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Soybean improvement has entered a new era with the advent of multi-omics strategies and bioinformatics innovations, enabling more precise and efficient breeding practices. This comprehensive review examines the application of multi-omics approaches in soybean—encompassing genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics. We first explore pre-breeding and genomic selection as tools that have laid the groundwork for advanced trait improvement. Subsequently, we dig into the specific contributions of each -omics field, highlighting how bioinformatics tools and resources have facilitated the generation and integration of multifaceted data. The review emphasizes the power of integrating multi-omics datasets to elucidate complex traits and drive the development of superior soybean cultivars. Emerging trends, including novel computational techniques and high-throughput technologies, are discussed in the context of their potential to revolutionize soybean breeding. Finally, we address the challenges associated with multi-omics integration and propose future directions to overcome these hurdles, aiming to accelerate the pace of soybean improvement. This review serves as a crucial resource for researchers and breeders seeking to leverage multi-omics strategies for enhanced soybean productivity and resilience. [ABSTRACT FROM AUTHOR]

Soybean breeding programs targeting tofu quality must evaluate their performance within zones of adaptation. A comprehensive study was carried out to examine soybean breeding lines from three maturity groups (MGs; MG0, MG00, and MG000) from 2018 to 2022. Several agronomic, chemical composition and tofu-related quality traits were evaluated, and the associations among traits were investigated. The results showed that genotypes in MG0 yielded higher and matured later, which confirmed that the selection of targeted genotypes for a specific maturity group was successful. Non-imbibed "stone seeds", an important quality trait for tofu processors, were higher in MG000 lines. Tofu texture using both GDL and MgCl2 coagulants was positively associated, indicating one coagulant might be enough for screening purposes. The MG by traits biplot showed very clear MG clustering for all genotypes tested from 2018 to 2022, signifying that the MG has a more pronounced effect on the investigated traits than the environmental effects seen in different years, regardless of the MG. Most tofu-related traits were higher and showed stronger associations in MG0 lines compared to the lines in earlier MGs, indicating a need for future effort in shorter season MGs. Overall, this study provided useful information for selecting soybean lines for tofu end-use application targeting specific MGs. [ABSTRACT FROM AUTHOR]

Climate change, resulting from increased atmospheric CO2, will affect temperature and precipitation amount and regularity. Changes in solar radiation have been observed in the recent past. Precipitation irregularity is a measure of rainfall distribution during a growing season (calculated as the standard error of the slope from regression of cumulative precipitation on day of the growing season). We investigated whether precipitation irregularity and solar radiation contributed to soybean yield. Fourteen short-season cultivars, released from 1930 to 1992, were grown from 1993 to 2019 at Ottawa, Canada. Stepwise multiple linear regression was used to investigate the contribution to seed yield of precipitation irregularity and solar radiation, and also previously modeled parameters genetic improvement, annual [CO2], and cumulative precipitation and average minimum temperature during the vegetative, flowering and podding, and seed filling growth stages. While solar radiation and precipitation irregularity did not trend over the years of our study and precipitation irregularity was not related to growing season precipitation, both were significant factors in our model, accounting for 2.5% and 6.5%, respectively, of the seed yield variability. Precipitation during all three stages were similar as they each accounted for 4%–7% of seed yield variability. We observed contrasting temperature effects where higher minimum temperature during vegetative and seed filling reduced yield, while during flowering and podding increased yield. Estimated yield improvement due to elevated [CO2] was 7.8 kg ha−1 ppm−1 and to genetic improvement over time was 7.1 kg ha−1 year−1. Over the extremes of our study we found that precipitation irregularity could cause up to a 30% yield reduction. [ABSTRACT FROM AUTHOR]

Soybean (Glycine max (L.) Merr.) is among the most valuable crops based on its nutritious seed protein and oil. Protein quality, evaluated as the ratio of glycinin (11S) to β-conglycinin (7S), can play a role in food and feed quality. To help uncover the underlying differences between high and low protein soybean varieties, we performed differential expression analysis on high and low total protein soybean varieties and high and low 11S soybean varieties grown in four locations across Eastern and Western Canada over three years (2018–2020). Simultaneously, ten individual differential expression datasets for high vs. low total protein soybeans and ten individual differential expression datasets for high vs. low 11S soybeans were assessed, for a total of 20 datasets. The top 15 most upregulated and the 15 most downregulated genes were extracted from each differential expression dataset and cross-examination was conducted to create shortlists of the most consistently differentially expressed genes. Shortlisted genes were assessed for gene ontology to gain a global appreciation of the commonly differentially expressed genes. Genes with roles in the lipid metabolic pathway and carbohydrate metabolic pathway were differentially expressed in high total protein and high 11S soybeans in comparison to their low total protein and low 11S counterparts. Expression differences were consistent between East and West locations with the exception of one, Glyma.03G054100. These data are important for uncovering the genes and biological pathways responsible for the difference in seed protein between high and low total protein or 11S cultivars. [ABSTRACT FROM AUTHOR]

