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Given high animal protein costs, protein deficiency is a prevalent form of malnutrition in sub‐Saharan Africa (SSA). Soybean [Glycine max (L.) Merr.] can provide a cheaper high‐quality protein source and fortify lysine‐limited cereal‐based diets. Breeding soybean for seed composition in SSA requires understanding genotype by environment interactions (G × E). African breeding programs submit cultivars for evaluation in the Pan‐African Soybean Variety Trials (PATs), providing the opportunity to examine G × E across diverse environments. With PAT data, we conducted additive main effects and multiplicative interaction (AMMI) and genotype plus genotype‐by‐environment (GGE) biplot analyses on seed protein and oil content of 17 cultivars grown with two replications in nine environments across Zimbabwe. Across environments, protein ranged from 322.8 to 445.1 g kg−1 and oil ranged from 164.8 to 242.7 g kg−1. For protein AMMI analysis, MAKWACHA performed best for both stability and a combination of stability plus content. For oil AMMI analysis, SC SPIKE performed best for stability and KALEYA performed best for a combination of stability plus content. GGE biplot analyses identified three different mega‐environments for protein and oil, with SC EXPT2, KALEYA, and SC EXPT1 having highest protein content and TGX 2002‐9FM, LUKANGA, and SC EXPT3 having highest oil content. We also evaluated genetic diversity of 19 PAT cultivars through phylogenetic analyses with 1059 USDA Germplasm Resources Information Network (GRIN) diversity panel accessions. We recommend stable and adaptable PAT cultivars to breeders and producers while highlighting genetically distinct accessions with valuable traits as a resource for breeding programs. Core Ideas: This is a comprehensive report on seed composition stability within Pan‐African Soybean Variety Trials (PATs).Genotype by environment interaction explained a significant amount of variation in seed protein and oil content.Additive main effects and multiplicative interaction (AMMI) and genotype plus genotype‐by‐environment (GGE) biplot analyses identified PAT cultivars with the highest stability and adaptability in Zimbabwe.We highlight the genetic relatedness of PAT cultivars relative to USDA Germplasm Resources Information Network (GRIN) diversity panel accessions. Plain Language Summary: Soybean is currently promoted in sub‐Saharan Africa as a high‐quality protein source. Breeding soybean for improved seed composition requires understanding how cultivars interact with these new environments. This study evaluated genotype by environment interactions and the genetic diversity of cultivars grown in the Pan‐African Soybean Variety Trials. We used stability analyses to evaluate how the environment, cultivar, and their interaction impacted protein and oil across Zimbabwe. We identified cultivars with increased protein or oil in specific environments or stable performance across environments. We also compared the genetic diversity of the African cultivars to over 1000 genetically diverse accessions from around the world. Our analyses showed that the African cultivars have relatively low genetic diversity and are most closely related to American accessions. Our results provide valuable resources for improving soybean seed composition in sub‐Saharan Africa. [ABSTRACT FROM AUTHOR]

Thirty soybean [Glycine max (L.) Merr.] genotypes, along with three checks, were evaluated over three seasons across five communes in Benin. The experiments were laid out in an alpha lattice design with three replicates. Additive multiplicative mean interaction (AMMI) and best linear unbiased predictor (BLUP) analysis were combined to assess differential agronomic performance and yield stability among genotypes. There was significant variation (p < 0.001) between genotypes for all traits, with highly significant environmental and genotype × environment interaction (GEI) effects on soybean grain yield (p < 0.001). The likelihood ratio test indicated that both genotype and interaction effects were highly significant (p < 0.001). The low R² (0.21) for GEI reflected the presence of high residual variation in the GEI component, in contrast to the AMMI analysis of variance, which explained a high proportion of the GEI through the first two interaction principal component axes (52%). The very high value of the predictive accuracy (0.89) confirmed the model’s reliability in selecting superior genotypes. The low (0.33) genotypic correlation between environments indicated that it was difficult to select superior genotypes for each environment. Based on the superiority index (weighted average absolute scores from BLUP for yield) of BLUP, simultaneous selection led to the identification of Jenguma 2.67 ± 0.06 t ha−1 as the most stable and productive genotype across environments, followed by Favour 2.34 ± 0.08 t ha−1, and Afayak 2.46 ± 0.08 t ha−1. The agronomic performance of soybean in this study suggested great potential for diversifying cotton-based cropping systems in Benin, thereby improving their sustainability. The effect of these soybean genotypes on the productivity of intercrop combinations and sequences of cash crops, such as cotton, is yet to be investigated. [ABSTRACT FROM AUTHOR]

Soybean is the most important legume crop worldwide and is grown mainly for its protein and oil rich seed, yet soybean production in Africa has largely lagged behind the increases [...]

