title: Genome-wide association study of rust traits in orchardgrass using SLAF-seq technology.
abstract: BACKGROUND
  While orchardgrass (Dactylis glomerataL.) 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.
  
  
  RESULTS
  In 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 r2of 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 analysis.
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: Department of Animal Science, Southwest University, Rongchang, Chongqing, 402460 China.
authors.forename: Bing
authors.initials: B
authors.lastname: Zeng
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China.
authors.forename: Haidong
authors.initials: H
authors.lastname: Yan
authors.affiliation: Agricultural College, Sichuan Agricultural University, Chengdu, 611130 China.
authors.forename: Xinchun
authors.initials: X
authors.lastname: Liu
authors.affiliation: College of Life Science, China West Normal University, Nanchong, 637009 China.
authors.forename: Wenjing
authors.initials: W
authors.lastname: Zang
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China.
authors.forename: Ailing
authors.initials: A
authors.lastname: Zhang
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China.
authors.forename: Sifan
authors.initials: S
authors.lastname: Zhou
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China.
authors.forename: Linkai
authors.initials: L
authors.lastname: Huang
authors.affiliation: College of Life Science, China West Normal University, Nanchong, 637009 China.
authors.forename: Jinping
authors.initials: J
authors.lastname: Liu
mesh_terms: D001487:Basidiomycota; D018744:DNA, Plant / Q000235:genetics; D031745:Dactylis / Q000235:genetics* / Q000382:microbiology; D060467:Disease Resistance / Q000235:genetics*; D017343:Genes, Plant; D056726:Genetic Association Studies; D008040:Genetic Linkage; D015810:Linkage Disequilibrium; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant
keywords: Genome-wide association study; Orchardgrass; Rust disease; SLAF-seq