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SummaryGlyceollins, a family of phytoalexin induced in legume species, play essential roles in responding to environmental stresses and in human health. However, little is known about the genetic basis and selection of glyceollin induction.We employed a metabolite-based genome-wide association (mGWA) approach to identify candidate genes involved in glyceollin induction from genetically diverse and understudied wild soybeans subjected to soybean cyst nematode stress.Eight SNPs on chromosomes 3, 9, 13, 15, and 20 showed significant association with glyceollin induction. Six genes close to one of the significant SNPs (ss715603454) on chromosome 9 fell into two clusters, and they encode enzymes in the glycosyltransferase class within the phenylpropanoid pathway. Transcription factors (TFs) genes, such asMYBandWRKYwere also found within the linkage disequilibrium of the significant SNPs on chromosome 9. Epistasis and a strong selection signal were detected on the four significant SNPs on chromosome 9.Gene clusters and transcription factors may play important roles in regulating glyceollin induction in wild soybeans. Additionally, as major evolutionary factors, epistatic interactions and selection may influence glyceollin variation in natural populations.

Saponins, prominent secondary plant metabolites, are recognized for their roles in plant defense and medicinal benefits. Soyasaponins, commonly derived from legumes, are a class of triterpenoid saponins that demonstrate significant potential for plant and human health applications. Previous research and reviews largely emphasize human health effects of soyasaponins. However, the biological effects of soyasaponins and their implications for plants in the context of human health have not been well-discussed. This review provides comprehensive discussions on the biological roles of soyasaponins in plant defense and rhizosphere microbial interactions; biosynthetic regulation and compound production; immunological effects and potential for therapeutics; and soyasaponin acquisition attributed to processing effects, bioavailability, and biotransformation processes based on recent soyasaponin research. Given the multifaceted biological effects elicited by soyasaponins, further research warrants an integrated approach to understand molecular mechanisms of regulations in their production as well as their applications in plant and human health.

Gamma-aminobutyric acid (GABA) analogs are being used by an increasing number of reproductive-age women. However, there is concern regarding the teratogenic potential of GABA analogs.We performed this systematic review and meta-analysis to assess the relationship between GABA analog exposure and risk of adverse neonatal outcomes.Eight cohort studies were included in the meta-analysis. Exposure to a GABA analog during pregnancy was not associated with an increased risk of congenital malformation (odds ratio [OR] 1.19, 95% confidence interval [CI] 0.96-1.46, P = 0.106) or a small for gestational age (SGA) infant (OR 1.99, 95% CI 0.78-5.1, P = 0.152) compared to no exposure. However, exposure to a GABA analog was associated with an increased risk of preterm birth (PB) (OR 1.56, 95% CI 1.04-2.35, P = 0.033), spontaneous abortion (SA) (OR 1.64, 95% CI 1.14-2.38, P = 0.008), or termination of pregnancy (TOP) (OR 3.02, 95% CI 2-4.56, P 0.001).Exposure to GABA analogs during pregnancy does not appear to be associated with congenital malformation, although there was some evidence of a higher risk of several other negative neonatal outcomes. Given the few studies included, larger prospective studies controlling for important confounders are needed to verify our findings.

This study aimed to investigate the role of estrogen in the differential diagnosis of depression and schizophrenia and its relationship with the curative effects, adverse events.From 2017 to 2019, patients with depression or schizophrenia treated with modern electroconvulsive therapy (MECT) were studied retrospectively. Their serum estrogen levels, Hamilton Depression Scale, and Brief Psychiatric Rating Scale scores were collected. Differences in the estrogen levels between patients with depression and schizophrenia before and after treatment and the correlation of the estrogen level with curative effect and adverse events was evaluated. In total, 67 patients with depression and 61 with schizophrenia were included.There were no significant differences in the baseline characteristics, except the estrogen level (p0.001). Serum estrogen levels increased in both groups after MECT (117 vs. 141 pmol/L, p0.001; 42 vs. 46 pmol/L, respectively; p0.001), and higher estrogen levels were positively correlated with better outcomes (p0.001).Post-MECT estrogen levels were not associated with the incidence rate of adverse events of MECT. Estrogen plays a promising role in distinguishing depression and schizophrenia and evaluating the therapeutic efficacy of MECT.

