Dynamics of cis-regulatory sequences and transcriptional divergence of duplicated genes in soybean

Profiling conserved transcription factor binding motifs in Phaseolus vulgaris through comparative genomics

Common bean (Phaseolus vulgaris), a staple food in Latin America and Africa, serves as a vital source of energy, protein, and essential minerals for millions of people. However, genomics knowledge that breeders could leverage for improvement of this crop is scarce. We have developed and validated a comparative genomics approach to predict conserved transcription factor binding sites (TFBS) in common bean and studied gene regulatory networks. We analyzed promoter regions and identified TFBS for 12,631 bean genes with an average of 6 conserved motifs per gene. Moreover, we discovered a statistically significant relationship between the number of conserved motifs and amount of available experimental evidence of gene regulation. Notably, ERF, MYB, and bHLH transcription factor families dominated conserved motifs, with implications for starch biosynthesis regulation. Furthermore, we provide gene regulatory data as a resource that can be interrogated for the regulatory landscape of any set of genes. Our results underscore the significance of TFBS conservation in legumes and aligns with the notion that core genes often exhibit a more conserved regulatory makeup. The study demonstrates the effectiveness of a comparative genomics approach for addressing genome information gaps in non-model organisms and provides valuable insights into the regulatory networks governing starch biosynthesis genes that can support crop improvement programs.

Unlocking soybean potential: genetic resources and omics for breeding

Soybean (Glycine max) is a vital foundation of global food security, providing a primary source of high-quality protein and oil for human consumption and animal feed. The rising global population has significantly increased the demand for soybeans, emphasizing the urgency of developing high-yield, stress-tolerant, and nutritionally superior cultivars. The extensive collection of soybean germplasm resources-including wild relatives, landraces, and cultivars-represents a valuable reservoir of genetic diversity critical for breeding advancements. Recent breakthroughs in genomic technologies, particularly high-throughput sequencing and multi-omics approaches, have revolutionized the identification of key genes associated with essential agronomic traits within these resources. These innovations enable precise and strategic utilization of genetic diversity, empowering breeders to integrate traits that improve yield potential, resilience to biotic and abiotic stresses, and nutritional quality. This review highlights the critical role of genetic resources and omics-driven innovations in soybean breeding. It also offers insights into strategies for accelerating the development of elite soybean cultivars to meet the growing demands of global soybean production.

Divergent evolutionary paces among eudicot plants revealed by simultaneously duplicated genes produced billions of years ago

Polyploidization often occurs more than once along an evolutionary lineage to form extant plants. Major core eudicot plants share a whole-genome triplication (ceWGT), through which thousands of simultaneously duplicated genes are retained in extant genomes, providing a valuable starting line to check the difference in their evolutionary paces. Here, by characterizing the synonymous nucleotide substitutions (Ks) between these duplicates from 28 representative plants from 21 families, we checked the various evolutionary rates among plants among plants subjected to different rounds of extra polyploidization events. We found up to 68.04% difference in evolutionary rates among the selected plants. A statistical correlation analysis (correlation coefficient =0.57, at significant level = 0.01) indicated that plants affected by extra polyploidies have evolved faster than plants without such extra polyploidies showing that (additional) polyploidization has resulted in elevated genetic diversity. Comparing the plants affected by additional polyploidization and plants without it, the duplicated genes produced by the ceWGT and retained in extant genomes have gathered 4.75% more nucleotide substitutions in the former plants. By identifying the fast- and slowly evolving genes, we showed that genes evolving at divergent rates were often related to different evolutionary paths. By performing correction to evolutionary rates using a genome-scale approach, we revised the estimated timing of key evolutionary events. The present effort exploited the simultaneously duplicated genes produced by the shared polyploidization and help deepen the understanding of the role of polyploidization, especially its long-term effect in plant evolution and biological innovation.

Soybean2035: A decadal vision for soybean functional genomics and breeding

Soybean, the fourth most important crop in the world, uniquely serves as a source of both plant oil and plant protein for the world's food and animal feed. Although soybean production has increased approximately 13-fold over the past 60 years, the continually growing global population necessitates further increases in soybean production. In the past, especially in the last decade, significant progress has been made in both functional genomics and molecular breeding. However, many more challenges should be overcome to meet the anticipated future demand. Here, we summarize past achievements in the areas of soybean omics, functional genomics, and molecular breeding. Furthermore, we analyze trends in these areas, including shortages and challenges, and propose new directions, potential approaches, and possible outputs toward 2035. Our views and perspectives provide insight into accelerating the development of elite soybean varieties to meet the increasing demands of soybean production.

