Impact of LDLR polymorphisms on lipid levels and atorvastatin's efficacy in a northern Chinese adult Han cohort with dyslipidemia.

BACKGROUND: Dyslipidemia, a significant risk factor for atherosclerotic cardiovascular disease (ASCVD), is influenced by genetic variations, particularly those in the low-density lipoprotein receptor (LDLR) gene. This study aimed to elucidate the effects of LDLR polymorphisms on baseline serum lipid levels and the therapeutic efficacy of atorvastatin in an adult Han population in northern China with dyslipidemia. METHODS: In this study, 255 Han Chinese adults receiving atorvastatin therapy were examined and followed up. The 3' untranslated region (UTR) of the LDLR gene was sequenced to identify polymorphisms. The associations between gene polymorphisms and serum lipid levels, as well as changes in lipid levels after intervention, were evaluated using the Wilcoxon rank sum test, with a P < 0.05 indicating statistical significance. Assessment of linkage disequilibrium patterns and haplotype structures was conducted utilizing Haploview. RESULTS: Eleven distinct polymorphisms at LDLR 3' UTR were identified. Seven polymorphisms (rs1433099, rs14158, rs2738466, rs5742911, rs17249057, rs55971831, and rs568219285) were correlated with the baseline serum lipid levels (P < 0.05). In particular, four polymorphisms (rs14158, rs2738466, rs5742911, and rs17249057) were in strong linkage disequilibrium (r2 = 1), and patients with the AGGC haplotype had higher TC and LDL-C levels at baseline. Three polymorphisms (rs1433099, rs2738467, and rs7254521) were correlated with the therapeutic efficacy of atorvastatin (P < 0.05). Furthermore, carriers of the rs2738467 T allele demonstrated a significantly greater reduction in low-density lipoprotein cholesterol (LDL-C) levels post-atorvastatin treatment (P = 0.03), indicating a potentially crucial genetic influence on therapeutic outcomes. Two polymorphisms (rs751672818 and rs566918949) were neither correlated with the baseline serum lipid levels nor atorvastatin's efficacy. CONCLUSIONS: This research outlined the complex genetic architecture surrounding LDLR 3' UTR polymorphisms and their role in lipid metabolism and the response to atorvastatin treatment in adult Han Chinese patients with dyslipidemia, highlighting the importance of genetic profiling in enhancing tailored therapeutic strategies. Furthermore, this investigation advocates for the integration of genetic testing into the management of dyslipidemia, paving the way for customized therapeutic approaches that could significantly improve patient care. TRIAL REGISTRATION: This multicenter study was approved by the Ethics Committee of Xiangya Hospital Central South University (ethics number K22144). It was a general ethic. In addition, this study was approved by The First Hospital of Hebei Medical University (ethics number 20220418).

Ivabradine Alleviates Experimental Autoimmune Myocarditis-Mediated Myocardial Injury.

