The effect of maturity (time to maturity) on seed composition in soybean [Glycine max (L.) Merr.] genotypes is not well understood because maturity is generally confounded with genotypic background. Therefore, the effects of maturity on seed composition were estimated in two sets of near isogenic soybean lines (‘Clark’ and ‘Harosoy’), where the maturity of each line within a set varied, but all had a common genotypic background. There was a positive linear relationship between protein concentration and maturity among isolines of the Clark set in 2004 (r2 = 0.75; P ≤ 0.001) and 2005 (r2 = 0.63; P ≤ 0.001). However, in Harosoy isolines there was no relationship between protein and maturity. There was a negative linear relationship between oil concentration and maturity for Clark (in 2004, r2 = 0.82, P ≤ 0.001; in 2005, r2 = 0.91, P ≤ 0.0001) and Harosoy (in 2004, r2 = 0.19, P ≤ 0.05; in 2005, r2 = 0.36, P ≤ 0.01). Maturity had greater effects on seed composition than maximum temperature. The results indicate that the relationship between seed composition and maturity was different between the Clark and Harosoy sets of isolines. However, the overall mean of protein and oil concentration was not different between genotypic backgrounds. This information will be useful for soybean breeding in developing new germplasm for seed composition.

Charcoal rot [Macrophomina phaseolina (Tassi) Goid] of soybean [Glycine max (L.) Merr.] is a disease of economic significance throughout the world. Progress in developing resistant genotypes has been hampered because of a lack of reliable and efficient methods for assessment of soybean genotypes. Researchers need a common system for classifying soybean genotypes for their reaction to M. phaseolina that is consistent across environments. We propose a classification system based on a colony‐forming unit index (CFUI), derived by dividing the colony‐forming unit (CFU) value of a given genotype by the CFU value of a susceptible standard. Four other assessment methods were compared and correlated to CFUI: percent height of stem discoloration measured at R7, foliar symptoms taken at R7, area under the disease progress curve based on foliar symptom data collected four times during the growing season up to R7, and the intensity of internal root and stem discoloration taken at R7 (root and stem severity [RSS]). Twenty‐four soybean genotypes in Maturity Groups III through V were evaluated in 2002 and 2003 in naturally and artificially infested fields. Based on the CFUI, four genotypes were classified as moderately resistant to M. phaseolina Among the disease assessment methods, RSS had the highest correlation with CFUI (r = 0.71 in 2002 and r = 0.69 in 2003). The CFUI provided a good measure of disease resistance across environments but was still time consuming. The RSS provided a less‐accurate but more‐rapid alternative that may be suitable for some breeding strategies.

Using genome-wide association studies, 39 SNP markers likely tagging 21 different loci for carbon isotope ratio (δ (13) C) were identified in soybean. Water deficit stress is a major factor limiting soybean [Glycine max (L.) Merr.] yield. Soybean genotypes with improved water use efficiency (WUE) may be used to develop cultivars with increased yield under drought. A collection of 373 diverse soybean genotypes was grown in four environments (2 years and two locations) and characterized for carbon isotope ratio (δ(13)C) as a surrogate measure of WUE. Population structure was assessed based on 12,347 single nucleotide polymorphisms (SNPs), and genome-wide association studies (GWAS) were conducted to identify SNPs associated with δ(13)C. Across all four environments, δ(13)C ranged from a minimum of -30.55‰ to a maximum of -27.74‰. Although δ(13)C values were significantly different between the two locations in both years, results were consistent among genotypes across years and locations. Diversity analysis indicated that eight subpopulations could contain all individuals and revealed that within-subpopulation diversity, rather than among-subpopulation diversity, explained most (80%) of the diversity among the 373 genotypes. A total of 39 SNPs that showed a significant association with δ(13)C in at least two environments or for the average across all environments were identified by GWAS. Fifteen of these SNPs were located within a gene. The 39 SNPs likely tagged 21 different loci and demonstrated that markers for δ(13)C can be identified in soybean using GWAS. Further research is necessary to confirm the marker associations identified and to evaluate their usefulness for selecting genotypes with increased WUE.

Few resistance loci to soybean rust (SBR), caused by Phakopsora pachyrhizi Syd., have been genetically mapped and linked to molecular markers that can be used for marker assisted selection. New technologies are available for single nucleotide polymorphism (SNP) genotyping that can be used to rapidly map traits controlled by single loci such as resistance to SBR. Our objective was to demonstrate that the high‐throughput SNP genotyping method known as the GoldenGate assay can be used to perform bulked segregant analysis (BSA) to find candidate regions to facilitate efficient mapping of a dominant resistant locus to SBR designated Rpp3 We used a 1536 SNP GoldenGate assay to perform BSA followed by simple sequence repeat (SSR) mapping in an F2 population segregating for SBR resistance conditioned by Rpp3 A 13‐cM region on linkage group C2 was the only candidate region identified with BSA. Subsequent F2 mapping placed Rpp3 between SSR markers BARC_Satt460 and BARC_Sat_263 on linkage group C2 which is the same region identified by BSA. These results suggest that the GoldenGate assay was successful at implementing BSA, making it a powerful tool to quickly map qualitative traits since the GoldenGate assay is capable of screening 1536 SNPs on 192 DNA samples in three days.