Episymbiotic Saccharibacteria TM7x modulates the susceptibility of its host bacteria to phage infection and promotes their coexistence.

Bacteriophages (phages) play critical roles in modulating microbial ecology. Within the human microbiome, the factors influencing the long-term coexistence of phages and bacteria remain poorly investigated. Saccharibacteria (formerly TM7) are ubiquitous members of the human oral microbiome. These ultrasmall bacteria form episymbiotic relationships with their host bacteria and impact their physiology. Here, we showed that during surface-associated growth, a human oral Saccharibacteria isolate (named TM7x) protects its host bacterium, a Schaalia odontolytica strain (named XH001) against lytic phage LC001 predation. RNA-Sequencing analysis identified in XH001 a gene cluster with predicted functions involved in the biogenesis of cell wall polysaccharides (CWP), whose expression is significantly down-regulated when forming a symbiosis with TM7x. Through genetic work, we experimentally demonstrated the impact of the expression of this CWP gene cluster on bacterial-phage interaction by affecting phage binding. In vitro coevolution experiments further showed that the heterogeneous populations of TM7x-associated and TM7x-free XH001, which display differential susceptibility to LC001 predation, promote bacteria and phage coexistence. Our study highlights the tripartite interaction between the bacterium, episymbiont, and phage. More importantly, we present a mechanism, i.e., episymbiont-mediated modulation of gene expression in host bacteria, which impacts their susceptibility to phage predation and contributes to the formation of "source-sink" dynamics between phage and bacteria in biofilm, promoting their long-term coexistence within the human microbiome.

Stability enhancing of perovskite LaCoO3 by compositing with oxygen doped MoS2 in Fenton-like reactions.

Perovskite materials are reported to be effective in peroxymonosulfate (PMS) based Fenton-like reactions, the leaching rates of chalcogenide materials in perovskite materials are however serious, thus leading to bad performance in long-term stability. In this study, an O-doped MoS2 is synthesized to composite with LaCoO3, and the high catalytic activity of LaCoO3 is well preserved with greatly decreased Co leaching. During the BPA degradation with PMS as oxidant, ∼100% degradation can be achieved in 20 min and this degradation efficiency can be maintained for ∼45 h in a simulated fixed bed reactor, which is almost 3 times longer than the pure LaCoO3. With the compositing of O-doped MoS2, the leached Co was greatly decreased and the dominated reactive oxidation species (ROS) transformed from SO4•- into O2•- with longer lifespan, thus resulting in the better stability. This study could promote the application of perovskite materials in the real industrial wastewater treatment.

Influence of resin modified glass ionomer cement incorporating protein-repellent and antimicrobial agents on supragingival microbiome around brackets: an in-vivo split-mouth 3-month study.

Objective: To explore the influence of resin modified glass ionomer cement (RMGIC) adhesives containing protein-repellent and quaternary ammonium salt agents on supragingival microbiome, enamel and gingival health around brackets. Materials and Methods: Ten patients (21.4 ± 3.5 years) about to receive fixed orthodontics were enrolled in this study. Unilateral upper teeth bonded with RMGIC incorporating 2-Methacryloyloxyethyl phosphorylcholine (MPC) and Dimethylaminohexadecyl methacrylate (DMAHDM) were regarded as experimental group (RMD), while contralateral upper teeth bonded with RMGIC were control group (RMGIC), using a split-mouth design. Supragingival plaque was collected from both groups before treatment (T0), and at 1 month (T1) and 3 months (T2) of treatment. High-throughput sequencing was performed targeting v3-v4 of 16S rRNA gene. Streptococcus mutans and Fusobacterium nucleatum quantification was done by qPCR analysis. Bracket failures, enamel decalcification index (EDI), DIAGNODent scores (Dd), plaque index (PI) and gingival index (GI) were monitored at indicated time points. Results: Within 3 months, alpha and beta diversity of supragingival plaque had no difference between RMGIC and RMD groups. From T0 to T2, the relative abundance of Streptococcus depleted in RMD but remained steady in RMGIC group. Streptococcus, Prevotella, and Fusobacterium became depleted in RMD, Haemophilus and Capnocytophaga became depleted in RMGIC group but Prevotella enriched. Quantification of Fusbacterium nucleatum and Streptococcus mutans showed significant difference between RMGIC and RMD groups at T2. Teeth bonded with RMD had significant lower plaque index (PI) and DIAGNODent (Dd) score at T2, compared with teeth bonded with RMGIC (p < 0.05). No difference in bracket failure rate was examined between both groups (p > 0.05). Conclusion: By incorporating MPC and DMAHDM into RMGIC, the material could affect the supragingival microbial composition, inhibit the progress of plaque accumulation as well as the key pathogens S. mutans and F. nucleatum in the early stage of orthodontic treatment.