Ivabradine (IVA) reduces heart rate by inhibiting hyperpolarization-activated cyclic nucleotide-gated channels (HCNs), which play a role in the promotion of pacemaker activity in cardiac sinoatrial node cells. HCNs are highly expressed in neural and myocardial tissues and are involved in the modulation of inflammatory neuropathic pain. However, whether IVA exerts any effect on myocardial inflammation in the pathogenesis of heart failure is unclear. We employed single-cell RNA sequencing (scRNA-seq) in porcine cardiac myosin-induced experimental autoimmune myocarditis rat model to determine the effects and mechanisms of IVA. Lewis rats (n = 32) were randomly divided into the normal, control, high-dose-IVA, and low-dose-IVA groups. Heart rate and blood pressure were measured on days 0 and 21, respectively. Echocardiography was performed on day 22, and inflammation of the myocardium was evaluated via histopathological examination. Western blot was employed to detect the expression of HCN1-4, MinK-related protein 1 (MiRP1), matrix metalloproteinase 2 (MMP-2), MMP-9, and transforming growth factor-ß (TGF-ß). Furthermore, enzyme-linked immunosorbent assay was performed to measure serum IL-1, IL-6, and TNF-α. The relative mRNA levels of collagen I, collagen III, and α-smooth muscle actin (α-SMA) were determined via qRT-PCR. We found that IVA reduced the total number of cells infiltrated into the myocardium, particularly in the subset of fibroblasts, endocardia, and monocytes. IVA administration ameliorated cardiac inflammation and reduced collagen production. Results of the echocardiography indicated that left ventricular internal diameter at end-systole LVIDs increased whereas left ventricular ejection fraction and left ventricular fractional shortening decreased in the control group. IVA improved cardiac performance. The expression of HCN4 and MiRP1 protein and the level of serum IL-1, IL-6, and TNF-α were decreased by IVA treatment. In conclusion, HCNs and the helper proteins were increased in the profile of myocardial inflammation. HCNs may be involved in the regulation of myocardial inflammation by inhibiting immune cell infiltration. Our findings can contribute to the development of IVA-based combination therapies for the future treatment of cardiac inflammation and heart failure.

Comparative Analysis of Commercially Available Flavor Oil Sausages and Smoked Sausages.

This study utilized gas chromatography-ion mobility spectrometry (GC-IMS) to analyze the volatile flavor compounds present in various commercially available sausages. Additionally, it conducted a comparative assessment of the distinctions among different samples by integrating sensory evaluation with textural and physicochemical parameters. The results of the GC-IMS analysis showed that a total of 65 volatile compounds were detected in the four samples, including 12 hydrocarbons, 11 alcohols, 10 ketones, 9 aldehydes, 12 esters, and 1 acids. Fingerprinting combined with principal component analysis (PCA) showed that the volatiles of different brands of sausages were significantly different (p < 0.05). The volatiles of S1 and S4 were more similar and significantly different from the other two samples (p < 0.05). Among them, there were 14 key volatile substances in the four samples, of which 3-hydroxy-2-butanone and diallyl sulfide were common to all four sausages. Combined textural and sensory evaluations revealed that smoked sausages exhibited superior characteristics in resilience, cohesiveness, springiness, gumminess, and chewiness. Additionally, smoked sausages were found to be more attractive in color, moderately spicy, and salty, while having a lower fat content. In conclusion, smoked sausages are preferred by consumers over flavored oil sausages.

Selection of GmSWEET39 for oil and protein improvement in soybean.

Soybean [Glycine max (L.) Merr.] was domesticated from wild soybean (G. soja Sieb. and Zucc.) and has been further improved as a dual-use seed crop to provide highly valuable oil and protein for food, feed, and industrial applications. However, the underlying genetic and molecular basis remains less understood. Having combined high-confidence bi-parental linkage mapping with high-resolution association analysis based on 631 whole sequenced genomes, we mapped major soybean protein and oil QTLs on chromosome15 to a sugar transporter gene (GmSWEET39). A two-nucleotide CC deletion truncating C-terminus of GmSWEET39 was strongly associated with high seed oil and low seed protein, suggesting its pleiotropic effect on protein and oil content. GmSWEET39 was predominantly expressed in parenchyma and integument of the seed coat, and likely regulates oil and protein accumulation by affecting sugar delivery from maternal seed coat to the filial embryo. We demonstrated that GmSWEET39 has a dual function for both oil and protein improvement and undergoes two different paths of artificial selection. A CC deletion (CC-) haplotype H1 has been intensively selected during domestication and extensively used in soybean improvement worldwide. H1 is fixed in North American soybean cultivars. The protein-favored (CC+) haplotype H3 still undergoes ongoing selection, reflecting its sustainable role for soybean protein improvement. The comprehensive knowledge on the molecular basis underlying the major QTL and GmSWEET39 haplotypes associated with soybean improvement would be valuable to design new strategies for soybean seed quality improvement using molecular breeding and biotechnological approaches.