Polyphenols, such as flavonoids and phenolic acids, are a group of specialized metabolites in plants that largely aid in plant defense by deterring biotic stressors and alleviating abiotic stress. Polyphenols offer a wide range of medical applications, acting as preventative and active treatments for diseases such as cancers and diabetes. Recently, researchers have proposed that polyphenols may contribute to certain applications aimed at tackling challenges related to the COVID-19 pandemic. Understanding the beneficial impacts of phytochemicals, such as polyphenols, could potentially help prepare society for future pandemics. Thus far, most reviews have focused on polyphenols in cancer prevention and treatment. This review aims to provide a comprehensive discussion on the critical roles that polyphenols play in both plant chemical defense and human health based on the most recent studies while highlighting prospective avenues for future research, as well as the implications for phytochemical-based applications in both agricultural and medical fields.

Climate change poses critical challenges for population persistence in natural communities, agriculture and environmental sustainability, and food security. In this review, we discuss recent progress in climatic adaptation in plants. We evaluate whether climate change exerts novel selection and disrupts local adaptation, whether gene flow can facilitate adaptive responses to climate change, and if adaptive phenotypic plasticity could sustain populations in the short term. Furthermore, we discuss how climate change influences species interactions. Through a more in-depth understanding of these eco-evolutionary dynamics, we will increase our capacity to predict the adaptive potential of plants under climate change. In addition, we review studies that dissect the genetic basis of plant adaptation to climate change. Finally, we highlight key research gaps, ranging from validating gene function, to elucidating molecular mechanisms, expanding research systems from model species to other natural species, testing the fitness consequences of alleles in natural environments, and designing multifactorial studies that more closely reflect the complex and interactive effects of multiple climate change factors. By leveraging interdisciplinary tools (e.g., cutting-edge omics toolkits, novel ecological strategies, newly-developed genome editing technology), researchers can more accurately predict the probability that species can persist through this rapid and intense period of environmental change, as well as cultivate crops to withstand climate change, and conserve biodiversity in natural systems.

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them., National Science Foundation 1916797 David W Ehrhardt, Kenneth D Birnbaum, Seung Yon Rhee; National Science Foundation 2052590 Seung Yon Rhee

Background: Seeds are the economic basis of oilseed crops, especially for soybean, thus far the most widely cultivated oilseed crop worldwide. Seed development is accompanied with a multitude of diverse cellular processes and revealing the underlying regulatory activities is critical for seed improvement. Results: Here, we profiled transcriptomes of developing seeds (20, 25, 30, 40 days after flowering) representing key points of seed development from early to full development. We identified a set of highly-abundant genes and highlighted the importance of these genes to support nutrient accumulation and transcriptional regulation in developing seeds. We identified 8,925 differentially expressed genes that exhibited temporal expression patterns over the course and had expression specificities in distinct tissues including seeds and non-seed tissues (roots, stems, leaves). Genes with specificities to non-seed tissues have tissue-specialized roles while remain relatively low transcript abundance in developing seeds, exhibiting their supportive roles spatially for seed development. Co-expression network analysis identified several under-explored genes in soybean that bridge tissue-specific gene modules. Conclusions: Our study provides a global view of gene activities and biological processes critical for seed formation in soybean and prioritizes a set of genes for further study. The results shed insight into the mechanism controlling seed development and storage reserves.

Background Seeds are the economic basis of oilseed crops, especially soybeans, the most widely cultivated oilseed crop worldwide. Seed development is accompanied by a multitude of diverse cellular processes, and revealing the underlying regulatory activities is critical for seed improvement. Results In this study, we profiled the transcriptomes of developing seeds at 20, 25, 30, and 40 days after flowering (DAF), as these stages represent critical time points of seed development from early to full development. We identified a set of highly abundant genes and highlighted the importance of these genes in supporting nutrient accumulation and transcriptional regulation for seed development. We identified 8925 differentially expressed genes (DEGs) that exhibited temporal expression patterns over the course and expression specificities in distinct tissues, including seeds and nonseed tissues (roots, stems, and leaves). Genes specific to nonseed tissues might have tissue-associated roles, with relatively low transcript abundance in developing seeds, suggesting their spatially supportive roles in seed development. Coexpression network analysis identified several underexplored genes in soybeans that bridge tissue-specific gene modules. Conclusions Our study provides a global view of gene activities and biological processes critical for seed formation in soybeans and prioritizes a set of genes for further study. The results of this study help to elucidate the mechanism controlling seed development and storage reserves.