Candida albicans enriched in orthodontic derived white spot lesions and shaped focal supragingival bacteriome.

White spot lesions (WSLs) are common enamel infectious diseases in fixed orthodontic treatment, which might attribute to the dysbiosis of oral microbiome. However, the correlation of Candida albicans with oral bacteriome in WSLs still remains unrevealed. This study investigated the carriage of C. albicans and how it shaped the bacterial community in disease or healthy supragingival plaque, to explore the potential role of interkingdom interaction in orthodontic WSLs. In this study, 31 patients with WSLs (WSLs) and 23 healthy patients (Health) undergoing fixed orthodontic treatment were enrolled. The supragingival microbiota in both groups were determined using 16S rRNA gene sequencing. Colonization and abundance of C. albicans in the plaque were determined via culture-dependent and -independent methods. Among WSLs patients, the correlation of C. albicans and bacteriome was analyzed under QIIME2-based bioinformatics and Spearman's correlation coefficient. The raw reads were deposited into the NCBI Sequence Read Archive (SRA) database (Accession Number: SRP404186). Significant differences in microbial diversity as well as composition were observed between WSLs and Health groups. Leptotrichia remarkably enriched in the WSLs group, while Neisseria and Cardiobacterium significantly enriched in the Health group. In addition, 45% of WSLs patients were C. albicans carriers but none in patients without WSLs. Among all WSLs patients, beta diversity and microbial composition were distinguished between C. albicans carriers and non-carriers. In C. albicans carriers, Corynebacterium matruchotii and Streptococcus mutans significantly enriched whereas Saccharibacteria_TM7_G-1 significantly depleted. The abundance of C. albicans was positively associated with bacteria such as Streptococcus mutans, while the negative correlation was detected between C. albicans and several bacteria such as Cardiobacterium hominis and Streptococcus sanguinis. Our study elucidated the distinguished supragingival plaque microbiome between orthodontic patients with and without WSLs. C. albicans frequently existed and enriched in orthodontic derived WSLs. The carriage of C. albicans shape plaque bacterial community in demineralized lesions and might play roles in WSLs pathogenesis.

Yttrium aluminum garnet-based filler resin composites used as clear aligner attachments.

The objective of this study was to develop a novel resin composite containing yttrium aluminum garnet (Y3Al5O12, YAG) nanoparticles for clear aligner attachments. After the silanization of YAG, their Fourier-transform infrared (FT-IR) and thermogravimetric (TGA) analyses were performed. By conducting flexural and compressive strength measurements, the optimal YAG concentration was selected for the subsequent experiments. Next, Vickers microhardness values, fluidities, attachment volumes, conversion degrees, and volumetric shrinkages of the resin were determined. The obtained FT-IR and TG results revealed that γ-methacryloxypropy ltrimethoxysilane coupling agent was successfully grafted onto the surface of YAG, which enabled their use as inorganic fillers. Furthermore, adding 9 wt% YAG in the resin can increase Vickers hardness and fluidity, reduce polymerization shrinkage, and enhance the restoration of the clear aligner attachment shape on the premise of guarantee proper flexural and compressive strength of the resin, which can help control tooth movement and increase orthodontic efficiency.

Exploitation of a Bacterium-Encoded Lytic Transglycosylase by a Human Oral Lytic Phage To Facilitate Infection.

