We report a large-scale analysis of the patterns of genome-wide genetic variation in soybeans. We re-sequenced a total of 17 wild and 14 cultivated soybean genomes to an average of approximately ×5 ...depth and >90% coverage using the Illumina Genome Analyzer II platform. We compared the patterns of genetic variation between wild and cultivated soybeans and identified higher allelic diversity in wild soybeans. We identified a high level of linkage disequilibrium in the soybean genome, suggesting that marker-assisted breeding of soybean will be less challenging than map-based cloning. We report linkage disequilibrium block location and distribution, and we identified a set of 205,614 tag SNPs that may be useful for QTL mapping and association studies. The data here provide a valuable resource for the analysis of wild soybeans and to facilitate future breeding and quantitative trait analysis.
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.
Summary
MicroRNAs (miRNAs) are important regulators of plant biological processes, including soybean nodulation. One miRNA, miR4407, was identified in soybean roots and nodules. However, the function ...of miR4407 in soybean is still unknown.
MiR4407, unique to soybean, positively regulates lateral root emergence and root structures and represses a root‐specific ISOPENTENYLTRANSFERASE (GmIPT3). By altering the expression of miR4407 and GmIPT3, we investigated the role of miR4407 in lateral root and nodule development.
Both miR4407 and GmIPT3 are expressed in the inner root cortex and nodule primordia. Upon rhizobial inoculation, miR4407 was downregulated while GmIPT3 was upregulated. Overexpressing miR4407 reduced the number of nodules in transgenic soybean hairy roots while overexpressing the wild‐type GmIPT3 or a miR4407‐resistant GmIPT3 mutant (mGmIPT3) significantly increased the nodule number. The mechanism of miR4407 and GmIPT3 functions was also linked to autoregulation of nodulation (AON), where miR4407 overexpression repressed miR172c and activated its target, GmNNC1, turning on AON. Exogenous CK mimicked the effects of GmIPT3 overexpression on miR172c, supporting the notion that GmIPT3 regulates nodulation by enhancing root‐derived CK.
Overall, our data revealed a new miRNA‐mediated regulatory mechanism of nodulation in soybean. MiR4407 showed a dual role in lateral root and nodule development.
SUMMARY
Plants that have experienced certain abiotic stress may gain tolerance to a similar stress in subsequent exposure. This phenomenon, called priming, was observed here in soybean (Glycine max) ...seedlings exposed to salt stress. Time‐course transcriptomic profiles revealed distinctively different transcriptional responses in the primed seedlings from those in the non‐primed seedlings under high salinity stress, indicating a stress response strategy of repressing unhelpful biotic stress responses and focusing on the promotion of those responses important for salt tolerance. To identify histone marks altered by the priming salinity treatment, a genome‐wide profiling of histone 3 lysine 4 dimethylation (H3K4me2), H3K4me3, and histone 3 lysine 9 acetylation (H3K9ac) was performed. Our integrative analyses revealed that priming induced drastic alterations in these histone marks, which coordinately modified the stress response, ion homeostasis, and cell wall modification. Furthermore, transcriptional network analyses unveiled epigenetically modified networks which mediate the strategic downregulation of defense responses. Altering the histone acetylation status using a chemical inhibitor could elicit the priming‐like transcriptional responses in non‐primed seedlings, confirming the importance of histone marks in forming the priming response.
Significance Statement
Understanding how plants adapt to stress conditions is important for developing strategies for crop improvement. In this study, a mild salt treatment of soybean (Glycine max) seedlings primed them for a more effective response against subsequent high salinity stress, by altering the genome‐wide distribution of histone marks to upregulate osmotic stress response genes and downregulate those for defense responses.
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.
SUMMARY
Root hair length (RHL) is an important character that affects nutrient acquisition in plants. The regulatory network in soybean controlling RHL is yet to be fully understood. In this study, ...we identified a quantitative trait locus (QTL) regulating RHL. One candidate causal gene in this QTL (GmbHLH113), preferentially expressed in root hairs, was annotated as encoding a basic helix–loop–helix transcription factor. In wild soybeans, the allelic type of GmbHLH113 with a glycine in the 13th residue, which was associated with a reduction in RHL, was shown to localize in the nucleus and activate gene transcription. Another allelic type with a single nucleotide polymorphism that resulted in a glutamate in the 13th residue is fixed in cultivated soybeans, and it lost the ability to localize to the nucleus or negatively regulate RHL. The ectopic expression of GmbHLH113 from W05 in Arabidopsis root hairs resulted in shorter RHL and reduced phosphorus (P) accumulation in shoots. Hence, a loss‐of‐function allele in cultivated soybeans might have been selected during domestication due to its association with a longer RHL and improved nutrient acquisition.