Seed protein, oil content and yield are highly correlated agronomically important traits that essentially account for the economic value of soybean. The underlying molecular mechanisms and selection of these correlated seed traits during soybean domestication are, however, less known. Here, we demonstrate that a CCT gene, POWR1, underlies a large-effect protein/oil QTL. A causative TE insertion truncates its CCT domain and substantially increases seed oil content, weight, and yield while decreasing protein content. POWR1 pleiotropically controls these traits likely through regulating seed nutrient transport and lipid metabolism genes. POWR1 is also a domestication gene. We hypothesize that the TE insertion allele is exclusively fixed in cultivated soybean due to selection for larger seeds during domestication, which significantly contributes to shaping soybean with increased yield/seed weight/oil but reduced protein content. This study provides insights into soybean domestication and is significant in improving seed quality and yield in soybean and other crop species.

Soybean cyst nematode (SCN, Heterodera glycine Ichinohe) is the most damaging soybean pest worldwide and management of SCN remains challenging. The current SCN resistant soybean cultivars, mainly developed from the cultivated soybean gene pool, are losing resistance due to SCN race shifts. The domestication process and modern breeding practices of soybean cultivars often involve strong selection for desired agronomic traits, and thus, decreased genetic variation in modern cultivars, which consequently resulted in limited sources of SCN resistance. Wild soybean (Glycine soja) is the wild ancestor of cultivated soybean (Glycine max) and it’s gene pool is indisputably more diverse than G. max. Our aim is to identify novel resistant genetic resources from wild soybean for the development of new SCN resistant cultivars. In this study, resistance response to HG type 2.5.7 (race 5) of SCN was investigated in a newly identified SCN resistant ecotype, NRS100. To understand the resistance mechanism in this ecotype, we compared RNA seq-based transcriptomes of NRS100 with two SCN-susceptible accessions of G. soja and G. max, as well as an extensively studied SCN resistant cultivar, Peking, under both control and nematode J2-treated conditions. The proposed mechanisms of resistance in NRS100 includes the suppression of the jasmonic acid (JA) signaling pathway in order to allow for salicylic acid (SA) signaling-activated resistance response and polyamine synthesis to promote structural integrity of root cell walls. Our study identifies a set of novel candidate genes and associated pathways involved in SCN resistance and the finding provides insight into the mechanism of SCN resistance in wild soybean, advancing the understanding of resistance and the use of wild soybean-sourced resistance for soybean improvement.

Porous metal–organic frameworks (MOFs) are structures made up of inorganic nodes and organic ligands, which can be used as crystalline vessels to accommodate various functional guests. This study reports on the drug delivery of a new porous metal–organic framework [Zn3(BTC)2(Aml)(H2O)2](MeOH)6 (1, H3BTC = 1,3,5-benzenetricarboxylic acid, Aml = ammeline). The Zn-MOF nanocomposites were synthesized by reaction of Zn(NO3)2·6H2O and the organic ligand with the aid of polyvinyl pyrrolidone. Stability and porosity of this nanostructure have been confirmed via the PXRD measurement and gas sorption studies. Due to its large BET surface areas, suitable window size, and high density of open free N sites, this MOF has been used for the anticancer drug 5-fluorouracil (5-Fu) storage/delivery, a moderate–high 5-Fu loading capacity, and pH-dependent drug release behavior which could be observed. Furthermore, the in vitro cytotoxicity of the nano-1 and the 5-Fu@nano-1 composite toward the human normal fibroblastic epithelial cell line (HFL1) and human liver cancer cell line HepG2 has been evaluated via the MTT assay.