Development of a versatile resource for post-genomic research through consolidating and characterizing 1500 diverse wild and cultivated soybean genomes.

BACKGROUND: With advances in next-generation sequencing technologies, an unprecedented amount of soybean accessions has been sequenced by many individual studies and made available as raw sequencing reads for post-genomic research. RESULTS: To develop a consolidated and user-friendly genomic resource for post-genomic research, we consolidated the raw resequencing data of 1465 soybean genomes available in the public and 91 highly diverse wild soybean genomes newly sequenced. These altogether provided a collection of 1556 sequenced genomes of 1501 diverse accessions (1.5 K). The collection comprises of wild, landraces and elite cultivars of soybean that were grown in East Asia or major soybean cultivating areas around the world. Our extensive sequence analysis discovered 32 million single nucleotide polymorphisms (32mSNPs) and revealed a SNP density of 30 SNPs/kb and 12 non-synonymous SNPs/gene reflecting a high structural and functional genomic diversity of the new collection. Each SNP was annotated with 30 categories of structural and/or functional information. We further identified paired accessions between the 1.5 K and 20,087 (20 K) accessions in US collection as genomic "equivalent" accessions sharing the highest genomic identity for minimizing the barriers in soybean germplasm exchange between countries. We also exemplified the utility of 32mSNPs in enhancing post-genomics research through in-silico genotyping, high-resolution GWAS, discovering and/or characterizing genes and alleles/mutations, identifying germplasms containing beneficial alleles that are potentially experiencing artificial selection. CONCLUSION: The comprehensive analysis of publicly available large-scale genome sequencing data of diverse cultivated accessions and the newly in-house sequenced wild accessions greatly increased the soybean genome-wide variation resolution. This could facilitate a variety of genetic and molecular-level analyses in soybean. The 32mSNPs and 1.5 K accessions with their comprehensive annotation have been made available at the SoyBase and Ag Data Commons. The dataset could further serve as a versatile and expandable core resource for exploring the exponentially increasing genome sequencing data for a variety of post-genomic research.

Artificial selection on GmOLEO1 contributes to the increase in seed oil during soybean domestication.

Increasing seed oil content is one of the most important breeding goals for soybean due to a high global demand for edible vegetable oil. However, genetic improvement of seed oil content has been difficult in soybean because of the complexity of oil metabolism. Determining the major variants and molecular mechanisms conferring oil accumulation is critical for substantial oil enhancement in soybean and other oilseed crops. In this study, we evaluated the seed oil contents of 219 diverse soybean accessions across six different environments and dissected the underlying mechanism using a high-resolution genome-wide association study (GWAS). An environmentally stable quantitative trait locus (QTL), GqOil20, significantly associated with oil content was identified, accounting for 23.70% of the total phenotypic variance of seed oil across multiple environments. Haplotype and expression analyses indicate that an oleosin protein-encoding gene (GmOLEO1), colocated with a leading single nucleotide polymorphism (SNP) from the GWAS, was significantly correlated with seed oil content. GmOLEO1 is predominantly expressed during seed maturation, and GmOLEO1 is localized to accumulated oil bodies (OBs) in maturing seeds. Overexpression of GmOLEO1 significantly enriched smaller OBs and increased seed oil content by 10.6% compared with those of control seeds. A time-course transcriptomics analysis between transgenic and control soybeans indicated that GmOLEO1 positively enhanced oil accumulation by affecting triacylglycerol metabolism. Our results also showed that strong artificial selection had occurred in the promoter region of GmOLEO1, which resulted in its high expression in cultivated soybean relative to wild soybean, leading to increased seed oil accumulation. The GmOLEO1 locus may serve as a direct target for both genetic engineering and selection for soybean oil improvement.

Transcriptome profiling reveals the spatial-temporal dynamics of gene expression essential for soybean seed development.

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.

