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Key Message: 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., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Background: The advancement of sequencing technologies today has made a plethora of whole-genome re-sequenced (WGRS) data publicly available. However, research utilizing the WGRS data without further configuration is nearly impossible. To solve this problem, our research group has developed an interactive Allele Catalog Tool to enable researchers to explore the coding region allelic variation present in over 1,000 re-sequenced accessions each for soybean, Arabidopsis, and maize., Results: The Allele Catalog Tool was designed originally with soybean genomic data and resources. The Allele Catalog datasets were generated using our variant calling pipeline (SnakyVC) and the Allele Catalog pipeline (AlleleCatalog). The variant calling pipeline is developed to parallelly process raw sequencing reads to generate the Variant Call Format (VCF) files, and the Allele Catalog pipeline takes VCF files to perform imputations, functional effect predictions, and assemble alleles for each gene to generate curated Allele Catalog datasets. Both pipelines were utilized to generate the data panels (VCF files and Allele Catalog files) in which the accessions of the WGRS datasets were collected from various sources, currently representing over 1,000 diverse accessions for soybean, Arabidopsis, and maize individually. The main features of the Allele Catalog Tool include data query, visualization of results, categorical filtering, and download functions. Queries are performed from user input, and results are a tabular format of summary results by categorical description and genotype results of the alleles for each gene. The categorical information is specific to each species; additionally, available detailed meta-information is provided in modal popups. The genotypic information contains the variant positions, reference or alternate genotypes, the functional effect classes, and the amino-acid changes of each accession. Besides that, the results can also be downloaded for other research purposes., Conclusions: The Allele Catalog Tool is a web-based tool that currently supports three species: soybean, Arabidopsis, and maize. The Soybean Allele Catalog Tool is hosted on the SoyKB website ( https://soykb.org/SoybeanAlleleCatalogTool/ ), while the Allele Catalog Tool for Arabidopsis and maize is hosted on the KBCommons website ( https://kbcommons.org/system/tools/AlleleCatalogTool/Zmays and https://kbcommons.org/system/tools/AlleleCatalogTool/Athaliana ). Researchers can use this tool to connect variant alleles of genes with meta-information of species., (© 2023. The Author(s).)

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. [ABSTRACT FROM AUTHOR]

Genome-to-phenome research in agriculture aims to improve crops through in silico predictions. Genome-wide association study (GWAS) is potent in identifying genomic loci that underlie important traits. As a statistical method, increasing the sample quantity, data quality, or diversity of the GWAS dataset positively impacts GWAS power. For more precise breeding, concrete candidate genes with exact functional variants must be discovered. Many post-GWAS methods have been developed to narrow down the associated genomic regions and, ideally, to predict candidate genes and causative mutations (CMs). Historical natural selection and breeding-related artificial selection both act to change the frequencies of different alleles of genes that control phenotypes. With higher diversity and more extensive GWAS datasets, there is an increased chance of multiple alleles with independent CMs in a single causal gene. This can be caused by the presence of samples from geographically isolated regions that arose during natural or artificial selection. This simple fact is a complicating factor in GWAS-driven discoveries. Currently, none of the existing association methods address this issue and need to identify multiple alleles and, more specifically, the actual CMs. Therefore, we developed a tool that computes a score for a combination of variant positions in a single candidate gene and, based on the highest score, identifies the best number and combination of CMs. The tool is publicly available as a Python package on GitHub, and we further created a web-based Multiple Alleles discovery (MADis) tool that supports soybean and is hosted in SoyKB (https://soykb.org/SoybeanMADisTool/). We tested and validated the algorithm and presented the utilization of MADis in a pod pigmentation L1 gene case study with multiple CMs from natural or artificial selection. Finally, we identified a candidate gene for the pod color L2 locus and predicted the existence of multiple alleles that potentially cause loss of pod pigmentation. In this work, we show how a genomic analysis can be employed to explore the natural and artificial selection of multiple alleles and, thus, improve and accelerate crop breeding in agriculture. [ABSTRACT FROM AUTHOR]