Two new three-dimensional coordination polymers (H2NMe2)[Dy4(µ3−OH)4(NMF)3(H2O)(L1)3](H2O)2 (1, NMF = N-methylformamide, H3L1 = 3,5-bis(4-(1H-tetrazol-5-yl)phenoxy)benzoic acid) and [Cu(L2)2(H2O)](H2O)2 (2, H2L2 = 4-(4-pyridyl)-isophthalic acid) have been successfully prepared using two N,O-mixed donor organic ligands. The structures of these complexes have been successfully determined by single crystal X-ray diffraction. In addition, in vitro antitumor activity of compounds 1 and 2 on four human liver cancer cells (SMMC7721, Bel-7402, MHCC97 and HCCLM3) was further determined and the results show that the two compounds showed promising activity.

Soybean [ Glycine max (L.) Merr.] is an important crop rich in vegetable protein and oil, and is a staple food for human and animals worldwide. However, soybean plants have been challenged by soybean cyst nematode (SCN, Heterodera glycines ), one of the most damaging pests found in soybean fields. Applying SCN-resistant cultivars is the most efficient and environmentally friendly strategy to manage SCN. Currently, soybean breeding and further improvement in soybean agriculture are hindered by severely limited genetic diversity in cultivated soybeans. G . soja is a soybean wild progenitor with much higher levels of genetic diversity compared to cultivated soybeans. In this study, transcriptomes of the resistant and susceptible genotypes of the wild soybean, Glycine soja Sieb & Zucc, were sequenced to examine the genetic basis of SCN resistance. Seedling roots were treated with infective second-stage juveniles (J2s) of the soybean cyst nematode (HG type 2.5.7) for 3, 5, 8 days and pooled for library construction and RNA sequencing. The transcriptome sequencing generated approximately 245 million (M) high quality (Q > 30) raw sequence reads (125 bp in length) for twelve libraries. The raw sequence reads were deposited in NCBI sequence read archive (SRA) database, with the accession numbers SRR5227314-25. Further analysis of this data would be helpful to improve our understanding of the molecular mechanisms of soybean-SCN interaction and facilitate the development of diverse SCN resistance cultivars.

Deleterious effects of climate change and human activities, as well as diverse environmental stresses, present critical challenges to food production and the maintenance of natural diversity. These challenges may be met by the development of novel crop varieties with increased biotic or abiotic resistance that enables them to thrive in marginal lands. However, considering the diverse interactions between crops and environmental factors, it is surprising that evolutionary principles have been underexploited in addressing these food and environmental challenges. Compared with domesticated cultivars, crop wild relatives (CWRs) have been challenged in natural environments for thousands of years and maintain a much higher level of genetic diversity. In this review, we highlight the significance of CWRs for crop improvement by providing examples of CWRs that have been used to increase biotic and abiotic stress resistance/tolerance and overall yield in various crop species. We also discuss the surge of advanced biotechnologies, such as next‐generation sequencing technologies and omics, with particular emphasis on how they have facilitated gene discovery in CWRs. We end the review by discussing the available resources and conservation of CWRs, including the urgent need for CWR prioritization and collection to ensure continuous crop improvement for food sustainability.

The legume family (Fabaceae) is the third-largest flowering family with over 18 000 species worldwide that are rich in proteins, oils, and nutrients. However, the production potential of legume-derived food cannot meet increasing global demand. Wild legumes represent a large group of wild species adaptive to diverse habitats and harbor rich genetic diversity for the improvement of the agronomic, nutritional, and medicinal values of the domesticated legumes. Accumulating evidence suggests that the genetic variation retained in these under-exploited leguminous wild relatives can be used to improve crop yield, nutrient contents, and resistance/tolerance to environmental stresses via the integration of omics, genetics, and genome-editing technologies.

