Soybean Germplasm Research Articles

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.

Transcription-Aided Selection (TAS) for Crop Disease Resistance: Strategy and Evidence

A transcription-aided selection (TAS) strategy is proposed in this paper, which utilizes the positive regulatory roles of genes involved in the plant immunity pathways to screen crops with high disease resistance. Increased evidence has demonstrated that upon pathogen attack, the expression of diverse genes involved in salicylic acid (SA)-mediated SAR are differentially expressed and transcriptionally regulated. The paper discusses the molecular mechanisms of the SA signaling pathway, which plays a central role in plant immunity, and identifies differentially expressed genes (DEGs) that could be targeted for transcriptional detection. We have conducted a series of experiments to test the TAS strategy and found that the level of GmSAGT1 expression is highly correlated with soybean downy mildew (SDM) resistance with a correlation coefficient R2 = 0.7981. Using RT-PCR, we screened 2501 soybean germplasms and selected 26 collections with higher levels of both GmSAGT1 and GmPR1 (Pathogenesis-related proteins1) gene expression. Twenty-three out of the twenty-six lines were inoculated with Peronospora manshurica (Pm) in a greenhouse. Eight showed HR (highly resistant), four were R (resistant), five were MR (moderately resistant), three were S (susceptible), and three were HS (highly susceptible). The correlation coefficient R2 between the TAS result and Pm inoculation results was 0.7035, indicating a satisfactory consistency. The authors anticipate that TAS provides an effective strategy for screening crops with broad-spectrum and long-lasting resistance.

Diversity Analysis and Comprehensive Evaluation of 101 Soybean (Glycine max L.) Germplasms Based on Sprout Quality Characteristics.

Soybean sprouts are a common culinary vegetable due to their high nutrition and tasty flavors. To select soybean varieties with excellent sprout quality, 101 soybean materials were collected from different regions of China, and eight sprout quality parameters were determined for overall evaluation. The results showed that eight sprout quality parameters achieved varying degrees of difference and correlation. Based on the principal component analysis (PCA), three principal components were extracted, with a cumulative contribution rate of 78.314%. Further, the comprehensive evaluation value (D) of soybean sprout quality was calculated by membership function analysis based on PCA, and the quality of soybean sprouts was ranked accordingly. Subsequently, a regression equation for the prediction of soybean sprout quality was established using a stepwise regression analysis, and the model showed a good prediction performance (correlation coefficient of prediction > 0.8; residual predictive deviation > 2.0). On these grounds, it was proposed that the quality of soybean sprouts could be comprehensively predicted by four parameters: hypocotyl length, edible rate, 100-seed weight, and total isoflavone content and saponin content. In conclusion, this study provides excellent varieties for soybean sprout production and new variety breeding, and it provides an important reference for the prediction of soybean sprout quality.

Morpho-physiological traits and stress indices reveal divergence in early-stage salt stress response in elite soybean germplasm