Bacteriophages (phages) are an integral part of the human oral microbiome. Their roles in modulating bacterial physiology and shaping microbial communities have been discussed but remain understudied due to limited isolation and characterization of oral phage. Here, we report the isolation of LC001, a lytic phage targeting human oral Schaalia odontolytica (formerly known as Actinomyces odontolyticus) strain XH001. We showed that LC001 attached to and infected surface-grown, but not planktonic, XH001 cells, and it displayed remarkable host specificity at the strain level. Whole-genome sequencing of spontaneous LC001-resistant, surface-grown XH001 mutants revealed that the majority of the mutants carry nonsense or frameshift mutations in XH001 gene APY09_05145 (renamed ltg-1), which encodes a putative lytic transglycosylase (LT). The mutants are defective in LC001 binding, as revealed by direct visualization of the significantly reduced attachment of phage particles to the XH001 spontaneous mutants compared that to the wild type. Meanwhile, targeted deletion of ltg-1 produced a mutant that is defective in LC001 binding and resistant to LC001 infection even as surface-grown cells, while complementation of ltg-1 in the mutant background restored the LC001-sensitive phenotype. Intriguingly, similar expression levels of ltg-1 were observed in surface-grown and planktonic XH001, which displayed LC001-binding and nonbinding phenotypes, respectively. Furthermore, the overexpression of ltg-1 failed to confer an LC001-binding and -sensitive phenotype to planktonic XH001. Thus, our data suggested that rather than directly serving as a phage receptor, ltg-1-encoded LT may increase the accessibility of phage receptor, possibly via its enzymatic activity, by cleaving the peptidoglycan structure for better receptor exposure during peptidoglycan remodeling, a function that can be exploited by LC001 to facilitate infection. IMPORTANCE The evidence for the presence of a diverse and abundant phage population in the host-associated oral microbiome came largely from metagenomic analysis or the observation of virus-like particles within saliva/plaque samples, while the isolation of oral phage and investigation of their interaction with bacterial hosts are limited. Here, we report the isolation of LC001, the first lytic phage targeting oral Schaalia odontolytica. Our study suggested that LC001 may exploit the host bacterium-encoded lytic transglycosylase function to gain access to the receptor, thus facilitating its infection.

Dissection of the practical soybean breeding pipeline by developing ZDX1, a high-throughput functional array.

KEY MESSAGE: We developed the ZDX1 high-throughput functional soybean array for high accuracy evaluation and selection of both parents and progeny, which can greatly accelerate soybean breeding. Microarray technology facilitates rapid, accurate, and economical genotyping. Here, using resequencing data from 2214 representative soybean accessions, we developed the high-throughput functional array ZDX1, containing 158,959 SNPs, covering 90.92% of soybean genes and sites related to important traits. By application of the array, a total of 817 accessions were genotyped, including three subpopulations of candidate parental lines, parental lines and their progeny from practical breeding. The fixed SNPs were identified in progeny, indicating artificial selection during the breeding process. By identifying functional sites of target traits, novel soybean cyst nematode-resistant progeny and maturity-related novel sources were identified by allele combinations, demonstrating that functional sites provide an efficient method for the rapid screening of desirable traits or gene sources. Notably, we found that the breeding index (BI) was a good indicator for progeny selection. Superior progeny were derived from the combination of distantly related parents, with at least one parent having a higher BI. Furthermore, new combinations based on good performance were proposed for further breeding after excluding redundant and closely related parents. Genomic best linear unbiased prediction (GBLUP) analysis was the best analysis method and achieved the highest accuracy in predicting four traits when comparing SNPs in genic regions rather than whole genomic or intergenic SNPs. The prediction accuracy was improved by 32.1% by using progeny to expand the training population. Collectively, a versatile assay demonstrated that the functional ZDX1 array provided efficient information for the design and optimization of a breeding pipeline for accelerated soybean breeding.

Genome-wide association of single nucleotide polymorphism loci and candidate genes for frogeye leaf spot (Cercospora sojina) resistance in soybean.

