Three molecular approaches to improving soybean: Gene discovery, genetic diversity, and allele-specific hybridization markers

Soybean [Glycine max (L.) Merrill] is the primary source of vegetable protein and oil worldwide, largely due to breeders' improvement of soybean's agronomically important traits over the years. Previously, breeders have utilized soybean diversity to make significant gains in cultivar traits through traditional breeding methods. To continue these improvements, breeders are turning to biotechnology for assistance in discovering genes, sources of diversity, and developing molecular methods to track important soybean genetic loci.; Complementary DNA libraries from soybean seedling root, mature root, seedling root 24 hours post Bradyrhizobium japonicus infection, mature nodule, and degenerating cotyledon organs were constructed. From these libraries, 25,132 expressed sequence tags (ESTs) were generated and analyzed. These were assembled into 14,018 unique sequences (contigs). The most abundant identified transcripts were consistent with organ type, but nearly 60% of the contigs had no functional protein identification. These EST clones are publicly available, significantly increasing the amount of material accessible for functional studies.; Breeders have exploited soybean genetic diversity to improve crop cultivars. The diversity available to breeders is limited by the small number of ancestral lines that have been used for cultivar development. The diversity and genetic structure of 20 soybean ancestors was assessed using DNA sequence and amplified fragment length polymorphism (AFLP) data. Five genetic loci were comparatively sequenced, yielding 66 polymorphic loci. The average Nei's diversity index (D) was 0.309; the combined haplotype D was 0.942. AFLP analyses were performed on the same ancestors. A set of 111 AFLP markers had average and combined haplotype Ds of 0.281 and 0.95, respectively. However, much less time and fewer resources were required to generate the AFLP markers. Ancestral plant introductions (Pls) and three southern ancestors appeared to be the best sources of diversity among these ancestors.; A high-throughput method, allele-specific hybridization (ASH), was adapted to soybean to track allele diversity. An example genetic locus was comparatively sequenced and allele-specific oligonucleotide hybridization probes designed that were able to distinguish between single-nucleotide polymorphisms. An adapted germplasm population was genotyped, yielding a combined haplotype diversity of 0.43 for two polymorphic loci, demonstrating the utility of ASH in a breeding context.