Abstract
BackgroundWhile orchardgrass (Dactylis glomerata L.) is a well-known perennial forage species, rust diseases cause serious reductions in the yield and quality of orchardgrass; however, genetic mechanisms of rust resistance are not well understood in orchardgrass.ResultsIn this study, a genome-wide association study (GWAS) was performed using specific-locus amplified fragment sequencing (SLAF-seq) technology in orchardgrass. A total of 2,334,889 SLAF tags were generated to produce 2,309,777 SNPs. ADMIXTURE analysis revealed unstructured subpopulations for 33 accessions, indicating that this orchardgrass population could be used for association analysis. Linkage disequilibrium (LD) analysis revealed an average r2 of 0.4 across all SNP pairs, indicating a high extent of LD in these samples. Through GWAS, a total of 4,604 SNPs were found to be significantly (P < 0.01) associated with the rust trait. The bulk analysis discovered a number of 5,211 SNPs related to rust trait. Two candidate genes, including cytochrome P450, and prolamin were implicated in disease resistance through prediction of functional genes surrounding each high-quality SNP (P < 0.01) associated with rust traits based on GWAS analysis and bulk analysisConclusionsThe large number of SNPs associated with rust traits and these two candidate genes may provide the basis for further research on rust resistance mechanisms and marker-assisted selection (MAS) for rust-resistant lineages.
Highlights
While orchardgrass (Dactylis glomerata L.) is a well-known perennial forage species, rust diseases cause serious reductions in the yield and quality of orchardgrass; genetic mechanisms of rust resistance are not well understood in orchardgrass
Specific-locus amplified fragment sequencing results In total, 76.74 M reads were generated for the 33 genotypes, encompassing 4.30 Gb of the orchardgrass genomic DNA sequence
These SLAF tags were divided into three types: Marker, No ploy, and Repeat (SLAF tags on repeat sequences) (Table 1)
Summary
While orchardgrass (Dactylis glomerata L.) is a well-known perennial forage species, rust diseases cause serious reductions in the yield and quality of orchardgrass; genetic mechanisms of rust resistance are not well understood in orchardgrass. Tajimi et al [4] studied orchardgrass clonal lines and found that the rusts of orchardgrass, Genome-wide association studies (GWASs) have become one of the most commonly strategies for identifying genes underlying complex traits in plants. In model species, such as Arabidopsis thaliana, the potential of GWAS to reveal genetic traits has been demonstrated
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