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North American soybean breeders have successfully developed a large number of elite cultivars with diverse maturity groups (MG) from a small number of ancestral landraces. To understand molecular and genetic basis underlying the large variation in their maturity and flowering times, we integrated pedigree and maturity data of 166 cultivars representing North American soybean breeding. Network analysis and visualization of their pedigree relationships revealed a clear separation of southern and northern soybean breeding programs, suggesting that little genetic exchange occurred between northern (MG 0–IV) and southern cultivars (MG V–VIII). We also analyzed the transcript sequence and expression levels of four major maturity genes ( E1  to  E4 ) and revealed their allelic variants in 75 major ancestral landraces and milestone cultivars. We observed that  e1-as  was the predominant  e  mutant allele in northern genotypes, followed by  e2  and  e3 . There was no allelic variation at  E4 . Transcript accumulation of the  e2  mutant allele was significantly reduced, which might be caused by its premature stop codon triggering the nonsense-mediated mRNA decay pathway. The large DNA deletion generating the  e3  mutant allele also created a gene fusion transcript. The  e  alleles found in milestone cultivars were traced through pedigrees to their ancestral landraces and geographic origins. Our analysis revealed an approximate correlation between dysfunctional alleles and maturity groups for most of the 75 cultivars. However, single  e  mutant alleles and their combinations were not sufficient to fully explain their maturity diversity, suggesting that additional genes/alleles are likely involved in regulating maturity time.   Electronic supplementary material  The online version of this article (doi:10.1007/s11032-016-0611-7) contains supplementary material, which is available to authorized users.

Genetic separation of southern and northern soybean breeding programs in North America and their associated allelic variation at four maturity loci