Integrating GWAS and gene expression data for functional characterization of resistance to white mould in soya bean.

White mould of soya bean, caused by Sclerotinia sclerotiorum (Lib.) de Bary, is a necrotrophic fungus capable of infecting a wide range of plants. To dissect the genetic architecture of resistance to white mould, a high-density customized single nucleotide polymorphism (SNP) array (52 041 SNPs) was used to genotype two soya bean diversity panels. Combined with resistance variation data observed in the field and greenhouse environments, genome-wide association studies (GWASs) were conducted to identify quantitative trait loci (QTL) controlling resistance against white mould. Results showed that 16 and 11 loci were found significantly associated with resistance in field and greenhouse, respectively. Of these, eight loci localized to previously mapped QTL intervals and one locus had significant associations with resistance across both environments. The expression level changes in genes located in GWAS-identified loci were assessed between partially resistant and susceptible genotypes through a RNA-seq analysis of the stem tissue collected at various time points after inoculation. A set of genes with diverse biological functionalities were identified as strong candidates underlying white mould resistance. Moreover, we found that genomic prediction models outperformed predictions based on significant SNPs. Prediction accuracies ranged from 0.48 to 0.64 for disease index measured in field experiments. The integrative methods, including GWAS, RNA-seq and genomic selection (GS), applied in this study facilitated the identification of causal variants, enhanced our understanding of mechanisms of white mould resistance and provided valuable information regarding breeding for disease resistance through genomic selection in soya bean.

Dynamic DNA Methylation in Plant Growth and Development.

DNA methylation is an epigenetic modification required for transposable element (TE) silencing, genome stability, and genomic imprinting. Although DNA methylation has been intensively studied, the dynamic nature of methylation among different species has just begun to be understood. Here we summarize the recent progress in research on the wide variation of DNA methylation in different plants, organs, tissues, and cells; dynamic changes of methylation are also reported during plant growth and development as well as changes in response to environmental stresses. Overall DNA methylation is quite diverse among species, and it occurs in CG, CHG, and CHH (H = A, C, or T) contexts of genes and TEs in angiosperms. Moderately expressed genes are most likely methylated in gene bodies. Methylation levels decrease significantly just upstream of the transcription start site and around transcription termination sites; its levels in the promoter are inversely correlated with the expression of some genes in plants. Methylation can be altered by different environmental stimuli such as pathogens and abiotic stresses. It is likely that methylation existed in the common eukaryotic ancestor before fungi, plants and animals diverged during evolution. In summary, DNA methylation patterns in angiosperms are complex, dynamic, and an integral part of genome diversity after millions of years of evolution.

The Inflammatory Transcription Factor C/EBPß Plays a Critical Role in Cardiac Fibroblast Differentiation and a Rat Model of Cardiac Fibrosis Induced by Autoimmune Myocarditis.

The aim of the present study was to investigate the mechanisms of CCAAT/enhancer-binding protein ß (C/EBPß) in cardiac myofibroblast (CMF) differentiation and in a rat model of cardiac fibrosis induced by experimental autoimmune myocarditis (EAM).In vitro studies performed in primary neonatal rat CMF revealed that silencing of C/EBPß expression (via lentiviral mediated shRNA strategies) was sufficient to reduce C/EBPß mRNA and protein levels as well as to decrease the expressions of actin cytoskeletal proteins, cofilin, and filamin A (FLNA). TGFß increased IL-1ß, IL-6 and TNF-a production in cardiac fibroblasts (CF), while C/EBPß knockdown reduced the secretion of these inflammatory mediators. In vivo studies performed in rats exhibiting EAM revealed that lentiviral-mediated silencing of C/EBPß was sufficient to reduce the expression of C/EBPß as well as inflammation and fibrosis in the hearts of EAM rats, when compared to controls. Echocardiography further revealed that C/EBPß knockdown was sufficient to significantly improve cardiac dimensions and function in EAM rats. Immunohistochemical results showed that C/EBPß knockdown attenuated the expression of C/EBPß protein as well as the expressions of collagen I, collagen III, MMP-2, MMP-9, and α-SMA in heart tissue sections from rats in the EAM + Lenti-shC/EBPß group.Strategies targeted at inhibiting C/EBPß expression can be potentially exploited to regulate cofilin and FLNA expression, thereby regulating actin polymerization/depolymerization, cytoskeleton rearrangement, and CF differentiation into CMF and the production of inflammatory cytokines. C/EBPß knock down reduces the degree of inflammation-mediated myocardial fibrosis in a rat model of EAM.

