Soybean Lines Research Articles

Investigating the Role of Soybean Genetic Resistance on the Production of Sclerotinia sclerotiorum Sclerotia.

Sclerotia serve as survival structures for many plant pathogens, including Sclerotinia sclerotiorum, which causes Sclerotinia stem rot (SSR) in soybeans and leads to significant yield losses. While partially resistant soybean varieties are effective in reducing SSR incidence, the relationship between resistance and sclerotial production remains unclear. This study investigated the sclerotial production of two soybean recombinant inbred lines (RILs) with differential levels of SSR resistance under both greenhouse and field conditions. In the greenhouse, three S. sclerotiorum isolates of varying aggressiveness were used to screen the two RILs, revealing differences in disease development and sclerotial characteristics. Under greenhouse conditions, the susceptible RIL resulted in greater SSR development, higher total sclerotia production, and greater sclerotial mass per plant than the resistant RIL. Field trials in 2022 and 2023 with the same two soybean RILs, demonstrated that the susceptible RIL consistently produced more sclerotia than the resistant. Further linear regressions between the SSR incidence (DI, %) and sclerotial mass were examined for the susceptible and resistant RILs, where on the susceptible each 10% increase in DI resulted in 28.5 kg ha-1 of sclerotia produced, and on the resistant RIL each 10% increase in DI resulted in 16.2 kg ha-1. These findings provide new insights into the impact of SSR resistance in soybeans on sclerotial production and highlight the importance of selecting resistant soybean varieties to reduce potential build-up of long-lasting inoculum loads.

Investigating the stability of phenotype, seed components and powdery mildew resistance of the <i>GmMLO</i> edited soybean plants

Previously, utilizing the CRISPR/Cas9 system, we had successfully induced targeted mutations in the GmMLO genes of the Vietnamese elite soybean cultivar ĐT26 for the first time. The mutant lines carried homozygous mutations of four or three GmMLO genes (including GmMLO02, GmMLO19, GmMLO23 and/or GmMLO20) with no pleiotrophic effects and increased powdery mildew resistance in the T3 generation. In this study, we selected two representative lines and evaluated them in the T4 generation to see if their phenotype and resistance were maintained stably. The analysis results of agronomic and yield parameters under the net-house conditions indicated that there were no undesired data in the two mutant lines in comparison with the wild-type. In addition, the major nutritional compositions of the seeds including the fatty acids, free amino acids and crude protein content of the mutant lines were similar to the control line. Importantly, the response to Erysiphe diffusa challenge of the quadruple mutant line was still maintained at a moderate resistance level (grade 2.5) as compared to the moderate infection level of the wild-type and the triple mutant line (approximately grade 4). These results again demonstrate that inducing targeted mutations of four tested GmMLO genes via the CRISPR/Cas9 system is not accompanied with undesired traits, and the quadruple mutant line is the potential one with increased powdery mildew resistance maintained stably through generations. This soybean mutant line will be valuable material for further breeding programs as well as being able to be propagated for production.

Characterization of high protein soybean using mass spectrometry based proteomic and metabolomic analyses.

We have created several high protein (HPBL) and low protein breeding lines (LPBL) by crossing between NC-Raleigh and PI407228. The NC-Raleigh is a low protein cultivar widely grown in North Carolina with excellent yield potential and a high protein wild soybean (Glycine soja) with low yield. We analyzed the F6 generation of this cross for protein and oil compositions using near-infrared spectroscopy (NIR). Two soybean lines HPBL and LPBL were selected for biochemical analysis using mass spectrometry-based proteomic and metabolomic techniques. We identified 4,538 proteins and 267 metabolites in these lines. The HPBL showed the enrichment of proteins associated with protein synthesis, processing, and storage in addition to higher content of primary and secondary metabolites. The mapping of metabolites on the global metabolic pathways revealed the increased protein content in the HPBL that may have resulted from increased arginine content routed from citrulline-argininosuccinic acid. This information will be useful for breeders and biotechnologists to produce a value-added soybean trait.