This study assessed the salt stress response of seventy soybean genotypes by exposing seedlings to sodium chloride (NaCl) concentrations of 0, 75, 100, and 125 mM. Salinity stress significantly reduced root length, shoot length, fresh and dry root/shoot weight, and root/shoot ratio. A total of 62 genotypes germinated at 125 mM, showing significant phenotypic variation in traits such as root length, shoot length, fresh shoot weight, and dry shoot weight. Pearson’s correlation analysis revealed a strong positive correlation between most morpho-physiological traits, suggesting their interdependence. Eight salinity tolerance indices i.e., Fresh Weight Stress Tolerance Index (FWSI), Dry Weight Stress Tolerance Index (DWSI), Root Length Salinity Index (RLSI), Shoot Length Salinity Index (SLSI), Salinity Tolerance Index (STI), Salinity Susceptibility Index (SSI), Tolerance Index (TI), and Percent Reduction (PR) were calculated to assess genotypes response. Na+ concentration and antioxidant activities significantly increased under salt stress compared to the control. The activities of antioxidant enzymes, as well as the levels of reactive oxygen species (ROS) such as H2O2 and O2−, were markedly higher under salt stress compared to the control. Hierarchical cluster analysis grouped genotypes into six clusters, with clusters V and VI comprising genotypes exhibiting higher salt tolerance based on high FWSI, DWSI, and STI values, and low PR, SSI, and TI values. Eight salinity tolerance indices, including Fresh Weight Stress Tolerance Index (FWSI), Dry Weight Stress Tolerance Index (DWSI), Root Length Salinity Index (RLSI), and Salinity Tolerance Index (STI), were used to evaluate the genotypes’ responses. The study revealed that the average FWSI value for all genotypes under treatments was 54.20 ± 12.93. The highest FWSI was recorded for the genotype Black (92.52), followed by NIBGE-224 (84.70) and NIBGE-183 (81.05). In contrast, Malakand-96 had the lowest FWSI (28.49), followed by SPS-10 (32.74) and SPS-08 (34.55). PGRA-91 had the highest STI (0.83), followed by SPS-9 (0.75) and NIBGE-115 (0.72), while NIBGE-335, SPS-24, and Malakand-96 had the lowest STI values. Positive correlations were observed between root length and shoot length (0.69**), shoot length and fresh shoot weight (0.63**), and other related traits. Overall, this study identified promising soybean genotypes with varying degrees of salt tolerance. These findings can be utilized in breeding programs to develop salt-tolerant soybean varieties for salinity-affected agricultural lands.

Advances in Soybean Genetic Improvement.

The soybean (Glycine max) is a globally important crop due to its high protein and oil content, which serves as a key resource for human and animal nutrition, as well as bioenergy production. This review assesses recent advancements in soybean genetic improvement by conducting an extensive literature analysis focusing on enhancing resistance to biotic and abiotic stresses, improving nutritional profiles, and optimizing yield. We also describe the progress in breeding techniques, including traditional approaches, marker-assisted selection, and biotechnological innovations such as genetic engineering and genome editing. The development of transgenic soybean cultivars through Agrobacterium-mediated transformation and biolistic methods aims to introduce traits such as herbicide resistance, pest tolerance, and improved oil composition. However, challenges remain, particularly with respect to genotype recalcitrance to transformation, plant regeneration, and regulatory hurdles. In addition, we examined how wild soybean germplasm and polyploidy contribute to expanding genetic diversity as well as the influence of epigenetic processes and microbiome on stress tolerance. These genetic innovations are crucial for addressing the increasing global demand for soybeans, while mitigating the effects of climate change and environmental stressors. The integration of molecular breeding strategies with sustainable agricultural practices offers a pathway for developing more resilient and productive soybean varieties, thereby contributing to global food security and agricultural sustainability.

Have We Selected for Higher Mesophyll Conductance in Domesticating Soybean?

Soybean (Glycine max) is the single most important global source of vegetable protein. Yield improvements per unit land area are needed to avoid further expansion onto natural systems. Mesophyll conductance (gm) quantifies the ease with which CO2 can diffuse from the sub-stomatal cavity to Rubisco. Increasing gm is attractive since it increases photosynthesis without increasing water use. Most measurements of gm have been made during steady-state light saturated photosynthesis. In field crop canopies, light fluctuations are frequent and the speed with which gm can increase following shade to sun transitions affects crop carbon gain. Is there variability in gm within soybean germplasm? If so, indirect selection may have indirectly increased gm during domestication and subsequent breeding for sustainability and yield. A modern elite cultivar (LD11) was compared with four ancestor accessions of Glycine soja from the assumed area of domestication by concurrent measurements of gas exchange and carbon isotope discrimination (∆13C). gm was a significant limitation to soybean photosynthesis both at steady state and through light induction but was twice the value of the ancestors in LD11. This corresponded to a substantial increase in leaf photosynthetic CO2 uptake and water use efficiency.

