Evolutionary and synteny analysis of HIS1, BADH2, GBSS1, and GBSS2 in rice: insights for effective introgression breeding strategies

The key genes BADH2, GBSS1, GBSS2, and HIS1 regulate the fragrance, starch synthesis, and herbicide resistance in rice. Although the molecular functions of four genes have been investigated in the Oryza sativa species, little is known regarding their evolutionary history in the Oryza genus. Here, we studied the evolution of four focal genes in 10 Oryza species using phylogenetic and syntenic approaches. The HIS1 family underwent several times of tandem duplication events in the Oryza species, resulting in copy number variation ranging from 2 to 7. At most one copy of BADH2, GBSS1, and GBSS2 orthologs were identified in each Oryza species, and gene loss events of BADH2 and GBSS2 were identified in three Oryza species. Gene transfer analysis proposed that the functional roles of GBSS1 and GBSS2 were developed in the Asian and African regions, respectively, and most allelic variations of BADH2 in japonica rice emerged after the divergence between the Asian and African rice groups. These results provide clues to determine the origin and evolution of the key genes in rice breeding as well as valuable information for molecular breeders and scientists to develop efficient strategies to simultaneously improve grain quality and yield potential in rice.

The enhancement effect of mungbean on the physical, functional, and sensory characteristics of soy yoghurt

Vegetable drinks offer a convenient way to increase the daily intake of vegetables containing vitamins, antioxidants, and fiber. In this study, we discovered that mungbean milk serves as a carbohydrate source during fermentation using lactic acid bacteria (LAB) and enhances the nutritional value of vegetable yoghurt. Mungbean milk reduces pH while titratable acidity increases faster than soybean milk during fermentation. M0S, Soybean milk 100% with added sucrose exhibited the highest titratable acidity after 16 h of fermentation. The acetic acid content of all samples did not show significant changes during fermentation, but the lactic acid content increased. Proximate analysis showed no significant change during fermentation, regardless of the fermentation time and mixing ratio of mungbean to soybean milk. The sucrose content of samples except M0S decreased after 16 h of fermentation. Mungbean milk exhibited high antioxidant activity both before and after fermentation, while M0S showed the lowest antioxidant activity. The results of this study demonstrated the potential application of mungbean milk to improve fermented vegetable drinks using LAB functionally. Fermented mungbean milk yoghurt can be a valuable addition to a healthy and balanced diet for those who consume plant-based diets.

Unraveling the maternal and paternal origins of allotetraploid Vigna reflexo-pilosa

The genomic structures of Vigna hirtella Ridl. and Vigna trinervia (B.Heyne ex Wight & Arn.) Tateishi & Maxted, key ancestral species of the allotetraploid Vigna reflexo-pilosa var. glabra (Roxb.) N.Tomooka & Maxted, remain poorly understood. This study presents a comprehensive genomic comparison of these species to deepen our knowledge of their evolutionary trajectories. By comparing the genomic profiles of V. hirtella and V. trinervia with those of V. reflexo-pilosa, we investigate the complex genomic mechanisms underlying allopolyploid evolution within the genus Vigna. Comparison of the chloroplast genome revealed that V. trinervia is closely related to V. reflexo-pilosa. De novo assembly of the whole genome, followed by synteny analysis and Ks value calculations, confirms that V. trinervia is closely related to the A genome of V. reflexo-pilosa, and V. hirtella to its B genome. Furthermore, the comparative analyses reveal that V. reflexo-pilosa retains residual signatures of a previous polyploidization event, particularly evident in higher gene family copy numbers. Our research provides genomic evidence for polyploidization within the genus Vigna and identifies potential donor species of allotetraploid species using de novo assembly techniques. Given the Southeast Asian distribution of both V. hirtella and V. trinervia, natural hybridization between these species, with V. trinervia as the maternal ancestor and V. hirtella as the paternal donor, seems plausible.

The complete mitochondrial genome of the biodiesel plant Jatropha curcas L

Jatropha curcas (Linnaeus, 1753) is a plant species in the order Malpighiales and the family Euphorbiaceae and is native to the tropical regions of America, such as Mexico and Argentina. Currently, this plant species inhabits tropical and subtropical regions of the world. Jatropha has been widely used as a biofuel plant to produce high-quality diesel engine fuel. In this study, the complete mitochondrial genome sequence of J. curcas was assembled into 561,839 bp circular nucleotides with a GC content of 44.6%. The mitochondrial genome of J. curcas comprises 33 known protein-coding genes, 22 tRNA genes, three rRNA genes, one ncRNA gene, and 85 open reading frame genes. Phylogenetic analysis showed this species is closely related to the castor bean (Ricinus communis).

Metabolic profiling and expression analysis of key genetic factors in the biosynthetic pathways of antioxidant metabolites in mungbean sprouts

Mungbeans (Vigna radiata L.), a major legume crop in Asia, contain higher amounts of functional substances than other legumes, such as catechin, chlorogenic acid, and vitexin. Germination can improve the nutritional value of legume seeds. Here, 20 functional substances were profiled in germinated mungbeans and the expression levels of the transcripts of key enzymes in targeted secondary metabolite biosynthetic pathways were identified. VC1973A, a reference mungbean elite cultivar, had the highest amount of gallic acid (99.93 ± 0.13 mg/100 g DW) but showed lower contents of most metabolites than the other genotypes. Wild mungbeans contained a large amount of isoflavones compared with cultivated genotypes, especially for daidzin, genistin and glycitin. The expression of key genes involved in biosynthetic pathways had significant positive or negative correlations with the target secondary metabolite contents. The results indicate that functional substance contents are regulated at the transcriptional level, which can be applied to improve the nutritional value of mungbean sprouts in molecular breeding or genetic engineering, and wild mungbeans are a useful resource to improve the quality of mungbean sprouts.

Identification of novel loci for flowering time in mungbean [Vigna radiata (L.) R. Wilczek] using genome-wide association study

BACKGROUND

Flowering time is an important crop trait. Mungbean flowers do not flower simultaneously, leading to asynchronous pod maturity and laborious multiple harvests per individual plant. The genomic and genetic mechanisms of flowering in mungbean are largely unknown.

OBJECTIVE

This study sought to discover new quantitative trait loci (QTLs) for days to first flowering in mungbean using a genome-wide association study (GWAS).

METHODS

In total, 206 mungbean accessions collected from 20 countries were sequenced using genotyping by sequencing. A GWAS was conducted using 3,596 single nucleotide polymorphisms (SNPs) using TASSEL v5.2.

RESULTS

Seven significant SNPs were associated with first flowering time. Based on the linkage disequilibrium (LD) decay distance, LD block was determined from upstream to downstream of each SNP up to 384 kb. The lead SNP (Chr2_51229568) was located in the DFF2-2 locus. Syntenic analysis between mungbean and soybean revealed the DFF2-2 locus had collinearity with soybean genomic regions containing flowering-related QTLs on Gm13 and Gm20.

CONCLUSION

Identification of flowering-related QTLs and SNPs is important for developing synchronous pod maturity and desirable flowering traits in mungbean.