Glycine soja, PI424025, is a valuable genetic resource to improve soybean seed-protein content and composition.

Soybean seed-protein content and composition is important because it contributes over half the value of this $61 billion crop. Historic negative correlation between seed-protein content and oil have been reported. Similarly, negative correlation between seed-protein content and yield have been reported but may be at least in part mitigated by increasing the genetic diversity of the elite soybean germplasm. Improvements in amino acid composition of seed-protein would increase the value of soybean meal and protein for animal and human consumption. We have identified a genetic resource in wild soybean germplasm, PI424025B, with elevated seed-protein, elevated cysteine in the seed and increased sulfur content in the seed. We have developed a population of Recombinant Inbred Lines derived from a cross between NC-Raleigh and PI424025B. We evaluated the carbon, nitrogen and sulfur (C, N and S) content of seeds from the progeny, the parents and other high-seed protein soybean lines. N content and C/N (ratio of C to N) were well correlated with protein content measured by NIR. PI424025B had a N content comparable to high-protein soybean lines and a superior N/S. These traits were inherited by some of the progeny. Quantitative Trait Loci (QTL) associated with high-seed protein were identified on chr2, chr20 and chr15 and colocalizes with well characterized loci on chr 15 and chr 20 known to affect seed-protein content and quality. A potentially unique QTL was identified on Chr15. Unlike the chr20 QTL, the chr15 QTL improved S content relative to N content and was superior to other high seed-protein phenotypes tested. These data indicate that PI424025B is a valuable resource to diversify the genetics of soybean while improving soybean seed-protein content and composition.

USING RETROSPECTIVE DATA TO ASSESS THE UNCERTAINTY OF INDICATORS OF BIOLOGICAL SAFETY OF FOOD AND FEED RAW MATERIALS

The results of the analysis of the advantages and disadvantages of the use of retrospective data for the implementation of the evaluation of uncertainty in the measurement of indicators of biological safety of food and feed raw materials are given. The model measurement procedure used quantitative determination of genetically modified organisms by means of polymerase chain reaction in real time 250 measurement results of certified reference material with a content of 0.1% genetically modified soybean line obtained under conditions of intra-laboratory reproducibility and 10 results of relevant inter-laboratory comparisons with the participation accredited provider. The suitability of retrospective data was assessed by the Shapiro-Wilk criterion and statistical controllability analysis using standardized score charts and modified Shewhart charts, uncertainty by 4 methods described in general and branch international guidelines and regulations. The results of using a combination of modified Shewhart maps demonstrate the acceptability of this approach for establishing the suitability of retrospective measurement results as input data for uncertainty assessment. By integrating additional "fitness limits" to a set of standardized control limits, this analysis acquires the ability to simultaneously establish not only stability, through the interpretation of geometric patterns, but also compliance with specific criteria. Using this approach, objective evidence of the suitability of retrospective data for estimating measurement uncertainty was obtained. The distribution of retrospective data obtained under conditions of intralaboratory reproducibility is assumed to be normal. As a result of the assessment of statistical controllability and compliance with the established criteria, objective evidence of the suitability of the data for uncertainty assessment was obtained. Analysis of uncertainty intervals of subgroups with the volume of 25 measurements, using 4 assessment methods, demonstrated significant variability in the results of measuring biological safety indicators. The uncertainty interval could narrow or widen by almost 100% of the value within fifty measurements. Median values obtained using different uncertainty estimation methods were 2.69%, 22.69%, 39.23, and 43.08%. This variability is due to the limited coverage of sources of uncertainty, which is inherent in each of the analyzed methods. The most optimal method is the evaluation based on the routine measurement of the certified reference material. Retrospective results of routine measurement of certified reference material and interlaboratory comparisons are an effective source of input data for assessing the uncertainty of the results of measuring biological safety indicators of agricultural raw materials. There is a need for further research to establish an assessment model that will provide an opportunity to take into account the optimal number of influential sources of uncertainty that are inherent in biological systems and cannot be simultaneously taken into account using existing approaches offered by standard assessment methods.