Strophostyles helvola is a close relative to common bean (Phaseolus vulgaris) and inhabits both coastal and non-coastal regions in North America. However, the mechanism of saline adaptation in S. helvola remains unclear. A transcriptome profiling would facilitate dissecting the underlying molecular mechanisms in salinity-adapted S. helvola. In this study, we reported the RNA-seq analyses of two genotypes (a salt-tolerant beach genotype and a salt-sensitive inland genotype) of S. helvola stressed with salt. S. helvola plants were grown in pots and treated with half lethal-guided dose of NaCl solution for 3 h, 24 h, and 7d. The plants supplied with the same amount of water were used as controls. The whole roots sampled from the three time points were equally pooled as one biological replicate, and three replicates were used for library construction and transcriptome sequencing on Illumina Hiseq 2500. The comparative analyses of root transcriptomes presented here provides a valuable resource for discovery of genes and networks involved in salt tolerance in S. helvola.

A fundamental goal in evolutionary biology is to understand how various evolutionary factors interact to affect the population structure of diverse species, especially those of ecological and/or agricultural importance such as wild soybean (Glycine soja). G. soja, from which domesticated soybeans (Glycine max) were derived, is widely distributed throughout diverse habitats in East Asia (Russia, Japan, Korea, and China). Here, we utilize over 39,000 single nucleotide polymorphisms genotyped in 99 ecotypes of wild soybean sampled across their native geographic range in northeast Asia, to understand population structure and the relative contribution of environment versus geography to population differentiation in this species. A STRUCTURE analysis identified four genetic groups that largely corresponded to the geographic regions of central China, northern China, Korea, and Japan, with high levels of admixture between genetic groups. A canonical correlation and redundancy analysis showed that environmental factors contributed 23.6% to population differentiation, much more than that for geographic factors (6.6%). Precipitation variables largely explained divergence of the groups along longitudinal axes, whereas temperature variables contributed more to latitudinal divergence. This study provides a foundation for further understanding of the genetic basis of climatic adaptation in this ecologically and agriculturally important species.

A worldwide food shortage has been projected as a result of the current increase in global population and climate change. In order to provide sufficient food to feed more people, we must develop crops that can produce higher yields. Plant early vigor traits, early growth rate (EGR), early plant height (EPH), inter-node length, and node count are important traits that are related to crop yield. Glycine soja, the wild counterpart to cultivated soybean, Glycine max, harbors much higher genetic diversity and can grow in diverse environments. It can also cross easily with cultivated soybean. Thus, it holds a great potential in developing soybean cultivars with beneficial agronomic traits. In this study, we used 225 wild soybean accessions originally from diverse environments across its geographic distribution in East Asia. We quantified the natural variation of several early vigor traits, investigated the relationships among them, and dissected the genetic basis of these traits by applying a Genome-Wide Association Study (GWAS) with genome-wide single nucleotide polymorphism (SNP) data. Our results showed positive correlation between all early vigor traits studied. A total of 12 SNPs significantly associated with EPH were identified with 4 shared with EGR. We also identified two candidate genes, Glyma.07G055800.1 and Glyma.07G055900.1, playing important roles in influencing trait variation in both EGR and EPH in G. soja.

There is a considerable demand for crop improvement, especially considering the increasing growth of world population, continuing climatic fluctuations, and rapidly evolving plant pests and pathogens. Crop wild relatives hold great potential in providing beneficial alleles for crop improvement. Wild soybean, Glycine soja (Siebold & Zucc.), the wild ancestor to the domesticated soybean (Glycine max (L.) Merr.), harbors a high level of genetic variation. Research on G. soja has been largely devoted to understanding the domestication history of the soybean, while little effort has been made to explore its genetic diversity for crop improvement. High genomic diversity and expanded traits make G. soja populations an excellent source for soybean improvement. This review summarizes recent successful research examples of applying wild soybeans in dissecting the genetic basis of various traits, with a focus on abiotic/biotic stress tolerance and resistance. We also discuss the limitations of using G. soja. Perspective future research is proposed, including the application of advanced biotechnology and emerging genomic data to further utilize the wild soybean to counterbalance the rising demand for superior crops. We proposed there is an urgent need for international collaboration on germplasm collection, resource sharing, and conservation. We hope to use the wild soybean as an example to promote the exploration and use of wild resources for crop improvement in order to meet future food requirements.