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.

Identification of Candidate Genes for Soybean Storability via GWAS and WGCNA Approaches

Soybean (Glycine max (L.) Merr.) is an important crop for both food and feed, playing a significant role in agricultural production and the human diet. During long-term storage, soybean seeds often exhibit reduced quality, decreased germination, and lower seedling vigor, ultimately leading to significant yield reductions in soybean crops. Seed storage tolerance is a complex quantitative trait controlled by multiple genes and is also influenced by environmental factors during seed formation, harvest, and storage. This study aimed to evaluate soybean germplasms for their storage tolerance, identify quantitative trait nucleotides (QTNs) associated with seed storage tolerance traits, and screen for candidate genes. The storage tolerance of 168 soybean germplasms was evaluated, and 23,156 high-quality single nucleotide polymorphism (SNP) markers were screened and analyzed through a genome-wide association study (GWAS). Ultimately, 14 QTNs were identified as being associated with seed storage tolerance and were distributed across the eight chromosomes of soybean, with five QTNs (rs25887810, rs27941858, rs33981296, rs44713950, and rs18610980) being newly reported loci in this study. In the linkage disequilibrium regions of these SNPs, 256 genes were identified. By combining GWAS and weighted gene co-expression network analysis (WGCNA), eight hub genes (Glyma.03G058300, Glyma.04G1921100, Glyma.04G192600, Glyma.04G192900, Glyma.07G002000, Glyma.08G329400, Glyma.16G074600, Glyma.16G091400) were jointly identified. Through the analysis of expression patterns, two candidate genes (Glyma.03G058300, Glyma.16G074600) potentially involved in seed storage tolerance were ultimately identified. Additionally, haplotype analysis revealed that natural variations in Glyma.03G058300 could affect seed storage tolerance. The findings of this research provide a theoretical foundation for understanding the regulatory mechanism underlying soybean storage.

Deciphering the genetic basis of salinity tolerance in a diverse panel of cultivated and wild soybean accessions by genome-wide association mapping

Key messageIn a genome-wide association study involving 269 cultivated and wild soybean accessions, potential salt tolerance donors were identified along with significant markers and candidate genes, such as GmKUP6 and GmWRKY33.Salt stress remains a significant challenge in agricultural systems, notably impacting soybean productivity worldwide. A comprehensive genome-wide association study (GWAS) was conducted to elucidate the genetic underpinnings of salt tolerance and identify novel source of salt tolerance among soybean genotypes. A diverse panel comprising 269 wild and cultivated soybean accessions was subjected to saline stress under controlled greenhouse conditions. Phenotypic data revealed that salt tolerance of soybean germplasm accessions was heavily compromised by the accumulation of sodium and chloride, as indicated by highly significant positive correlations of leaf scorching score with leaf sodium/chloride content. The GWAS analysis, leveraging a dataset of 32,832 SNPs, unveiled 32 significant marker-trait associations (MTAs) across seven traits associated with salt tolerance. These markers explained a substantial portion of the phenotypic variation, ranging from 14 to 52%. Notably, 11 markers surpassed Bonferroni’s correction threshold, exhibiting highly significant associations with the respective traits. Gene Ontology enrichment analysis conducted within a 100 Kb range of the identified MTAs highlighted candidate genes such as potassium transporter 6 (GmKUP6), cation hydrogen exchanger (GmCHX15), and GmWRKY33. Expression levels of GmKUP6 and GmWRKY33 significantly varied between salt-tolerant and salt-susceptible soybean accessions under salt stress. The genetic markers and candidate genes identified in this study hold promise for developing soybean varieties resilient to salinity stress, thereby mitigating its adverse effects.

No Common Candidate Genes for Resistance to Fusarium graminearum, F. proliferatum, F. sporotrichioides, and F. subglutinans in Soybean Accessions from Maturity Groups 0 and I: Findings from Genome-wide Association Mapping.

