Soybean Pedigree Analysis Using Map‐Based Molecular Markers: I. Tracking RFLP Markers in Cultivars

Abstract

The history of soybean [Glycine max (L.) Merr.] cultivar development is relatively short. Approximately 80% of the germplasm present in modern cultivars can be traced back to just 12 ancestral lines which were introduced into the USA in the early 1900s. This limited number of ancestral contributors and short history make soybean a promising system for marker‐facilitated, pedigree‐based, genetic analysis. The overall objectives of this project were to (i) identify a core set of markers that would be useful for pedigree‐based analyses of elite soybean cultivars, (ii) trace markers and chromosomal regions from ancestral to descendent cultivars, (iii) determine if the observed and theoretical contribution of parental genomes to cultivar progeny were comparable, and (iv) demonstrate the utility of pedigree‐based or codescent mapping in the detection of putative linkages between molecular markers and phenotypic traits. Sixty‐four soybean lines including ancestral and milestone cultivars were analyzed at 217 RFLP loci to identify a core set of markers to use in evaluating these, and other elite breeding lines. A core set of 97 polymorphic loci were identified for genetic analysis. Results demonstrated that genomic regions contributed by a parent can be traced, often for more than a generation. Six generations of cultivar development were included in this analysis, and one RFLP allele, R013‐l‐b, could be traced through all six generations. Results also revealed that two pedigrees, that of Lincoln and Ogden, could not be supported by RFLP analysis, although it is possible that the pedigrees reported are correct and the incorrect accessions are maintained in the USDA collection. Comparison of the predicted amount of germplasm contributed by a parent, and the amount observed by RFLP analysis revealed that in only four out of 26 instances did one parent provide more genetic information than expected. Codescent analysis of markers and phenotypes demonstrated putative linkages with B and Dtl. The ability to follow regions of chromosomes from parent to offspring through multiple generations should provide an understanding of what transpired at the molecular level during the breeding of cultivars over the last 55 yr. Graphical genotypes of the cultivars analyzed in this study, and the raw RFLP data, are available for electronic transfer.