Enhanced stability of the SARS CoV-2 spike glycoprotein following modification of an alanine cavity in the protein core

The spike (S) glycoprotein of SARS CoV-2 is the target of neutralizing antibodies (NAbs) that are crucial for vaccine effectiveness. The S1 subunit binds ACE2 while the S2 subunit mediates virus-cell membrane fusion. S2 is a class I fusion glycoprotein subunit and contains a central coiled coil that acts as a scaffold for the conformational changes associated with fusion function. The coiled coil of S2 is unusual in that the 3-4 repeat of inward-facing positions are mostly occupied by polar residues that mediate few inter-helical contacts in the prefusion trimer. We examined how insertion of bulkier hydrophobic residues (Val, Leu, Ile, Phe) to fill a cavity next to Ala1016 and Ala1020 in the 3-4 repeat affects the stability and antigenicity of S trimers. Substitution of Ala1016 with bulkier hydrophobic residues in the context of a prefusion-stabilized S trimer, S2P-FHA, was associated with increased thermal stability. S glycoprotein membrane fusion function was retained with Ala1016/Ala1020 cavity-filling mutations associated with improved recombinant S2P-FHA thermostability, however 2 mutants, A1016L and A1016V/A1020I, lacked ability to mediate entry of S-HIV-1 pseudoparticles into 293-ACE2 cells. When assessed as immunogens, two thermostable S2P-FHA mutants derived from the ancestral isolate, A1016L (16L) and A1016V/A1020I (VI) elicited neutralizing antibody with 50%-inhibitory dilutions (ID50s) in the range 2,700-5,110 for ancestral and Delta-derived viruses, and 210-1,744 for Omicron BA.1. The antigens elicited antibody specificities directed to the receptor-binding domain (RBD), N-terminal domain (NTD), fusion peptide and stem region of S2. The VI mutation enabled the production of intrinsically stable Omicron BA.1 and Omicron BA.4/5 S2P-FHA-like ectodomain oligomers in the absence of an external trimerization motif (T4 foldon), thus representing an alternative approach for stabilizing oligomeric S glycoprotein vaccines.

Development of an inclusive 580K SNP array and its application for genomic selection and genome-wide association studies in rice

Rice is a globally cultivated crop and is primarily a staple food source for more than half of the world's population. Various single-nucleotide polymorphism (SNP) arrays have been developed and utilized as standard genotyping methods for rice breeding research. Considering the importance of SNP arrays with more inclusive genetic information for GWAS and genomic selection, we integrated SNPs from eight different data resources: resequencing data from the Korean World Rice Collection (KRICE) of 475 accessions, 3,000 rice genome project (3 K-RGP) data, 700 K high-density rice array, Affymetrix 44 K SNP array, QTARO, Reactome, and plastid and GMO information. The collected SNPs were filtered and selected based on the breeder's interest, covering all key traits or research areas to develop an integrated array system representing inclusive genomic polymorphisms. A total of 581,006 high-quality SNPs were synthesized with an average distance of 200 bp between adjacent SNPs, generating a 580 K Axiom Rice Genotyping Chip (580 K _ KNU chip). Further validation of this array on 4,720 genotypes revealed robust and highly efficient genotyping. This has also been demonstrated in genome-wide association studies (GWAS) and genomic selection (GS) of three traits: clum length, heading date, and panicle length. Several SNPs significantly associated with cut-off, -log₁₀ p-value >7.0, were detected in GWAS, and the GS predictabilities for the three traits were more than 0.5, in both rrBLUP and convolutional neural network (CNN) models. The Axiom 580 K Genotyping array will provide a cost-effective genotyping platform and accelerate rice GWAS and GS studies.

β-Delayed One and Two Neutron Emission Probabilities Southeast of ^{132}Sn and the Odd-Even Systematics in r-Process Nuclide Abundances

The β-delayed one- and two-neutron emission probabilities (P_{1n} and P_{2n}) of 20 neutron-rich nuclei with N≥82 have been measured at the RIBF facility of the RIKEN Nishina Center. P_{1n} of ^{130,131}Ag, ^{133,134}Cd, ^{135,136}In, and ^{138,139}Sn were determined for the first time, and stringent upper limits were placed on P_{2n} for nearly all cases. β-delayed two-neutron emission (β2n) was unambiguously identified in ^{133}Cd and ^{135,136}In, and their P_{2n} were measured. Weak β2n was also detected from ^{137,138}Sn. Our results highlight the effect of the N=82 and Z=50 shell closures on β-delayed neutron emission probability and provide stringent benchmarks for newly developed macroscopic-microscopic and self-consistent global models with the inclusion of a statistical treatment of neutron and γ emission. The impact of our measurements on r-process nucleosynthesis was studied in a neutron star merger scenario. Our P_{1n} and P_{2n} have a direct impact on the odd-even staggering of the final abundance, improving the agreement between calculated and observed Solar System abundances. The odd isotope fraction of Ba in r-process-enhanced (r-II) stars is also better reproduced using our new data.

Metabolomic and transcriptomic changes in mungbean (Vigna radiata (L.) R. Wilczek) sprouts under salinity stress

Mungbean (Vigna radiata) sprouts are consumed globally as a healthy food with high nutritional values, having antioxidant and anticancer capacity. Under mild salinity stress, plants accumulate more secondary metabolites to alleviate oxidative stress. In this study, metabolomic and transcriptomic changes in mungbean sprouts were identified using a reference cultivar, sunhwa, to understand the regulatory mechanisms of secondary metabolites in response to salinity stress. Under salinity conditions, the contents of phenylpropanoid-derived metabolites, including catechin, chlorogenic acid, isovitexin, p-coumaric acid, syringic acid, ferulic acid, and vitexin, significantly increased. Through RNA sequencing, 728 differentially expressed genes (DEGs) were identified and 20 DEGs were detected in phenylpropanoid and flavonoid biosynthetic pathways. Among them, 11 DEGs encoding key enzymes involved in the biosynthesis of the secondary metabolites that increased after NaCl treatment were significantly upregulated, including dihydroflavonol 4-reductase (log₂FC 1.46), caffeoyl-CoA O-methyltransferase (1.38), chalcone synthase (1.15), and chalcone isomerase (1.19). Transcription factor families, such as MYB, WRKY, and bHLH, were also identified as upregulated DEGs, which play a crucial role in stress responses in plants. Furthermore, this study showed that mild salinity stress can increase the contents of phenylpropanoids and flavonoids in mungbean sprouts through transcriptional regulation of the key enzymes involved in the biosynthetic pathways. Overall, these findings will provide valuable information for molecular breeders and scientists interested in improving the nutritional quality of sprout vegetables.

The association between frailty and physical performance in elderly patients with heart failure

Background

Frailty is known to be an important prognostic indicator in heart failure (HF). The Korean version of the frail scale for Koreans (K-FRAIL) has been developed and verified. The purpose of this study is to analyze the relationship between the K-FRAIL scale and physical performance, including muscular fitness and aerobic capacity in patients with HF.