Investigating the Role of Known Arabidopsis Iron Genes in a Stress Resilient Soybean Line.

Genes involved in iron deficiency responses have been well characterized in Arabidopsis thaliana, but their roles in crop species have not been well explored. Reliance on model species may fail to identify novel iron stress mechanisms present within crop species, likely selected by hundreds of years of selection. Fiskeby III (PI 438471) is a soybean line from Sweden that demonstrates high levels of resilience to numerous stresses. Earlier Fiskeby III studies have identified a suite of genes responding to iron deficiency stress in Fiskeby III that are also associated with Arabidopsis iron deficiency responses. We were interested in determining how canonical iron genes function in Fiskeby III under normal and iron stress conditions. To investigate this, we used virus-induced gene silencing to knock down gene expression of three iron deficiency response genes (FER-like iron deficiency induced transcription factor (FIT), elongated hypocotyl 5 (HY5) and popeye (PYE)) in Fiskeby III. Analyses of RNAseq data generated from silenced plants in iron-sufficient and -deficient conditions found silencing FIT and HY5 altered general stress responses but did not impact iron deficiency tolerance, confirming Fiskeby III utilizes novel mechanisms to tolerate iron deficiency stress.

Morphological Characterization-based Optimal Trait Selection for Improving Yield and Stability of Soybean (Glycine max L. Merrill)

The present investigation was convened during kharif, 2022 (July–October), rabi-Summer 2023 (January–May) and kharif, 2023 (July–October) at J.N.K.V.V., Jabalpur, Madhya Pradesh, India to characterize 165 diverse soybean germplasm lines in pursuance of DUS (Distinctness, Uniformity, and Stability) guidelines focusing on integrating optimal morphological traits to pre-fine soybean crop improvement. The study revealed significant variation among soybean genotypes. The hypocotyl color, controlled by a monogenic trait, was found in 77 genotypes, closely associated with violet flower color, whereas non-pigmented hypocotyls present in 88 genotypes were linked to white flowers. Growth habits were categorized as determinate (59), semi-determinate (103), and indeterminate (3), demonstrating that semi-determinate genotypes offer balanced resource allocation and reduced lodging. Most genotypes displayed medium flowering time (159) and medium plant height (134). Leaf shape was predominantly pointed ovate (121), with lanceolate leaves associated with higher number of seeds-1 pod. The presence of dark green leaves in 108 genotypes indicated higher chlorophyll content and enhanced photosynthetic efficiency to strengthen plant type. Semi-erect growth habit was prevalent in 152 genotypes, providing better soil coverage and moisture retention, while 13 genotypes showed erect growth. Pod pubescence was observed in 106 genotypes, offering protection against pests. These traits are found stable across the environment and may be used as an identification key for different varieties and donor germplasm lines.

Genetic variability increase by gamma irradiation of soybean seeds

The increase of genetic variability by the appearance of new genes of agronomic interest may be favored by the use of gamma radiation. The objective of this study was to evaluate different doses of gamma irradiation on dry seeds of VX04-5692 soybean line, aiming to increase the genetic variability and, with this, the identification of possible mutant plants. The doses of 0, 50, 150 and 250 Gy of gamma radiation were applied from a60Co source. The newly irradiated seeds were sown in the field, giving rise to the M1 cycle. Selected plants originated the M2 cycle. The number of seedlings was counted on the 21st day after sowing. Ten plants of each row were identified and evaluated for the various agronomic characteristics and for chemical composition. The data were submitted to analysis of variance. The F test was applied and the results were presented by boxplots and biplot (canonical variables). There was effect of gamma radiation doses at plant height at full bloom and maturity, number of nodes, pods with one seed and seeds per pod. The use of gamma radiation increases the variability in soybean, with consequent increase in the probabilities of identification of new mutants and gains in the chemical composition, useful for breeding programs that aim at better agronomic performance and gains in oil and protein contents. More satisfactory results in the generation of variability are obtained by the application of gamma radiation on soybean dry seeds between 50 and 150 Gy.