Seedling diseases and root rot, caused by species of Fusarium, can limit soybean (Glycine max L.) production in the United States. Currently, there are few commercially available cultivars resistant to Fusarium. This study was conducted to assess the resistance of soybean maturity group (MG) accessions from 0 and I to Fusarium proliferatum, F. sporotrichioides, and F. subglutinans, as well as to identify common quantitative trait loci (QTLs) for resistance to these pathogens, in addition to F. graminearum, using a genome-wide association study (GWAS). A total of 155, 91, and 48 accessions from the United States Department of Agriculture (USDA) soybean germplasm collection from MG 0 and I were screened with a single isolate each of F. proliferatum, F. sporotrichioides, and F. subglutinans, respectively, using the inoculum layer inoculation method in the greenhouse. The disease severity was assessed 21 days postinoculation and analyzed using nonparametric statistics to determine the relative treatment effects (RTEs). Eleven and seven accessions showed significantly lower RTEs when inoculated with F. proliferatum and F. subglutinans, respectively, compared with the susceptible cultivar 'Williams 82'. One accession was significantly less susceptible to both F. proliferatum and F. subglutinans. The GWAS conducted with 41,985 single-nucleotide markers identified one QTL associated with resistance to both F. proliferatum and F. sporotrichioides, as well as another QTL for resistance to both F. subglutinans and F. graminearum. However, no common QTLs were identified for the four pathogens. The USDA accessions and QTLs identified in this study can be utilized to selectively breed resistance to multiple species of Fusarium.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Development of simplex and quintuplex RT-PCR for simultaneous detection of soybean viruses

Five simplex and a multiplex-RT-PCR (m-RT-PCR) protocols were developed for detection and differentiation of bean pod mottle virus (BPMV), cherry leaf roll virus (CLRV), raspberry ringspot virus (RpRSV), soybean mosaic virus (SMV) and tomato ringspot virus (ToRSV) infecting soybean. The simplex RT-PCR protocols produced virus-specific amplicons of 538 bp for BPMV, 139 bp for CLRV, 298 bp for RpRSV, 403 bp for SMV, and 282 bp for ToRSV, with sensitivity down to 10−4 diluted cDNA. Further, to detect all the five viruses simultaneously in a single tube a quintuplex RT-PCR protocol was optimized with as low as 10−3 diluted cDNA and 0.05 µM primer. To validate the reliability of the simplex RT-PCR protocol, imported soybean samples were tested by ELISA as well as RT-PCR. The results revealed that the developed protocol could detect the viruses in imported soybean, and found to be efficient than ELISA in resolving ambiguity in detection of seed borne viruses. The developed simplex and quintuplex RT-PCR protocol will be quite helpful for the diagnosis of soybean germplasm co-infected with viruses during the quarantine processing for ensuring virus free long term seed conservation in the National Gene Bank as well as for quarantine certification.

Artificial selection of mutations in two nearby genes gave rise to shattering resistance in soybean

Resistance to pod shattering is a key domestication-related trait selected for seed production in many crops. Here, we show that the transition from shattering in wild soybeans to shattering resistance in cultivated soybeans resulted from selection of mutations within the coding sequences of two nearby genes - Sh1 and Pdh1. Sh1 encodes a C2H2-like zinc finger transcription factor that promotes shattering by repressing SHAT1-5 expression, thereby reducing the secondary wall thickness of fiber cap cells in the abscission layers of pod sutures, while Pdh1 encodes a dirigent protein that orchestrates asymmetric lignin distribution in inner sclerenchyma, creating torsion in pod walls that facilitates shattering. Integration analyses of quantitative trait locus mapping, genome-wide association studies, and allele distribution in representative soybean germplasm suggest that these two genes are primary modulators underlying this domestication trait. Our study thus provides comprehensive understanding regarding the genetic, molecular, and cellular bases of shattering resistance in soybeans.