The adoption of dicamba-tolerant (DT) soybean in the United States resulted in extensive off-target dicamba damage to non-DT vegetation across soybeanproducing states. Although soybeans are highly sensitive to dicamba, the intensity of observed symptoms and yield losses are affected by the genetic background of genotypes. Thus, the objective of this study was to detect novel marker-trait associations and expand on previously identified genomic regions related to soybean response to off-target dicamba. A total of 551 non-DT advanced breeding lines derived from 232 unique bi-parental populations were phenotyped for off-target dicamba across nine environments for three years. Breeding lines were genotyped using the Illumina Infinium BARCSoySNP6K BeadChip. Filtered SNPs were included as predictors in Random Forest (RF) and Support Vector Machine (SVM) models in a forward stepwise selection loop to identify the combination of SNPs yielding the highest classification accuracy. Both RF and SVM models yielded high classification accuracies (0.76 and 0.79, respectively) with minor extreme misclassifications (observed tolerant predicted as susceptible, and vice-versa). Eight genomic regions associated with off-target dicamba tolerance were identified on chromosomes 6 [Linkage Group (LG) C2], 8 (LG A2), 9 (LG K), 10 (LG O), and 19 (LG L). Although the genetic architecture of tolerance is complex, high classification accuracies were obtained when including the major effect SNP identified on chromosome 6 as the sole predictor. In addition, candidate genes with annotated functions associated with phases II (conjugation of hydroxylated herbicides to endogenous sugar molecules) and III (transportation of herbicide conjugates into the vacuole) of herbicide detoxification in plants were co-localized with significant markers within each genomic region. Genomic prediction models, as reported in this study, can greatly facilitate the identification of genotypes with superior tolerance to off-target dicamba. [ABSTRACT FROM AUTHOR]

The widespread adoption of genetically modified (GM) dicamba-tolerant (DT) soybean was followed by numerous reports of off-target dicamba damage and yield losses across most soybean-producing states. In this study, a subset of the USDA Soybean Germplasm Collection consisting of 382 genetically diverse soybean accessions originating from 15 countries was used to identify genomic regions associated with soybean response to off-target dicamba exposure. Accessions were genotyped with the SoySNP50K BeadChip and visually screened for damage in environments with prolonged exposure to off-target dicamba. Two models were implemented to detect significant marker-trait associations: the Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) and a model that allows the inclusion of population structure in interaction with the environment (G×E) to account for variable patterns of genotype responses in different environments. Most accessions (84%) showed a moderate response, either moderately tolerant or moderately susceptible, with approximately 8% showing tolerance and susceptibility. No differences in off-target dicamba damage were observed across maturity groups and centers of origin. Both models identified significant associations in regions of chromosomes 10 and 19. The BLINK model identified additional significant marker-trait associations on chromosomes 11, 14, and 18, while the G×E model identified another significant marker-trait association on chromosome 15. The significant SNPs identified by both models are located within candidate genes possessing annotated functions involving different phases of herbicide detoxification in plants. These results entertain the possibility of developing non-GM soybean cultivars with improved tolerance to off-target dicamba exposure and potentially other synthetic auxin herbicides. Identification of genetic sources of tolerance and genomic regions conferring higher tolerance to off-target dicamba may sustain and improve the production of other non-DT herbicide soybean production systems, including the growing niche markets of organic and conventional soybean. [ABSTRACT FROM AUTHOR]

Studies have indicated that exon and intron size and intergenic distance are correlated with gene expression levels and expression breadth. Previous reports on these correlations in plants and animals have been conflicting. In this study, next-generation sequence data, which has been shown to be more sensitive than previous expression profiling technologies, were generated and analyzed from 14 tissues. Our results revealed a novel dichotomy. At the low expression level, an increase in expression breadth correlated with an increase in transcript size because of an increase in the number of exons and introns. No significant changes in intron or exon sizes were noted. Conversely, genes expressed at the intermediate to high expression levels displayed a decrease in transcript size as their expression breadth increased. This was due to smaller exons, with no significant change in the number of exons. Taking advantage of the known gene space of soybean, we evaluated the positioning of genes and found significant clustering of similarly expressed genes. Identifying the correlations between the physical parameters of individual genes could lead to uncovering the role of regulation owing to nucleotide composition, which might have potential impacts in discerning the role of the noncoding regions. Key words: expression level, expression breadth, next-generation sequencing, physical clustering. Des etudes ont montre que la taille des introns et des exons ainsi que la distance intergeenique seraient corretees avec le niveau et l'etendue de l'expression geenique. Les etudes anteerieures sur ce sujet chez les plantes et les animaux se sont averees contradictoires. Dans cette etude, des domtoes de sequence de seconde generation, lesquelles fournissent des donnees transcriptomiques plus sensibles que celles obtenues a l'aide des techniques anteerieures, ont ete produites et analysees chez 14 tissus. Les resultats des auteurs revelent une nouvelle dichotomie. Chez les genes faiblement exprimes, un accroissement de l'etendue de l'expression etait correle avec un accroissement de la taille des transcrits attribuable a une augmentation du nombre d'exons et d'introns. Aucun changement quant a la taille des introns ou des exons n'a ete note;. Inversement, les genes exprimes de maniere intermeidiaire ou forte presentaient des transcrits dont la taille diminuait au fur et a mesure que s'accroissait l'etendue de leur expression. Cette reduction etait due a une reduction de la taille des exons, sans qu'il y ait eu reduction du nombre de ceux-ci. En tirant avantage de la connaissance de l'espace geenique chez le soya, les auteurs ont examine; le positionnement des genes et ont observe un groupement significatif des genes qui presentent un niveau d'expression semblable. L'identification de correlations entre les parameitres physiques de genes individuels pourrait permettre de mieux comprendre la re;gulation ge;nique de;coulant de la composition nucle;otidique, laquelle pourrait aider a discerner le role des regions non-codantes. Mots-cles: niveau d'expression, eetendue de l'expression, seequencage de seconde generation, groupement physique. [Traduit par la Redaction], Introduction The uniqueness of living organisms is dependent not only upon the suite of genic material available to them but also upon the subtleties of gene expression patterns. Some genes [...]

