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We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.

Soybean (Glycine max L.) is gaining in importance due to its many uses, including as a food crop and a source of industrial products, among others. Increasing efforts are made to accelerate soybean research and develop new soybean varieties to meet global demands. Soybean research, breeding, identification, and variety protection all rely on precise genomic information. While DNA markers are invaluable tools for these purposes, the older generations, especially those developed before the advent of genome sequencing, lack precision and specificity. Thankfully, advancements in genome sequencing technologies have generated vast amounts of sequence data over the past decade, allowing precise and high-resolution analyses. However, making sense of the genomic information requires a certain level of professional training and computational power, which are not universally available to researchers. To address this, we generated a set of PCR-based DNA markers out of the existing genomic data from 228 popular soybean varieties that offer precise, unambiguous genomic information and can be easily adapted in various applications. A standard operating procedure (SOP) was also designed for these markers and validated on diverse soybean varieties to ensure their reproducibility. This user-friendly universal panel of DNA markers, along with the SOP, will facilitate soybean research and breeding programs through simple applications. [ABSTRACT FROM AUTHOR]

Summary: Copy number variations (CNVs) play important roles in crop domestication. However, there is only very limited information on the involvement of CNVs in soybean domestication. Trailing growth and long shoots are soybean adaptations for natural habitats but cause lodging that hampers yield in cultivation. Previous studies have focused on Dt1/2 affecting the indeterminate/determinate growth habit, whereas the possible role of the gibberellin pathway remained unclear. In the present study, quantitative trait locus (QTL) mapping of a recombinant inbred population of 460 lines revealed a trailing‐growth‐and‐shoot‐length QTL. A CNV region within this QTL was identified, featuring the apical bud‐expressed gibberellin 2‐oxidase 8A/B, the copy numbers of which were positively correlated with expression levels and negatively with trailing growth and shoot length, and their effects were demonstrated by transgenic soybean and Arabidopsis thaliana. Based on the fixation index, this CNV region underwent intense selection during the initial domestication process. Significance Statement: Copy number variations (CNVs) play important roles in crop domestication. Two gibberellin 2‐oxidase 8 (GA2ox8) genes in a CNV region within a quantitative trait locus under intensive selection were identified to suppress soybean shoot length and trailing growth phenotype and the physiological functions of these two GA2ox8 genes were validated by transgenic soybean and transgenic Arabidopsis thaliana. [ABSTRACT FROM AUTHOR]

To obtain a comprehensive understanding of transcriptomic reprogramming under salt stress, we performed whole‐transcriptome sequencing on the leaf and root of soybean seedlings subjected to salt treatment in a time‐course experiment (0, 1, 2, 4, 24, and 48 hr). This time series dataset enabled us to identify important hubs and connections of gene expressions. We highlighted the analysis on phytohormone signaling pathways and their possible crosstalks. Differential expressions were also found among those genes involved in carbon and nitrogen metabolism. In general, the salt‐treated seedlings slowed down their photosynthetic functions and ramped up sugar catabolism to provide extra energy for survival. Primary nitrogen assimilation was shut down whereas nitrogen resources were redistributed. Overall, the results from the transcriptomic analyses indicate that the plant uses a multipronged approach to overcome salt stress, with both fast‐acting, immediate physiological responses, and longer term reactions that may involve metabolic adjustment. We performed time‐course experiments to analyse the changes in gene expression profiles in conjunction with physiological adaptations and metabolic adjustments under salt stress. Using multiple time points, we are able to identify important hubs and connections of gene expressions. Our data indicate that soybean seedlings uses a multipronged approach to overcome salt stress, with both fast‐acting, immediate physiological responses, and longer term reactions that may involve metabolic adjustments. [ABSTRACT FROM AUTHOR]

Prokaryotes benefit from having accessory genes, but it is unclear how accessory genes can be linked with the core regulatory network when developing adaptations to new niches. Here we determined hierarchical core/accessory subsets in the multipartite pangenome (composed of genes from the chromosome, chromid and plasmids) of the soybean microsymbiont Sinorhizobium fredii by comparing twelve Sinorhizobium genomes. Transcriptomes of two S. fredii strains at mid-log and stationary growth phases and in symbiotic conditions were obtained. The average level of gene expression, variation of expression between different conditions, and gene connectivity within the co-expression network were positively correlated with the gene conservation level from strain-specific accessory genes to genus core. Condition-dependent transcriptomes exhibited adaptive transcriptional changes in pangenome subsets shared by the two strains, while strain-dependent transcriptomes were enriched with accessory genes on the chromid. Proportionally more chromid genes than plasmid genes were co-expressed with chromosomal genes, while plasmid genes had a higher within-replicon connectivity in expression than chromid ones. However, key nitrogen fixation genes on the symbiosis plasmid were characterized by high connectivity in both within- and between-replicon analyses. Among those genes with host-specific upregulation patterns, chromosomal znu and mdt operons, encoding a conserved high-affinity zinc transporter and an accessory multi-drug efflux system, respectively, were experimentally demonstrated to be involved in host-specific symbiotic adaptation. These findings highlight the importance of integrative regulation of hierarchical core/accessory components in the multipartite genome of bacteria during niche adaptation and in shaping the prokaryotic pangenome in the long run. [ABSTRACT FROM AUTHOR]

Differential gene expression profiles often provide important clues for gene functions. While reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is an important tool, the validity of the results depends heavily on the choice of proper reference genes. In this study, we employed new and published RNA-sequencing (RNA-Seq) datasets (26 sequencing libraries in total) to evaluate reference genes reported in previous soybean studies. In silico PCR showed that 13 out of 37 previously reported primer sets have multiple targets, and 4 of them have amplicons with different sizes. Using a probabilistic approach, we identified new and improved candidate reference genes. We further performed 2 validation tests (with 26 RNA samples) on 8 commonly used reference genes and 7 newly identified candidates, using RT-qPCR. In general, the new candidate reference genes exhibited more stable expression levels under the tested experimental conditions. The three newly identified candidate reference genes Bic-C2, F-box protein2, and VPS-like gave the best overall performance, together with the commonly used ELF1b. It is expected that the proposed probabilistic model could serve as an important tool to identify stable reference genes when more soybean RNA-Seq data from different growth stages and treatments are used. [ABSTRACT FROM AUTHOR]

Natural antisense transcripts (NATs) have been generally reported as negative regulators of their sense counterparts. Multidrug and toxic compound extrusion (MATE) proteins mediate the transport of various substrates. Although MATEs have been identified genome-wide in various plant species, their transcript regulators remain unclear. Here, using the publicly available strand-specific RNA-seq datasets of Glycine soja (wild soybean) which have the data from various tissues including developing pods, developing seeds, embryos, cotyledons and hypocotyls, roots, apical buds, stems, and flowers, we identified 35 antisense transcripts of MATEs from 28 gene loci after transcriptome assembly. Spearman correlation coefficients suggested the positive expression correlations of eight MATE antisense and sense transcript pairs. By aligning the identified transcripts with the reference genome of Glycine max (cultivated soybean), the MATE antisense and sense transcript pairs were identified. Using soybean C08 (Glycine max), in developing pods and seeds, the positive correlations between MATE antisense and sense transcript pairs were shown by RT-qPCR. These findings suggest that soybean antisense transcripts are not necessarily negative transcription regulators of their sense counterparts. This study enhances the existing knowledge on the transcription regulation of MATE transporters by uncovering the previously unknown MATE antisense transcripts and their potential synergetic effects on sense transcripts. [ABSTRACT FROM AUTHOR]