An Integrated Resource for Barley Linkage Map and Malting Quality QTL Alignment

Abstract

Barley (Hordeum vulgare L.) is an economically important model plant for genetics research. Barley is currently served by an increasingly comprehensive set of tools for genetic analysis that have recently been augmented by high‐density genetic linkage maps built with gene‐based single nucleotide polymorphisms (SNPs). These SNP‐based maps need to be aligned with earlier generation maps, which were used for quantitative trait locus (QTL) detection, by integrating multiple types of markers into a single map. A 2383 locus linkage map was developed using the Oregon Wolfe Barley (OWB) Mapping Population to allow such alignments. The map is based on 1472 SNP, 722 DArT, and 189 prior markers which include morphological, simple sequence repeat (SSR), Restriction Fragment Length Polymorphism (RFLP), and sequence tagged site (STS) loci. This new OWB map forms, therefore, a useful bridge between high‐density SNP‐only maps and prior QTL reports. The application of this bridge concept is shown using malting‐quality QTLs from multiple mapping populations, as reported in the literature. This is the first step toward developing a Barley QTL Community Curation workbook for all types of QTLs and maps, on the GrainGenes website. The OWB‐related resources are available at OWB Data and GrainGenes Tools (OWB‐DGGT) (http://wheat.pw.usda.gov/ggpages/maps/OWB/).

Structural and functional characterization of a winter malting barley

“…In this study, we focus on 40 of the 55 QTL for which Szűcs et al (2009) assigned precise map coordinates based on the presence of markers in common between the original QTL report and the integrated OWB map (Table 2). Only the QTL for the seven traits for which we have phenotypic measurements (Table 1) were placed on the map.…”

“…Malting quality QTL reported in the literature were assigned map positions on the 88Ab536 graphical haplotype based on the integrated OWB map (Szűcs et al 2009). In this study, we focus on 40 of the 55 QTL for which Szűcs et al (2009) assigned precise map coordinates based on the presence of markers in common between the original QTL report and the integrated OWB map (Table 2).…”

“…Malting quality and winter hardiness-related genes and/or QTL were assigned to map positions based on their presence in POPA-3 or their position was inferred based on the Oregon Wolfe Barley (OWB) integrated map (Szűcs et al 2009). …”

“…However, only a few of these genes have been fully characterized Szűcs et al 2009). Large-scale gene expression technologies such as cDNA-and oligonucleotide-based arrays, and serial analysis of gene expression (SAGE) have proved to be useful to conduct transcript profiling during germination and malting (Lapitan et al 2009;Potokina et al 2002Potokina et al , 2004Watson and Henry 2005;White et al 2006), and to identify candidate genes for malting quality (Lapitan et al 2009;Potokina et al 2004Potokina et al , 2006.…”

“…Many quantitative trait locus (QTL) studies have been carried out to dissect the genetics of malting and 154 malting-quality QTL associated with 18 traits have been recently summarized and placed on the Oregon Wolfe Barley (OWB) map (Szűcs et al 2009). …”