Brown stem rot (BSR) of soybean [Glycine max (L.) Merr.], caused by Phialophora gregata (Allington & D.W. Chamb.) W. Gams 1971, is an economically important disease prevalent in soybean producing regions of the north-central United States and Canada. To date, all BSR resistant genes identified are located on chromosome 16 (formerly molecular linkage group J). The objective of this study was to determine if four plant introductions from south-central China identified as BSR resistant have resistance genes mapping to the same location on chromosome 16 as previously mapped BSR resistance genes. The four plant introductions, PI 594637, PI 594638B, PI 594650A, and PI 594858B, were crossed to the BSR-susceptible cultivar 'Century 84' to develop four [F.sub.2] populations. Each segregating population and the parental lines were screened for BSR resistance in growth chamber conditions. The [F.sub.2:3] individual plants of each population were tested with the sire ale sequence repeat (SSR) markers Satt431 or Satt547, which map closely to BSR resistance quantitative trait loci (QTL) on chromosome 16. Associations between molecular data and phenotypic data used to validate QTL were analyzed using single factor ANOVA. Three of the four populations had markers on chromosome 16 significantly associated with BSR resistance with [R.sup.2] values from 24 to 48%. However, when marker Satt547 was regressed on BSR resistance in population PI 594637 x Century 84, no significant association was observed. This result suggests that PI 594637 could have a new BSR resistance gene. Transgressive segregation also was observed in this population, and highly BSR resistant progeny could be used in the development of BSR resistant cultivars. Additional research and testing in this population will be conducted to identify resistance QTL(s) from this source. doi: 10.2135/cropsci2010.03.0159

From 1970 to 2008 there were 2242 soybean [Glycine max (L) Merr.] cultivars registered in North America through U.S. Plant Variety Protection (PVP), U.S. utility patent, and journal registration. Of these, 80% were developed through proprietary and 20% through public programs. Our objective was to characterize the development and genetic diversity of North American soybean cultivars. The most frequently used germplasm for cultivar development were the cultivars Williams (parent used in last cross before inbreeding in 70 cultivars), A3127 (63), Essex (45), Amsoy (38), Corsoy (33), Wayne (30), Forrest (27), Hutcheson (25), MO13404 (23), and Bedford (23). Genetic diversity (1 - coefficient of parentage), estimated from pedigree lineage, was 0.89 overall. Genetic diversity was the same within public (0.89) and proprietary (0.89) cultivars. The cultivar A3127 is a major progenitor of recently developed proprietary cultivars registered from 1999 to 2008. Of these 494 cultivars, 23% have a genetic contribution of at least 25% from A3127. New cultivars were predominantly developed from the following crosses: two-parent (70% of cultivars developed), complex (12%), three-parent (5%), one backcross (5%), multiple (two, three, or four) backcrosses (3%), and five or greater backcrosses (2%). In comparisons where both parent and progeny were evaluated together, seed yield increased 3.2% per breeding cycle. In these comparisons, seed yield had a correlation of 0.29 with parental diversity. doi: 10.2135/cropsci2009.08.0456

The soybean aphid (Aphis glycines Matsumura) is a new invasive soybean [Glycine max (L.) Merr.] insect pest first identified in North America in 2000. A major aphid resistance gene Rag1 was identified and mapped from the maturity group VIII cultivar Dowling, and the gene has been introgressed into Midwest-adapted germplasm. The objective of this study was to test the associated effects of Rag1 on yield and several important agronomic traits in two elite Midwest-adapted soybean backgrounds. To do this, we tested two backcross populations that segregate for Rag1 with simple sequence repeat markers linked to the gene in field tests conducted in multiple environments with no detectable soybean aphid infestations. Across environments, Rag1 had no significant (P = 0.05) associated effects on yield, plant height, and lodging score in either population. However, Rag1 was significantly associated with a 2-d delay in maturity in one population. This delay in maturity is likely caused by linkage drag between Rag1 and gene(s) that delayed maturity. These results indicate that breeders can incorporate Rag1 into Midwest-adapted backgrounds without an associated yield reduction.