Southern root-knot nematode [RKI; Meloidogyne incognita (Kofoid and White) Chitwood] is an important soybean [Glycine max (L.) Merr.] pest. When RKI resistance was introgressed from the highly resistant, gray pubescent breeding line G93-9009 into moderately resistant, tawny pubescent cultivars BoggsRR and BenningRR, higher than expected proportions of two advanced backcross populations had gray pubescence. Introgressing genes from unadapted breeding lines into cultivars may reduce seed yield or quality of the resulting lines. This study's objectives were to determine if (i) an RKI resistance quantitative trait locus (QTL) is linked to the T-locus conditioning pubescence color in G93-9009, and (ii) a yield or seed quality loss is associated with introgressing G93-9009 RKI resistance QTL into BenningRR and BoggsRR. Tawny and gray pubescent F2:4 lines of BoggsRR(6) x G93-9009 and BenningRR(5) x G93-9009 were evaluated in greenhouse experiments for RKI resistance and in field experiments grown in four environments for seed yield and quality. Gray lines of both populations averaged 75% fewer RKI eggs per plant than tawny lines. There were no significant differences in seed yield. Differences in agronomic traits such as plant height, seed size, and oil and protein content were observed. These results suggest an RKI resistance QTL exists near the T-locus and the potential to introgress resistance from G93-9009 into other genetic backgrounds without a loss in yield or major impact on other agronomic traits.