The protein meal of soybean [Glycine max (L.) Merr.] lines homozygous for the mips allele (mips lines) has reduced phytate phosphorus and raffinose saccharides. Less phytate is desirable for reducing the phosphorus content of manure from non-ruminant animals and less raffinose saccharides increases the amount of metabolizable energy available to them. An objective of this study was to determine the association of the reduced raffinose saccharides and phytate phosphorus with agronomic and seed traits. A total of 48 F 3:5 mips lines with the same number of lines with the Mips Mips genotype (Mips lines) were compared in replicated field tests at two Iowa locations during 2001. Mean field emergence of mips lines was 46% less than the Mips lines. Mean seed yield adjusted for plant density by covariate analysis was 4% less in the mips lines than the Mips lines. Differences between mips lines and Mips lines for maturity, lodging, plant height, protein, and oil were not consistently significant. If reduced field emergence can be overcome, it should be possible to develop mips cultivars equivalent to Mips cultivars for agronomic and seed traits.;A second research objective was to determine if field emergence of mips lines is influenced by the environment used for seed production. Seed of six mips lines and four Mips lines produced in four temperate and 12 subtropical environments during two years was evaluated for field emergence percentage. The field emergence of mips lines was significantly less than mips lines for all seed sources. The mips lines had a mean field emergence of 63% for temperate sources and 8% for subtropical sources while mips lines had a mean field emergence of 77% for temperate sources and 83% for subtropical sources. Seed source should be a consideration when evaluating the field emergence of mips lines in a breeding program.;A third research objective was to locate the region of the soybean genome containing the mips locus. A total of 87 of the 269 (32%) simple sequence repeat (SSR) markers that were evaluated were polymorphic between the parents of the F2 mapping populations. Bulked segregant analysis was conducted on two bulked DNA samples composed of 10 homozygous mips and 10 homozygous Mips F2 individuals. The mips locus was not located because none of the 87 SSRs were polymorphic between the two bulked DNA samples. The mips locus was probably not located because none of the SSRs were close enough to the mips locus. There were 17 regions on 13 chromosomes where the distance between polymorphic markers was at least 40 centimorgans. Mapping alternatives were considered, but not pursued due to their time and cost.