The genetic model for maturity in soybean [Glycine max (L.) Merr.] is a series of near-isogenic lines, but they do not span the natural variation for early maturity. The objectives of this study were to determine if a single gene in OT98-17 controls early maturity and if this is a new locus. A cross was made between 'Maple Presto' and OT98-17, an early-maturing Maple Presto-derived backcross line. A total of 201 [F.sub.3] progeny rows from this population and Maple Presto were grown at Ottawa, ON, in 1999. In 2000, [F.sub.4] progeny rows were grown and 150 late-maturing and 51 early-maturing families were observed to fit a 3:1 ratio (n = 201, [X.sup.2] = 0.01, P = 0.90). The early-maturing allele was transferred to a 'Harosoy' background, and isolines were grown from 2002 to 2006 at Ottawa, ON. The isolines were 9 and 6 d earlier maturing in Maple Presto and Harosoy backgrounds, respectively. To determine the independence of this locus, simple sequence repeat molecular markers were used to identify three candidate regions. The gene E8 specifically mapped to linkage group C1 between Sat_404 and Satt136. No other maturity gene has been mapped to this region. The two other candidate regions were both related to maturity quantitative trait loci on molecular linkage group L and may be inadvertently selected along with early maturity. The gene symbol E8e8 has been assigned by the Soybean Genetics Committee. E8E8 results in later maturity and e8e8 results in early maturity. The earliest Harosoy maturity isoline is now rated as maturity group 000. doi: 10.2135/cropsci2009.04.0174

Natto soybean [Glycine max (L.) Merr.] cultivars are typically small seeded and seed yield is generally lower than that of oilseed cultivars. We investigated the effects of mass selection for small seed size on seed yield. Two sets of populations were developed, from crosses of natto and larger-seeded parents, using mass selection; nine tested in three site-years in 2003 and 2004, and four tested from 2002 to 2004. Populations were advanced with mass selection for seed size applied to [F.sub.3] and [F.sub.4] seeds using either no. 14 of 15 round-hole sieves. [F.sub.4:5] recombinant inbred lines (RILs) from AC Colibri/ OT91-3, unselected for seed size, were evaluated from 2002 to 2004. Selection for small seed reduced seed weight but did not affect yield or days to maturity when comparing two sieve sizes. The seed yield of natto selections remained at about 80% of the oilseed check cultivars in this study. In nine populations, among progenies resulting from mass-selection for seed size, random selections were significantly higher yielding and later maturing but did not differ in seed weight compared to visually selected lines. In four populations segregating for leaflet shape, mass selection for small seed size resulted in more narrow-leaflet lines. Selection for narrow leaflets may aid in reducing seed size in some populations. The seed size distribution of the RILs suggests that selection for small seed size may cause a bottleneck in mass selected populations and result in small effective population sizes.

Studies with a series of historic soybean [Glycine max (L.) Merr.] cultivars have found genetic improvement rates for seed yield of about 0.5% per year since soybean was first cultivated in Canada. Work with maize (Zea mays L.) has shown seed yield differences between old and new hybrids are more pronounced under higher seeding rates. The objective of our research was to determine the effect of plant populations on the rate of genetic improvement of short-season soybeans. Soybean cultivars released from 1934 to 1996 were grown in 40-cm-wide rows at several seeding rates (Exp. 1, 42 cultivars grown at 25, 50, 75 seeds [m.sup.-2] in 1998 and 1999; and Exp. 2, seven cultivars grown at 25, 50, 100, 150, 200 seeds [m.sup.-2] in 1999 and 2000) in two fields for 2 yr at Ottawa, ON. Genetic improvement rates were based on cultivar year of release and were compared across plant populations. In Exp. 1, seed yields did not reach a plateau. In Exp. 2, a seed yield plateau was reached and genetic improvement rates generally increased with plant population. Maximum rates of genetic improvement occurred at plant populations three to four times greater than current commercial practice (40 plants [m.sup.-2]). A plateau for seed yield was reached at lower plant populations compared to plateaus for genetic improvement rates which were reached at higher plant populations (>80 plants [m.sup.-2]). Higher plant populations also resulted in earlier maturity, increased plant height, and increased lodging. Seed protein increased and seed oil decreased with higher plant populations. New soybean cultivars appear more tolerant to plant population stress than older cultivars., ACCORDING to Donald (1963) a successful crop plant should be intraspecifically noncompetitive while still exhibiting sufficient plasticity to respond in size and shape to available conditions. Duncan (1969) concluded that [...]