Fine mapping of the soybean aphid-resistance genes Rag6 and Rag3c from Glycine soja 85-32.

KEY MESSAGE: Rag6 and Rag3c were delimited to a 49-kb interval on chromosome 8 and a 150-kb interval on chromosome 16, respectively. Structural variants in the exons of candidate genes were identified. The soybean aphid, an invasive species, has significantly threatened soybean production in North America since 2000. Host-plant resistance is known as an ideal management strategy for aphids. Two novel aphid-resistance loci, Rag6 and Rag3c, from Glycine soja 85-32, were previously detected in a 10.5-cM interval on chromosome 8 and a 7.5-cM interval on chromosome 16, respectively. Defining the exact genomic position of these two genes is critical for improving the effectiveness of marker-assisted selection for aphid resistance and for identification of the functional genes. To pinpoint the locations of Rag6 and Rag3c, four populations segregating for Rag6 and Rag3c were used to fine map these two genes. The availability of the Illumina Infinium SoySNP50K/8K iSelect BeadChip, combined with single-nucleotide polymorphism (SNP) markers discovered through the whole-genome re-sequencing of E12901, facilitated the fine mapping process. Rag6 was refined to a 49-kb interval on chromosome 8 with four candidate genes, including three clustered nucleotide-binding site leucine-rich repeat (NBS-LRR) genes and an amine oxidase encoding gene. Rag3c was refined to a 150-kb interval on chromosome 16 with 11 candidate genes, two of which are a LRR gene and a lipase gene. Moreover, by sequencing the whole-genome exome-capture of the resistant source (E12901), structural variants were identified in the exons of the candidate genes of Rag6 and Rag3c. The closely linked SNP markers and the candidate gene information presented in this study will be significant resources for integrating Rag6 and Rag3c into elite cultivars and for future functional genetics studies.

Identification and characterization of large DNA deletions affecting oil quality traits in soybean seeds through transcriptome sequencing analysis.

KEY MESSAGE: Identification and characterization of a 254-kb genomic deletion on a duplicated chromosome segment that resulted in a low level of palmitic acid in soybean seeds using transcriptome sequencing. A large number of soybean genotypes varying in seed oil composition and content have been identified. Understanding the molecular mechanisms underlying these variations is important for breeders to effectively utilize them as a genetic resource. Through design and application of a bioinformatics approach, we identified nine co-regulated gene clusters by comparing seed transcriptomes of nine soybean genotypes varying in oil composition and content. We demonstrated that four gene clusters in the genotypes M23, Jack and N0304-303-3 coincided with large-scale genome rearrangements. The co-regulated gene clusters in M23 and Jack mapped to a previously described 164-kb deletion and a copy number amplification of the Rhg1 locus, respectively. The coordinately down-regulated gene clusters in N0304-303-3 were caused by a 254-kb deletion containing 19 genes including a fatty acyl-ACP thioesterase B gene (FATB1a). This deletion was associated with reduced palmitic acid content in seeds and was the molecular cause of a previously reported nonfunctional FATB1a allele, fap nc . The M23 and N0304-304-3 deletions were located in duplicated genome segments retained from the Glycine-specific whole genome duplication that occurred 13 million years ago. The homoeologous genes in these duplicated regions shared a strong similarity in both their encoded protein sequences and transcript accumulation levels, suggesting that they may have conserved and important functions in seeds. The functional conservation of homoeologous genes may result in genetic redundancy and gene dosage effects for their associated seed traits, explaining why the large deletion did not cause lethal effects or completely eliminate palmitic acid in N0304-303-3.

Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content.

BACKGROUND: Variation in seed oil composition and content among soybean varieties is largely attributed to differences in transcript sequences and/or transcript accumulation of oil production related genes in seeds. Discovery and analysis of sequence and expression variations in these genes will accelerate soybean oil quality improvement. RESULTS: In an effort to identify these variations, we sequenced the transcriptomes of soybean seeds from nine lines varying in oil composition and/or total oil content. Our results showed that 69,338 distinct transcripts from 32,885 annotated genes were expressed in seeds. A total of 8,037 transcript expression polymorphisms and 50,485 transcript sequence polymorphisms (48,792 SNPs and 1,693 small Indels) were identified among the lines. Effects of the transcript polymorphisms on their encoded protein sequences and functions were predicted. The studies also provided independent evidence that the lack of FAD2-1A gene activity and a non-synonymous SNP in the coding sequence of FAB2C caused elevated oleic acid and stearic acid levels in soybean lines M23 and FAM94-41, respectively. CONCLUSIONS: As a proof-of-concept, we developed an integrated RNA-seq and bioinformatics approach to identify and functionally annotate transcript polymorphisms, and demonstrated its high effectiveness for discovery of genetic and transcript variations that result in altered oil quality traits. The collection of transcript polymorphisms coupled with their predicted functional effects will be a valuable asset for further discovery of genes, gene variants, and functional markers to improve soybean oil quality.

Effects of ivabradine on myocardial autophagia and apoptosis in isoprenaline-induced heart failure in mice.

Objectives: To investigate the effects and mechanisms of ivabradine (IVA) on isoprenaline-induced cardiac injury. Materials and Methods: Forty male C57BL/6 mice were randomly divided into control group, model group, high-dose IVA group, and low-dose IVA group. The control group was given saline, other groups were given subcutaneous injections of isoproterenol (ISO) 5 mg/kg/d to make the myocardial remodeling model. A corresponding dose of IVA (high dose 50 mg/kg/d, low dose 10 mg/kg/d) was given by gavage (30 days). A transthoracic echocardiogram was obtained to detect the structure and function of the heart. An electron microscope was used to explore the cardiomyocytes' apoptosis and autophagy. HE staining and Masson's trichrome staining were performed to explore myocardial hypertrophy and fibrosis. Western blot was used to detect Bax, Bcl-2, cleaved caspase-3, Becline-1, LC3, phosphorylated p38 mitogen-activated protein kinase (p-p38MAPK), phosphorylated extracellular regulated protein kinases1/2 (p-ERK1/2), phosphorylated c-Jun N-terminal kinase (p-JNK), and α-smooth muscle actin (α-SMA) in the myocardium. Results: Heart rate in the IVA groups was reduced, and the trend of heart rate reduction was more obvious in the high-dose group. Echocardiography showed that IVA improved the cardiac structure and function compared to the model group. IVA attenuated cardiac fibrosis, decreased cardiomyocyte apoptosis, and increased autophagy. The phosphorylated MAPK in the ISO-induced groups was increased. IVA treatment decreased the p-p38MAPK level. There were no differences in p-ERK and p-JNK levels. Conclusion: The beneficial effects of IVA on myocardial injury are related to blocking the p38MAPK signal pathway, decreasing cardiomyocyte apoptosis, and increasing cardiomyocyte autophagy.

Identification and characterization of a temperature sensitive chlorotic soybean mutant.

