A novel locus conferring resistance to Puccinia hordei maps to the genomic region corresponding to Rph14 on barley chromosome 2HS

Authors: MEHNAZ, MEHNAZ - University Of Sydney; DRACATOS, PETER - Agribio, Centre For Agribioscience; DINH, HOAN - University Of Sydney; FOREST, KERRIE - Agriculture Victoria; Rouse, Matthew; PARK, ROBERT - University Of Sydney; SINGH, DAVINDER - University Of Sydney

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/24/2022
Publication Date: 10/6/2022
Citation: Mehnaz, M., Dracatos, P., Dinh, H.X., Forest, K., Rouse, M.N., Park, R.F., Singh, D. 2022. A novel locus conferring resistance to Puccinia hordei maps to the genomic region corresponding to Rph14 on barley chromosome 2HS. Frontiers in Plant Science. 13. Article 980870. https://doi.org/10.3389/fpls.2022.980870.
DOI: https://doi.org/10.3389/fpls.2022.980870

Interpretive Summary: Barley is grown on over 2.5 million acres in the United States. The rust diseases of barley can cause devastating yield losses. In order to mitigate barley leaf rust, disease-resistant barley varieties need to be developed. Barley breeding programs targeting leaf rust resistance need effective barley leaf rust resistance genes and markers linked to these genes. In our studies reported here, three barley lines ('AGG 396', 'AGG397' and 'AGG 403') from Israel carrying uncharacterized resistance to P. hordei were crossed with the leaf rust susceptible barley 'Gus' to develop genetic populations to characterize the resistance in each. Genetic analysis of phenotypic data from rust testing revealed single gene inheritance in all three populations. Targeted genotype-by-sequencing of the three populations detected marker trait associations in the same genomic region suggesting that the resistance in all three lines is conferred by the same locus (tentatively designated RphAGG396). Four molecular markers co-segregated with RphAGG396 in a high-resolution mapping population. A closely linked marker was developed for RphAGG396 that can be used for marker assisted selection. The molecular markers linked to barley leaf rust resistance and the three barley lines identified with resistance to barley leaf rust can be used in barley breeding to develop rust-resistant barley varieties for the United States.

Technical Abstract: Barley leaf rust (BLR), caused by Puccinia hordei, is best controlled through genetic resistance. An efficient resistance breeding program prioritizes the need to identify, characterize, and map new sources of resistance as well as understanding the effectiveness, structure, and function of resistance genes. In our studies reported here, three barley lines ('AGG 396', 'AGG397' and 'AGG 403') from Israel carrying uncharacterized resistance to P. hordei were crossed with the leaf rust susceptible barley 'Gus' to develop genetic populations to characterize the resistance in each. Genetic analysis of phenotypic data from rust testing F3s with a defined P. hordei pathotype revealed monogenic inheritance in all three populations. Targeted genotype-by-sequencing of the three populations detected marker trait associations in the same genomic region on the short arm of chromosome 2H between 39-57 Mb (AGG-396/Gus), 44-64 Mb (AGG-397/Gus) and 31-58 Mb (AGG-403/Gus), suggesting that the resistance in all three lines is conferred by the same locus (tentatively designated RphAGG396). Two KASP markers, HvGBSv2-902 and HvGBSv2-932, defined a genetic distance of 3.8 cM proximal and 7.1 cM distal to RphAGG396, respectively. To increase the marker density at the RphAGG396 locus, 75 CAPS markers were designed between two flanking markers. Integration of marker data resulted in the identification of two critical recombinants and mapping RphAGG396 between markers- Mloc-28 (40.75 Mb) and Mloc-41 (41.92 Mb) narrowing the physical window to 1.17 Mb based on the Morex v2.0 reference genome assembly. To enhance map resolution, 600 F2s were genotyped with markers- Mloc-28 and Mloc-41 and nine recombinants were identified, placing the gene at a genetic distance of 0.5 and 0.2 cM between the two markers, respectively. Two annotated NLR genes (r2.2HG0093020 and r2.2HG0093030) were identified as the best candidates for RphAGG396. Markers MLoc-29 and MLoc-31 designed to the coding sequences of NLR gene- r2.2HG0093020, and further two MLoc-70 and MLoc-71 designed to the CDS of second NLR gene- r2.2HG0093030, co-segregated with RphAGG396 in a high-resolution mapping population. A closely linked marker was developed for RphAGG396 that can be used for marker assisted selection.