Methods

This study included 143 HF patients aged over 65 years from a single tertiary hospital. In these subjects, muscular fitness was assessed using the handgrip test and knee extensor strength measurement, and aerobic capacity was assessed by cardiopulmonary exercise test and 6-minute walk test. Frailty status was measured using the K-FRAIL questionnaire and was classified as robust (K-FRAIL scale: 0), prefrail (1–2), and frail (3–5).

Results

Mean age of participants with robust (N=37), prefrail (N=75), and frail (N=31) were 72.5, 73.5, and 76.3 years, respectively. There was no difference in sex and left ventricular ejection fraction (LVEF) among groups, but the estimated glomerular filtration rate (eGFR) was significantly lower as frailty status increased (75.6±17.2 vs. 70.0±20.5 vs. 56.1±23.7 mL/min/1.73 m2; P<0.001). Hand-grip strength and knee extensor muscle strength did not differ among groups. However, peak oxygen consumption (peak VO2; 22.8±5.0 vs. 19.3±4.6 vs. 16.9±4.7 mL/kg/min, P<0.001) and 6-min walk distance (458.4±68.2 vs. 404.5±92.3 vs. 311.2±120.5 m; p<0.001) significantly decreased according to frailty severity. In multivariate regression analysis adjusted for age, sex, haemoglobin, eGFR and LVEF, peak VO2 (β=−0.311; P=0.002) and 6-min walk distance (β=−0.384; P<0.001) showed a significant inverse association with the K-FRAIL scale. With the cut-off value from receiver-operating characteristic curve analysis, peak VO2 (hazard ratio, 5.08; p=0.023) and 6MWT (hazard ratio, 3.99; p=0.020) were independent predictor of frailty according to K-FRAIL scale.

Conclusion

In elderly HF patients, physical performance differs according to frailty status, peak VO2 and 6-min walk distance correlates with the K-FRAIL scale better than muscular fitness.

Funding Acknowledgement

Type of funding sources: None.

Identification of noble candidate gene associated with sensitivity to phytotoxicity of etofenprox in soybean

Phytotoxicity is caused by the interaction between plants and a chemical substance, which can cause critical damage to plants. Understanding the molecular mechanism underlying plant-chemical interactions is important for managing pests in crop fields and avoiding plant phytotoxicity by insecticides. The genomic region responsible for sensitivity to phytotoxicity of etofenprox (PE), controlled by a single dominant gene, was detected by constructing high density genetic map using recombination inbred lines (RILs) in soybean. The genomic region of ~ 80 kbp containing nine genes was identified on chromosome 16 using a high-throughput single nucleotide polymorphism (SNP) genotyping system using two different RIL populations. Through resequencing data of 31 genotypes, nonsynonymous SNPs were identified in Glyma.16g181900, Glyma.16g182200, and Glyma.16g182300. The genetic variation in Glyma.16g182200, encoding glycosylphosphatidylinositol-anchored protein (GPI-AP), caused a critical structure disruption on the active site of the protein. This structural variation of GPI-AP may change various properties of the ion channels which are the targets of pyrethroid insecticide including etofenprox. This is the first study that identifies the candidate gene and develops SNP markers associated with PE. This study would provide genomic information to understand the mechanism of phytotoxicity in soybean and functionally characterize the responsive gene.

Effect of follow-up raloxifene therapy after denosumab discontinuation in postmenopausal women

Follow-up raloxifene therapy after denosumab discontinuation resulted in a decrease in bone mass to the pre-denosumab levels and a rebound increase of bone turnover markers. The decrease in lumbar bone mineral density was particularly evident when the body mass index was low, there were previous vertebral fractures, or lumbar bone mineral density before denosumab administration was low.

INTRODUCTION

Selective estrogen receptor modulators may be an alternative to bisphosphonates for treating rebound resorption after discontinuing denosumab. This study aimed to investigate the effects of follow-up raloxifene therapy after denosumab discontinuation in postmenopausal women.

METHODS

This retrospective observational study included 61 patients who received 12-month follow-up raloxifene therapy after denosumab discontinuation. The primary endpoint was the bone mineral density change. The secondary endpoints were the changes in bone turnover markers and the incidence of new vertebral fractures.

RESULTS

Raloxifene administration for 12 months after denosumab discontinuation resulted in a significantly lower bone mineral density at all sites compared to the level at 6 months after the last denosumab treatment (lumbar spine, - 5.48%; femoral neck, - 2.95%; total hip, - 3.52%; all, p < 0.001). The decrease in lumbar bone mineral density was particularly evident when the body mass index was low, there were previous vertebral fractures, or lumbar bone mineral density before denosumab administration was low. Marked increases in the bone turnover markers from baseline were noted after switching to raloxifene. However, no new vertebral fractures occurred during raloxifene treatment.

CONCLUSIONS

Follow-up raloxifene therapy after denosumab discontinuation resulted in a decrease in bone mass to the pre-denosumab levels and a rebound increase of bone turnover markers. Therefore, raloxifene administered sequentially after denosumab discontinuation was not effective in preventing rebound phenomenon.

Glaucoma and biomechanics

PURPOSE OF REVIEW

Biomechanics is an important aspect of the complex family of diseases known as the glaucomas. Here, we review recent studies of biomechanics in glaucoma.

RECENT FINDINGS

Several tissues have direct and/or indirect biomechanical roles in various forms of glaucoma, including the trabecular meshwork, cornea, peripapillary sclera, optic nerve head/sheath, and iris. Multiple mechanosensory mechanisms and signaling pathways continue to be identified in both the trabecular meshwork and optic nerve head. Further, the recent literature describes a variety of approaches for investigating the role of tissue biomechanics as a risk factor for glaucoma, including pathological stiffening of the trabecular meshwork, peripapillary scleral structural changes, and remodeling of the optic nerve head. Finally, there have been advances in incorporating biomechanical information in glaucoma prognoses, including corneal biomechanical parameters and iridial mechanical properties in angle-closure glaucoma.

SUMMARY

Biomechanics remains an active aspect of glaucoma research, with activity in both basic science and clinical translation. However, the role of biomechanics in glaucoma remains incompletely understood. Therefore, further studies are indicated to identify novel therapeutic approaches that leverage biomechanics. Importantly, clinical translation of appropriate assays of tissue biomechanical properties in glaucoma is also needed.

Comparison of fracture risk between type 1 and type 2 diabetes: a comprehensive real-world data

Population-based cohort study of 6,548,784 Korean subjects demonstrates that the risk of fracture was higher in patients with diabetes than in nondiabetic subjects. Furthermore, patients with type 1 diabetes were associated with a higher risk of fracture than patients with type 2 diabetes for all measurement sites.

INTRODUCTION

Diabetes mellitus is associated with increased fracture risk. Although the pathophysiologic effect on bone metabolism differs according to the type of diabetes, a higher risk of fracture in patients with diabetes than in nondiabetic patients has been consistently demonstrated. Considering the ever-increasing number of patients with diabetes, we aimed to provide updated information on whether this phenomenon remains valid in real-world settings by using large-scale population datasets.

