88 L.M. MERTZ, F.A. HENNING, S. BORSUK, L.C. DA MAIA, O.A. DELLAGOSTIN, S.T. PESKE AND P.D. ZIMMER Mertz, L.M., Henning, F.A., Borsuk, S., Da Maia, L.C., Dellagostin, O.A., Peske S.T. and Zimmer, P.D. (2010), Seed Sci. & Technol., 38, 88-95 cDNA-AFLP analyses between black and yellow soybean seed coats L.M. MERTZ 1 , F.A. HENNING 1 , S. BORSUK 2 , L.C. DA MAIA 3 , O.A. DELLAGOSTIN 2 , S.T. PESKE 1 AND P.D. ZIMMER 1 1 Programa de Pós-Graduação em Ciência e Tecnologia de Sementes, Universidade Federal de Pelotas (UFPel), 354, 96010-970, Pelotas, RS, Brazil (E-mail: lilianemertz@yahoo.com.br) 2 Centro de Biotecnologia, Instituto de Biologia, (UFPel), Pelotas, RS, Brazil 3 Programa de Pós-Graduação em Agronomia, área de concentração Fitomelhoramento, (UFPel), Pelotas, RS, Brazil (Accepted September 2009) Summary Some soybean genotypes have black seed coat, which are semi-permeable to water, less susceptible to mechanical damages, less affected by weather adversities, deterioration by humidity and pathogen occurrence. Identifying structures and proteins that are responsible for these characteristics can help the development of varieties with higher seed quality. cDNA-AFLP analyses were used to isolate cDNA fragments differentially expressed between soybean seed coats from two contrasting genotypes, the BC (one soybean isoline, with black seed coat ) and the YC (the commercial cultivar CD-202, with yellow seed coat). cDNA-AFLP analysis revealed 47 cDNA fragments differentially expressed between these genotypes, 25 from BC genotype and 22 from YC genotype. Fragments present just in BC genotype were recovered from the gel, cloned and sequenced. This approach allowed the identification of putative proteins related to soybean seed coat characteristics. The characterization of these proteins can help to explain the phenotypical differences in soybean seed coats from BC and YC genotypes. Introduction Commercial soybean varieties have yellow seed coat, however, some soybean genotypes are pigmented and accumulate anthocyanins within the epidermal layer of the seed coat. Seed coat pigmentation is correlated with low rates of imbibition in several legumes species. Compared with unpigmented seed coats, a higher degree of shrinkage of the pigmented ones and, hence, a greater adherence to the cotyledons during maturation results in low rates of imbibition in Vigna (Asiedu and Powell, 1998). Browning of seed coat during seed maturation was associated with its impermabilization in Phaseolus vulgaris, Vigna unguiculata (Legesse and Powell, 1996) an Pisum (Werker et al., 1979). Black soybean seed coats have lower initial imbibition rates, higher resistent to field deterioration, thicker and tougher testas, higher lignin contents and fungicidal properties in comparison with non-black seed coated cultivars (Peske and Pereira, 1983; Tavares et al., 1986; Kuo, 1989; Chachalis and Smith 2000).