Variability in predicted deleterious mutations among barley accessions conserved ex situ

AbstractUnderstanding the genetic cost for long‐term conservation of more than 7 million plant germplasm accessions in 1750 genebanks worldwide requires knowledge about the extent and variation of deleterious mutations within and among conserved germplasm collections. Our recent study revealed a wide range of mutations predicted to be deleterious to gene function and averaged sample‐wise mutation burden per deleterious locus across barley, wheat, oat, soybean, maize, rapa, and sunflower germplasm collections. Here we report the extent and variation of predicted deleterious mutations among nine accessions of a barley (Hordeum vulgare L.) collection from an RNA‐Seq analysis of 16 individual samples of each accession. The assayed accessions were found to vary significantly in the number and proportion of single nucleotide polymorphisms (SNPs) predicted to be deleterious mutations (ranging from 242 to 314 with a mean of 270 and from 0.00073 to 0.00099 with a mean of 0.00086, respectively). Similarly, a significant variation was also observed in the averaged sample‐wise mutation burden estimates per deleterious locus, ranging from 0.541 to 0.747 with a mean of 0.681. Cultivar accessions had higher averages in the proportions of the predicted deleterious SNPs and in the averaged sample‐wise mutation burden estimates than landrace accessions (0.00090 vs. 0.00082 and 0.695 vs. 0.663, respectively). The estimates of deleterious base‐substitution mutations (×10−8) for the nine accessions varied from 0.313 to 0.406 with a mean of 0.349. These within‐collection findings are useful for understanding the genetic cost in conserved germplasm and have implications for long‐term germplasm management and conservation.

Genetic diversity and genome-wide association study of partial resistance to Sclerotinia stem rot in a Canadian soybean germplasm panel.

Developing genetically resistant soybean cultivars is key in controlling the destructive Sclerotinia Stem Rot (SSR) disease. Here, a GWAS study in Canadian soybeans identified potential marker-trait associations and candidate genes, paving the way for more efficient breeding methods for SSR. Sclerotinia stem rot (SSR), caused by the fungal pathogenSclerotinia sclerotiorum, is one of the most important diseases leading to significant soybean yield losses in Canada and worldwide. Developing soybean cultivars that are genetically resistant to the disease is the most inexpensive and reliable method to control the disease. However, breeding for resistance is hampered by the highly complex nature of genetic resistance to SSR in soybean. This study sought to understand the genetic basis underlying SSR resistance particularly in soybean grown in Canada. Consequently, a panel of 193 genotypes was assembled based on maturity group and genetic diversity as representative of Canadian soybean cultivars. Plants were inoculated and screened for SSR resistance in controlled environments, where variation for SSR phenotypic response was observed. The panel was also genotyped via genotyping-by-sequencing and the resulting genotypic data were imputed using BEAGLE v5 leading to a catalogue of 417K SNPs. Through genome-wide association analyses (GWAS) using FarmCPU method with threshold of FDR-adjustedp-values < 0.1, we identified significant SNPs on chromosomes 2 and 9 with allele effects of 16.1 and 14.3, respectively. Further analysis identified three potential candidate genes linked to SSR disease resistance within a 100Kb window surrounding each of the peak SNPs. Our results will be important in developing molecular markers that can speed up the breeding for SSR resistance in Canadian grown soybean.

Joint GWAS and WGCNA Identify Genes Regulating the Isoflavone Content in Soybean Seeds.

