Fine structure mapping of the barley chromosome-1 centromere region containing malting-quality QTLs

Current techniques for quantitative trait locus (QTLs) analyses provide only approximate locations of QTLs on chromosomes. Further resolution of identified QTL regions is often required for detailed characterization. An important region containing malting-quality QTLs on barley (Hordeum vulgare L.) chromosome 1 was identified by previous QTL analyses in a Steptoe x Morex cross. This region contains two putative adjacent overlapping QTLs, each of which has effects on malt-extract percentage, alpha-amylase activity, diastatic power, and malt beta-glucan content. All favorable alleles for these traits are attributed to Morex. The objective of the present study was fine structure mapping of this complex QTL region to elucidate whether these two putative overlapping QTLs are really one QTL. Another question was whether the apparently overlapping QTLs are due to the pleiotropic effects of a single gene, or the independent effects of several genes. A high-resolution map in the target region was developed which spans approximately 27 cM. Molecular-marker-assisted backcrossing was employed to create isogenic lines with a Steptoe background differing only in the region containing the QTLs of interest. A total of 32 different recombinants were identified, of which eight most-informative isogenic lines plus one reconstructed Steptoe control were selected for field testing. The additive effects on malt-extract percentage, alpha-amylase activity, diastatic power, and malt beta-glucan content from eight isogenic lines were calculated based on malting data from three locations. By comparing the significant additive effects among isogenic lines carrying different Morex fragments, two QTLs each for malt extract and for alpha-amylase, and two to three for diastatic power were identified in certain environments and resolved into 1-8-cM genome fragments. There was a significant QTL x environment interaction for diastatic power, and there are indications that epistatic interactions for malt beta-glucan content occur between the QTLs on chromosome 1 and QTLs on other chromosomes.