METHODS

We conducted a retrospective longitudinal study using data from the Korean National Health Insurance Service dataset of preventive health check-ups between January 2009 and December 2016. The hazard ratios were calculated for any fracture, vertebral fracture, and hip fracture and were analyzed according to the presence and type of diabetes. Among 10,585,818 subjects, 6,548,784 were eligible for the analysis (2418 patients with type 1 diabetes mellitus [T1DM] and 506,208 patients with type 2 diabetes mellitus [T2DM]).

RESULTS

The mean follow-up duration (in years) was 7.0 ± 1.3 for subjects without diabetes, 6.4 ± 2.0 for those with T1DM, and 6.7 ± 1.7 for T2DM. Patients with T1DM had a higher incidence rate for all types of fractures per 1000 person-years. The fully adjusted hazard ratios (HRs) for any fracture, vertebral fracture, and hip fracture were higher in T1DM than in T2DM (1.37 [95% confidence interval (CI): 1.23-1.52] for any fracture, 1.33 [95% CI: 1.09-1.63] for vertebral fracture, and 1.99 [95% CI: 1.56-2.53] for hip fracture).

CONCLUSIONS

In this large-scale population analysis, diabetes was associated with a higher risk of all types of fractures. Patients with T1DM had a higher risk of fracture than those with T2DM for all measurement sites, and hip fractures had the highest risk. Therefore, fracture prevention training for patients with diabetes is advisable.

Development of postbiotics by whey bioconversion with Enterococcus faecalis M157 KACC81148BP and Lactococcus lactis CAU2013 KACC81152BP for treating periodontal disease and improving gut health

This study developed postbiotics with whey bioconversion product produced by Enterococcus faecalis M157 KACC 81148BP, and mixed whey bioconversion products produced by E. faecalis M157 KACC 81148BP and Lactococcus lactis ssp. lactis CAU2013 KACC 81152BP to alleviate periodontitis (PD) and to improve gut health. The powdered whey bioconversion product (EF) produced by E. faecalis M157 KACC 81148BP, mixed whey bioconversion products (EF+LL) from E. faecalis M157 KACC 81148BP and L. lactis CAU2013 KACC 81152BP, and phosphate-buffered saline (PBS; control) were administered orally to PD-induced rats for 8 wk. Infiltration of inflammatory cells and epithelial proliferation in periodontal tissue were found in control, but the lesions were reduced in PD+EF group (administration of EF to PD-induced rats), and no lesions were observed in PD+EF+LL group (administration of EF+LL to PD-induced rats). The bone loss volumes in PD+EF and PD+EF+LL groups were lower than in control. Cytokine production levels related to inflammation were lower and antioxidative stress markers were higher in PD+EF and PD+EF+LL groups than in control for both periodontal tissue and gut. The ratios of Lactobacillus spp. in gut microbiome of PD+EF and PD+EF+LL groups were higher than in control. These results indicate that the whey bioconversion product produced by E. faecalis M157 KACC 81148BP, and mixed whey bioconversion products produced by E. faecalis M157 KACC 81148BP and L. lactis CAU2013 KACC 81152BP are effective on relieving periodontitis and improving the gut health.

A near-complete genome sequence of mungbean (Vigna radiata L.) provides key insights into the modern breeding program

Mungbean (Vigna radiata L.), a fast-growing legume species, is an important source of carbohydrates and proteins in developing countries of Asia. Here, we constructed a near-complete genome sequence of mungbean with a scaffold N50 value of 5.2 Mb and only a 0.4% gap, with a total scaffold size of 475 Mb. We identified several misassembled pseudomolecules (Chr03, Chr04, Chr05, and Chr08) in the previous draft assembly; Chr03, Chr04, and Chr08 were assembled into one chromosome, and Chr05 was broken into two chromosomes in the improved reference genome assembly, thus providing more accurate linkage information to breeders. Additionally, using an ultra-high-resolution linkage map constructed based on resequencing data, we identified several quantitative trait loci (QTLs) and the underlying candidate genes affecting synchronous pod maturity (SPM). Mungbean homologs of two soybean ([Glycine max (L.) Merr.] flowering genes, E3 (phytochrome A) and J (early flowering 3), were identified as candidate genes for the QTLs, and the candidate genes for plant height, node number, and SPM showed critical nucleotide substitutions between the reference cultivar and other genotypes (landraces and wild accessions). Based on the analysis of genetic diversity among 276 accessions collected from 23 countries, we identified 36 selective sweep regions and observed that the overall genetic diversity of cultivars decreased to 30% of that in wild accessions postdomestication. The near-complete genome sequence of mungbean represents an important resource for genome-assisted improvement in the mungbean breeding program.

Metabolomics Changes of Serum and Tissues in Mice Died of Acute Tetracaine Poisoning

Abstract

Objective To study the changes of metabolites in serum and tissues （kidney, liver and heart） of mice died of acute tetracaine poisoning by metabolomics, to search for potential biomarkers and related metabolic pathways, and to provide new ideas for the identification of cause of death and research on toxicological mechanism of acute tetracaine poisoning. Methods Forty ICR mice were randomly divided into control group and acute tetracaine poisoning death group. The model of death from acute poisoning was established by intraperitoneal injection of tetracaine, and the metabolic profile of serum and tissues of mice was obtained by ultra-high performance liquid chromatography-electrostatic field orbitrap high resolution mass spectrometry （UPLC-Orbitrap HRMS）. Multivariate statistical principal component analysis （PCA） and orthogonal partial least square-discriminant analysis （OPLS-DA） were used, combined with t-test and fold change to identify the differential metabolites associated with death from acute tetracaine poisoning. Results Compared with the control group, the metabolic profiles of serum and tissues in the mice from acute tetracaine poisoning death group were significantly different. Eleven differential metabolites were identified in serum, including xanthine, spermine, 3-hydroxybutylamine, etc.; twenty-five differential metabolites were identified in liver, including adenylate, adenosine, citric acid, etc.; twelve differential metabolites were identified in heart, including hypoxanthine, guanine, guanosine, etc; four differential metabolites were identified in kidney, including taurochenodeoxycholic acid, 11, 12-epoxyeicosatrienoic acid, dimethylethanolamine and indole. Acute tetracaine poisoning mainly affected purine metabolism, tricarboxylic acid cycle, as well as metabolism of alanine, aspartic acid and glutamic acid. Conclusion The differential metabolites in serum and tissues of mice died of acute tetracaine poisoning are expected to be candidate biomarkers for this cause of death. The results can provide research basis for the mechanism and identification of acute tetracaine poisoning.

Identification of a novel trait associated with phytotoxicity of an insecticide etofenprox in soybean

Synthetic insecticides are widely used to control pests in various crop fields. Especially in soybean [Glycine max (L.) Merr.] fields, the insecticide etofenprox, which is a pyrethroid derivative, has been used to manage hemiptera pests. To date, soybean phytotoxicity response has not been reported to etofenprox derivatives, two Korean cultivars, Danbaek and Kwangan, were first identified to show leaf shape shrinkage damage after etofenprox application. We confirmed that the causal substance for phytotoxicity is etofenprox and that it had dosage effects. Through genetic analysis using three F₂ populations, sensitivity to etofenprox is confirmed to be managed by a single dominant gene, and that gene is the same in Danbaek and Kwangan. Although further genetic research is required to identify the gene responsible for sensitivity to etofenprox, the results of this study will help to elucidate the interaction between plants and chemicals when breeding new cultivars or developing pesticides.