Optimization of plant architecture by modifying stem termination and timing of flowering and maturity of soybean is a promising strategy to improve its adaptability to specific production environments. Therefore, it is important to choose a proper stem termination type and to understand morphological differences between each stem termination type under various environmental conditions. Variations in abruptness of stem termination have been generally classified into three classical genetic types, indeterminate (Dt1), determinate (dt1), and semi-determinate (Dt2). However, an additional stem termination type, termed tall determinate, and its genetic symbol, dt1-t , were introduced about 25 years ago. The tall determinate soybean lines show delayed cessation of apical stem growth and about 50% taller plant heights than the typical determinate soybeans, even though the genetic control of the tall determinate phenotype was found to be allelic to dt1. Despite the potential agronomic merits of the alternative stem termination type, knowledge about the tall determinate soybean remains limited. We clarified the molecular basis of the tall determinate stem termination type and examined potential agronomic merits of the alternative stem type under three different production environments in the US. Sequence analysis of the classical tall determinate soybean lines revealed that the dt1-t allele responsible for tall determinate stem architecture is caused by two of the identified independent missense alleles of dt1, dt1-t1 (R130K), and dt1-t2 (R62S). Also, from the comparison among soybean accessions belonging to each of the genotype categories for stem termination types, soybean accessions with tall determinate alleles were found to have a high discrepancy rate in phenotyping. Newly developed tall determinate late-maturing soybean germplasm lines had taller plant heights and a greater number of nodes with a similar stem diameter and similar pod density at the apical stem compared to typical determinate soybeans having dt1 (R166W) alleles in Southern environments in the US. The phenotype of increased pod-bearing nodes with lodging resistance has the potential to improve yield, especially grown in high yield environments. This study suggests an alternative strategy to remodel the shape of soybean plants, which can possibly lead to yield improvement through the modification of soybean plant architecture. [ABSTRACT FROM AUTHOR]

Adaptation of soybean cultivars to the photoperiod in which they are grown is critical for optimizing plant yield. However, despite its importance, only the major loci conferring variation in flowering time and maturity of US soybean have been isolated. By contrast, over 200 genes contributing to floral induction in the model organism Arabidopsis thaliana have been described. In this work, putative alleles of a library of soybean orthologs of these Arabidopsis flowering genes were tested for their latitudinal distribution among elite US soybean lines developed in the United States. Furthermore, variants comprising the alleles of genes with significant differences in latitudinal distribution were assessed for amino acid conservation across disparate genera to infer their impact on gene function. From these efforts, several candidate genes from various biological pathways were identified that are likely being exploited toward adaptation of US soybean to various maturity groups. [ABSTRACT FROM AUTHOR]

Background: Soybean is native to the temperate zones of East Asia. Poor yields of soybean in West African countries may be partially attributed to inadequate adaptation of soybean to tropical environments. Adaptation will require knowledge of the effects of allelic combinations of major maturity genes (E1, E2, and E3) and stem architecture. The long juvenile trait (J) influences soybean flowering time in short, ~ 12 h days, which characterize tropical latitudes. Soybean plant architecture includes determinate or indeterminate stem phenotypes controlled by the Dt1 gene. Understanding the influence of these genetic components on plant development and adaptation is key to optimize phenology and improve soybean yield potential in tropical environments. Results: Soybean lines from five recombinant inbred populations were developed that varied in their combinations of targeted genes. The soybean lines were field tested in multiple environments and characterized for days to flowering (DTF), days to maturity (DTM), and plant height in locations throughout northern Ghana, and allelic combinations were determined for each line for associating genotype with phenotype. The results revealed significant differences based on genotype for DTF and DTM and allowed the comparison of different variant alleles of those genes. The mutant alleles of J and E1 had significant impact on DTF and DTM, and alleles of those genes interacted with each other for DTF but not DTM. The Dt1 gene significantly influenced plant height but not DTF or DTM. Conclusions: This research identified major and minor effect alleles of soybean genes that can be combined to control DTF, DTM, and plant height in short day tropical environments in Ghana. These phenotypes contribute to adaptation to a low latitude environment that can be optimized in a soybean breeding program with targeted selection of desired allele combinations. The knowledge of the genetic control of these traits will enhance molecular breeding to produce optimally adapted soybean varieties targeted to tropical environments. [ABSTRACT FROM AUTHOR]

Soybean [Glycine max (L.) Merr.] oil with high oleic acid (>75%) has increased oxidative stability and health benefits that are valuable for food, fuel, and industrial products. It has been determined that two naturally occurring mutations in genes FAD2‐1A and FAD2‐1B can combine to produce high oleic soybeans. The objective of this study was to test the effect of these mutant alleles on seed yield and oil and protein concentration. Molecular markers assisted in the creation of a population of 48 BC3F2:4 lines (93.75% expected genome commonality). Each line was classified into one of four genotypic groups where both FAD2‐1A and FAD2‐1B genes were either homozygous wild type or mutant, respectively. Twelve lines for each genotypic group were evaluated in three replications at six locations across Tennessee. There was no seed yield difference between the high oleic genotypic group and the other groups (P < 0.05). On the other hand, there were differences in fatty acid profiles and oil and protein concentrations. In combination, the mutant FAD2‐1A and FAD2‐1B alleles produced a mean of 803.1 g kg−1 oleic acid. This is, on average, approximately 500 g kg−1 more oleic acid compared to soybean lines with only one mutant FAD2‐1 allele. The high oleic double mutant group had more total oil (228.0 g kg−1) and protein (401.0 g kg−1) compared to all other genotypic groups (P < 0.05). Overall, this specific combination of mutant FAD2‐1A and FAD2‐1B alleles appears to generate conventional high oleic soybeans without a yield drag. [ABSTRACT FROM AUTHOR]

