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BackgroundA landmark in soybean research, Glyma1.01, the first whole genome sequence of variety Williams 82 (Glycine max L. Merr.) was completed in 2010 and is widely used. However, because the assembly was primarily built based on the linkage maps constructed with a limited number of markers and recombinant inbred lines (RILs), the assembled sequence, especially in some genomic regions with sparse numbers of anchoring markers, needs to be improved. Molecular markers are being used by researchers in the soybean community, however, with the updating of the Glyma1.01 build based on the high-resolution linkage maps resulting from this research, the genome positions of these markers need to be mapped.ResultsTwo high density genetic linkage maps were constructed based on 21,478 single nucleotide polymorphism loci mapped in the Williams 82 x G. soja (Sieb. & Zucc.) PI479752 population with 1083 RILs and 11,922 loci mapped in the Essex x Williams 82 population with 922 RILs. There were 37 regions or single markers where marker order in the two populations was in agreement but was not consistent with the physical position in the Glyma1.01 build. In addition, 28 previously unanchored scaffolds were positioned. Map data were used to identify false joins in the Glyma1.01 assembly and the corresponding scaffolds were broken and reassembled to the new assembly, Wm82.a2.v1. Based upon the plots of the genetic on physical distance of the loci, the euchromatic and heterochromatic regions along each chromosome in the new assembly were delimited. Genomic positions of the commonly used markers contained in BARCSOYSSR_1.0 database and the SoySNP50K BeadChip were updated based upon the Wm82.a2.v1 assembly.ConclusionsThe information will facilitate the study of recombination hot spots in the soybean genome, identification of genes or quantitative trait loci controlling yield, seed quality and resistance to biotic or abiotic stresses as well as other genetic or genomic research.

Test weight (TW) is a unit of bulk density that is influenced by several factors, including both genetics and environment. A subset of the trials in the Uniform Soybean Tests—Southern States was used to correlate seed composition traits of oil and protein percentages, and seed weight (SW) with TW to investigate the interaction of these traits in multi‐environments for four different maturity group (MG) tests. The results indicate that environment (location and year combination) had a larger impact on TW than genetic effect in all MG tests. This difference was greater in the earlier MGs, compared to MG VI and MG VII. In all tests across four MGs, the genotype interaction with environment effect was significant, but practically was not as important as genotype or environment effects. Significant negative correlations between TW and SW (MG V, VI, and VII tests), and TW and oil (MG V and VI tests) were observed but not consistent in all environments within these tests. TW and protein correlations were inconsistent with a negative relationship in MG V but a positive relationship in MG VII. As anticipated, the inconsistencies in the relationships across MGs for TW and seed composition traits suggest that selection strategies for improving TW will differ across soybean breeding programs. In the future, a similar study using a diverse panel of cultivars that do not change from year to year may shed more light on the influence of seed composition and environmental conditions on TW. Core Ideas: Soybean test weights are heritable.Test weight and seed trait correlations differ across maturity groups.Test weight values across Uniform Soybean Test—Southern States were lower than the standard 60 lb bu‐1. [ABSTRACT FROM AUTHOR]

Soybean oil is an abundant commodity crop that has garnered attention for its use as a feedstock for sustainable materials. Soybean oil is high in polyunsaturated fatty acid content, which can promote undesirable properties in biodiesel and lubricant applications. In this work, we characterized the fatty acid composition of commercial soybean oil along with two other soybean oil varieties, Ellis and TN18‐4110. Ellis and commercial soybean oils had similar fatty acid compositions, while TN18‐4110 was enriched in the monounsaturated oleic acid. Biodiesel and estolides were prepared from the three varieties and the relevant physical properties were measured. In comparison to commercial soybean diesel, both Ellis and TN18‐4110 exhibited unique advantages. As estolide‐based lubricants, all three varieties had advantageous cold flow properties, but TN18‐4110 also possessed excellent oxidative stability and lower viscosity. The physical properties and structural property relationships of the biodiesel and estolides are discussed. [ABSTRACT FROM AUTHOR]

'TN14‐5021' (Reg. no. CV‐543, PI 699124) is a late maturity group IV (relative maturity 4.9) determinate conventional soybean [Glycine max (L.) Merr.] cultivar developed and released by the University of Tennessee soybean breeding program. Soybean cultivars with resistance to soybean cyst nematode (SCN) race 2 are rare, but race 2 is becoming a predominant SCN population infecting farmers' fields in regions of the U.S. Southeast and Mid‐South. TN14‐5021 also conveys resistance to stem canker [caused by Diaporthe phaseolorum (Cooke & Ellis) Sacc. var. caulivora K.L. Athow & R.M. Caldwell] and strong resistance to SCN races 3 and 5. In replicated trials across 70 environments from the Mid‐South to the Southeast, TN‐5021 showed high yield potential and adaptation to a broad range of growing conditions. TN14‐5021 has white flowers and gray pubescence. The pods have a tan pod coat, and the seeds are yellow with smooth seed coats. Across 48 environments over a 4‐yr period, with testing locations from Kansas to Alabama, TN14‐5021 averaged 406 and 226 g kg–1 protein and oil content, respectively. In comparison, the average protein and oil content of commercial cultivars grown in the same tests averaged 397 and 224 g kg–1, respectively. Its high yield coupled with elevated seed protein concentration and nematode resistance package make TN14‐5021 a valuable cultivar for Tennessee and the Mid‐South region. [ABSTRACT FROM AUTHOR]

