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Background Soybean is an economically important crop which flowers predominantly in response to photoperiod. Several major loci controlling the quantitative trait for reproductive timing have been identified, of which allelic combinations at three of these loci, E1, E2, and E3, are the dominant factors driving time to flower and reproductive period. However, functional genomics studies have identified additional loci which affect reproductive timing, many of which are less understood. A better characterization of these genes will enable fine-tuning of adaptation to various production environments. Two such genes, E1La and E1Lb, have been implicated in flowering by previous studies, but their effects have yet to be assessed under natural photoperiod regimes. Results Natural and induced variants of E1La and E1Lb were identified and introgressed into lines harboring either E1 or its early flowering variant, e1-as. Lines were evaluated for days to flower and maturity in a Maturity Group (MG) III production environment. These results revealed that variation in E1La and E1Lb promoted earlier flowering and maturity, with stronger effects in e1-as background than in an E1 background. The geographic distribution of E1La alleles among wild and cultivated soybean revealed that natural variation in E1La likely contributed to northern expansion of wild soybean, while breeding programs in North America exploited e1-as to develop cultivars adapted to northern latitudes. Conclusion This research identified novel alleles of the E1 paralogues, E1La and E1Lb, which promote flowering and maturity under natural photoperiods. These loci represent sources of genetic variation which have been under-utilized in North American breeding programs to control reproductive timing, and which can be valuable additions to a breeder’s molecular toolbox.

Soybean plays an important role in seed oil production for foods and industrial products in the USA. Chemical hydrogenation of commodity soybean oil increased functionality but unavoidably created trans fat which has been linked to many health issues in humans. An alternative to using hydrogenation of the oil to enhance oxidative stability is to genetically increase the level of oleic acid in the seed oil. Our goal was to develop a soybean germplasm as a source for more functional soybean oil with a high oleic acid, increased stearic acid, and low linolenic acid profile utilizing new and existing variant alleles of key fatty acid desaturase genes. Using forward genetics, novel alleles of FAD2-1A were discovered and characterized from a mutant soybean population already containing elevated seed stearic acid content. One of the two new FAD2-1A alleles, when combined with existing mutant alleles of FAD2-1B created a high oleic acid seed oil phenotype in soybean germplasm lines. The other new FAD2-1A allele produced lower and more variable oleic acid levels when combined with existing mutant alleles of FAD2-1B. Seed stearic acid increased to ~ 10–11% in lines containing combinations of FAD2-1A and FAD2-1B mutant alleles plus the SACPD-C missense mutant alleles; however, the increase in stearic acid was associated with a decrease in the oleic acid content and did not meet the target of at least 20% stearic acid in the seed oil. In addition, existing FAD3 mutant alleles were incorporated into the novel high oleic acid and high oleic/elevated stearic acid soybean lines with four or five targeted alleles combined (FAD2-1A, FAD2-1B, FAD3A, FAD3C, and SACPD-C) to create soybean germplasm with more functional soybean oil. This study is beneficial for improving the quality of soybean oil based on nutritional value and oxidative stability.