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At the reproductive development stage of rice (Oryza sativa L.), temperature stress can decrease spikelet fertility, ultimately resulting in a yield loss. In this study, a total of 98 rice varieties were used in genome-wide association study (GWAS) to understand spikelet fertility under a high temperature (SFHT). GWAS results revealed that two lead SNPs were significantly associated with SFHT. Candidate genes located within ± 250 kb of the corresponding SNP position were discovered, resulting in a total of 21 candidate genes on chromosome 10 and 18 candidate genes on chromosome 11. Based on previously reported function and haplotype analysis, Os10g0177200 (EF-HAND 2domain containing protein) as one candidate gene showed significant differences among groups of haplotypes. This candidate gene will be further evaluated for its function to determine whether it is useful for improving molecular breeding studies and developing new high temperature tolerant rice varieties.

Rice (Oryza sativa L.) pollen grains are highly sensitive to extreme temperatures. Studies on the proteomic analysis of pollen at different developmental stages are limited. In this study, to identify proteins expressed during pollen development, we performed shotgun proteomic analysis of rice anthers harvested at 8, 3, and 0 days before heading (DBH). A total of 4509 non-redundant proteins were identified in rice anthers at each of the three time points with three replications per time point. Among these, 2968 proteins were reproducible, of which 1919 were specifically expressed at a given stage of anther development. Clustering and gene ontology (GO) enrichment analyses categorized the specifically expressed proteins into four groups. Group I comprised proteins involved in cell differentiation, reproduction, and stress response; Group II contained proteins related to cell growth and carbohydrate metabolic process; Group III included proteins related to starch accumulation and lipid metabolic process; Group IV comprised proteins related to structure morphogenesis and cellular components. Proteins in Group I steadily increased during anther development, whereas those in Group I steadily decreased. Group III proteins showed the highest expression at 3 DBH, whereas Group IV proteins exhibited the lowest expression at 3 DBH.

Superhongmi is a new rice variety, which was developed for the enrichment of bioactive compounds through cross-breeding three varieties of rice breeds in Korea. The high-performance liquid chromatography coupled with a photodiode array detector quadrupole and tandem time-of-flight mass spectrometry (HPLC/PDA/QTOF-MS) analysis has revealed that superhongmi bran extract contained four taxifolin derivatives as well as cyanidin 3-glucoside. The high-performance countercurrent chromatography (CCC) and reversed-phase HPLC led to the isolation of aforementioned five compounds, and spectroscopic analysis identified cyanidin 3-glucoside (1), along with (2R,3R)-taxifolin 3-O-β-d-glucopyranoside (2), (2R,3R)-4'-O-methyltaxifolin 3-O-β-d-glucopyranoside (a novel compound) (3), (2R,3R)-taxifolin (4), and (2R,3R)-4'-O-methyltaxifolin (5). Compound 2 had the highest rat small intestinal sucrase inhibitory activity (0.54 mM) relevant for potentially managing postprandial hyperglycemia, followed by compound 1 (0.97 mM) and compound 4 (1.74 mM, IC50). The anti-hyperglycemic effect of compound 4 (taxifolin), a main peak in HPLC analysis was investigated using a Sprague-Dawley (SD) rat model. Compared to a control, taxifolin treatment (p < 0.001) reduced significantly after sucrose loading the observed postprandial blood glucose and the maximum blood glucose (Cmax) by 15% (203.60 ± 15.86 to 172.30 ± 12.74). These results indicate that taxifolin derivatives that inhibit the activity of carbohydrate-hydrolyzing enzymes resulting in reduced dietary carbohydrate absorption can potentially be used as a strategy to manage diabetes.

We conducted a genome-wide association study (GWAS) of cold tolerance in a collection of 127 rice accessions, including 57 Korean landraces at the seedling stage. Cold tolerance of rice seedlings was evaluated in a growth chamber under controlled conditions and scored on a 0–9 scale, based on their low-temperature response and subsequent recovery. GWAS, together with principal component analysis (PCA) and kinship matrix analysis, revealed four quantitative trait loci (QTLs) on chromosomes 1, 4, and 5 that explained 16.5% to 18.5% of the variance in cold tolerance. The genomic region underlying the QTL on chromosome four overlapped with a previously reported QTL associated with cold tolerance in rice seedlings. Similarly, one of the QTLs identified on chromosome five overlapped with a previously reported QTL associated with seedling vigor. Subsequent bioinformatic and haplotype analyses revealed three candidate genes affecting cold tolerance within the linkage disequilibrium (LD) block of these QTLs: Os01g0357800, encoding a pentatricopeptide repeat (PPR) domain-containing protein, Os05g0171300, encoding a plastidial ADP-glucose transporter, and Os05g0400200, encoding a retrotransposon protein, Ty1-copia subclass. The detected QTLs and further evaluation of these candidate genes in the future will provide strategies for developing cold-tolerant rice in breeding programs.