Fermented milk with Lactobacillus curvatus SMFM2016-NK alleviates periodontal and gut inflammation, and alters oral and gut microbiota

This study aimed to analyze the effect of milk fermented with Lactobacillus curvatus SMFM2016-NK on periodontal diseases and gut health in a rat model. To improve the effect of Lb. curvatus SMFM2016-NK-fermented milk administration for relieving periodontitis, the periodontitis rat models were treated with the following for 4 wk: 10% skim milk (normal), periodontitis + 10% skim milk (negative control), periodontitis + Lactobacillus rhamnosus GG-fermented milk (positive control), and periodontitis + Lb. curvatus SMFM2016-NK-fermented milk (PD+LCFM). Transcriptional analysis of inflammatory cytokines [tumor necrosis factor α (TNF-α), IL-1β, IL-6, and IL-10] was performed via quantitative reverse-transcription PCR. The changes in the oral and gut microbiomes after administering Lb. curvatus SMFM2016-NK-fermented milk were analyzed with metagenomics sequencing using DNA extracted from the oral gingival tissues and feces from the cecum of the rat models. After treatment with Lb. curvatus SMFM2016-NK-fermented milk, the relative gene expression levels of TNFA and IL1B in the gingiva decreased in the PD+LCFM group compared with those in the negative control group. In the oral microbiome, the proportion of the phylum Proteobacteria in the PD+LCFM group was lower than that in the negative control after treatment with Lb. curvatus SMFM2016-NK-fermented milk. For the effect in the gut, the relative gene expression levels of inflammatory cytokines in the colon between the normal and negative control groups were not different; however, the expression levels of TNFA and IL1B in the PD+LCFM and positive control groups, respectively, were lower than those in the negative control group. The composition and diversity of the gut microbiome differed among normal, periodontitis, and Lb. curvatus SMFM2016-NK-fermented milk treatment groups. These results indicate that Lb. curvatus SMFM2016-NK-fermented milk could alleviate periodontal and gut inflammation and change oral and gut microbiota.

Anti-fibrotic activity of a rho-kinase inhibitor restores outflow function and intraocular pressure homeostasis

Glucocorticoids are widely used as an ophthalmic medication. A common, sight-threatening adverse event of glucocorticoid usage is ocular hypertension, caused by dysfunction of the conventional outflow pathway. We report that netarsudil, a rho-kinase inhibitor, decreased glucocorticoid-induced ocular hypertension in patients whose intraocular pressures were poorly controlled by standard medications. Mechanistic studies in our established mouse model of glucocorticoid-induced ocular hypertension show that netarsudil both prevented and reduced intraocular pressure elevation. Further, netarsudil attenuated characteristic steroid-induced pathologies as assessed by quantification of outflow function and tissue stiffness, and morphological and immunohistochemical indicators of tissue fibrosis. Thus, rho-kinase inhibitors act directly on conventional outflow cells to prevent or attenuate fibrotic disease processes in glucocorticoid-induced ocular hypertension in an immune-privileged environment. Moreover, these data motivate the need for a randomized prospective clinical study to determine whether netarsudil is indeed superior to first-line anti-glaucoma drugs in lowering steroid-induced ocular hypertension.

Identification of a Locus Controlling Compound Raceme Inflorescence in Mungbean [Vigna radiata (L.) R. Wilczek]

Mungbean [Vigna radiata (L.) R. Wilczek] produces a compound raceme inflorescence that branches into secondary inflorescences, which produce flowers. This architecture results in the less-domesticated traits of asynchronous pod maturity and multiple harvest times. This study identified the genetic factors responsible for the compound raceme of mungbean, providing a unique biological opportunity to improve simultaneous flowering. Using a recombinant inbred line (RIL) population derived from VC1973A, an elite cultivar with a compound raceme type, and IT208075, a natural mutant with a simple raceme type, a single locus that determined the inflorescence type was identified based on 1:1 segregation ratio in the F₈ generation, and designated Comraceme. Linkage map analysis showed Comraceme was located on chromosome 4 within a marker interval spanning 520 kb and containing 64 genes. RILs carrying heterozygous fragments around Comraceme produced compound racemes, indicating this form was dominant to the simple raceme type. Quantitative trait loci related to plant architecture and inflorescence have been identified in genomic regions of soybean syntenic to Comraceme. In IT208075, 15 genes were present as distinct variants not observed in other landrace varieties or wild mungbean. These genes included Vradi04g00002481, a development-related gene encoding a B3 transcriptional factor. The upstream region of Vradi04g00002481 differed between lines producing the simple and compound types of raceme. Expression of Vradi04g00002481 was significantly lower at the early vegetative stage and higher at the early reproductive stage, in IT208075 than in VC1973A. Vradi04g00002481 was therefore likely to determine inflorescence type in mungbean. Although further study is required to determine the functional mechanism, this finding provides valuable genetic information for understanding the architecture of the compound raceme in mungbean.

Genetic Diversity and Genome-Wide Association Study of Seed Aspect Ratio Using a High-Density SNP Array in Peanut (Arachis hypogaea L.)

Peanut (Arachis hypogaea L.) is one of the important oil crops of the world. In this study, we aimed to evaluate the genetic diversity of 384 peanut germplasms including 100 Korean germplasms and 284 core collections from the United States Department of Agriculture (USDA) using an Axiom_Arachis array with 58K single-nucleotide polymorphisms (SNPs). We evaluated the evolutionary relationships among 384 peanut germplasms using a genome-wide association study (GWAS) of seed aspect ratio data processed by ImageJ software. In total, 14,030 filtered polymorphic SNPs were identified from the peanut 58K SNP array. We identified five SNPs with significant associations to seed aspect ratio on chromosomes Aradu.A09, Aradu.A10, Araip.B08, and Araip.B09. AX-177640219 on chromosome Araip.B08 was the most significantly associated marker in GAPIT and Regularization method. Phosphoenolpyruvate carboxylase (PEPC) was found among the eleven genes within a linkage disequilibrium (LD) of the significant SNPs on Araip.B08 and could have a strong causal effect in determining seed aspect ratio. The results of the present study provide information and methods that are useful for further genetic and genomic studies as well as molecular breeding programs in peanuts.

Machine learning for predicting fractional flow reserve based on optical coherence tomography in intermediate coronary stenosis

Background

Machine learning approaches using intravascular optical coherence tomography (OCT) to predict fractional flow reserve (FFR) have not been previously investigated. The objective of the study was to evaluate a machine learning method to estimate FFR based on intravascular OCT images in intermediate coronary lesions.

Methods

Data from both OCT- and wire-based FFR methods were obtained for lesions of the left anterior descending artery in 125 patients. Based on the total number of lesions, training and testing groups were partitioned at a ratio of 5:1. For the training group, 36 features, including 16 clinical and lesion characteristics, and 21 OCT features, were used to model machine learning-FFR. machine learning-FFR values were then derived for the testing group and compared with wire-based FFR values in terms of a diagnosis of ischemia (FFR &lt;0.8).

