Despite the importance of grain yield potential to plant breeders and society in general, it has been difficult to identify grain yield quantitative trait loci (QTL) effective for marker‐assisted selection (MAS) across a wide range of genetic and/or environmental contexts. However, as genotyping becomes more cost effective, it might be feasible to use preliminary yield trials to model a target genotype within each context and immediately select the progeny that approach that target genotype in real time. In the present study, elite soybean cultivars with residual heterogeneity were leveraged as populations (the genetic context) to detect yield QTL within a limited set of environments (the environmental context), to model a target genotype, and to select subline haplotypes that comprised the target genotype. The yield potential of the selected subline haplotypes were then compared to their respective mother lines in highly replicated yield trials across multiple environments and years. Statistically significant yield gains of up to 5.8% were confirmed in some of the selected sublines, and two of the improved sublines were released as improved cultivars. This context‐specific MAS (CSM) approach might also be applicable to the more typical biparental and backcross populations commonly used in plant breeding programs. Factors that can affect the efficiency and applicability of CSM are discussed.

Genetic improvement for yield in soybean [Glycine max (L.) Merrill] has beenaccomplished by breeding within a narrow elite gene pool. Plant introductions (Pis) may be useful for obtaining additional increases in yield if unique and desirable alleles at quantitative trait loci (QTL) can be identified. The objectives of the study were to identify QTL for yield in elite and PI germplasm and to determine if the Pis possessed favorable alleles for yield.Allele frequencies were measured with simple sequence repeat (SSR) markers in three populations that differed in their percentage of PI parentage. AP10 had 40 PI parents, API 2 had 40 PI and 40 elite parents, and API 4 had 40 elite parents. Four cycles of recurrent selection for yield had been conducted in the three populations. Nei's genetic distance indicated that AP10, AP12, and AP14 remained distinct through cycle 4 (C4), but that the genetic diversity narrowed within each population. Less gametic phase disequilibrium (GPD) was observed in the parents used to form the cycle 0 (CO) populations than in C4 of AP12 and AP14. Allele frequencies of the highest-yielding C4 lines in the three populations were compared with the parents used to form the populations of the initial cycles. Allele flow was simulated to account for genetic drift. Ninety-two SSRs were associated with 56 yield QTL. Nine of the QTL had been identified in previous research. Thirty-three favorable marker alleles were unique to the PI parents. The restriction of alleles from the 40 CO parents to the 20 cycle 1 (CI) parents of AP10 was reflected in the number of alleles that had frequency changes and could explain the reduced genetic variance for yield in the C4 of AP10. Genetic asymmetry may account for the different genetic gain for yield that had been observed between AP10 and AP14.

The use of soybean [Glycine max (L.) Merr.] in animal feed without heat treatment may be possible by reducing protease inhibitors. The objectives of this study were to determine to what extent soybean protease inhibitors would be reduced genetically by combining the Brazil nut protein (BNP) gene from the transgenic line BX4P9341B6 with the ti allele for the Kunitz trypsin inhibitor from the cultivar Kunitz and their effect on agronomic traits. Soybean seed from 42 F2‐derived lines from the cross BX4P9341B6 × Kunitz were evaluated in replicated trials in 1995 for trypsin inhibitor (TI), chymotrypsin inhibitor (CI) activity, and agronomic traits. There were six lines homogeneous for presence of the BNP gene and the Ti allele (BNP+, Ti), 18 lines homogeneous for presence of the BNP gene and the ti allele (BNP+, ti), six lines homogeneous for absence of the BNP gene and presence of the Ti allele (BNP−, Ti), and 12 lines homogeneous for absence of the BNP gene and presence of the ti allele (BNP−, ti). The mean TI activity of the BNP+, ti lines was 85.1% less than for the BNP−, Ti lines representative of conventional soybean cultivars. The mean CI activity of the BNP+, ti lines was 61.4% less than the BNP−, Ti lines. The means of the four genotypic classes were not significantly different (P > 0.05) for seed yield, maturity, lodging, and protein content. It should be possible to develop high‐yielding cultivars with the BNP+, ti genotype that have major reductions in TI and CI activity.

Development of soybean [Glycine max (L.) Merr.] cultivars with reduced palmitate and stearate will lower the total saturated fatty ester content of the seed oil, and reduction of linolenate will improve its oxidative stability. The objective of this study was to compare the family and line methods of selection for reduced palmitate, palmitate + stearate (saturates), and linolenate in four populations segregating for the major alleles fap1 and fap3 for reduced palmitate or the fan1(A5) and fan2 for reduced linolenate. Four random F3‐derived lines from 21 F2 families from each population were evaluated in a plant‐row‐yield test in 1995 and replicated trials at four locations in 1996. For the family method, the mean palmitate, saturates, and linolenate of the four F3‐derived lines of each F2 family was used to identify families from which to select individual lines. For the line method, lines were selected without regard to the family structure. The fatty ester contents of the selected and unselected lines based on data from one environment were compared with their mean fatty ester contents in the other environments. The number of lines selected for each of the traits by the family method was less than for the line method in all populations. There was a greater percentage of lines incorrectly rejected by the family method than by the line method. For development of cultivars with reduced palmitate, saturates, and linolenate, breeding methods that rely on family performance would not be more effective or efficient than methods that ignore family structure.

Plant‐row‐yield tests (PRYT) are used by soybean [Glycine max (L.) Merr.] breeders for the initial evaluation of experimental lines. The highest yielding lines in the PRYT are advanced for additional testing in replicated tests. The objective of this study was to determine the reliability of selection for seed yield in unreplicated plots by the family and line methods of selection. Four F3‐derived lines from each of 21 F2 families from four populations were grown in a PRYT during 1995 and in replicated tests at four environments in 1996. For the family method, the mean seed yield of the four F3‐derived lines of each F2 family was used to identify superior families from which to select individual lines. For the line method, lines were selected without regard to the family structure. The seed yield of the selected and unselected lines on the basis of data from the PRYT was compared with their mean seed yield in the 1996 environments. The total number of lines selected by the family method was less than for the line method in all populations. The percentage of selected lines that were correctly classified was similar for both methods. There was a greater percentage of lines incorrectly rejected by the family method than by the line method. The use of replication at an individual location did not improve the selection of lines by the family or line methods of selection. For the selection of lines for seed yield in unreplicated plots, breeding methods that rely on family performance would not be more effective or efficient than methods that ignore family structure. To obtain lines for yield tests at multiple locations, selection of lines by the line method on the basis of their performance in a PRYT would be better than the use of random lines.