Spring orchid (Cymbidium goeringii) is one of the most important species belonging to Orchidaceae owing to its aesthetic appeal, fragrant flowers and ideal characteristics for using as a houseplant. In this study, the complete chloroplast genome of Korean C. goeringii acc. smg222 was determined by Illumina sequencing. The circular double-stranded DNA of 148,441 bp consisted of two inverted repeat regions of 25,610 bp each, a large single copy region of 83,311 bp, and a small single copy region of 13,910 bp. The genome contained 122 genes, of which 104 were unique and 18 were duplicated within the IRs. The 104 unique genes included 70 protein-coding genes, 30 distinct tRNA genes, and four rRNA genes. Phylogenetic tree analysis revealed that C. goeringii acc. smg222 was clustered with Cymbidium kanran, a cymbidium species native to Korea.

Rice varieties with suitable flour-making qualities are required to promote the rice processed-food industry and to boost rice consumption. A rice mutation, Namil(SA)-flo1, produces grains with floury endosperm. Overall, grains with low grain hardness, low starch damage, and fine particle size are more suitable for use in flour processing grains with waxy, dull endosperm with normal grain hardness and a high amylose content. In this study, fine mapping found a C to T single nucleotide polymorphism (SNP) in exon 2 of the gene encoding cytosolic pyruvate phosphate dikinase (cyOsPPDK). The SNP resulted in a change of serine to phenylalanine acid at amino acid position 101. The gene was named FLOURY ENDOSPERM 4-5 (FLO4-5). Co-segregation analysis with the developed cleaved amplified polymorphic sequence (CAPS) markers revealed co-segregation between the floury phenotype and the flo4-5. This CAPS marker could be applied directly for marker-assisted selection. Real-time RT-PCR experiments revealed that PPDK was expressed at considerably higher levels in the flo4-5 mutant than in the wild type during the grain filling stage. Plastid ADP-glucose pyrophosphorylase small subunit (AGPS2a and AGPS2b) and soluble starch synthase (SSIIb and SSIIc) also exhibited enhanced expression in the flo4-5 mutant.

The complete chloroplast genome sequence of Korean Cymbidium goeringii acc. smg222 was analyzed. Based on a comparison with Chinese C. goeringii, losses of nine ndh subunits (ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhH, ndhJ, and ndhK), three protein-coding genes (ycf 1-like, ycf 15, and ycf 68), six transfer RNAs, and one conserved open reading frame (orf 42). In addition, 219 InDels (insertion or deletion) and 171 simple sequence repeats were observed. Twenty-Five of which InDel markers have been evaluated, that useful for distinguishing Korean and Chinese Cymbidium associations based on the polymorphisms of chloroplast genomes between Korean Cymbidium goeringii acc. smg222 and Chinese C. goeringii and evaluation of genetic diversity. Finally, the phylogenetic relationships of the 39 Korean and 22 Chinese species was constructed based on the five InDel markers of them and obtained high support, indicating that our data may be useful in resolving relationships in this genus. The information about chloroplast DNA structure and gene variants of C. goeringii acc. smg222 chloroplast genome will provide sufficient phylogenetic information for resolving evolutionary relationships. The molecular markers developed in here will contribute to further research of Cymbidium species and conservation of endemic Cymbidium species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-019-2020-1) contains supplementary material, which is available to authorized users.

A genome-wide association study (GWAS) was used to investigate the genetic basis of chilling tolerance in a collection of 117 rice accessions, including 26 Korean landraces and 29 weedy rices, at the reproductive stage. To assess chilling tolerance at the early young microspore stage, plants were treated at 12 °C for 5 days, and tolerance was evaluated using seed set fertility. GWAS, together with principal component analysis and kinship matrix analysis, revealed five quantitative trait loci (QTLs) associated with chilling tolerance on chromosomes 3, 6, and 7. The percentage of phenotypic variation explained by the QTLs was 11–19%. The genomic region underlying the QTL on chromosome 3 overlapped with a previously reported QTL associated with spikelet fertility. Subsequent bioinformatic and haplotype analyses suggested three candidate chilling-tolerance genes within the QTL linkage disequilibrium block: Os03g0305700, encoding a protein similar to peptide chain release factor 2, Os06g0495700, encoding a beta tubulin, autoregulation binding-site-domain-containing protein, and Os07g0137800, encoding a protein kinase, core-domain-containing protein. Further analysis of the detected QTLs and the candidate chilling-tolerance genes will facilitate strategies for developing chilling-tolerant rice cultivars in breeding programs.

