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

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 this study, three mapping populations were developed by crossing Israelian barley lines “AGG-396,” “AGG-397,” and “AGG-403” (carrying unknown leaf rust resistance) with a susceptible variety “Gus” to characterize and map resistance. Genetic analysis of phenotypic data from rust testing F3s with a P. hordei pathotype 5457 P+ revealed monogenic inheritance in all three populations. Targeted genotyping-by-sequencing of the three populations detected marker trait associations in the same genomic region on the short arm of chromosome 2H between 39 and 57 Mb (AGG-396/Gus), 44 and 64 Mb (AGG-397/Gus), and 31 and 58 Mb (AGG-403/Gus), suggesting that the resistance in all three lines is likely conferred by the same locus (tentatively designated RphAGG396). Two Kompetitive allele-specific PCR (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 (nucleotide-binding domain leucine-rich repeat) genes (r2.2HG0093020 and r2.2HG0093030) were identified as the best candidates for RphAGG396. A closely linked marker was developed for RphAGG396 that can be used for marker-assisted selection.

Mining the Australian Grains Gene Bank for Rust Resistance in Barley

“…Seedling infection types were scored on a 0–4 scale as described in [ 3 ] for barley leaf and crown rust. Assays for barley seedling response to P. coronata var hordei were performed like those for P. hordei except plants were maintained at 20–22 °C after inoculation through disease assessment [ 5 , 16 ]. The seedling infection type data were linearized to a 0–9 scale according to Gao et al [ 17 ], however the linearized data were not transformed.…”

A pathogen-induced putative NAC transcription factor mediates leaf rust resistance in barley

“…Rph7-avirulent (200 P+, 276 P+ and 5477 P-) and virulent (5553 P+) pathotypes were used to validate the resistance gene function and specificity in the T 1 generation of Golden Promise + Rph7 transgenic plants. These pathotypes were isolated and increased as described by Dinh et al (2022) before being stored in liquid nitrogen at the Plant Breeding Institute, the University of Sydney, Australia. Rust testing of barley seedlings in the greenhouse with P. hordei pathotypes listed above was performed as described in Dinh et al (2022) and plants were phenotyped 10 days post-inoculation using the "0"-"4" infection type (IT) scale as described by (Park et al, 2015).…”

“…Cebada Capa, Bowman + Rph7 (BW758) and Bowman seedlings were grown in trays as described by Dinh et al (2022) and then inoculated using either oil (mock control) and oil mixed with 30 mg of P. hordei urediniospores (pt. 5457 P+).…”

“…However, recent evidence suggests race-specific resistance is also governed by non-canonical gene classes (Dinh et al, 2020;Sánchez-Martín and Keller, 2021;Zhang et al, 2020). Two recent studies utilised sequenced chromosome scale assemblies from the wheat and barley pangenomes to clone the race-specific leaf rust resistance genes Lr14a (Kolodziej et al, 2021) and Rph3 (Dinh et al, 2022). Interestingly, Lr14a and Rph3 encode a membrane-bound ankyrin repeat containing protein and a putative executor protein, respectively.…”

“…Resistance to leaf rust in Hordeum spp. is well characterised and widely available due to the numerous genetic (Dracatos et al, 2015; Elmansour et al, 2017; Jost et al, 2020; Mehnaz et al, 2021; Mehnaz et al, 2022; Park et al ., 2015; Qi et al, 1998; Rothwell et al, 2020; Singh et al, 2016; Singh et al, 2018) and cloning studies undertaken (Chen et al, 2020; Dinh et al, 2022; Dracatos et al, 2019; Wang et al, 2019). However, in most cases the underlying genes responsible for resistance are not known, limiting effective and efficient deployment in agricultural settings (Dinh et al, 2020; Park et al, 2015).…”