Understanding the control of flowering time in photoperiod-sensitive plants has been furthered by grafting experiments. In soybean [Glycine max (L.) Merr.], genes which control flowering time have been identified and their responses to photoperiod characterized. Grafting experiments allow the study of interactions between genotypes. The objective of our study was to characterize the flowering response of scions from a grafted series of early- to late-flowering soybean near-isogenic lines. Seedling scions were grafted to 1-wk-older rootstocks and grown under noninductive 16-h days. Rootstocks were allowed to develop a single axillary shoot to allow interaction between rootstock and scion shoots. Late-flowering rootstocks did not delay flowering of the earliest-flowering isolines but delayed flowering of intermediate-flowering isolines. Some floral inhibition was also seen within scions since defoliated late-flowering scions grafted to early-flowering rootstocks flowered earlier compared with nondefoliated scions of the same graft combination. Early-flowering rootstocks promoted flowering of late-flowering scions both within and across genetic backgrounds. Early-flowering scions flowered early (27 to 30 d) regardless of rootstock genotype. This early flowering was observed even when the scions were defoliated, indicating that floral promoters might be produced or sensed in unexpanded leaves or buds. The activity of floral promoters and inhibitors was demonstrated in soybean and these factors appeared to mediate flowering time antagonistically., THE CONTROL OF floral initiation in plants has been studied for many years. Levy and Dean (1998) reviewed models for the control of flowering time including the florigen concept postulated [...]

Oxalic acid is an important pathogenic factor for the fungus Sclerotinia sclerotiorum (Lib.) de Bary. An oxalate degrading enzyme, oxalate oxidase (OxO), in transgenic soybean [Glycine max (L.) Merr.] has reduced pathogen growth in indoor seedling studies. The objective of this study was to characterize the response of this OxO transgenic soybean line to white mold under field conditions and also to characterize the agronomic performance of this transgenic line under noninfected conditions. The transgenic line 80(30)-1contains the wheat germin gene gf-2.8 that codes for OxO. This line was compared with 80(30)-9, a sib line which does not contain the gene, as well as resistant and susceptible cultivars. Field tests were conducted at three sites infested with white mold in Ontario and Quebec across 3 yr. The Sainte-Foy site provided the highest infection potential and the transgenic line had a disease severity index (DSI) of 7 compared with 80(30)-9 with a DSI of 46, across 3 yr. Across 2 yr, resistant commercial cultivars had an average DSI of 2 and susceptible cultivars a DSI of 46. Stem inoculations were performed in the field at Elora and the transgenic line was significantly less infected compared with 80(30)-9. In noninfested trials, no significant differences were found between the transgenic, the negative sib, and the parental lines for seed yield, maturity, seed weight, or seed protein and oil content. The transgene provided white mold resistance equivalent to the best commercial cultivars in a white mold susceptible background., SCLEROTINIA SCLEROTIORUM is a fungal pathogen which causes sclerotinia stem rot, also known as white mold, in soybean. White mold has become an important soybean disease in parts of Canada, [...]

A new locus (E7) controlling flowering and maturity time, and photoperiod response in soybean [Glycine max (L.) Merr.] was identified by means of 20-h days of low (0.7) red:far-red (R:FR) light quality. The objective of this study was to characterize light quality and photoperiod responses of E7E7 and e7e7 soybean near-isogenic lines. E7E7 and e7e7 lines, in two genetic backgrounds, were grown in 20-h photoperiods with four R:FR light qualities (0.7, 1.2, 2.3, 2.7) and in 12-h photoperiods with 0.7 and 2.7 R:FR light quality. Under high R:FR, all isolines flowered early and similarly in both 12- and 20-h photoperiods. In 20-h photoperiods, as R:FR light quality approached that of natural day light (1.2), E7E7 lines flowered 6 to 7 d later than e7e7 lines, while under low R:FR (0.7), E7E7 lines flowered about 15 d later than e7e7 lines. Under low R:FR, all isolines flowered later under 20-h compared with 12-h photoperiods. Six `Harosoy' isolines (e7e7 and 5 E7E7 lines) were grown in 1998 and 1999 in the field under natural daylength and daylength extended to 20 h with incandescent lamps (ILD). The e7e7 line matured 6 d earlier than the E7E7 line under natural and ILD photoperiod. An ILD treatment was simulated in growth cabinets with 4 + 12 + 4 h of incandescent light and was compared with 12-, 20-, and 24-h photoperiods. All lines flowered early and similarly under 12-h photoperiod. The 4 + 12 + 4-h treatment delayed flowering less than the 20-h photoperiod. Flowering was not delayed further when the photoperiod was extended from 20 to 24 h. The E7E7 lines were sensitive to light quality. They did not perceive long days of high R:FR light quality, but under natural daylight and under low R:FR light quality, E7 delayed flowering., TIME TO FLOWERING AND MATURITY in soybean is controlled genetically by the E series of loci: E1, E2 (Bernard, 1971), E3 (Buzzell, 1971), E4 (Buzzell and Voldeng, 1980), E5 (McBlain [...]