BACKGROUND: Frogeye leaf spot (FLS) is a destructive fungal disease that affects soybean production. The most economical and effective strategy to control FLS is the use of resistant cultivars. However, the use of a limited number of resistant loci in FLS management will be countered by the emergence of new high-virulence Cercospora sojina races. Therefore, we identified quantitative trait loci (QTL) that control resistance to FLS and identified novel resistant genes using a genome-wide association study (GWAS) on 234 Chinese soybean cultivars. RESULTS: A total of 30,890 single nucleotide polymorphism (SNP) markers were used to estimate linkage disequilibrium (LD) and population structure. The GWAS results showed four loci (p < 0.0001) distributed over chromosomes (Chr.) 5 and 20, that are significantly associated with FLS resistance. No previous studies have reported resistance loci in these regions. Subsequently, 45 genes in the two resistance-related haplotype blocks were annotated. Among them, Glyma20g31630 encoding pyruvate dehydrogenase (PDH), Glyma05g28980, which encodes mitogen-activated protein kinase 7 (MPK7), and Glyma20g31510, Glyma20g31520 encoding calcium-dependent protein kinase 4 (CDPK4) in the haplotype blocks deserves special attention. CONCLUSIONS: This study showed that GWAS can be employed as an effective strategy for identifying disease resistance traits in soybean and narrowing SNPs and candidate genes. The prediction of candidate genes in the haplotype blocks identified by disease resistance loci can provide a useful reference to study systemic disease resistance.

Episymbiotic Saccharibacteria suppresses gingival inflammation and bone loss in mice through host bacterial modulation.

Saccharibacteria (TM7) are obligate epibionts living on the surface of their host bacteria and are strongly correlated with dysbiotic microbiomes during periodontitis and other inflammatory diseases, suggesting they are putative pathogens. However, due to the recalcitrance of TM7 cultivation, causal research to investigate their role in inflammatory diseases is lacking. Here, we isolated multiple TM7 species on their host bacteria from periodontitis patients. These TM7 species reduce inflammation and consequential bone loss by modulating host bacterial pathogenicity in a mouse ligature-induced periodontitis model. Two host bacterial functions involved in collagen binding and utilization of eukaryotic sialic acid are required for inducing bone loss and are altered by TM7 association. This TM7-mediated downregulation of host bacterial pathogenicity is shown for multiple TM7/host bacteria pairs, suggesting that, in contrast to their suspected pathogenic role, TM7 could protect mammalian hosts from inflammatory damage induced by their host bacteria.

Effects of Fluoride and Calcium Phosphate Materials on Remineralization of Mild and Severe White Spot Lesions.

Fixed orthodontic treatments often lead to enamel demineralization and cause white spot lesions (WSLs). The aim of this study was to evaluate the mineralization degree of 2 types of WSLs based on ICDAS index and compare the remineralizing efficacy of 3 oral hygiene practices after 1 month and 3 months. 80 mild demineralized and 80 severe demineralized enamel specimens were randomized into three treatments: fluoride toothpaste (FT), fluoride varnish plus fluoride toothpaste (FV+FT), and CPP-ACP plus fluoride toothpaste (CPP-ACP+FT). Microhardness tester, DIAGNODent Pen 2190, and scanning electron microscope were used to evaluate the changes of mineralization degree. Both qualitative and quantitative indicators suggested that the mild and severe white spot lesions were different in the degree of mineralization. Severe WSLs demineralized much more seriously than mild lesions even after 3 months of treatment. Despite the variation in severity, both lesions had the same variation trend after each measure was applied: FT had weak therapeutic effect, FV + FT and CPP-ACP + FT were effective for remineralization. Their remineralizing efficacy was similar after 1 month, and combined use of CPP-ACP plus F toothpaste was more effective after 3 months. In order to fight WSLs, early diagnosis was of great importance, and examination of the tooth surface after air-dry for 5 seconds was recommended. Also, when WSLs were found, added remineralizing treatments were required.

Design and synthesis of amine-functionalized cellulose with multiple binding sites and their application in CC bond forming reactions.