Two novel organic-inorganic hybrid materials {(Hbiz)6[AsIII2AsVMoVI18O62]}·H2O (1, biz = benzimidazole) and (dim)[AsIII2AsVMoVI18O62] [2, dim = 1,6-bis(imidazol)hexane] have been successfully obtained by using the molybdenum arsenate and different N donor organic compounds and determined through X-ray single-crystal diffraction technique. The in vitro cytotoxicity of compounds 1 and 2 was then investigated against three human liver tumor cell lines (SMMC7721, Bel-7402, and MHCC97) by MTT assay. It was found that the two compounds showed potent use as antitumor agents against the aforementioned cell lines.

Crop wild relatives harbor exotic and novel genetic resources, which hold great potential for crop improvement. Ipomoea imperati is a wild diploid relative of sweet potato with the capability of high salinity tolerance. We compared the transcriptomes of I. imperati under salt stress vs. control to identify candidate genes and pathways involved in salt response. De novo assembly produced 67,911 transcripts with a high depth of coverage. A total of 39,902 putative genes were assigned annotations, and 936 and 220 genes involved in salt response in roots and leaves, respectively. Functional analysis indicated a whole system response during salt stress in I. imperati, which included four metabolic processes: sensory initiation, transcriptional reprogramming, cellular protein component change, and cellular homeostasis regulation. We identified a number of candidate genes involved in the ABA signaling pathway, as well as transcription factors, transporters, antioxidant enzymes, and enzymes associated with metabolism of synthesis and catalysis. Furthermore, two membrane transporter genes, including vacuole cation/proton exchanger and inositol transporter, were considered to play important roles in salt tolerance. This study provided valuable information not only for understanding the genetic basis of ecological adaptation but also for future application in sweet potato and other crop improvements.

Soybean cyst nematode (SCN) is the most damaging pest of soybean worldwide. The molecular mechanism of SCN resistance remains largely unknown. We conducted a global RNA-seq comparison between a resistant genotype (S54) and a susceptible genotype (S67) of Glycine soja, the wild progenitor of soybean, to understand its regulatory network in SCN defense. The number of differentially expressed genes (DEGs) in S54 (2,290) was much larger than that in S67 (555). A number of defense-related genes/pathways were significantly induced only in S54, while photosynthesis and several metabolic pathways were affected in both genotypes with SCN infection. These defense-associated DEGs were involved in pathogen recognition, calcium/calmodulin-mediated defense signaling, jasmonic acid (JA)/ethylene (ET) and sialic acid (SA)-involved signaling, the MAPK signaling cascade, and WRKY-involved transcriptional regulation. Our results revealed a comprehensive regulatory network involved in SCN resistance and provided insights into the complex molecular mechanisms of SCN resistance in wild soybean.

A set of nested association mapping (NAM) families was developed by crossing 40 diverse soybean [ (L.) Merr.] genotypes to the common cultivar. The 41 parents were deeply sequenced for SNP discovery. Based on the polymorphism of the single-nucleotide polymorphisms (SNPs) and other selection criteria, a set of SNPs was selected to be included in the SoyNAM6K BeadChip for genotyping the parents and 5600 RILs from the 40 families. Analysis of the SNP profiles of the RILs showed a low average recombination rate. We constructed genetic linkage maps for each family and a composite linkage map based on recombinant inbred lines (RILs) across the families and identified and annotated 525,772 high confidence SNPs that were used to impute the SNP alleles in the RILs. The segregation distortion in most families significantly favored the alleles from the female parent, and there was no significant difference of residual heterozygosity in the euchromatic vs. heterochromatic regions. The genotypic datasets for the RILs and parents are publicly available and are anticipated to be useful to map quantitative trait loci (QTL) controlling important traits in soybean.