Significance Statement
The genetic mechanism behind root hair length (RHL) regulation in soybean is not yet fully understood. This study functionally characterized a novel negative regulator of RHL in wild soybeans and a loss‐of‐function allelic type fixed in cultivated soybeans resulting in longer root hairs and possibly more efficient nutrient acquisition, suggesting this loss‐of‐function allele could have been indirectly selected during soybean domestication.
Single nucleotide polymorphism (SNP) markers play significant roles in accelerating breeding and basic crop research. Several soybean SNP panels have been developed. However, there is still a lack of ...SNP panels for differentiating between wild and cultivated populations, as well as for detecting polymorphisms within both wild and cultivated populations.
This study utilized publicly available resequencing data from over 3,000 soybean accessions to identify differentiating and highly conserved SNP and insertion/deletion (InDel) markers between wild and cultivated soybean populations. Additionally, a naturally occurring mutant gene library was constructed by analyzing large-effect SNPs and InDels in the population.
The markers obtained in this study are associated with numerous genes governing agronomic traits, thus facilitating the evaluation of soybean germplasms and the efficient differentiation between wild and cultivated soybeans. The natural mutant gene library permits the quick identification of individuals with natural mutations in functional genes, providing convenience for accelerating soybean breeding using reverse genetics.
The superior agronomic and human nutritional properties of grain legumes (pulses) make them an ideal foundation for future sustainable agriculture. Legume‐based farming is particularly important in ...Africa, where small‐scale agricultural systems dominate the food production landscape. Legumes provide an inexpensive source of protein and nutrients to African households as well as natural fertilization for the soil. Although the consumption of traditionally grown legumes has started to decline, the production of soybeans (Glycine max Merr.) is spreading fast, especially across southern Africa. Predictions of future land‐use allocation and production show that the soybean is poised to dominate future production across Africa. Land use models project an expansion of harvest area, whereas crop models project possible yield increases. Moreover, a seed change in farming strategy is underway. This is being driven largely by the combined cash crop value of products such as oils and the high nutritional benefits of soybean as an animal feed. Intensification of soybean production has the potential to reduce the dependence of Africa on soybean imports. However, a successful “soybean bonanza” across Africa necessitates an intensive research, development, extension, and policy agenda to ensure that soybean genetic improvements and production technology meet future demands for sustainable production.
Soybean is fast becoming an increasingly attractive cash crop in Africa. We have examined current and future legume production in Sub‐Saharan Africa using a modelling approach based on available FAO data to provide projections for 2050. These data predict a large expansion in African soybean production. The resultant great potential for the amelioration of poverty, hunger, and malnutrition will be a major driver for farmers and producers to overcome the significant challenges that might otherwise impede soybean production in Africa.
It has been commonly accepted that soybean domestication originated in East Asia. Although East Asia has the historical merit in soybean production, the USA has become the top soybean producer in the ...world since 1950s. Following that, Brazil and Argentina have been the major soybean producers since 1970s and 1990s, respectively. China has once been the exporter of soybean to Japan before 1990s, yet she became a net soybean importer as Japan and the Republic of Korea do. Furthermore, the soybean yield per unit area in East Asia has stagnated during the past decade. To improve soybean production and enhance food security in these East Asian countries, much investment has been made, especially in the breeding of better performing soybean germplasms. As a result, China, Japan, and the Republic of Korea have become three important centers for soybean genomic research. With new technologies, the rate and precision of the identification of important genomic loci associated with desired traits from germplasm collections or mutants have increased significantly. Genome editing on soybean is also becoming more established. The year 2019 marked a new era for crop genome editing in the commercialization of the first genome-edited plant product, which is a high-oleic-acid soybean oil. In this review, we have summarized the latest developments in soybean breeding technologies and the remarkable progress in soybean breeding-related research in China, Japan, and the Republic of Korea.
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