Weighted Gene Co-Expression Network Analysis Uncovers Critical Genes and Pathways Involved in Soybean Response to Soybean Mosaic Virus

Background: Soybean mosaic virus (SMV) is a globally prevalent and detrimental virus that belongs to the Potyvirus genus. Pathogenic viruses of this genus are typically linear in shape, with dimensions ranging between 630 and 750 nm, and are composed of single-stranded RNA and proteins. We have developed an SMV-resistant soybean line, Dongnong 93-046, which has no significant changes in disease resistance identification in the adult plants and has neat grains with no obvious brown or black markings. To explore the defense mechanisms of soybean against SMV, we performed comparative transcriptomic sequencing of the leaves between the Dongnong 93-046 inoculated with SMV at 8 h (T) and the non-inoculated control (C) on the HiSeq2000 platform. In addition, we performed non-targeted metabolomic sequencing of leaves from the treatment and control groups. Results: We identified a total of 41,189 differentially expressed genes (DEGs). A total of 9809 differentially expressed genes (DEGs) met the criteria of |Log2FC (Fold Change)| ≥ 1 and adjusted p-value ≤ 0.001. Among the 41,189 DEGs identified, 9196 exhibited FPKM values greater than 10. KEGG pathway enrichment analysis of the 9809 DEGs revealed significant enrichment of genes involved in resistance-related pathways such as plant–pathogen interaction, linoleic acid metabolism, mitogen-activated protein kinase (MAPK) signaling pathway, and plant hormone signaling transduction. Functional analysis using MapMan software identified multiple DEGs that were associated with pathways such as jasmonate synthesis and phenylpropanoid biosynthesis. Weighted gene co-expression network analysis (WGCNA) using the differential metabolites and the 9196 DEGs revealed a strong correlation between gene clusters within the Turquoise module and the content of jasmonate-related metabolites. Further functional enrichment analysis of the 894 genes within the gene clusters showed a significant and repeated enrichment of pathways related to plant–pathogen interaction, linoleic acid metabolism, and plant hormone signaling transduction. Subsequent focused pathway analysis identified key genes involved in plant hormone signaling transduction pathways, such as the jasmonate ZIM domain protein Glyma.16G010000, the gene Glyma.01G235600 encoding the essential diterpene reductase required for jasmonate synthesis in the jasmonate biosynthesis pathway, and the transcription factor Glyma.02G232600 involved in the plant–pathogen interaction pathway, among others. This study provides a theoretical framework for understanding the resistance mechanism of soybean cultivar Dongnong 93-046 against the SMV N1 strain, offers potential gene resources for breeding soybean varieties with resistance to SMV, and paves the way for new strategies to control SMV infection, enhance resistance, and improve crop yield and quality.

Impact of Sulfur Deficiency and Excess on the Growth and Development of Soybean Seedlings.

Sulfur is a critical element for plant growth and development, serving as a component of amino acids (cysteine and methionine), iron-sulfur clusters, proteins, glutathione, coenzymes, and auxin precursors. Deficiency or low concentrations of sulfur in the soil can lead to significant growth retardation in plants. The objective of our study was to examine the effects of sulfur (S) deficiency and excess on morphological symptoms, sulfur and nitrogen (N) metabolism, as well as antioxidant activity in soybean. We found that S starvation decreased the fine root length, biomass, and activity, and the chlorophyll content was reduced, while excess sulfur promotes lateral root growth. In contrast to sulfur excess, sulfur deficiency inhibits N and S metabolism levels in both subsurface and above-ground parts, and induced the expression of some sulfur transporters (SULTRs). In this study, we created soybean hairy root lines overexpressing the SULTR gene (GmSULTR2;1a) to observe metabolic changes following sulfur deficiency treatment. The results showed that GmSULTR2;1a saved the sulfur-deficient phenotype, and the antioxidant enzyme activity was much higher than that of the wildtype in the absence of sulfur. Our study revealed the important role of sulfur element in soybean growth and development and the regulation of sulfur deficiency by GmSULTR2;1a.