Soybean [Glycine max (L.) Merr.] is an important crop in the United States that is processed into two main products: a vegetable oil and a high‐protein meal used in livestock rations. Soybean cultivar development involves the incorporation of new traits that enhance value for the producer, processor, or end user. Soybean varieties that have seed composition characteristics that improve the value of the meal while still allowing high yields are desirable. The raffinose family of oligosaccharides (RFO) are antinutritional carbohydrates that reduce the nutritional energy of soybean meal, whereas sucrose can be considered nutritionally beneficial in soybean meal. The objective of this study was to expand the understanding of the environmental stability of the carbohydrate profiles for soybean lines containing different allele combinations of two key raffinose synthase (RS2 and RS3) genes, as well as targeted maturity gene combinations in a range of US soybean production environments. The results indicated that soybean genotypes with combinations of variant alleles of the RS2 and RS3 genes, as well as maturity genes appropriate for their targeted environment, produced characteristic carbohydrate profiles. Environmental factors did have an effect on carbohydrate components, particularly for sucrose. None of the genotype classes was stable for sucrose, although most of the variant RS2 genotypes accumulated at least 7% sucrose over the studied environments. In addition, five of the six genotype classes were stable for stachyose. The results establish the genotype classes with rs2W331− alleles suitable to develop soybean cultivars in broad maturity group backgrounds that have an enhanced energy meal trait. [ABSTRACT FROM AUTHOR]

Abstract: Oil value is determined by the functional qualities imparted from the fatty acid profile. Soybean oil historically had excellent use in foods and industry; the need to increase the stability of the oil without negative health consequences has led to a decline in soybean oil use. One solution to make the oil stable is to have high oleic acid (>70%) and lower linolenic acid content in the oil. Other fatty acid profile changes are intended to target market needs: low‐saturated fatty acid and high stearic acid content in the oil. The objective of this study is to determine the interaction of the high oleic acid oil trait with other alleles controlling fatty acid profiles. Soybean lines containing high oleic acid allele combinations plus other fatty acid modifying alleles were produced, and the seed was produced in multiple field environments over 2 years. Stable high oleic acid with low linolenic acid (<3.0%) was achieved with a 4‐allele combination. The target of >20% stearic acid in the seed oil was not achieved. Reducing total saturated fatty acids below 7% in a high oleic acid background was possible with mutant alleles of both an acyl‐ACP thioesterase B and a β‐ketoacyl‐[acyl‐carrier‐protein] synthase III gene. The results identified allele combinations that met the target fatty acid profile thresholds and were most stable across environments. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Pod shattering is an ancestral trait that promotes seed dispersal; however, shattering can have substantial yield losses in cultivated soybean. During the improvement process, American soybean breeders virtually eliminated the shatter phenotype for released varieties, but in other countries, such as Ghana, shatter persists. The objective of our research was to find a molecular tool to implicate genetic shatter susceptibility, validate its usefulness, and apply this knowledge to identify shattering potential in parental lines. Previous research revealed the gene Pdh1 on chromosome 16 plays a crucial role in determining the shatter phenotype. A perfect molecular marker assay was developed to detect alleles of the Pdh1 gene. A genome-wide association study (GWAS) was performed using the Pdh1 allele status as a phenotype and identified a highly associated marker in the SoySNP50K array. Soybean accessions from the National Plant Germplasm System (GRIN-NPGS) with shatter score and SoySNP50K data were evaluated to determine the impact of the predicted Pdh1 alleles on early and late pod shattering. An online tool was developed to enable researchers to query the GRIN collection for the predicted Pdh1 allele status. Lines from an African soybean germplasm collection were analyzed, and it was determined that 22.5% of lines had the shatter-susceptible alleles of Pdh1; two of seven Ghanaian released soybean varieties had the shatter-susceptible alleles of Pdh1. Soybean breeding programs that access germplasm from the GRIN or the African collection can utilize these resources to eliminate the Pdh1 effects on pod shatter and thus improve yield potential. [ABSTRACT FROM AUTHOR]