Straw is a green and promising material in nature. However, as is the case for all other biopolymers, straw have to face the challenge of underutilization thereby resulting in environmental and economic issues. To overcome these drawbacks, the urgent exploitation of straw is needed for its comprehensive utilization. In this paper, we chose cellulose as the straw model to prepare two amine ligands functionalized environmentally-friendly cellulose supported catalyst. The ethylenediamine functionalized cellulose catalyst (ADC) was effective in the reaction of aromatic aldehydes with nitromethane to synthesize nitroalkenes and 1,3­dinitroalkanes. Based on ADC, the diethylenetriamine functionalized cellulose (CL-DETA-Cl) could capture Pd firmly by virtue of the covalent bonding between diethylenetriamine functionalized cellulose and palladium nanoparticles. The synthesized catalyst (CL-DETA-Pd) was then illuminated by using FT-IR, TGA, XRD, TEM, ICP-OES and XPS. The multifunctional complex could catalyze the Suzuki-Miyaura reactions efficiently and prevented the metal leaching through the multiple capturing sites (hydroxyl and amine groups) with palladium. Also, the catalyst could be completely regenerated in a few cycles with simple centrifugation. This study will provide reliable foundation and extensive application way to further utilization of straw.

Differences in Zwitterionic Sulfobetaine and Carboxybetaine Dextran-Based Hydrogels.

Zwitterionic sulfobetaine (SB) and carboxybetaine (CB) have been extensively investigated for their noticeable antifouling properties. Both SB and CB have cationic and anionic groups in the molecule, but they differ in negatively charged groups. Molecular simulations have been conducted to investigate the different properties induced by structure changes. However, few studies have focused on the differences between SB and CB materials, especially zwitterionic polysaccharides. Two zwitterionic sulfobetaine and carboxybetaine dextran hydrogels were designed and used as models to compare their properties. Results showed that the equilibrium swelling ratios of the SB-DEX hydrogels were much higher than CB-DEX ones, and larger interior pores were observed in the SB-DEX hydrogels due to their higher hydrophilicity. The rheological storage modulus of the SB-DEX hydrogels was lower than that of CB-DEX ones as a result of higher water content of SB-DEX. These results were consistent with molecular modeling. Additionally, both CB-DEX and SB-DEX had remarkable biocompatibilities, and the in vitro release studies showed that the SB-DEX and CB-DEX hydrogels released DOX in a sustained manner under acidic condition (pH 5.0), indicating their promise as an effective drug-delivery system.

Genome-wide association mapping of QTL underlying seed oil and protein contents of a diverse panel of soybean accessions.

To investigate the genetic basis of variation in oil and protein contents in soybean seeds, a diverse collection of 421 mainly Chinese soybean cultivars was genotyped using 1536 SNPs, mostly from candidate genes related to acyl-lipid metabolism and from regions harboring known QTL. Six significant associations were identified for each of seed oil and protein contents which individually explained 2.7-5.9% of the phenotypic variance. Six associations occurred in or near known QTL and the remaining are putative novel QTL. Ten significant associations influenced the oil content without decreasing protein content, and vice versa. One SNP was pleiotropic, with opposite effects on oil and protein contents. The genetic region covering Map-6076 and-6077 was shown to be involved in controlling oil content in soybean by integrating the results of association mapping with information on known QTL and tissue-specific expression data. This region was subject to strong selection during the genetic improvement of soybean. Our results not only confirm and refine the map positions of known QTL but also contribute to a further elucidation of the genetic architecture of protein and oil contents in soybean seeds by identifying new associations exhibiting pleiotropic effects on seed protein and oil contents.

Current Insights into the Modulation of Oral Bacterial Degradation of Dental Polymeric Restorative Materials.

