Abstract: On the basis of our previous results of SSR loci associated with the 16 traits, alleles of loci significantly associated with the traits were analyzed further in the present paper. The phenotypic allele effect was estimated through comparison between the average phenotypic value over accessions with the specific allele and that of accessions with “null allele”, and then the average positive (negative) allele effect (AAE) of a locus was calculated over the estimated phenotypic effects of all positive (negative) alleles. The results showed that a set of elite alleles, loci and their carrier materials were screened out. Among the elite alleles existed in Glycine max and Glycine soja, some were consistent, some inconsistent and some complementary. The phenotypic effects of posi-tive (negative) alleles were different from each other, and therefore, the average positive (negative) effects of a locus were also different from each other, indicating the potential of genetic recombination for breeding purposes. A same marker locus could associate with multiple traits with its alleles performed in their own way in direction and size, and the covariation of a same allele performed in two related traits might be the genetic basis of their phenotypic correlation. In summary, the results implied that association mapping could offer further genetic information complementary to the family-based linkage mapping for the im-provement of breeding procedures. In addition, further detailed information on elite alleles and phenotypic effects of the 16 traits were shown in the text.

Key words: Cultivated soybean [Glycine max (L.) Merr.], Wild soybean (Glycine soja Sieb. et Zucc.), Simple-sequence repeat (SSR), Association mapping, Elite allele, Allele effect