Background Soybean seed weight is not only a yield component, but also a critical trait for various soybean food products such as sprouts, edamame, soy nuts, natto and miso. Linkage analysis and genome-wide association study (GWAS) are two complementary and powerful tools to connect phenotypic differences to the underlying contributing loci. Linkage analysis is based on progeny derived from two parents, given sufficient sample size and biological replication, it usually has high statistical power to map alleles with relatively small effect on phenotype, however, linkage analysis of the bi-parental population can’t detect quantitative trait loci (QTL) that are fixed in the two parents. Because of the small seed weight difference between the two parents in most families of previous studies, these populations are not suitable to detect QTL that have considerable effects on seed weight. GWAS is based on unrelated individuals to detect alleles associated with the trait under investigation. The ability of GWAS to capture major seed weight QTL depends on the frequency of the accessions with small and large seed weight in the population being investigated. Our objective was to identify QTL that had a pronounced effect on seed weight using a selective population of soybean germplasm accessions and the approach of GWAS and fixation index analysis. Results We selected 166 accessions from the USDA Soybean Germplasm Collection with either large or small seed weight and could typically grow in the same location. The accessions were evaluated for seed weight in the field for two years and genotyped with the SoySNP50K BeadChip containing >42,000 SNPs. Of the 17 SNPs on six chromosomes that were significantly associated with seed weight in two years based on a GWAS of the selective population, eight on chromosome 4 or chromosome 17 had significant Fst values between the large and small seed weight sub-populations. The seed weight difference of the two alleles of these eight significant SNPs varied from 8.1 g to 11.7 g/100 seeds in two years. We also identified haplotypes in three haplotype blocks with significant effects on seed weight. These findings were validated in a panel with 3753 accessions from the USDA Soybean Germplasm Collection. Conclusion This study highlighted the usefulness of selective genotyping populations coupled with GWAS and fixation index analysis for the identification of QTL with substantial effects on seed weight in soybean. This approach may help geneticists and breeders to more efficiently identify major QTL controlling other traits. The major regions and haplotypes we have identified that control seed weight differences in soybean will facilitate the identification of genes regulating this important trait. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3922-0) contains supplementary material, which is available to authorized users.

The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants the molecular signals of genome duplications have remained largely unexplored. High-throughput transcriptome data from next-generation sequencing have set the stage for novel investigations of genome evolution using new bioinformatic and methodological tools in a phylogenetic framework. Here we compare ten de novo-assembled transcriptomes representing the major lineages of the angiosperm genus Cornus (dogwood) and relevant outgroups using a customized pipeline for analyses. Using three distinct approaches, molecular dating of orthologous genes, analyses of the distribution of synonymous substitutions between paralogous genes, and examination of substitution rates through time, we detected a shared WGD event in the late Cretaceous across all taxa sampled. The inferred doubling event coincides temporally with the paleoclimatic changes associated with the initial divergence of the genus into three major lineages. Analyses also showed an acceleration of rates of molecular evolution after WGD. The highest rates of molecular evolution were observed in the transcriptome of the herbaceous lineage, C. canadensis, a species commonly found at higher latitudes, including the Arctic. Our study demonstrates the value of transcriptome data for understanding genome evolution in closely related species. The results suggest dramatic increase in sea surface temperature in the late Cretaceous may have contributed to the evolution and diversification of flowering plants.

Many biological species are threatened with extinction because of a number of factors such as climate change and habitat loss, and their preservation depends on an accurate understanding of the extent of their genetic variability within and among populations. In this study, we assessed the genetic divergence of five quantitative traits in 10 populations of an endangered cruciferous species, Boechera fecunda, found in only several populations in each of two geographic regions (WEST and EAST) in southwestern Montana. We analyzed variation in quantitative traits, neutral molecular markers, and environmental factors and provided evidence that despite the restricted geographical distribution of this species, it exhibits a high level of genetic variation and regional adaptation. Conservation efforts therefore should be directed to the preservation of populations in each of these two regions without attempting transplantation between regions. Heritabilities and genetic coefficients of variation estimated from nested ANOVAs were generally high for leaf and rosette traits, although lower (and not significantly different from 0) for water-use efficiency. Measures of quantitative genetic differentiation, Q ST, were calculated for each trait from each pair of populations. For three of the five traits, these values were significantly higher between regions compared with those within regions (after adjustment for neutral genetic variation, F ST). This suggested that natural selection has played an important role in producing regional divergence in this species. Our analysis also revealed that the B. fecunda populations appear to be locally adapted due, at least in part, to differences in environmental conditions in the EAST and WEST regions.