Studies were conducted to (i) identify molecular probes that have a high probability of detecting polymorphisms among soybean [Glycine max (L.) Merr.] genotypes, (ii) determine the potential for analyzing genome structure using a molecular genetic map, and (iii) demonstrate the feasibility of a molecular pedigree analysis using mapped RFLP markers. Genomic DNA of 51 genotypes representing U.S. midwestern soybean germplasm was digested with the restriction enzymes HindIII, DraI, EcoRI, EcoRV, and TaqI. A random sample of 32 probes detected polymorphisms between paired comparisons of the 51 genotypes with a frequency from 0 to 72%. On average, no enzyme was strikingly better than any other for detecting polymorphisms. Homeologous chromosomal segments were detected, although they were clearly only remnants with recombination distance disparities and many rearrangements. The soybean genome, if indeed an ancient tetraploid, appears to be highly shuffled or diploidized. RFLP data were compared with the pedigrees of the cultivars Harosoy, Corsoy, Williams, and Clark, using from 58 to 105 mapped markers. Markers on Linkage Groups A and E were analyzed in detail to determine the map positions of polymorphisms and to identify chromosomal segments involved in cultivar development. The polymorphism percentage as detected by molecular markers coincided with genetic distance expectations based on pedigrees. These studies have demonstrated that probe‐enzyme combinations can be identified that will be applicable to discerning differences among a broad range of genotypes. Additionally, it has been demonstrated that a detailed RFLP map can be used to increase our understanding of genome evolution and genome structure and, when combined with pedigrees, can be used to determine the ancestral sources of markers in a given cultivar's genome.

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.

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An analysis of the genome structure of soybean cultivars was conducted to determine if cultivars are composed of large regions of chromosomes inherited intact from one parent (indicative of minimal recombination) or if the chromosomes are a mixture of one parent's DNA interspersed with the DNA from the other parent (indicative of maximal recombination). Twenty-one single-cross-derived and 5 single-backcross-derived soybean cultivars and their immediate parents (47 genotypes) were analyzed at 89 RFLP loci to determine the minimal number and distribution of recombination events detected. Cultivars derived from single-cross and single-backcross breeding programs showed an average of 5.2 and 8.0 recombination events per cultivar, respectively. A homogeneity Chi-square test based upon a Poisson distribution of recombination events across 13 linkage groups indicated that the number of recombinations observed among linkage groups was random for the single-cross cultivars, but not for the single-backcross-derived cultivars. A twotailed t-test demonstrated that for some linkage groups, the number of recombinations per map unit exceeded the confidence interval developed from a t-distribution of recombinations standardized for map unit distance. Paired t-tests of the number of recombinations observed between linkage-group ends and the mid-portion of the linkage groups indicated that during the development of the cultivars analyzed in this study more recombinations were associated with the ends of linkage groups than with the middle region. Detailed analysis of each linkage group revealed that large portions of linkage groups D, F, and G were inherited intact from one parent in several cultivars. A portion of linkage group G, in contrast, showed more recombination events than expected, based on genetic distance. These analyses suggest that breeders may have selected against recombination events where agronomically favorable combinations of alleles are present in one parent, and for recombination in areas where agronomically favorable combinations of alleles are not present in either parent.

, made significant contributions to the first paper, entitled "Soybean Pedigree Analysis Using Map-Based Molecular Markers I. Tracking Chromosomal Regions". Jim Specht assisted in the experimental design, and in the identification of germplasm sources, as well contributing valuable suggestions during a review of the manuscript. Nevin Young and Sam Boutin were responsible for creating the software, Supergene™, that was used in the visualization of RFLP data. I assisted in the design of Supergene™, but not in the actual writing of the "code". References cited in the general introduction and literature review are listed in "LITERATURE CITED", following the General Conclusion. LITERATURE REVIEW History Historical common names for domesticated soybean include "soya bean", "soja bean", and "soy bean" (Anonymous, 1882; Brooks, 1892; Brooks, 1895; Brooks, 1896). Taxonomically, domesticated soybean has been classified as Phaseolus max, Dolichos so/a. Glycine hispida, Soy hispida, Soja hispida, and Soja max, before the current classification of Glycine max (Brooks, 1892; Dodson and Stubbs, 1898; Piper, 1914; Morse, 1950). "The Soybean bears the climate of Pennsylvania very well. The bean ought therefore to be cultivated." This was one of the earliest accounts of the mention of soybean in American literature (Mease, 1804). Hymowitz and Harlan (1983) reported that Samuel Bowen planted soybeans on his plantation in Georgia and used them to produce soy sauce and vermicelli in 1765. Benjamin Franklin was also credited for an early introduction of soybean. In 1770, he sent soybean seeds from London to Philadelphia (Hymowitz and Harlan, 1983). Soybean Plant Introductions were brought to the United States primarily from Japan, China, and Korea (Delannay et al. 1983). The earliest written record of soybean was in 2207 B.C., suggesting that soybean may have been one of the first crops cultivated by man (Morse, 1950). The first soybeans cultivated in the United States were used as forage crops (Anonymous,

Before hybridization programs began in the 1930s, new soybean cultivars in the USA were primarily plant introductions from Japan, China, and Korea, or “off type, pure line” selections from existing U.S. cultivars. These “off type, pure‐line” selections were sometimes thought to have arisen as mutations. Current study of this hypothesis is difficult because numerous accessions with names similar or identical to“pre ‐1930” cultivars occur in the USDA soybean germplasm collection. This study was conducted to determine if selections made from old cultivars were likely derived from mutation and to determine the genetic diversity between accessions with the same or similar old cultivar names. One hundred‐six old entries, which belonged to 17 cultivar groups, were analyzed at between 37 and 50 RFLP loci. “Group” was defined as all accessions with a similar common name, and subsequent selections made from them. Genetic diversity values suggested that mutation did not appear to play a key role in the derivation of selections from most old cultivars. Mutation may have contributed to selections made from Habaro, Mandarin, and Wilson, but this could not be determined unambiguously. AK was previously known to be a heterogeneous seed mixture, and the old cultivar Manchu was suspected as such. The RFLP analysis supported the hypothesis that both AK and Manchu were introduced as a heterogeneous line. Most old cultivars with the same or similar common names could be easily distinguished by genotypic (RFLP) or phenotypic diversity. In 44 instances, phenotypic diversity values between two members of a group equalled zero. In only four cases were genotypic diversity values unable to resolve differences between the two accessions.

The Phytophthora root and stem resistance locus Rps1 has been mapped to linkage group N of the USDA-ARS soybean molecular map, approximately 2 cM from locus A071-1. To determine if A071-1 polymorphisms exist that distinguish and tag different Rps1 alleles, germplasms containing the seven Rps1 alleles were screened with eight enzymes for pA071-detectable polymorphisms. Six enzymes revealed at least one polymorphic fragment. All six detected a polymorphism at A071-1 as determined by restriction fragment length polymorphism mapping, comparison to an EMBL3 clone containing locus A071-1, and Southern hybridization with probes specific for locus A071-1. Screening of the Rps1 donors and 24 Rps1-and 15 Rps1-containing U.S. soybean varieties showed that locus A071-1 exhibited three polymorphisms with each enzyme. The polymorphisms detected by one enyme did not always correlate with those detected by the other four, suggesting that multiple mutation events may be responsible for the different A071-1 polymorphisms. Although no combination of alleles distinguished Rps1-and Rps1-containing genotypes, polymorphism at A071-1 made it possible to distinguish five groups of soybean germplasms. Thus, the unusual polymorphism of locus A071-1 should useful for following Rps1 inheritance in many breeding programs.

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