A spatially resolved multi-omic single-cell atlas of soybean development

Cis-regulatory elements (CREs) precisely control spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of gene expression with chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible chromatin regions (ACRs). Nearly 40% of the ACRs showed cell-type-specific patterns and were enriched for transcription factor (TF) motifs defining diverse cell identities. We identified de novo enriched TF motifs and explored the conservation of gene regulatory networks underpinning legume symbiotic nitrogen fixation. With comprehensive developmental trajectories for endosperm and embryo, we uncovered the functional transition of the three sub-cell types of endosperm, identified 13 sucrose transporters sharing the DNA binding with one finger 11 (DOF11) motif that were co-upregulated in late peripheral endosperm, and identified key embryo cell-type specification regulators during embryogenesis, including a homeobox TF that promotes cotyledon parenchyma identity. This resource provides a valuable foundation for analyzing gene regulatory programs in soybean cell types across tissues and life stages.

Genome-Wide Identification and Comprehensive Analysis of the PPO Gene Family in Glycine max and Glycine soja

BACKGROUND

Polyphenol oxidases (PPOs) form a multigene family that is widely distributed in plants, animals, and insects. To date, PPOs have been identified in plants such as Populus L. and Solanum tuberosum L., but studies on PPOs in soybean (Glycine max (L.) Merr.) and wild soybean (Glycine soja Sieb. and Zucc.) remain limited.

METHODS

To clarify the nature, structure, evolution, expression pattern, and interaction network of PPOs in these plants, we performed bioinformatics analysis and evaluated the expression patterns of PPOs in soybean and wild soybean throughout the growth period and under salt stress.

RESULTS

We identified 17 and 15 genes belonging to the PPO family. These genes were distributed across chromosomes 7 and 6 and could be divided into three groups. Most of these genes only contained one coding sequence (CDS), and their gene structure, conserved motifs, and 3D structures were very similar. Although there were a few intraspecies gene duplications, 75 gene replication pairs between soybean and wild soybean were detected. A Ka/Ks analysis showed that the PPOs in these plants were mainly subjected to purity selection. Moreover, the expression of the PPO genes varied greatly during different stages of the growth period and under salt stress, showing high temporal and spatial specificity. The protein interaction networks of these genes appeared to be quite distinct. Through the interaction analysis of the candidate gene GmPPO2 selected under salt stress, Glyma.07G059000, Glyma.10G279000, and Glyma.03G167900 were identified as the candidate genes regulating salt stress tolerance in soybean.

CONCLUSIONS

These findings provide a foundation for further research on the evolution of soybean and wild soybean, as well as the functions of the PPO gene family.

Genome-Wide Identification and Expression Profiling Analysis of the Mitochondrial Calcium Uniporter Gene Family Under Abiotic Stresses in Medicago sativa

The mitochondrial calcium uniporters (MCUs) are a family of calcium unidirectional transporters important for cytoplasmic Ca2+ signals. Though the MCU proteins in several plant species have been investigated, genome-wide analysis of MCUs in alfalfa is lacking. Here, via genome-wide analysis, a total of 5, 20, and 6 MCU genes were identified in three different alfalfa cultivars, namely Medicago truncatula Jemalong A17, Medicago sativa XinJiangDaYe, and M. sativa Zhongmu No. 1, respectively. They were further phylogenetically classified into three subfamilies. Most MCU genes have only one intron, and gene duplication events of MCU genes were observed within each alfalfa accession and between different accessions. All alfalfa MCU proteins contained a highly conserved MCU domain and 10 conserved motifs, featuring two transmembrane domains and a DI/VME motif. According to the tissue expression data of M. sativa Zhongmu No. 1, MsMCU6.2 was the most abundant transcript with the highest expression in the leaf, and MsMCU5 and MsMCU1.2 showed higher expression levels in the stem than other tissues. We analyzed the expression profiles of five MCU genes (MsMCU1.1/1.2/5/6.1/6.2) under salt, drought, and cold stresses via qRT-PCR assays. All five MCU genes were induced by drought stress, except MsMCU5, whose expression was up-regulated by salt stress, while cold stress slightly altered MsMCU expression. Nine potential interacting proteins and three miRNAs targeting MtMCUs were predicted. These results provide detailed knowledge of alfalfa MCU genes and suggest their potential functions in abiotic stress response.

Evolution, Gene Duplication, and Expression Pattern Analysis of CrRLK1L Gene Family in Zea mays (L.)

Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) plays pivotal roles in regulating plant growth and development, mediating intercellular signal transduction, and modulating responses to environmental stresses. However, a comprehensive genome-wide identification and analysis of the CrRLK1L gene family in maize remains elusive. In this study, a total of 24 CrRLK1L genes were identified in the maize whole genome. A phylogenetic analysis further revealed that CrRLK1L proteins from Arabidopsis, rice, and maize were grouped into nine distinct subgroups, with subgroup IV being unique to maize. Gene structure analysis demonstrated that the number of introns varied greatly among ZmCrRLK1L genes. Notably, the genome-wide duplication (WGD) events promoted the expansion of the ZmCrRLK1L gene family. Compared with Arabidopsis, there were more collinear gene pairs between maize and rice. Tissue expression patterns indicated that ZmCrRLK1L genes are widely expressed in various tissues, with ZmCrRLK1L5/9 specifically highly expressed in roots, and ZmCrRLK1L8/14/16/21/22 expressed in anthers. Additionally, RNA-seq and RT-qPCR analyses revealed that the expression of ZmCrRLK1L1/2/20/22 genes exhibited different expression patterns under drought and salt stresses. In summary, our study lays a foundation for elucidating the biological roles of ZmCrRLK1L genes in maize growth and development, reproductive development, and stress responses.

Revolutionizing soybean genomics: How CRISPR and advanced sequencing are unlocking new potential

Soybean Glycine max L., paleopolyploid genome, poses challenges to its genetic improvement. However, the development of reference genome assemblies and genome sequencing has completely changed the field of soybean genomics, allowing for more accurate and successful breeding techniques as well as research. During the single-cell revolution, one of the most advanced sequencing tools for examining the transcriptome landscape is single-cell RNA sequencing (scRNA-seq). Comprehensive resources for genetic improvement of soybeans may be found in the SoyBase and other genomics databases. CRISPR-Cas9 genome editing technology provides promising prospects for precise genetic modifications in soybean. This method has enhanced several soybean traits, including as yield, nutritional value, and resistance to both biotic and abiotic stresses. With base editing techniques that allow for precise DNA modifications, the use of CRISPR-Cas9 is further increased. With the availability of the reference genome for soybeans and the following assembly of wild and cultivated soybeans, significant chromosomal rearrangements and gene duplication events have been identified, offering new perspectives on the complex genomic structure of soybeans. Furthermore, major single nucleotide polymorphisms (SNPs) linked to stachyose and sucrose content have been found through genome-wide association studies (GWAS), providing important tools for enhancing soybean carbohydrate profiles. In order to open up new avenues for soybean genetic improvement, future research approaches include investigating transcriptional divergence processes, enhancing genetic resources, and incorporating CRISPR-Cas9 technologies.

Phosphorus-Use-Efficiency Gene Identification in Fabaceae and RSL2 Expansion in Lupinus albus Is Associated with Low-Phosphorus Adaptation

Phosphorus is critical for plant growth but often becomes less accessible due to its precipitation with cations in soil. Fabaceae, a diverse plant family, exhibits robust adaptability and includes species like Lupinus albus, known for its efficient phosphorus utilization via cluster roots. Here, we systematically identified phosphorus-utilization-efficiency (PUE) gene families across 35 Fabaceae species, highlighting significant gene amplification in PUE pathways in Fabaceae. Different PUE pathways exhibited variable amplification, evolution, and retention patterns among various Fabaceae crops. Additionally, the number of homologous genes of the root hair development gene RSL2 in L. albus was far more than that in other Fabaceae species. Multiple copies of the RSL2 gene were amplified and retained in L. albus after whole genome triplication. The gene structure and motifs specifically retained in L. albus were different from homologous genes in other plants. Combining transcriptome analysis under low-phosphorus treatment, it was found that most of the homologous genes of RSL2 in L. albus showed high expression in the cluster roots, suggesting that the RSL2 gene family plays an important role in the adaptation process of L. albus to low-phosphorus environments and the formation of cluster roots.

A spatially resolved multiomic single-cell atlas of soybean development

Cis-regulatory elements (CREs) precisely control spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of gene expression with chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible chromatin regions (ACRs). Nearly 40% of the ACRs showed cell-type-specific patterns and were enriched for transcription factor (TF) motifs defining diverse cell identities. We identified de novo enriched TF motifs and explored conservation of gene regulatory networks underpinning legume symbiotic nitrogen fixation. With comprehensive developmental trajectories for endosperm and embryo, we uncovered the functional transition of the three sub-cell types of endosperm, identified 13 sucrose transporters sharing the DOF11 motif that were co-up-regulated in late peripheral endosperm and identified key embryo cell-type specification regulators during embryogenesis, including a homeobox TF that promotes cotyledon parenchyma identity. This resource provides a valuable foundation for analyzing gene regulatory programs in soybean cell types across tissues and life stages.

