Abstract This study identified QTLs influencing seed quality characters in a cross of two early maturing soy- bean (Glycine max [L.] Merr.) cultivars (Ma.Belle and Proto) adapted to the short growing seasons of Central Europe. A molecular linkage map was constructed by us- ing 113 SSR, 6 RAPD and 1 RFLP markers segregating in 82 individuals of an F 2 population. The map consists of 23 linkage groups and corresponds well to previously published soybean maps. Using phenotypic data of the F 2 -derived lines grown in five environments, four markers for protein content, three for oil content and eight for seed weight were identified. Four from fifteen seed quality QTL-regions identified in the present study were also found by other authors. Markers associated with seed weight QTLs were consistent across all envi- ronments and proved to have effects large enough to be useful in a marker-assisted breeding program, whereas protein and oil QTLs showed environmental interactions. Keywords Glycine max (L.) · SSR · RAPD · RFLP · Marker-assisted selection Introduction Soybean [Glycine max (L.) Merr., 2n=2x=40] is one of the World’s major crops grown for seed protein and oil con- tent. In Asia it is used mainly for its protein content in hu- man consumption. In North America, it is used mostly for animal feed and for oil production (Smith and Huyser 1987). In Europe it is almost exclusively grown for its pro- tein content to feed livestock. However, soybean varieties of early maturity groups adapted to short-season growing conditions of Central Europe have a lower average protein content than available on the world market (Vollmann et al. 2000). Therefore, to improve the competitive value of Aus- trian grown soybean varieties, increasing the seed protein content of adapted germplasm is highly desirable. Recent developments in the use of molecular markers can make plant breeding more efficient (Paterson et al. 1991). Marker-aided selection (Lande and Thompson 1990) can serve as a tool to substantially increase the efficiency of selecting appropriate genotypes. The first molecular genetic maps of soybean were constructed using different kinds of parents and segregating popula- tions. Shoemaker and Olson (1993) used an interspecific cross between Glycine max and Glycine soja, Lark et al. (1993) used recombinant inbred lines from a cross between Minsoy and Noir, and Muehlbauer et al. (1991) used near-isogenic lines (NILs) between the varieties Clark and Harosoy. Meanwhile, a large number of reports on the molecular mapping of characters such as seed pro- tein and oil content (Diers et al. 1992; Mansur et al. 1993, 1996; Lark et al. 1994; Lee et al. 1996; Brummer et al. 1997; Qiu et al. 1999) shows the great interest for using molecular markers in soybean breeding. In this study, molecular markers associated with seed quality characters were identified in a segregating soy- bean population of the early maturity gene pool. As a first step a molecular-marker map was established and compared with the already published maps. Microsatel- lite markers, frequently referred to as simple sequence repeats (SSRs), were used in constructing the core map. Such a map can later be saturated by other markers such as RFLPs, RAPDs and AFLPs. In a second step, markers associated with seed protein content, oil content and seed weight were identified by means of a single-marker ap- proach and interval mapping. Communicated by J.W. Snape G. Csanádi · G. Stift · T. Lelley ( ✉ ) Department of Plant Biotechnology, Institute for Agrobiotechnology, Konrad Lorenz Strasse 20, A-3430 Tulln, Austria e-mail: lelley@ifa-tulln.ac.at Tel.: +43 2272/66280 204 J. Vollmann Department of Plant Breeding, University of Agricultural Sciences Vienna, Gregor Mendel Strasse 33, A-1180 Vienna, Austria Present address: G. Csanádi, Department of Biotechnology, University of Szeged, Temesvari krt. 62, H-6726 Szeged, Hungary Theor Appl Genet (2001) 103:912–919 © Springer-Verlag 2001 ORIGINAL ARTICLE G. Csanádi · J. Vollmann · G. Stift · T. Lelley Seed quality QTLs identified in a molecular map of early maturing soybean Received: 9 October 2000 / Accepted: 26 February 2001