Isoflavone is a secondary metabolite of the soybean phenylpropyl biosynthesis pathway with physiological activity and is beneficial to human health. In this study, the isoflavone content of 205 soybean germplasm resources from 3 locations in 2020 showed wide phenotypic variation. A joint genome-wide association study (GWAS) and weighted gene coexpression network analysis (WGCNA) identified 33 single-nucleotide polymorphisms and 11 key genes associated with soybean isoflavone content. Gene ontology enrichment analysis, gene coexpression, and haplotype analysis revealed natural variations in the Glyma.12G109800 (GmOMT7) gene and promoter region, with Hap1 being the elite haplotype. Transient overexpression and knockout of GmOMT7 increased and decreased the isoflavone content, respectively, in hairy roots. The combination of GWAS and WGCNA effectively revealed the genetic basis of soybean isoflavone and identified potential genes affecting isoflavone synthesis and accumulation in soybean, providing a valuable basis for the functional study of soybean isoflavone.

Soybean pod shattering resistance allele pdh1 and marker-assisted selection.

Pod shattering is a major production constraint of soybean [Glycine max (L.)]. The objectives of this study were to (i) estimate heritability for pod shattering resistance, (ii) determine the frequency of the pod shattering resistance allele pdh1 in the International Institute for Tropical Agriculture (IITA) soybean germplasm and Zambian commercial varieties, and (iii) determine the effectiveness of the DNA marker for the pod shattering resistance allele pdh1. A total of 59 genotypes were evaluated for pod shattering in field trials conducted in Malawi and Zambia and genotyped with a marker for pdh1. TGx2002-8FM and TGx2002-9FM were the most resistant among genotypes in early and medium maturity classes and can be used for genetic enhancement of pod shattering resistance in these specific maturity classes. Narrow sense heritability estimates for pod shattering ranged from 0.27 to 0.80. Of the 59 genotypes, 57 (96.6%) carried the resistance allele pdh1 while only two genotypes (3.6%) carried the susceptible allele, suggesting near-fixation of the resistance allele pdh1 in the IITA germplasm. The marker for pdh1 was highly effective in selecting resistant genotypes.

CRISPR/CasRx-mediated resistance to Soybean mosaic virus in soybean

Soybean mosaic virus (SMV), an RNA virus, is the most common and destructive pathogenic virus in soybean fields. The newly developed CRISPR/Cas immune system has provided a novel strategy for improving plant resistance to viruses; hence, this study aimed to engineer SMV resistance in soybean using this system. Specifically, multiple sgRNAs were designed to target positive- and/or negative-sense strands of the SMV HC-Pro gene. Subsequently, the corresponding CRISPR/CasRx vectors were constructed and transformed into soybeans. After inoculation with SMV, 39.02%, 35.77%, and 18.70% of T1 plants were confirmed to be highly resistant (HR), resistant (R), and mildly resistant (MR) to SMV, respectively, whereas only 6.50% were identified as susceptible (S). Additionally, qRT-PCR and DAS-ELISA showed that, both at 15 and 30 d post-inoculation (dpi), SMV accumulation significantly decreased or was even undetectable in HR and R plants, followed by MR and S plants. Additionally, the expression level of the CasRx gene varied in almost all T1 plants with different resistance level, both at 15 and 30 dpi. Furthermore, when SMV resistance was evaluated in the T2 generation, the results were similar to those recorded for the T1 generation. These findings provide new insights into the application of the CRISPR/CasRx system for soybean improvement and offer a promising alternative strategy for breeding for resistance to biotic stress that will contribute to the development of SMV-immune soybean germplasm to accelerate progress towards greater soybean crop productivity.

Genome-Wide Association and RNA-Seq Analyses Reveal a Potential Candidate Gene Related to Oil Content in Soybean Seeds.