Identification of the New GmJAG1 Transcription Factor Binding Motifs Using DAP-Seq

Interaction between transcription factors (TFs) and motifs is essential for gene regulation and the subsequent phenotype formation. Soybean (Glycine max) JAGGEED 1 (GmJAG1) is a key TF that controls leaf shape, seed number and flower size. To understand the GmJAG1 binding motifs, in this study, we performed the GmJAG1 DNA affinity purification sequencing (DAP-seq) experiment, which is a powerful tool for the de novo motif prediction method. Two new significant GmJAG1 binding motifs were predicted and the EMSA experiments further verified the ability of GmJAG1 bound to these motifs. The potential binding sites in the downstream gene promoter were identified through motif scanning and a potential regulatory network mediated by GmJAG1 was constructed. These results served as important genomic resources for further understanding the regulatory mechanism of GmJAG1.

Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton

Polyploidy is a prominent mechanism of plant speciation and adaptation, yet the mechanistic understandings of duplicated gene regulation remain elusive. Chromatin structure dynamics are suggested to govern gene regulatory control. Here, we characterized genome-wide nucleosome organization and chromatin accessibility in allotetraploid cotton, Gossypium hirsutum (AADD, 2n = 4X = 52), relative to its two diploid parents (AA or DD genome) and their synthetic diploid hybrid (AD), using DNS-seq. The larger A-genome exhibited wider average nucleosome spacing in diploids, and this intergenomic difference diminished in the allopolyploid but not hybrid. Allopolyploidization also exhibited increased accessibility at promoters genome-wide and synchronized cis-regulatory motifs between subgenomes. A prominent cis-acting control was inferred for chromatin dynamics and demonstrated by transposable element removal from promoters. Linking accessibility to gene expression patterns, we found distinct regulatory effects for hybridization and later allopolyploid stages, including nuanced establishment of homoeolog expression bias and expression level dominance. Histone gene expression and nucleosome organization are coordinated through chromatin accessibility. Our study demonstrates the capability to track high-resolution chromatin structure dynamics and reveals their role in the evolution of cis-regulatory landscapes and duplicate gene expression in polyploids, illuminating regulatory ties to subgenomic asymmetry and dominance.

Molecular dissection of an intronic enhancer governing cold-induced expression of the vacuolar invertase gene in potato

Potato (Solanum tuberosum) is the third most important food crop in the world. Potato tubers must be stored at cold temperatures to minimize sprouting and losses due to disease. However, cold temperatures strongly induce the expression of the potato vacuolar invertase gene (VInv) and cause reducing sugar accumulation. This process, referred to as "cold-induced sweetening," is a major postharvest problem for the potato industry. We discovered that the cold-induced expression of VInv is controlled by a 200 bp enhancer, VInvIn2En, located in its second intron. We identified several DNA motifs in VInvIn2En that bind transcription factors involved in the plant cold stress response. Mutation of these DNA motifs abolished VInvIn2En function as a transcriptional enhancer. We developed VInvIn2En deletion lines in both diploid and tetraploid potato using clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9)-mediated gene editing. VInv transcription in cold-stored tubers was significantly reduced in the deletion lines. Interestingly, the VInvIn2En sequence is highly conserved among distantly related Solanum species, including tomato (Solanum lycopersicum) and other non-tuber-bearing species. We conclude that the VInv gene and the VInvIn2En enhancer have adopted distinct roles in the cold stress response in tubers of tuber-bearing Solanum species.

Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry

Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and are more highly expressed than those from other subgenome(s). However, the molecular mechanisms responsible for subgenome dominance remain poorly understood. Here, we develop genome-wide map of accessible chromatin regions (ACRs) in cultivated strawberry (2n = 8x = 56, with A, B, C, D subgenomes). Each ACR is identified as an MNase hypersensitive site (MHS). We discover that the dominant subgenome A contains a greater number of total MHSs and MHS per gene than the submissive B/C/D subgenomes. Subgenome A suffers fewer losses of MHS-related DNA sequences and fewer MHS fragmentations caused by insertions of transposable elements. We also discover that genes and MHSs related to stress response have been preferentially retained in subgenome A. We conclude that preservation of genes and their cognate ACRs, especially those related to stress responses, play a major role in the establishment of subgenome dominance in octoploid strawberry.