Screening a transposon-mutagenized soybean population led to the discovery of a recessively inherited chlorotic phenotype. This "vir1" phenotype results in smaller stature, weaker stems, and a smaller root system with smaller nodules. Genome sequencing identified 15 candidate genes with mutations likely to result in a loss of function. Amplicon sequencing of a segregating population was then used to narrow the list to a single candidate mutation, a single-base change in Glyma.07G102300 that disrupts splicing of the second intron. Single cell transcriptomic profiling indicates that this gene is expressed primarily in mesophyll cells and RNA sequencing data indicates it is upregulated in germinating seedlings by cold stress. Previous studies have shown that mutations to Os05g34040, the rice homolog of Glyma.07G102300, produced a chlorotic phenotype that was more pronounced in cool temperatures. Growing soybean vir1 mutants at lower temperatures also resulted in a more severe phenotype. In addition, transgenic expression of wild type Glyma.07G102300 in the knockout mutant of the Arabidopsis homolog At4930720 rescues the chlorotic phenotype, further supporting the hypothesis that the mutation in Glyma.07G102300 is causal of the vir1 phenotype.

Genetic architecture of protein and oil content in soybean seed and meal.

Soybean is grown primarily for the protein and oil extracted from its seed and its value is influenced by these components. The objective of this study was to map marker-trait associations (MTAs) for the concentration of seed protein, oil, and meal protein using the soybean nested association mapping (SoyNAM) population. The composition traits were evaluated on seed harvested from over 5000 inbred lines of the SoyNAM population grown in 10 field locations across 3 years. Estimated heritabilities were at least 0.85 for all three traits. The genotyping of lines with single nucleotide polymorphism markers resulted in the identification of 107 MTAs for the three traits. When MTAs for the three traits that mapped within 5 cM intervals were binned together, the MTAs were mapped to 64 intervals on 19 of the 20 soybean chromosomes. The majority of the MTA effects were small and of the 107 MTAs, 37 were for protein content, 39 for meal protein, and 31 for oil content. For cases where a protein and oil MTAs mapped to the same interval, most (94%) significant effects were opposite for the two traits, consistent with the negative correlation between these traits. A coexpression analysis identified candidate genes linked to MTAs and 18 candidate genes were identified. The large number of small effect MTAs for the composition traits suggest that genomic prediction would be more effective in improving these traits than marker-assisted selection.

Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs.

BACKGROUND: MicroRNAs (miRNAs) have recently emerged as important gene regulators in plants. MiRNAs and their targets have been extensively studied in Arabidopsis and rice. However, relatively little is known about the characterization of miRNAs and their target genes in peach (Prunus persica), which is a complex crop with unique developmental programs. RESULTS: We performed small RNA deep sequencing and identified 47 peach-specific and 47 known miRNAs or families with distinct expression patterns. Together, the identified miRNAs targeted 80 genes, many of which have not been reported previously. Like the model plant systems, peach has two of the three conserved trans-acting siRNA biogenesis pathways with similar mechanistic features and target specificity. Unique to peach, three of the miRNAs collectively target 49 MYBs, 19 of which are known to regulate phenylpropanoid metabolism, a key pathway associated with stone hardening and fruit color development, highlighting a critical role of miRNAs in the regulation of peach fruit development and ripening. We also found that the majority of the miRNAs were differentially regulated in different tissues, in part due to differential processing of miRNA precursors. Up to 16% of the peach-specific miRNAs were differentially processed from their precursors in a tissue specific fashion, which has been rarely observed in plant cells. The miRNA precursor processing activity appeared not to be coupled with its transcriptional activity but rather acted independently in peach. CONCLUSIONS: Collectively, the data characterizes the unique expression pattern and processing regulation of peach miRNAs and demonstrates the presence of a complex, multi-level miRNA regulatory network capable of targeting a wide variety of biological functions, including phenylpropanoid pathways which play a multifaceted spatial-temporal role in peach fruit development.

POWR1 is a domestication gene pleiotropically regulating seed quality and yield in soybean.

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.

Transcriptional regulatory programs underlying barley germination and regulatory functions of Gibberellin and abscisic acid.

