Molecular markers associated with barley yellow dwarf virus tolerance in spring oat and their utilization in predictive breeding
type: CreativeWork
description: Barley yellow dwarf viruses (BYDVs) are responsible for the disease barley yellow dwarf (BYD), which causes significant yield losses in many cereals including oat (Avena sativa L.). Phenotyping for disease sensitivity is time consuming, laborious and requires viruliferous aphids for inoculations. Until recently, the molecular marker technology in oat has not allowed for many marker-trait association studies to determine the genetic mechanisms for tolerance and as a result, marker-assisted selection (MAS) and genomic selection (GS) have not been extensively used in breeding for BYD tolerance. In the first study, a genome-wide association study (GWAS) was performed on 428 spring oat lines using a recently developed high-density oat single nucleotide polymorphism (SNP) array as well as a SNP-based consensus map. Marker-trait associations were performed using a Q-K mixed model approach to control for population structure and relatedness. Six significant SNP-trait associations representing two QTL were found on chromosomes 3C and 18D. This is the first report of BYDV tolerance QTL on chromosome 3C and 18D. Haplotypes using the two QTL were evaluated, and distinct classes for tolerance were identified based on the number of favorable alleles. In the second study, GS and MAS models were compared in their accuracy to predict barley yellow dwarf virus tolerance in 428 spring oat lines from North America and Europe. Several GS models were evaluated using 2305 SNPs and included models with previously identified or randomly selected markers as fixed effects. Model accuracies were evaluated using five-fold cross evaluation. GS models used ridge regression-best linear unbiased predictor (RR-BLUP) for marker effect estimation while MAS models used ordinary least square (OLS). Moderate to high prediction accuracies (0.5-0.9) were observed across the models. GS models containing fixed effects (GS-GWAS, GS-3C18D) from previously identified QTL performed better than the GS model with …
abstract: Barley yellow dwarf viruses (BYDVs) are responsible for the disease barley yellow dwarf (BYD), which causes significant yield losses in many cereals including oat (Avena sativa L.). Phenotyping for disease sensitivity is time consuming, laborious and requires viruliferous aphids for inoculations. Until recently, the molecular marker technology in oat has not allowed for many marker-trait association studies to determine the genetic mechanisms for tolerance and as a result, marker-assisted selection (MAS) and genomic selection (GS) have not been extensively used in breeding for BYD tolerance. In the first study, a genome-wide association study (GWAS) was performed on 428 spring oat lines using a recently developed high-density oat single nucleotide polymorphism (SNP) array as well as a SNP-based consensus map. Marker-trait associations were performed using a Q-K mixed model approach to control for population structure and relatedness. Six significant SNP-trait associations representing two QTL were found on chromosomes 3C and 18D. This is the first report of BYDV tolerance QTL on chromosome 3C and 18D. Haplotypes using the two QTL were evaluated, and distinct classes for tolerance were identified based on the number of favorable alleles. In the second study, GS and MAS models were compared in their accuracy to predict barley yellow dwarf virus tolerance in 428 spring oat lines from North America and Europe. Several GS models were evaluated using 2305 SNPs and included models with previously identified or randomly selected markers as fixed effects. Model accuracies were evaluated using five-fold cross evaluation. GS models used ridge regression-best linear unbiased predictor (RR-BLUP) for marker effect estimation while MAS models used ordinary least square (OLS). Moderate to high prediction accuracies (0.5-0.9) were observed across the models. GS models containing fixed effects (GS-GWAS, GS-3C18D) from previously identified QTL performed better than the GS model with …
author: Foresman, Bradley
language: en
keywords: Barley yellow dwarf (BYD), Barley yellow dwarf viruses (BYDV), genomic selection, Genome-wide association study (GWAS), Marker-assisted selection, Genomic prediction, Oat
date published: 2016-07-07T19:52:34Z
date modified: 2026-07-22T22:26:32Z
provider: University of Illinois - Urbana-Champaign
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: University of Illinois at Urbana-Champaign

PropertyValue
property ID: Handle
value: http://hdl.handle.net/2142/90455