Genome-wide association study for crown rust (Puccinia coronata f. sp. avenae) and powdery mildew (Blumeria graminis f. sp. avenae) resistance in an oat (Avena sativa) collection of commercial varieties and landraces

Abstract

Diseases caused by crown rust (Puccinia coronata f. sp. avenae) and powdery mildew (Blumeria graminis f. sp. avenae) are among the most important constraints for the oat crop. Breeding for resistance is one of the most effective, economical, and environmentally friendly means to control these diseases. The purpose of this work was to identify elite alleles for rust and powdery mildew resistance in oat by association mapping to aid selection of resistant plants. To this aim, 177 oat accessions including white and red oat cultivars and landraces were evaluated for disease resistance and further genotyped with 31 simple sequence repeat and 15,000 Diversity Arrays Technology (DArT) markers to reveal association with disease resistance traits. After data curation, 1712 polymorphic markers were considered for association analysis. Principal component analysis and a Bayesian clustering approach were applied to infer population structure. Five different general and mixed linear models accounting for population structure and/or kinship corrections and two different statistical tests were carried out to reduce false positive. Five markers, two of them highly significant in all models tested were associated with rust resistance. No strong association between any marker and powdery mildew resistance at the seedling stage was identified. However, one DArT sequence, oPt-5014, was strongly associated with powdery mildew resistance in adult plants. Overall, the markers showing the strongest association in this study provide ideal candidates for further studies and future inclusion in strategies of marker-assisted selection.

A combination of genome-wide association and transcriptome analysis reveals candidate genes controlling harvest index-related traits in Brassica napus

“…In the current study, six models, involving different combinations of K, Q, and PCA were used to analyze all of the traits examined this our study. As with early studies, the mixed PCA + K model was best in removing false-positive association signals (Table 2), indicating that population structure correction in a PCA model was more efficient than the STRUCTURE algorithm at eliminating false positives34. Hence, to reduce the number of false positives and negatives, only optimal models for each trait were considered when identifying association signals.…”

Puccinia coronata f. sp. avenae: a threat to global oat production

“…Newly developed high‐throughput genetic marker assay systems, such as SNP, KASP and diversity arrays technology (DArT), are of benefit in oat breeding, with the construction of dense genetic maps enabling the discovery of additional resistance QTLs against crown rust in different oat crosses and RILs (Babiker et al ., ; Barbosa et al ., ; Chaffin et al ., ; Jackson et al ., ; Zhu and Kaeppler, ). In parallel, such systems are also used for genome‐wide association study (GWAS) as an alternative route to locate crown rust resistance QTLs (Klos et al ., ; Montilla‐Bascón et al ., ). Apart from their application in marker‐assisted selection, molecular markers are essential for map‐based cloning of resistance genes (Cabral et al ., ) as a basic step towards the determination of the mechanisms by which these genes exert their function.…”

Genome‐Wide Association Mapping of Crown Rust Resistance in Oat Elite Germplasm

“…In addition, QTL for adult‐plant rust resistance have been mapped and can be placed on linkage groups Mrg02, Mrg06, Mrg08, Mrg12, Mrg17, and Mrg20 (Zhu and Kaeppler, 2003; Portyanko et al, 2005; Acevedo et al, 2010; Lin et al, 2014; Babiker et al, 2015). Association mapping using samples or subsamples of oat accessions numbering <200 lines have identified QTL on linkage groups Mrg01, Mrg03, Mrg08, Mrg20, Mrg23, and Mrg28 (Montilla‐Bascón et al, 2015; Winkler et al, 2016). Given the overlap in map locations and the variation in methods of assessing resistance, some QTL may be either the same as, or allelic to the Pc genes.…”