu ◽

R. F. Park

Keyword(s):

Microsatellite Markers ◽

Leaf Rust ◽

Causal Agent ◽

Puccinia Hordei ◽

Barley Leaf Rust ◽

Isolation And Characterization ◽

Barley Leaf

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Barley leaf rust (Puccinia hordei Otth) in three production systems and practices in Ethiopia

Crop Protection ◽

10.1016/j.cropro.2006.10.016 ◽

2007 ◽

Vol 26 (8) ◽

pp. 1193-1202 ◽

Cited By ~ 5

Author(s):

G. Woldeab ◽

J. Yuen ◽

C. Fininsa ◽

H. Singh

Keyword(s):

Leaf Rust ◽

Production Systems ◽

Puccinia Hordei ◽

Barley Leaf Rust ◽

Barley Leaf

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First Detection of Puccinia hordei Virulence to Barley Leaf Rust Resistance Gene Rph3 and Combination with Virulence to Rph7 in North America

Plant Disease ◽

10.1094/pdis-08-12-0785-pdn ◽

2013 ◽

Vol 97 (6) ◽

pp. 838-838 ◽

Cited By ~ 1

Author(s):

M. N. Rouse ◽

C. A. Griffey ◽

W. S. Brooks

Keyword(s):

North America ◽

Leaf Rust ◽

Rust Resistance ◽

Leaf Rust Resistance ◽

Puccinia Hordei ◽

Barley Leaf Rust ◽

Barley Leaf ◽

Infection Types ◽

Rust Resistance Genes ◽

Leaf Rust Resistance Genes

Barley leaf rust, caused by Puccinia hordei Otth., has been problematic in United States barley (Hordeum vulgare L.) production in the Mid-Atlantic coast region and California. During the early 1990s, P. hordei pathotypes with virulence to resistance gene Rph7 caused average yield losses from 6 to 16% (3). ‘Doyce’ barley was released in 2003 and was described as being resistant to leaf rust (2). Initially in April 2010 and subsequently in spring 2011 and 2012, high severities and infection responses were observed on experimental plots of ‘Doyce’ in Warsaw and Blacksburg, Virginia. Three single uredinial isolates of P. hordei were derived from collections made from ‘Doyce’ barley. The isolates were characterized for virulence to barley leaf rust resistance genes by inoculating at least two replicates of a barley leaf rust differential set including 12 Rph genes (1). Previous methods used for inoculation, incubation, and pathotyping were followed (1). Infection types were scored on a 0 to 4 scale where 2 and below indicated resistance and 3 and above indicated susceptibility (4). The three isolates collected from Doyce barley displayed large pustules with infection types 3,3+ to cultivars Estate (Rph3) and Cebada Capa (Rph7). Avirulent isolates of P. hordei displayed infection types 0; to 0;1c to Estate and ;n to 0;1n to Cebada Capa (1). The data indicated that all three isolates were virulent to both barley leaf rust resistance genes Rph3 and Rph7. Though combined Rph3 and Rph7 virulence has been reported in the Mediterranean region, this is the first report of Rph3 virulence in North America. These isolates of P. hordei are virulent to important sources of resistance to barley leaf rust and threaten barley production in environments conducive for disease development in North America. References: (1) W. S. Brooks et al. Phytopathology 90:1131, 2000. (2) W. S. Brooks et al. Crop Sci. 45:792, 2005. (3) C. A. Griffey et al. Plant Dis. 78:256, 1994. (4) M. N. Levine and W. J. Cherewick. U.S. Dept. Agric. Tech. Bull. 1056, 1952.

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