It is necessary to understand the differences in physiological responses to water deficit stress of soybean [Glycine max (L.) Merr.] genotypes in order to breed for drought‐tolerant soybean genotypes better suited to water‐limited environments in the U.S. mid‐South region. Using controlled environment and field trials, this study identified soybean genotypes that conserve water through differences in their stomatal response under soil water deficit to determine if this trait confers a yield advantage. Research was conducted from 2017 to 2020 at the West Tennessee Research and Education Center in Jackson, TN. Seventeen mid‐South soybean genotypes (i.e., both, breeding lines and modern commercial soybean) were investigated for an early stomatal closure trait during progressive soil drying under controlled environment conditions. Under field conditions, portable rainout shelters installed when the plant canopies of most genotypes had reached at least 80% canopy closure to impose water deficit stress to nine selected genotypes for field observation of wilting score (WS) and early stomatal closure. Differences were observed among genotypes in their early stomatal closure thresholds with progressive soil drying in the controlled environment. The range in fraction of transpirable soil water (FTSW) thresholds among 17 tested genotypes was 0.33–0.76. Based on our experimental approaches in 4 yr of field studies, genotypes Ellis and USG Allen consistently expressed an early decrease in transpiration rate with progressive soil drying, delayed wilting in the field when soil water deficit developed under rainout shelters, and greater yield when grown in simulated drought conditions. Core Ideas: Effective plant water use is a priority in crop yield production.Crop water saving was evident by early stomatal closure during soil drying.Mid‐South soybean with less wilting are likely the best candidates for use in water‐limited environments.Less wilted lines are a source of germplasm for future breeding efforts of a water‐saving soybean. [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]

The use of soybean [Glycine max (L.) Merrill] is widespread, with applications in food, fuel, livestock feed, and industrial products. We developed a soybean population of 239 F4‐derived recombinant inbred lines (RIL) from the cross "5601T" × U99‐310255 to estimate the heritability and genetic gain for seed protein, oil, and yield, and to assess the utility of making selections for these important traits. Heritability estimates on an entry means basis for protein (0.78), oil (0.65), seed yield (0.38) varied by trait with regard to genetic influence. Genetic gain was calculated for each trait at 5%, 10%, 15%, and 20% selection intensities. With the genetic gain that was obtained through the selections for each trait, some lines excelled above that of the checks and parents in this population. The second and third highest yielding selections (56U99‐081 and 56U99‐244) are notable in producing 50.2% and 49.8% meal protein, respectively, while maintain high yields above the high‐yielding parent, 5601T. Seeking balance for these important soybean traits is essential for breeders looking to make optimal improvements for the wide variety of soybean uses. Further research on this population could prove to be of value to breeding programs wishing to increase seed yield, oil, and protein. [ABSTRACT FROM AUTHOR]

DNA methylation is a dynamic and reversible type of epigenetic mark that contributes to cellular physiology by affecting transcription activity, transposon mobility and genome stability. When plants are infected with pathogens, plant DNA methylation patterns can change, indicating an epigenetic interplay between plant host and pathogen. In most cases methylation can change susceptibility. While DNA hypomethylation appears to be a common phenomenon during the susceptible interaction, the levels and patterns of hypomethylation in transposable elements and genic regions may mediate distinct responses against various plant pathogens. The effect of DNA methylation on the plant immune response and other cellular activities and molecular functions is established by localized differential DNA methylation via cis-regulatory mechanisms as well as through trans-acting mechanisms. Understanding the epigenetic differences that control the phenotypic variations between susceptible and resistant interactions should facilitate the identification of new sources of resistance mediated by epigenetic mechanisms, which can be exploited to endow pathogen resistance to crops. [ABSTRACT FROM AUTHOR]

Background: A landmark in soybean research, Glyma1.01, the first whole genome sequence of variety Williams 82 (Glycine max L. Merr.) was completed in 2010 and is widely used. However, because the assembly was primarily built based on the linkage maps constructed with a limited number of markers and recombinant inbred lines (RILs), the assembled sequence, especially in some genomic regions with sparse numbers of anchoring markers, needs to be improved. Molecular markers are being used by researchers in the soybean community, however, with the updating of the Glyma1.01 build based on the high-resolution linkage maps resulting from this research, the genome positions of these markers need to be mapped. Results: Two high density genetic linkage maps were constructed based on 21,478 single nucleotide polymorphism loci mapped in the Williams 82 x G. soja (Sieb. & Zucc.) PI479752 population with 1083 RILs and 11,922 loci mapped in the Essex x Williams 82 population with 922 RILs. There were 37 regions or single markers where marker order in the two populations was in agreement but was not consistent with the physical position in the Glyma1.01 build. In addition, 28 previously unanchored scaffolds were positioned. Map data were used to identify false joins in the Glyma1.01 assembly and the corresponding scaffolds were broken and reassembled to the new assembly, Wm82.a2.v1. Based upon the plots of the genetic on physical distance of the loci, the euchromatic and heterochromatic regions along each chromosome in the new assembly were delimited. Genomic positions of the commonly used markers contained in BARCSOYSSR_1.0 database and the SoySNP50K BeadChip were updated based upon the Wm82.a2.v1 assembly. Conclusions: The information will facilitate the study of recombination hot spots in the soybean genome, identification of genes or quantitative trait loci controlling yield, seed quality and resistance to biotic or abiotic stresses as well as other genetic or genomic research. [ABSTRACT FROM AUTHOR]