High-protein soybean lines with stable seed protein content under heat and drought stresses

A significant factor determining the value of soybean is protein content, in addition to its importance as an oilseed. Increasing the seed protein content in soybean will make it a more valuable food and feedstock and enhance its importance in the international market. Due to this reason, developing high-protein soybean varieties is gaining increased industrial interest. To ensure profitable production, the stability of the high-protein trait needs to be verified under environmental stresses. The objectives of this study were to test whether the high-protein soybean genotypes can maintain their high seed protein content under heat and drought stresses imposed during seed filling and to assess the changes in their oil composition under stress conditions. The changes in seed protein and oil contents and oil composition of the high-protein lines NLM09–77, N14-7017, and N16-9924 under heat and drought stresses were assessed and compared against those of a recently released high-yielding, high-protein variety Benning HP; elite cultivars NC-Dunphy, NC-Raleigh, and NC-Dilday; low-protein breeding lines N11–9228 and N09-2505; heat-tolerant line DS25-1; and heat-susceptible line DT97-4290. We found that the high-protein genotypes NLM09–77, N16–9924, N14-7017, and Benning HP maintained their high seed protein contents under heat and drought stresses (46–55 %). Among them, NLM09–77 and N14-7017 were unique with no apparent negative relationship between the seed protein and oil contents. In terms of oil composition, N14-7017, NLM09-77, and Benning HP were similar to the elite cultivars NC-Dunphy and NC-Dilday. Additionally, the high-protein genotypes N14-7017, NLM09-77, and Benning HP did not exhibit any yield drag (2993–3150 kg ha−1vs 3289–3368 kg ha−1 for the elite cultivars). Taken together, our study demonstrates the usefulness of the advanced breeding lines NLM09–77 and N14-7017 and cultivar Benning HP for developing new varieties with enhanced nutritional value under climate change-associated stresses.

Screening Germplasms and Detecting Quantitative Trait Loci for High Sucrose Content in Soybean

Sucrose is a desirable component of processed soybean foods and animal feed, and thus, its content is used as an important characteristic for assessing the quality of soybean seeds. However, few studies have focused on the quantitative trait loci (QTLs) associated with sucrose regulation in soybean seeds. This study aims to measure the sucrose content of 1014 soybean accessions and identify genes related to high sucrose levels using QTL analysis. Colorimetric analysis based on the enzymatic reaction of invertase (INV) and glucose oxidase (GOD) was employed to test the germplasms. A total of six high-sucrose genetic resources (IT186230, IT195321, IT263138, IT263276, IT263286, and IT276521) and two low-sucrose genetic resources (IT025668 and IT274054) were identified. Two F2:3 populations, IT186230 × IT025668 and Ilmi × IT186230, were then established from these germplasms. QTL analysis identified four QTLs (qSUC6.1, qSUC11.1, qSUC15.1, and qSUC17.1), explaining 7.3–27.6% of the phenotypic variation in the sugar content. Twenty candidate genes were found at the four QTLs. Notably, Glyma.17G152300, located in the qSUC17.1 QTL region, exhibited a 17-fold higher gene expression in the high-sucrose germplasm IT186230 compared to the control germplasm Ilmi, confirming its role as a major gene regulating the sucrose content in soybean. These results may assist in marker-assisted selection for breeding programs that aim to develop soybean lines with a higher sucrose content.

