ARS | Publication request: An integrated resource for barley linkage map and malting quality QTL alignment

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 6, 2009
Publication Date: July 1, 2009
Repository URL: http://hdl.handle.net/10113/42087
Citation: Szucs, P., Blake, V.C., Chao, S., Marcos-Cuesta, A., Muehlbauer, G.J., Ramsay, L., Waugh, R., Hayes, P.M. 2009. An integrated resource for barley linkage map and malting quality QTL alignment. The Plant Genome. 2(2):134-140, 2009

Interpretive Summary: Barley is an economically important plant and a genetic model system. There is a long and rich history of genetics research in barley. To facilitate genetic analysis and gene discovery, DNA markers have been developed and genetic maps were constructed by placing these markers on each of the seven barley chromosomes. In the past twenty years, steady progress has been made in improving the marker density mapped on each chromosome. Previously a framework map consisting of 189 morphological and DNA markers have been developed using the Oregon Wolfe Barley (OWB) mapping population. The high polymorphism rate has made OWB population an important international resource for collaborative mapping of all types of markers, including both DNA and morphological markers. Single nucleotide polymorphism (SNP) is a new marker system that can differentiate individuals based on variations detected at the level of a single nucleotide base in the genome. Such variations are present in high abundance in the genomes of higher organisms including plants. Therefore, it is possible to tag the entire genome with SNP markers. In this report, we describe the development of a high-density genetic map by adding 1,472 gene-based SNP markers to the framework OWB map that resulted in a map containing a total of 2,383 markers. High-density genetic maps constructed from the inheritance of robust gene-based SNPs provide a seamless connection between gene sequence and the genetic coordinates of Quantitative Trait Loci (QTL) underlying the important agronomic traits. A set of SNPs found closely associated with the important traits can be implemented in the barley breeding programs through a process known as marker-assisted selection. In this report, we demonstrate the utility of the maps by integrating the OWB map with malting quality QTL reported in the literature previously published. This is the first step toward developing a Barley QTL Community Curation Workbook to provide access to all QTL reports available on the GrainGenes website, a database that hosts and disseminates genetic information related to the small grains, such as barley, wheat and oat.

Technical Abstract: Barley (Hordeum vulgare subsp. vulgare) is an economically important model plant for genetics research that is currently served by a comprehensive set of tools for genetic analysis. High density genetic linkage maps constructed from the inheritance of robust gene-based Single Nucleotide Polymorphisms (SNPs) provide a seamless connection between gene sequence and the genetic coordinates of Quantitative Trait Loci (QTL), and provide orthologous gene anchors directly to the DNA sequence of genomic models. We describe the development of a 2383 locus linkage map in the Oregon Wolfe Barley Mapping Population. The map is based on 1472 SNP, 722 DArT, and 189 prior markers. Prior markers include morphological, SSR, and RFLP markers. This map serves as a useful bridge, or “Rosetta stone”, between high-density SNP-only maps and maps that were widely used for QTL detection. The latter were largely based on RFLPs, SSRs, and - more recently - DArTs. In this report we describe integration of the OWB map with malting quality QTL reported in the literature. This is the first step toward developing a Barley QTL Community Curation workbook on the GrainGenes website.