BACKGROUND: Seed germination is a complex multi-stage developmental process, and mainly accomplished through concerted activities of many gene products and biological pathways that are often subjected to strict developmental regulation. Gibberellins (GA) and abscisic acid (ABA) are two key phytohormones regulating seed germination and seedling growth. However, transcriptional regulatory networks underlying seed germination and its associated biological pathways are largely unknown. RESULTS: The studies examined transcriptomes of barley representing six distinct and well characterized germination stages and revealed that the transcriptional regulatory program underlying barley germination was composed of early, late, and post-germination phases. Each phase was accompanied with transcriptional up-regulation of distinct biological pathways. Cell wall synthesis and regulatory components including transcription factors, signaling and post-translational modification components were specifically and transiently up-regulated in early germination phase while histone families and many metabolic pathways were up-regulated in late germination phase. Photosynthesis and seed reserve mobilization pathways were up-regulated in post-germination phase. However, stress related pathways and seed storage proteins were suppressed through the entire course of germination. A set of genes were transiently up-regulated within three hours of imbibition, and might play roles in initiating biological pathways involved in seed germination. However, highly abundant transcripts in dry barley and Arabidopsis seeds were significantly conserved. Comparison with transcriptomes of barley aleurone in response to GA and ABA identified three sets of germination responsive genes that were regulated coordinately by GA, antagonistically by ABA, and coordinately by GA but antagonistically by ABA. Major CHO metabolism, cell wall degradation and protein degradation pathways were up-regulated by both GA and seed germination. Those genes and metabolic pathways are likely to be important parts of transcriptional regulatory networks underlying GA and ABA regulation of seed germination and seedling growth. CONCLUSIONS: The studies developed a model depicting transcriptional regulatory programs underlying barley germination and GA and ABA regulation of germination at gene, pathway and systems levels, and established a standard transcriptome reference for further integration with various -omics and biological data to illustrate biological networks underlying seed germination. The studies also generated a great amount of systems biological evidence for previously proposed hypotheses, and developed a number of new hypotheses on transcriptional regulation of seed germination for further experimental validation.

Identification of Glutathione Peroxidase Gene Family in Ricinus communis and Functional Characterization of RcGPX4 in Cold Tolerance.

Glutathione peroxidases (GPXs) protect cells against damage caused by reactive oxygen species (ROS) and play key roles in regulating many biological processes. Here, five GPXs were identified in the Ricinus communis genome. Phylogenetic analysis displayed that the GPXs were categorized into five groups. Conserved domain and gene structure analyses showed that the GPXs from different plant species harbored four highly similar motifs and conserved exon-intron arrangement patterns, indicating that their structure and function may have been conserved during evolution. Several abiotic stresses and hormone-responsive cis-acting elements existed in the promoters of the RcGPXs. The expression profiles indicated that the RcGPXs varied substantially, and some RcGPXs were coordinately regulated under abiotic stresses. Overexpression of RcGPX4 in Arabidopsis enhanced cold tolerance at seed germination but reduced freezing tolerance at seedlings. The expression of abscisic acid (ABA) signaling genes (AtABI4 and AtABI5), ABA catabolism genes (AtCYP707A1 and AtCYP707A2), gibberellin acid (GA) catabolism gene (AtGA2ox7), and cytokinin (CTK)-inducible gene (AtARR6) was regulated in the seeds of transgenic lines under cold stress. Overexpression of RcGPX4 can disturb the hydrogen peroxide (H2O2) homeostasis through the modulation of some antioxidant enzymes and compounds involved in the GSH-ascorbate cycle in transgenic plants. Additionally, RcGPX4 depended on the MAPK3-ICE1-C-repeat-binding factor (CBF)-COR signal transduction pathway and ABA-dependent pathway to negatively regulate the freezing tolerance of transgenic plants. This study provides valuable information for understanding the potential function of RcGPXs in regulating the abiotic stress responses of castor beans.