Genotype x environment interaction and yield stability of soybean (Glycine max l.) genotypes in multi-environment trials (METs) in Nigeria

Genotype × environment interaction (GEI) poses a critical challenge to plant breeders by complicating the identification of stable variety (ies) for performance across diverse environments. GGE biplot and AMMI analyses have been identified as the most effective and appropriate statistical techniques for identifying stable and high-performing genotypes across diverse environments. The objective of this study was to identify widely adapted and high-yielding soybean genotypes from Multi-Locational Trials (MLTs) using GGE and AMMI biplot analyses. Fifteen IITA-bred elite soybean lines and three standard checks were evaluated for stability of performance in a 3 × 6 alpha lattice design with three replications across seven locations in Nigeria. Significant (p < 0.001) differences were detected among genotypes, environments, and GEI for grain yield, which ranged between 979.8 kg ha−1 and 3645 kg ha−1 with a mean of 2324 kg ha−1. To assess the stability of genotypes, analyses were conducted using the general linear method, GGE, and the Additive Main Effect and Multiplicative Interaction (AMMI) approach, as well as WAAS and ASV rank indices. In the GGE biplot model, the first two principal components accounted for 67.4 % of the total variation, while in the AMMI model, the first two Interaction Principal Component Axes (IPCA1 and IPCA2) explained 73.20 % and 11.40 % of the variation attributed to genotype by environment interaction, respectively. GGE biplot identified G10 and G16 as the most stable and productive genotypes, while WAASB index revealed G16, G10, G9, G4 and G2 as the most adaptive, stable and productive genotypes across locations, and ASV identified G9, G13, G4, G14 and G10 as the most stable and productive.Consequently, genotypes G2, G4, G9, G10 and G16 displayed outstanding and stable grain yield performance across the test locations and are, therefore, recommended for release as new soybean varieties suitable for cultivation in the respective mega environment where they performed best. More importantly, the two genotypes are recommended for recycling as sources of high-yield and yield stability genes, and as parental lines for high-yield and stable performance for future breeding and genomic selection.

Utility of Arabidopsis KASII Promoter in Development of an Effective CRISPR/Cas9 System for Soybean Genome Editing and Its Application in Engineering of Soybean Seeds Producing Super-High Oleic and Low Saturated Oils.

This study reports the use of the Arabidopsis KASII promoter (AtKASII) to develop an efficient CRISPR/Cas9 system for soybean genome editing. When this promoter was paired with Arabidopsis U6 promoters to drive Cas9 and single guide RNA expression, respectively, simultaneous editing of the three fatty acid desaturase genes GmFAD2-1A, GmFAD2-1B, and GmFAD3A occurred in more than 60% of transgenic soybean lines at T2 generation, and all the triple mutants possessed desirable high-oleic traits. In sharp contrast, not a single line underwent simultaneous editing of the three target genes when AtKASII was replaced by the widely used AtEC1.2 promoter. Furthermore, our study showed that the stable and inheritable mutations in the high-oleic lines did not alter the overall contents of oil and protein or amino acid composition while increasing the oleic acid content up to 87.6% from approximately 23.8% for wild-type seeds, concomitant with 34.4- and 3.7-fold reductions in linoleic and linolenic acid, respectively. Collectively, this study demonstrates that the AtKASII promoter is highly promising for optimization of the CRISPR/Cas9 system for genome editing in soybean and possibly beyond.

Redesigning soybean with improved oil and meal traits.

Soybean seed oil and meal composition traits can be combined without interference to provide additional value to the crop. Soybean [Glycine max (L.) Merr.] is an important crop worldwide; its overall value comes from seed oil and high protein meal. The development of soybean varieties with allele combinations for improved oil and meal quality is expected to provide a compositional value bundle for soybean. The high oleic and low linolenic acid seed oil trait (HOLL; > 70% oleic and < 3% linolenic acid) is targeted to optimize the health and functional properties of soybean oil. For soybean meal, metabolizable energy is improved by altering the carbohydrate profile with increased sucrose and decreased anti-nutritional factors, raffinose family of oligosaccharides (RFOs). Previous research identified four variant alleles of fatty acid desaturase (FAD) genes and two raffinose synthase (RS) genes necessary for the HOLL trait in soybean oil and Low or Ultra-Low (UL) RFO traits in soybean meal, respectively. We employed a molecular marker-assisted breeding approach to combine six alleles conferring the desired soybean oil and meal value traits. Eight environment field trials were conducted with twenty-four soybean lines to evaluate phenotypic interactions among the variant alleles of FAD and RS genes. The results indicated that the four FAD gene alleles conditioned the HOLL fatty acid profile of the seed oil regardless of the allele status of the RS genes. Independent of the allele combination of the FAD genes, soybean with two variant alleles of the RS genes had the desired RFO trait in the seeds. The results confirm the feasibility of soybean variety development with this unique combination of oil and meal traits.