Dental polymeric composites have become the first choice for cavity restorations due to their esthetics and capacity to be bonded to the tooth. However, the oral cavity is considered to be harsh environment for a polymeric material. Oral biofilms can degrade the polymeric components, thus compromising the marginal integrity and leading to the recurrence of caries. Recurrent caries around restorations has been reported as the main reason for restoration failure. The degradation of materials greatly compromises the clinical longevity. This review focuses on the degradation process of resin composites by oral biofilms, the mechanisms of degradation and its consequences. In addition, potential future developments in the area of resin-based dental biomaterials with an emphasis on anti-biofilm strategies are also reviewed.

Novel multifunctional dental cement to prevent enamel demineralization near orthodontic brackets.

OBJECTIVES: White spot lesions due to biofilm acid-induced enamel demineralization are prevalent in orthodontic treatments. The aim of this study was to develop a novel bioactive multifunctional cement with protein-repellent, antibacterial and remineralizing capabilities, and investigate the effects on enamel hardness and lesion depth in vitro for the first time. MATERIALS AND METHODS: 2-Methacryloyloxyethyl phosphorylcholine (MPC), dimethylaminohexadecyl methacrylate (DMAHDM), and nanoparticles of amorphous calcium phosphate (NACP) were incorporated into a resin-modified glass ionomer (RMGI). Extracted human premolars had brackets bonded via four groups: (1) Transbond XT (TB), (2) RMGI (GC Ortho LC), (3) RMGI+MPC+DMAHDM, (4) RMGI+MPC+DMAHDM+NACP. Demineralization was induced via a dental plaque microcosm biofilm model. Samples were tested using polarized light microscopy (PLM) for lesion depth. Enamel hardness was tested for different groups. RESULTS: Incorporating MPC, DMAHDM and NACP did not affect enamel bond strength. "RMGI+MPC+DMAHDM+NACP" group had the least lesion depth in enamel (p<0.05). Groups with NACP had the highest enamel hardness (p<0.05). Mineral loss (ΔS) in enamel for NACP group was about one third that for RMGI control. "RMGI+MPC+DMAHDM" had greater effect on demineralization-inhibition, compared to RMGI and TB controls. "RMGI+MPC+DMAHDM+NACP" was more effective in protecting enamel prisms from dissolution by biofilm acids, compared to RMGI and TB control groups. CONCLUSION: The Novel "RMGI+MPC+DMAHDM+NACP" cement substantially reduced enamel demineralization adjacent to orthodontic brackets, yielding much less lesion depth and greater enamel hardness under biofilm acid attacks than commercial controls. The clinical significance is that the novel multi-agent (RMGI+MPC+DMAHDM+NACP) method is promising for a wide range of preventive and restorative applications to combat caries.

Development and utilization of a new chemically-induced soybean library with a high mutation density .

Mutagenized populations have provided important materials for introducing variation and identifying gene function in plants. In this study, an ethyl methanesulfonate (EMS)-induced soybean (Glycine max) population, consisting of 21,600 independent M2 lines, was developed. Over 1,000 M4 (5) families, with diverse abnormal phenotypes for seed composition, seed shape, plant morphology and maturity that are stably expressed across different environments and generations were identified. Phenotypic analysis of the population led to the identification of a yellow pigmentation mutant, gyl, that displayed significantly decreased chlorophyll (Chl) content and abnormal chloroplast development. Sequence analysis showed that gyl is allelic to MinnGold, where a different single nucleotide polymorphism variation in the Mg-chelatase subunit gene (ChlI1a) results in golden yellow leaves. A cleaved amplified polymorphic sequence marker was developed and may be applied to marker-assisted selection for the golden yellow phenotype in soybean breeding. We show that the newly developed soybean EMS mutant population has potential for functional genomics research and genetic improvement in soybean.

Potential of marker selection to increase prediction accuracy of genomic selection in soybean (Glycine max L.).