Results

Clinical and lesion characteristics and OCT features between the training and testing groups were similar. During the machine learning modeling of the training group, six important features of machine learning-FFR were identified: minimal luminal area, percentage of the stenotic area, lesion length, proximal luminal area, pre-procedural platelet count, and hypertension. machine learning-FFR values showed a good correlation (r=0.853, P&lt;0.001) with wire-based FFR values (Figure 1A). The diagnostic power of an FFR value less than 0.8, sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of machine learning-FFR values for the testing group were 85.7%, 100%, 100%, 77.8%, and 90.5%, respectively (Figure 1B). Additionally, OCT-based machine learning-FFR values showed a good diagnostic accuracy compared with other image-based FFR values.

Conclusions

The OCT-based machine learning-FFR method can be used to simultaneously acquire information on both image and functional modalities using one invasive procedure, suggesting that it may be used to optimize treatments for intermediate coronary artery stenosis, as well as save time and cost.

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): Funded by the Korean government (MSIT) (no. 2017R1A2B2003191)

Identification of epigenetic variation associated with synchronous pod maturity in mungbean (Vigna radiata L.)

Cytosine methylation in genomic DNA affects gene expression, potentially causing phenotypic variation. Mungbean, an agronomically and nutritionally important legume species, is characterized by nonsynchronous pod maturity, resulting in multiple harvest which costs extra time and labor. To elucidate the epigenetic influences on synchronous pod maturity (SPM) in mungbean, we determined the genome-wide DNA methylation profiles of eight mungbean recombinant inbred lines (RILs) and their parental genotypes, and compared DNA methylation profiles between high SPM and low SPM RILs, thus revealing differentially methylated regions (DMRs). A total of 3, 18, and 28 pure DMRs, defined as regions showing no significant correlation between nucleotide sequence variation and methylation level, were identified in CpG, CHG, and CHH contexts, respectively. These DMRs were proximal to 20 genes. Among the 544 single nucleotide polymorphisms identified near the 20 genes, only one caused critical change in gene expression by early termination. Analysis of these genome-wide DNA methylation profiles suggests that epigenetic changes can influence the expression of proximal genes, regardless of nucleotide sequence variation, and that SPM is mediated through gibberellin-mediated hormone signaling pathways. These results provide insights into how epialleles contribute to phenotypic variation and improve SPM in mungbean cultivars.

Transcriptomic and biochemical analyses of the accumulation of sucrose in mungbean (Vigna radiata (L.) Wilczek) leaves after pod removal

Synchronous pod maturity is critical for increasing grain yield. The candidate genes involved in synchronous pod maturity were identified through RNA-seq and HPLC. Mungbean (Vigna radiata [L.] Wilczek), an important source of carbohydrate and protein in Asia, is characterized by nonsynchronous pod maturity; consequently, harvesting is labor intensive. Because pod maturity is associated with synthesis and remobilization of sucrose, we examined changes in sucrose levels and transcriptome in leaf (source) tissues after pod (sink) removal using two genotypes, VC1973A and V2984; VC1973A had higher synchronicity in pod maturity than V2984. After pod removal, much higher number of pods were produced in V2984 than VC1973A. The sucrose content of leaf tissues significantly decreased in V2984 because it continued to utilize assimilates from leaves for producing new pods, but significantly increased in VC1973A because of the loss of sink. Transcriptome analysis revealed that the number of differentially expressed genes was approximately fourfold higher in VC1973A than in those of V2984 after pod removal. The expression of two paralogous genes (Vradi01g05010 and Vradi10g08240), encoding beta-glucosidase enzymes, significantly decreased in VC1973A after pod removal and was significantly lower in depodded VC1973A than depodded V2984, indicating these two genes may participate in sucrose utilization for seed development by regulating the level of glucose. The results of this study will help elucidate the genetic basis of synchronous pod maturity in mungbean and facilitate the development of new cultivars with synchronous pod maturity.

Transplant outcomes in kidney recipients with lupus nephritis, and systematic review

Background

Despite improved survival of patients with lupus nephritis (LN), some require kidney transplantation because of progression to end-stage renal disease (ESRD). However, the transplant outcomes of these patients and other recipients have not been thoroughly compared.

Methods

In total, 1848 Korean kidney recipients who underwent transplantation from 1998 to 2017 at two tertiary referral centers were evaluated retrospectively. Among them, 28 recipients with LN, and 50 control recipients matched by age, sex, and donor type, were compared with respect to graft and patient survival. We pooled our data with 17 previous cohort studies in which the graft survival of recipients with LN was described in detail.

Results

During the median follow-up period of 9.5 years (maximum 21 years), graft failure (GF) occurred in 10.7% and 16.0% of LN and control recipients, respectively. No differences were found in the rates of GF and death-censored graft failure or patient survival between the two groups. The risks of acute T cell-mediated and antibody-mediated rejection were also similar between the two groups. The pooled analysis showed similar 1- and 5-year graft survival rates between LN and control recipients.

Conclusions

Kidney transplantation is an acceptable option in patients with concurrent LN and ESRD.

Updates on Legume Genome Sequencing

Legumes (Fabaceae) are agronomically and economically one of the most important crops. Because legumes serve as a source of food, feed, and industrial materials, many studies in the field of legume genomics, including genome sequencing, have been conducted over the last decade. Here, we update the progress in genome sequencing of legume crops, including soybean (Glycine max [L.] Merr.), mung bean (V. radiata var. radiata), adzuki bean (V. angularis var. angularis), common bean (Phaseolus vulgaris L.), pigeon pea (Cajanus cajan), chickpea (Cicer arietinum), and peanut (Arachis hypogaea). Since the publication of the first reference genome sequence of each species, many accessions have been resequenced to study genetic diversity, speciation, and polyploidization in the legume lineage.

P5731Optimal blood pressure in diabetic hypertensive patients with overt proteinuria

Background

Evidence for the benefit of intensive blood pressure lowering in diabetic nephropathy is not clear at this time. The objective of this study was to demonstrate whether lower mean blood pressure (BP) in treated hypertensive patients with diabetic nephropathy is associated with better prognosis.

Methods

From the National Health Insurance Service (NHIS) Health Examination Database, diabetic hypertensive subjects with proteinuria between 2009 and 2010 were selected and followed-up until 2015 (N=8,663). Mean of the recorded systolic and diastolic BP during follow-up health examinations were stratified into five categories (SBP: <120, 120 to <130, 130 to <140, 140 to <150, and ≥150 mmHg; DBP: <70, 70 to <80, 80 to <90, 90 to <100, and ≥100 mmHg). All-cause death, myocardial infarction (MI), stroke, and renal outcome (progression to end stage renal disease or doubling of serum creatinine) were examined by Cox proportional hazard models with the propensity scores adjusted method.