Genes of photoperiod sensitivity and early maturity E1-E4: dynamics of soybean growth in different daylength conditions

Background. Morphometric indicators are crucial for evaluating the development and productivity of soybeans. They are influenced by genetic and environmental factors. The use of nearly isogenic soybean lines is a convenient model for determining the impact of early maturity genes and daylength on growth indicators. The aim of this study was to determine the influence of different daylengths and early maturity genes on soybean morphometric indicators under conditions of the temperate zone (at the latitude of Kharkiv – 50° N). Materials and Methods. The study involved nearly isogenic soybean lines of the “Clark” cultivar with varying sensitivity to daylength. The research covers the results of field experiments over three seasons using different soybean lines. After reaching the V3 stage, some plants were subjected to short-day conditions for 14 days. Morphological indicators of ten plants per experimental variant were determined: plant height, dry weight, leaf number, and leaf surface area of soybean plants. Morphometric measurements were taken on the day of the beginning of different daylength treatments and on days 7, 14 and 21. The study results are presented as the mean values of the investigated parameters (plant height, dry weight, number of leaves and leaf surface area of soybean plants). Results. It was shown that under long-day conditions, dominant alleles of the E1 and E3 genes increased the dry weight of plants, while the dominant allele E2 increased plant height. The dominant allele E4 had no significant effect on plant height and weight indicators of soybean plants. Plants with dominant alleles of genes E1-E4 under long-day conditions had smaller leaf area compared to lines with recessive alleles of these genes. Conclusions. The obtained results on the relationships between genetic and environmental factors in influencing soybean plant height, weight, and leaf area can be useful in improving soybean yield and selecting cultivars that will be productive in high latitude conditions.

DNA methylation analysis reveals local changes in resistant and susceptible soybean lines in response to Phytophthora sansomeana.

Phytophthora sansomeana is an emerging oomycete pathogen causing root rot in many agricultural species including soybean. However, as of now, only one potential resistance gene has been identified in soybean, and our understanding of how genetic and epigenetic regulation in soybean contributes to responses against this pathogen remains largely unknown. In this study, we performed whole genome bisulfite sequencing (WGBS) on two soybean lines, Colfax (resistant) and Williams 82 (susceptible), in response to P. sansomeana at two time points: 4 and 16 hours post-inoculation to compare their methylation changes. Our findings revealed that there were no significant changes in genome-wide CG, CHG (H = A, T, or C), and CHH methylation. However, we observed local methylation changes, specially an increase in CHH methylation around genes and transposable elements (TEs) after inoculation, which occurred earlier in the susceptible line and later in the resistant line. After inoculation, we identified differentially methylated regions (DMRs) in both Colfax and Williams 82, with a predominant presence in TEs. Notably, our data also indicated that more TEs exhibited changes in their methylomes in the susceptible line compared to the resistant line. Furthermore, we discovered 837 DMRs within or flanking 772 differentially expressed genes (DEGs) in Colfax and 166 DMRs within or flanking 138 DEGs in Williams 82. These DEGs had diverse functions, with Colfax primarily showing involvement in metabolic process, defense response, plant and pathogen interaction, anion and nucleotide binding, and catalytic activity, while Williams 82 exhibited a significant association with photosynthesis. These findings suggest distinct molecular responses to P. sansomeana infection in the resistant and susceptible soybean lines.

