Genetic diversity analysis of North Dakota public soybean breeding program cultivars

Soybean [Glycine max (L.) Merr.] is a critical crop globally, valued for its protein and oil content. However, historical bottlenecks have constrained genetic diversity in soybean, particularly in high-latitude regions such as North Dakota, where environmental conditions necessitate maturity group (MG) 00 and 0 cultivars. This genetic diversity study examines the North Dakota State University (NDSU) soybean breeding program using pedigree, coefficient of parentage (CP), and SNP-based analyses. Pedigree tracing of 40 NDSU cultivars revealed a genetic base derived from 49 founders. CP analysis confirmed these findings, emphasizing dependence on limited germplasm, with the top ten founders accounting for over 70% of the genetic background and Mandarin (Ottawa) alone contributing 24%. SNP-based dendrograms and genetic relationship structures demonstrate the relationships among cultivars and founders. Notably, the specialty food grade natto cultivars formed a distinct cluster unrelated to commodity soybean. Population structure analyses emphasized the reliance on specific ancestral germplasm for breeding. This study underscores the need to diversify breeding materials to prevent genetic gain plateaus in MG 00 and 0 soybeans, thereby enhancing yield potential and adaptability in high-latitude regions.