Results

Compared to SBP of 130 to <140 mmHg, SBP of 120 to <130 mmHg was associated with lower risk of all-cause death (HR=0.78; 95% CI, 0.64–0.95), stroke (HR: 0.65; 95% CI, 0.45–0.94), and renal outcome (HR: 0.81; 95% CI, 0.68–0.97). SBP of <120 mmHg was associated with benefit for renal outcomes (HR: 0.69; 95% CI 0.55–0.88) but not with elevated risk of other outcomes. Compared to DBP of 80 to <90 mmHg, DBP of 70 to <80 mmHg were associated with lower risk of all-cause death (HR: 0.75; 95% CI, 0.64–0.88) but with higher risk of MI (HR: 1.52; 95% CI, 1.05–2.21). DBP of <70 mmHg was associated with reduced risk of all-cause death (HR: 0.79; 95% CI, 0.64–0.98).

Conclusion

In diabetic hypertensive subjects with overt proteinuria, deterioration of renal function decreased with decreasing SBP and the lowest risk of all-cause death and stroke were observed in SBP <130 mmHg. Low DBP was associated with low risk of all-cause death but there was a J curve phenomenon for MI in DBP of 70 to <80 mmHg.

P3555Lower native T1, extracellular volume and T2 on cardiac magnetic resonance imaging is related to more left ventricular reverse remodeling in nonischemic dilated cardiomyopathy

Introduction

Guideline-directed medical therapy can induce left ventricular reverse remodeling (LVRR) in nonischemic dilated cardiomyopathy (NIDCM). Some predictors for LVRR have been reported but, there were few studies about the relationship between cardiac magnetic resonance imaging (CMR) parameters and LVRR in NIDCM on optimal GDMT.

Methods

We retrospectively analyzed echocardiogram and CMR data of newly diagnosed 142 NIDCM patients (age: 57±16 years old, 71.8% male) in a single center from Jan 2012 to Dec 2017. NIDCM was defined as left ventricular ejection fraction (LVEF) <45% and the ischemic etiology was excluded by CMR, coronary angiography or coronary CT or SPECT scan. LVRR was defined as improvement in LVEF ≥10% during follow-up period (median 403 days).

Results

Baseline LVEF and LV end diastolic dimension (LVEDD) were 27±8% and 64±8 mm. There were 87 patients (61.3%) of LVRR in our cohort. In LVRR group, native T1 value was significantly lower (1326±66 for LVRR vs 1369±72ms, p<0.001), extracellular volume (ECV) was significantly lower (28.3±3.6 for LVRR vs 32.4±4.4%, p<0.001), and T2 value was significantly lower (49.6±4.6 for LVRR vs 52.1±5.4ms, p=0.004) compared with non-LVRR group. ECV was an independent predictor for LVRR after adjusting current LVRR predictors such as age, sex, LVEF, LVEDD, systolic blood pressure, heart rate and QRS duration (Odd ratio 0.706, 95% confidence interval 0.616–0.809, p<0.001).

Conclusion

Lower native T1, ECV and T2 on CMR is related to higher incidence of LVRR in NIDCM. Further larger prospective study should be warranted to confirm the relationship between CMR parameters and LVRR in NIDCM.

Soybean-VCF2Genomes: a database to identify the closest accession in soybean germplasm collection

BACKGROUND

The development of next generation sequencer (NGS) and the analytical methods allowed the researchers to profile their samples more precisely and easier than before. Especially for agriculture, the certification of the genomic background of their plant materials would be important for the reliability of seed market and stable yield as well as for quarantine procedure. However, the analysis of NGS data is still difficult for non-computational researchers or breeders to verify their samples because majority of current softwares for NGS analysis require users to access unfamiliar Linux environment.

MAIN BODY

Here, we developed a web-application, "Soybean-VCF2Genomes", http://pgl.gnu.ac.kr/soy_vcf2genome/ to map single sample variant call format (VCF) file against known soybean germplasm collection for identification of the closest soybean accession. Based on principal component analysis (PCA), we simplified genotype matrix for lowering computational burden while maintaining accurate clustering. With our web-application, users can simply upload single sample VCF file created by more than 10x resequencing strategy to find the closest samples along with linkage dendrogram of the reference genotype matrix.

CONCLUSION

The information of the closest soybean cultivar will allow breeders to estimate relative germplasmic position of their query sample to determine soybean breeding strategies. Moreover, our VCF2Genomes scheme can be extended to other plant species where the whole genome sequences of core collection are publicly available.

QTL Analysis of Resistance to High-Intensity UV-B Irradiation in Soybean (Glycine max [L.] Merr.)

High-intensity ultraviolet-B (UV-B) irradiation is a complex abiotic stressor resulting in excessive light exposure, heat, and dehydration, thereby affecting crop yields. In the present study, we identified quantitative trait loci (QTLs) for resistance to high-intensity UV-B irradiation in soybean (Glycine max [L.]). We used a genotyping-by-sequencing approach using an F6 recombinant inbred line (RIL) population derived from a cross between Cheongja 3 (UV-B sensitive) and Buseok (UV-B resistant). We evaluated the degree of leaf damage by high-intensity UV-B radiation in the RIL population and identified four QTLs, UVBR12-1, 6-1, 10-1, and 14-1, for UV-B stress resistance, together explaining 20% of the observed phenotypic variation. The genomic regions containing UVBR12-1 and UVBR6-1 and their syntenic blocks included other known biotic and abiotic stress-related QTLs. The QTL with the highest logarithm of odds (LOD) score of 3.76 was UVBR12-1 on Chromosome 12, containing two genes encoding spectrin beta chain, brain (SPTBN, Glyma.12g088600) and bZIP transcription factor21/TGACG motif-binding 9 (bZIP TF21/TGA9, Glyma.12g088700). Their amino acid sequences did not differ between the mapping parents, but both genes were significantly upregulated by UV-B stress in Buseok but not in Cheongja 3. Among five genes in UVBR6-1 on Chromosome 6, Glyma.06g319700 (encoding a leucine-rich repeat family protein) had two nonsynonymous single nucleotide polymorphisms differentiating the parental lines. Our findings offer powerful genetic resources for efficient and precise breeding programs aimed at developing resistant soybean cultivars to multiple stresses. Furthermore, functional validation of the candidate genes will improve our understanding of UV-B stress defense mechanisms.

Abstract P1-08-24: Conditional survival of breast cancer patients: Korean nationwide registry

Purpose: Conditional relative survival (CRS) could provide more relevant information on the current prognosis of cancer survivors than standard 5-year relative survival (RS). This study aimed to estimate the 5-year CRS of Korean breast cancer patients.

Patients and Methods: We identified 145,083 breast cancer cases with diagnosis between 2002 and 2013 in the Korea Central Cancer Registry. The CRS was estimated for every year after diagnosis, according to sex, age, histologic types, stage, and year of diagnosis.