Identification of QTLs and candidate genes for water-soluble protein content in soybean seeds

Soybean represents a vital source of premium plant-based proteins for human nutrition. Importantly, the level of water-soluble protein (WSP) is crucial for determining the overall quality and nutritional value of such crops. Enhancing WSP levels in soybean plants is a high-priority goal in crop improvement. This study aimed to elucidate the genetic basis of WSP content in soybean seeds by identifying quantitative trait loci (QTLs) and set the foundation for subsequent gene cloning and functional analysis. Using 180 F10 recombinant inbred lines generated by crossing the high-protein soybean cultivar JiDou 12 with the wild variety Ye 9, our researcher team mapped the QTLs influencing protein levels, integrating Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and gene expression profiling to identify candidate genes. During the 2020 and 2022 growing seasons, a standard bell-shaped distribution of protein content trait data was observed in these soybean lines. Eight QTLs affecting protein content were found across eight chromosomes, with LOD scores ranging from 2.59 to 7.30, explaining 4.15–11.74% of the phenotypic variance. Notably, two QTLs were newly discovered, one with a elite allele at qWSPC-15 from Ye 9. The major QTL, qWSPC-19, on chromosome 19 was stable across conditions and contained genes involved in nitrogen metabolism, amino acid biosynthesis, and signaling. Two genes from this QTL, Glyma.19G185700 and Glyma.19G186000, exhibited distinct expression patterns at maturity, highlighting the influence of these genes on protein content. This research revealed eight QTLs for WSP content in soybean seeds and proposed a gene for the key QTL qWSPC-19, laying groundwork for gene isolation and enhanced soybean breeding through the use of molecular markers. These insights are instrumental for developing protein-rich soybean cultivars.

Evaluation of Physiological and biochemical traits of selected soybean line in Makurdi

Twelve genotypes of soybean were selected for physiological and seed biochemical evaluations at Joseph Sarwuan Tarka University, Makurdi. These seeds were collected from NCRI Badegi; Niger State- Nigeria. Ten of these genotypes S1075-6-93, S1179-6-58, S1239-6-135, S1240-6-288, S1252-6-277, S1252-6-156, S1268-6-15, S1273-6-65, S1365-6L-20 and SC SENTINEL is newly introduced to Makurdi while SC SIGNA and SLO1 used as checks have been released. The seed crop field was laid out in a Randomized Complete Block Design (RCBD) with three replications in 4-rows of 5m long. Seed samples were collected and subjected to seed quality tests at the Department of Plant Breeding and Seed Science Laboratory of the University. Data were collected on germination count which was expressed as germination percentage and its (germination rate and germination rate index) were consequentially obtained. These seeds were also subjected to proximate analysis and percentage protein, fat, ash, moisture content and crude fibre were determined using soxhlet method. The result showed that significant differences existed for germination rate index (GRI) and germination index (GI) while other seedling traits were not different in magnitude from each other. Protein was highest in three varieties (S1075-6-93, S1239-6-135 and S1252-6-156) with 40.25%, respectively and significantly different from others and the checks. SC SENTINEL had the least protein content (37.19) and highest oil content (20.82). Meanwhile, genotype S1239-6-135 had the least oil content (18.83). Compositionally, an inverse relationship existed between protein oil in genotypes studied. Biochemical composition has more effect on seed quality of these soybean genotypes than physiological traits. Genotypes (S1075-6-93, S1239-6-135 and S1252-6-156) had higher protein content than the checks. Also, Sc SENTINEL, S1365-6L-20, S1273-6-65, S1268-6-15 and S1240-6-288 had higher oil content than the checks. Soybean oil producers could use SC SENTINEL for their productions and (S1075-6-93, S1239-6-135 and S1252-6-156) could be used for protein-based products.

Breeding a black soybean line with green cotyledon free from lectin, KTI, P34, lipoxygenase, and stachyose

Breeding a black soybean line with green cotyledon free from lectin, KTI, P34, lipoxygenase, and stachyose