Abstract
Key messageSix new PCR-based markers for the Pc39 crown rust resistance gene in Avena sativa L. were developed. Pc39 was mapped to Mrg11 of the oat consensus map using BLASTn analysis.The aim of this study was the identification of molecular markers for the Pc39 gene in cultivated oat (Avena sativa L.). Pc39 is a major race-specific crown rust resistance gene originally found in an Israeli accession of the wild hexaploid Avena sterilis. The effectiveness of this gene in Europe has decreased in recent years, but is still relatively high and breeding programs would benefit from the availability of molecular markers to aid in its mapping and deployment. The complexity of the oat genome poses a significant obstacle to genetic research. No oat rust resistance genes have yet been cloned, and even the number of relevant molecular markers is very limited. Here, genotyping of a segregating population derived from a cross ‘Celer’ (Pc39)/STH9210 (susceptible) was conducted using RAPD- and SRAP-PCR-based methods, as well as microarray-based DArT™ and next-generation sequencing DArTseq™ techniques. Markers associated with Pc39 were placed on the hexaploid oat consensus linkage group Mrg11 at 3.7–6.7 cM. Six new PCR-based markers were developed to allow identification of the resistant Pc39 allele. These tightly linked markers will be useful in marker-assisted selection, with the closest, SCAR_3456624, being within 0.37 cM of Pc39. The newly developed markers could find applications in the fine mapping or positional cloning of this gene. Moreover, easy-to-use PCR-based markers linked to Pc39 could facilitate the utilization of this gene in oat breeding programs, especially as a component of crown rust resistance gene pyramids.
Highlights
Fungal diseases are an important constraint to cereal production
The objective of this study was the identification of molecular markers linked to the Pc39 gene using a F 2 population derived from a cross ‘Celer’/STH9210, and development of simple, PCR-based markers for this gene, supporting effective Pc39 gene introduction in breeding programs
The only marker for Pc39 identified to date was a RFLP marker cdo666 found in the Pendek3948 population and located 6 cM away from the gene (Wight et al 2004)
Summary
Fungal diseases are an important constraint to cereal production. In oats (Avena spp.), crown rust caused by Puccinia coronata Cda. f. (Pca) is considered the most destructive fungal disease, causing great yield and grain quality loses (Simons 1985). The chief method of control for crown rust is resistance conditioned by major resistance (R) genes (Cabral et al 2014). Large-scale cultivation of varieties containing a single R gene increases the probability of emergence of new pathogen races able.
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