Results: The 5-year RS at diagnosis was 90.8% and 10-year RS was 85.7%. Five-year CRS was 91.0% and 94.3% at 1-year and 5-year after diagnosis. Women had better 5-year CRS than men after 5 years of survival (94.3% vs. 79.5%), and very young and very old patients had worse 5-year CRS after 5 years of survival than other age groups (92.2% in &lt;40yr, 92.6% in ≥70yr vs. 95.4% in 40-49, 94.3% in 50-59, and 93.7% in 60-69, relatively). In histologic types, CRS of metaplastic carcinoma has improved from 82.0% to 95.2%, compared to CRS of lobular carcinoma (from 93.1% to 92.5%). Hardly any excess mortality (5-year CRS ≥ 95%) was seen since 7 years after diagnosis. There was hardly any excess mortality at 5 years of survival, for the patients with 40-49 years (95.4%), with localized disease (97.8%), and with metaplastic carcinoma (95.2%).

Conclusion: This study showed that CRS of breast cancer survivors in Korea has been improved, which varied by sex, age, stage, and histologic types. These CRS analysis could provide a more detailed information for survival to breast cancer survivors and clinicians.

Citation Format: Jung S-Y, Jung K-W, Won Y-J, Kwon Y, Ha J, Kim YA, Kong S-Y, Lee ES. Conditional survival of breast cancer patients: Korean nationwide registry [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-08-24.

Comprehensive RNA sequencing and co-expression network analysis to complete the biosynthetic pathway of coumestrol, a phytoestrogen

Coumestrol (CMS), a coumestan isoflavone, plays key roles in nodulation through communication with rhizobia, and has been used as phytoestrogens for hormone replacement therapy in humans. Because CMS content is controlled by multiple genetic factors, the genetic basis of CMS biosynthesis has remained unclear. We identified soybean genotypes with consistently high (Daewonkong) or low (SS0903-2B-21-1-2) CMS content over 2 years. We performed RNA sequencing of leaf samples from both genotypes at developmental stage R7, when CMS levels are highest. Within the phenylpropanoid biosynthetic pathway, 41 genes were tightly connected in a functional co-expression gene network; seven of these genes were differentially expressed between two genotypes. We identified 14 candidate genes involved in CMS biosynthesis. Among them, seven were annotated as encoding oxidoreductases that may catalyze the transfer of electrons from daidzein, a precursor of CMS. Two of the other genes, annotated as encoding a MYB domain protein and a MLP-like protein, may increase CMS accumulation in response to stress conditions. Our results will help to complete our understanding of the CMS biosynthetic pathway, and should facilitate development of soybean cultivars with high CMS content that could be used to promote the fitness of plants and human beings.

Genome sequence of Jatropha curcas L., a non-edible biodiesel plant, provides a resource to improve seed-related traits

Jatropha curcas (physic nut), a non-edible oilseed crop, represents one of the most promising alternative energy sources due to its high seed oil content, rapid growth and adaptability to various environments. We report ~339 Mbp draft whole genome sequence of J. curcas var. Chai Nat using both the PacBio and Illumina sequencing platforms. We identified and categorized differentially expressed genes related to biosynthesis of lipid and toxic compound among four stages of seed development. Triacylglycerol (TAG), the major component of seed storage oil, is mainly synthesized by phospholipid:diacylglycerol acyltransferase in Jatropha, and continuous high expression of homologs of oleosin over seed development contributes to accumulation of high level of oil in kernels by preventing the breakdown of TAG. A physical cluster of genes for diterpenoid biosynthetic enzymes, including casbene synthases highly responsible for a toxic compound, phorbol ester, in seed cake, was syntenically highly conserved between Jatropha and castor bean. Transcriptomic analysis of female and male flowers revealed the up-regulation of a dozen family of TFs in female flower. Additionally, we constructed a robust species tree enabling estimation of divergence times among nine Jatropha species and five commercial crops in Malpighiales order. Our results will help researchers and breeders increase energy efficiency of this important oil seed crop by improving yield and oil content, and eliminating toxic compound in seed cake for animal feed.

Overexpression of the Soybean NAC Gene GmNAC109 Increases Lateral Root Formation and Abiotic Stress Tolerance in Transgenic Arabidopsis Plants

NACs are plant-specific transcription factors that have crucial roles in plant development and biotic and/or abiotic stress responses. This study characterized the functions of the soybean NAC gene GmNAC109 using an overexpression construct in Arabidopsis lines. Sequence analysis revealed that GmNAC109 is highly homologous to ATAF1 (Arabidopsis Transcription Activation Factor 1), which regulates biotic and abiotic stress responses. GmNAC109 protein localized to the nucleus and its C-terminal domain exhibited transcriptional activation activity. Salt, dehydration, and cold stresses significantly increased expression of GmNAC109 in soybean. Similarly, Arabidopsis plants overexpressing GmNAC109 were more tolerant to drought and salt stress than wild-type Col-0 plants. Stress response-related genes, such as DREB1A (drought-responsive element-binding 1A), DREB2A, AREB1 (ABSCISIC ACID-RESPONSIVE ELEMENT BINDING PROTEIN 1), AREB2, RD29A (RESPONSIVE TO Desiccation 29A), and COR15A (COLD REGULATED 15A) were upregulated in GmNAC109-overexpressing transgenic Arabidopsis lines. The transgenic lines showed upregulation of the ABA-responsive genes ABI1 (ABA INSENSITIVE 1) and ABI5 and hypersensitivity to ABA. However, GmNAC109 did not increase expression of the ABA-biosynthetic gene NCED3 (NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3) and endogenous ABA content in the transgenic lines. Overexpression of GmNAC109 significantly increased lateral root formation in transgenic Arabidopsis lines. Expression of AIR3 (AUXIN-INDUCED IN ROOT CULTURES 3) and ARF2 (AUXIN RESPONSE FACTOR 2) was increased and decreased in these transgenic lines, respectively, indicating that GmNAC109 is involved in the auxin signaling pathway and thereby helps to regulate hairy root formation. Our results provide a basis for development of soybean lines with improved tolerance to abiotic stresses via genetic manipulation.

GmBRC1 is a Candidate Gene for Branching in Soybean (Glycine max (L.) Merrill)

Branch number is one of the main factors affecting the yield of soybean (Glycine max (L.)). In this study, we conducted a genome-wide association study combined with linkage analysis for the identification of a candidate gene controlling soybean branching. Five quantitative trait nucleotides (QTNs) were associated with branch numbers in a soybean core collection. Among these QTNs, a linkage disequilibrium (LD) block qtnBR6-1 spanning 20 genes was found to overlap a previously identified major quantitative trait locus qBR6-1. To validate and narrow down qtnBR6-1, we developed a set of near-isogenic lines (NILs) harboring high-branching (HB) and low-branching (LB) alleles of qBR6-1, with 99.96% isogenicity and different branch numbers. A cluster of single nucleotide polymorphisms (SNPs) segregating between NIL-HB and NIL-LB was located within the qtnBR6-1 LD block. Among the five genes showing differential expression between NIL-HB and NIL-LB, BRANCHED1 (BRC1; Glyma.06G210600) was down-regulated in the shoot apex of NIL-HB, and one missense mutation and two SNPs upstream of BRC1 were associated with branch numbers in 59 additional soybean accessions. BRC1 encodes TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTORS 1 and 2 transcription factor and functions as a regulatory repressor of branching. On the basis of these results, we propose BRC1 as a candidate gene for branching in soybean.