Soybean is a crucial crop globally, serving as a significant source of unsaturated fatty acids and protein in the human diet. However, further enhancements are required for the related genes that regulate soybean oil synthesis. In this study, 155 soybean germplasms were cultivated under three different environmental conditions, followed by phenotypic identification and genome-wide association analysis using simplified sequencing data. Genome-wide association analysis was performed using SLAF-seq data. A total of 36 QTLs were significantly associated with oil content (-log10(p) > 3). Out of the 36 QTLs associated with oil content, 27 exhibited genetic overlap with previously reported QTLs related to oil traits. Further transcriptome sequencing was performed on extreme high-low oil soybean varieties. Combined with transcriptome expression data, 22 candidate genes were identified (|log2FC| ≥ 3). Further haplotype analysis of the potential candidate genes showed that three potential candidate genes had excellent haplotypes, including Glyma.03G186200, Glyma.09G099500, and Glyma.18G248900. The identified loci harboring beneficial alleles and candidate genes likely contribute significantly to the molecular network's underlying marker-assisted selection (MAS) and oil content.

Comparison of grain traits and genetic diversity between Chinese and Uruguayan soybeans (Glycine max L.).

Soybeans (Glycine max L.), originating in China, were introduced to South America in the late 19th century after passing through North America. South America is now a major soybean-producing region, accounting for approximately 40% of the global soybean production. Crops like soybeans gradually adapt to the local climate and human-selected conditions, resulting in beneficial variations during cultivation in different regions. Comparing the phenotypic and genetic variations in soybeans across different regions is crucial to determining the variations that may enhance soybean productivity. This study identified seed-related traits and conducted a genetic diversity analysis using 46 breeding soybean varieties from China and Uruguay. Compared to the Chinese soybean germplasm, the Uruguayan equivalent had a lower 100-grain weight, higher oil content, lower protein content, and higher soluble sugar content. Using ZDX1 gene chips, genetic typing was performed on the 46 breeding varieties. Cluster analysis based on SNP sites revealed significant differences in the genetic basis of Sino-Uruguayan soybean germplasm. Selection analysis, including nucleotide polymorphism (π) and fixation indexes (Fst), identified several genomic regions under selection between Sino-Uruguayan soybean germplasm. The selected intervals significantly enriched gene ontology (GO) terms related to protein metabolism. Additionally, differentiation occurred in genes associated with the oil content, seed weight, and cyst nematodes between Sino-Uruguayan soybean germplasm, such as GmbZIP123 and GmSSS1. These findings highlight the differences in seed-related phenotypes between Sino-Uruguay soybean germplasm and provide genomic-level insights into the mechanisms behind phenotypic differences, offering valuable references for understanding soybean evolution and molecular breeding.

Development and implementation of nested single-nucleotide polymorphism (SNP) assays for breeding and genetic research applications.

SoySNP50K and SoySNP6K are commonly used for soybean (Glycine max) genotyping. The SoySNP50K assay has been used to genetically analyze the entire USDA Soybean Germplasm Collection, while the SoySNP6K assay, containing a subset of 6000 single-nucleotide polymorphisms (SNPs) from SoySNP50K, has been used for quantitative trait loci mapping of different traits. To meet the needs for genomic selection, selection of parents for crosses, and characterization of breeding populations, especially early selection of ideal offspring from thousands of lines, we developed two assays, SoySNP3K and SoySNP1K, containing 3072 and 1252 SNPs, respectively, based on SoySNP50K and SoySNP6K mark sets. These two assays also contained the trait markers reported or contributed by soybean breeders. The SNPs in the SoySNP3K are a subset from SoySNP6K, while the SNPs in the SoySNP1K are a subset from SoySNP3K. These SNPs were chosen to reduce the SNP number in the large linkage blocks while capturing as much of the haplotype diversity as possible. They are highly polymorphic and of high quality. The mean minor allele frequencies of the SNPs in the southern and northern US elites were 0.25 and 0.27 for SoySNP3K, respectively, and 0.29 and 0.33 for SoySNP1K. The selected SNPs are a valuable source for developing targeted amplicon sequencing assay or beadchip assay in soybean. SoySNP3K and SoySNP1K assays are commercialized by Illumina Inc. and AgriPlex Genomics, respectively. Together with SoySNP50K and SoySNP6K, a series of nested assays with different marker densities will serve as additional low-cost genomic tools for genetic, genomic, and breeding research.