Genomic selection is a promising molecular breeding strategy enhancing genetic gain per unit time. The objectives of our study were to (1) explore the prediction accuracy of genomic selection for plant height and yield per plant in soybean [Glycine max (L.) Merr.], (2) discuss the relationship between prediction accuracy and numbers of markers, and (3) evaluate the effect of marker preselection based on different methods on the prediction accuracy. Our study is based on a population of 235 soybean varieties which were evaluated for plant height and yield per plant at multiple locations and genotyped by 5361 single nucleotide polymorphism markers. We applied ridge regression best linear unbiased prediction coupled with fivefold cross-validations and evaluated three strategies of marker preselection. For plant height, marker density and marker preselection procedure impacted prediction accuracy only marginally. In contrast, for grain yield, prediction accuracy based on markers selected with a haplotype block analyses-based approach increased by approximately 4 % compared with random or equidistant marker sampling. Thus, applying marker preselection based on haplotype blocks is an interesting option for a cost-efficient implementation of genomic selection for grain yield in soybean breeding.

Identification and Validation of Loci Governing Seed Coat Color by Combining Association Mapping and Bulk Segregation Analysis in Soybean.

Soybean seed coat exists in a range of colors from yellow, green, brown, black, to bicolor. Classical genetic analysis suggested that soybean seed color was a moderately complex trait controlled by multi-loci. However, only a couple of loci could be detected using a single biparental segregating population. In this study, a combination of association mapping and bulk segregation analysis was employed to identify genes/loci governing this trait in soybean. A total of 14 loci, including nine novel and five previously reported ones, were identified using 176,065 coding SNPs selected from entire SNP dataset among 56 soybean accessions. Four of these loci were confirmed and further mapped using a biparental population developed from the cross between ZP95-5383 (yellow seed color) and NY279 (brown seed color), in which different seed coat colors were further dissected into simple trait pairs (green/yellow, green/black, green/brown, yellow/black, yellow/brown, and black/brown) by continuously developing residual heterozygous lines. By genotyping entire F2 population using flanking markers located in fine-mapping regions, the genetic basis of seed coat color was fully dissected and these four loci could explain all variations of seed colors in this population. These findings will be useful for map-based cloning of genes as well as marker-assisted breeding in soybean. This work also provides an alternative strategy for systematically isolating genes controlling relative complex trait by association analysis followed by biparental mapping.

Targeted association mapping demonstrating the complex molecular genetics of fatty acid formation in soybean.

BACKGROUND: The relative abundance of five dominant fatty acids (FAs) (palmitic, stearic, oleic, linoleic and linolenic acids) is a major factor determining seed quality in soybean. METHODS: To clarify the currently poorly understood genetic architecture of FAs in soybean, targeted association analysis was conducted in 421 diverse accessions phenotyped in three environments and genotyped using 1536 pre-selected SNPs. RESULTS: The population of 421 soybean accessions displayed significant genetic variation for each FA. Analysis of the molecular data revealed three subpopulations, which reflected a trend depending on latitude of cultivation. A total of 37 significant (p < 0.01) associations with FAs were identified by association mapping analysis. These associations were represented by 33 SNPs (occurring in 32 annotated genes); another four SNPs had a significant association with two different FAs due to pleiotropic interactions. The most significant associations were cross-verified by known genes/QTL or consistency across cultivation year and subpopulations. CONCLUSION: The detected marker-trait associations represent a first important step towards the implementation of molecular-marker-based selection of FA composition with the potential to substantially improve the seed quality of soybean with benefits for human health and for food processing.

Detecting SNPs underlying domestication-related traits in soybean.

BACKGROUND: Cultivated soybean (Glycine max) experienced a severe genetic bottleneck during its domestication and a further loss in diversity during its subsequent selection. Here, a panel of 65 wild (G. soja) and 353 cultivated accessions was genotyped at 552 single-nucleotide polymorphism loci to search for signals of selection during and after domestication. RESULTS: The wild and cultivated populations were well differentiated from one another. Application of the Fst outlier test revealed 64 loci showing evidence for selection. Of these, 35 related to selection during domestication, while the other 29 likely gradually became monomorphic as a result of prolonged selection during post domestication. Two of the SNP locus outliers were associated with testa color. CONCLUSIONS: Identifying genes controlling domestication-related traits is important for maintaining the diversity of crops. SNP locus outliers detected by a combined forward genetics and population genetics approach can provide markers with utility for the conservation of wild accessions and for trait improvement in the cultivated genepool.