Lectin protein is a main antinutritional factor in mature soybean seed. The Le gene controls a lectin protein. Plant breeders can use molecular markers to select indirectly individuals in segregating populations that carry a gene for a favorable trait if a tight linkage exists between a marker locus and the genetic locus controlling that trait. The objective of this research was to identify RAPD markers linked to Le allele using bulked segregant analysis. Cultivar "Gaechuck#2" (LeLe) was crossed with PI548391(lele, absence of lectin protein) and F1 seeds were planted. The F1 plants were grown in the greenhouse to produce F2 seeds. Each F2 seed from F1 plants was analysed electrophoretically to determine the presence of the lectin protein band. F2 individual plants were grown in the greenhouse. Young leaf tissues from each F2 plant were collected. At maturity, single F2 plants were harvested. Random F3 seeds from individual F3 seeds harvested were selected and were used to confirm the presence of the lectin protein band. The dominant and recessive F2 plant leaf bulks consisted with ten F2 individual plants were made. 1,000 Operon random primers were used to screen polymorphic band between dominant and recessive bulk. The presence of lectin protein is dominant to the lack of a lectin protein and lectin protein was controlled by a single locus. A few primers that shows polymorphism in bulked samples were selected and were used to obtain segregating data in F2 individual plants.

Lipoxygenase is responsible for the beany flavor and soybean kunitz trypsin inhibitor protein is responsible for the inferior nutritional quality of unheated or incompletely heated soybean meal. Anthocyanins from black soybean seed coat are known to have many pharmaceutical effect. The object of this study is to select black soybean genotype with absence of lipoxygenase-2,3 (Lx1Lx1lx2lx2lx3lx3) and small seed size. Two cultivars (“Seomoktae” and "Gaechuck#1") were used. "Seomoktae" cultivar has the traits of small seed size, black seed coat, green cotyledon and lipoxygenase protein. "Gaechuck#1" has the traits of big seed size, black seed coat, green cotyledon and lipoxygenase free protein. In the F2 population, the several plants with small seed size and lipoxygenase free protein were selected. In F3 and F4 generation, seed size and lipoxygenase protein was comfirmed from the bulked seed harvested at field. The F5 seeds with small seed size and Lx1Lx1lx2llx2lx3lx3 genotype were planted in the field. Several agronomic traits were evaluated. The lines with appropriate agronomic traits were selected.