Rice crops are vulnerable to low temperatures. During development, the reproductive stage is particularly sensitive to cold exposure, which causes abnormal pollen development and a high degree of male sterility. In this study, shotgun proteomic analysis was used to analyze rice anthers containing pollen grains from a cold-tolerant variety, Dianxi 4. Protein expression was compared between normal anthers and anthers exposed to cold temperatures at the young microspore stage. In total, 3835 non-redundant proteins were identified in the rice anther. Of these, 441 proteins were differentially expressed between normal and cold-treated anthers. Pollen allergens, ATP synthase, actin, profilin, and β-expansin proteins were highly abundant, reflecting anther development, pollen germination, and pollen tube elongation. Starch and sucrose metabolic proteins such as α-amylase precursor and 4-α-glucanotransferase exhibited reduced expression after cold exposure. Among the proteins that exhibited increased expression after cold exposure, C2 domain proteins, and GRPs were identified as candidate signaling factors for mediation of the cold tolerance response. Through high-throughput proteomic analysis we were able to reveal proteomic changes against cold stress and suggest two signaling factors as the candidate genes.

Women experience physical, mental, and social changes during menopause. It is important to maintain a healthy diet for effective menopause management. The effect of germinated Superjami, a deep violet colored rice cultivar, on the body weight, glucose level, antioxidant defense system, and bone metabolism in a menopausal rat model was investigated. The animals were randomly divided into three groups and fed with a normal diet (ND), a control diet supplemented with 20% (w/w) non-germinated Superjami flour (NGSF), or germinated Superjami flour (GSF) for eight weeks. The NGSF and GSF groups exhibited significantly lower body weight and fat, glucose and insulin contents, adipokine concentrations, and bone resorption biomarker levels, and higher antioxidant enzyme activities and 17-&beta, estradiol content than the ND group (p &lt, 0.05). The GSF group showed greater glucose homeostasis, antioxidative, and bone metabolism-improving effects compared with the NGSF group. These findings demonstrate that germination could further improve the health-promoting properties of Superjami and that this germinated pigmented rice cultivar could be useful in the treatment and management of menopause-induced hyperglycemia, oxidative stress, and bone turnover imbalance.

To increase coverage of protein identification of an Agaricus bisporus fruiting body, we analyzed the crude protein fraction of the fruiting body by using a shotgun proteomics approach where 7 MudPIT (Multi-Protein identification Technology) runs were conducted and the MS/MS spectra from the 7 MudPIT runs were merged. Overall, 3093 non-redundant proteins were identified to support the expression of those genes annotated in the genome database of Agaricus bisporus. The physicochemical properties of the identified proteins, i.e., wide pI value range and molecular mass range, were indicative of unbiased protein identification. The relative quantification of the identified proteins revealed that K5XI50 (Aldedh domain-containing protein) and K5XEW1 (Ubiquitin-like domain-containing protein) were highly abundant in the fruiting body. Based on the information in the Uniprot (Universal Protein Resource) database for A. bisporus, only approximately 53% of the 3093 identified proteins have been functionally described and approximately 47% of the proteins remain uncharacterized. Gene Ontology analysis revealed that the majority of proteins were annotated with a biological process, and proteins associated with coiled-coil (12.8%) and nucleotide binding (8.21%) categories were dominant. The Kyoto Encyclopedia of Genes and Genome analysis revealed that proteins involved in biosynthesis of secondary metabolites and tyrosine metabolism were enriched in a fruiting body of Agaricus bisporus, suggesting that the proteins are associated with antioxidant metabolites.

and non-allelopathic parents of &lsquo, Nong-an&rsquo, The performance of allelopathic traits were evaluated with inhibition rate on root length, shoot length, total length, root weight, shoot weight, and total weight of lettuce as a receiver plant. With 785 polymorphic DNA markers, we constructed a linkage map showing a total of 2489.75 cM genetic length and 3.17 cM of average genetic distance between each adjacent marker. QTL analysis detected on QTL regions on chromosome 8 responsible for the inhibition of shoot length and inhibition of total length. The qISL-8 explained 20.38% of the phenotypic variation for the inhibition on the shoot length. The qITL-8 explained 14.93% of the phenotypic variation for the inhibition on total length. The physical distance of the detected QTL region was 194 Kbp where 31 genes are located., Sathi&rsquo, In rice there are few genetic studies reported for allelopathy traits, which signify the ability of plants to inhibit or stimulate growth of other plants in the environment, by exuding chemicals. QTL analysis for allelopathic traits were conducted with 98 F8 RILs developed from the cross between the high allelopathic parents of &lsquo

In this study, relative germination percentage (RGP) and delayed mean germination time (DMGT) were measured in various rice accessions at the germination stage and carried out association analysis to identify candidate genes related to low temperature germination (LTG) using a natural population comprising 137 rice cultivars and inbred lines selected from the Korean rice core set. Genome-wide association study using ~ 1.44 million high-quality SNPs, which were identified by re-sequencing all rice collections, revealed 48 candidate genes on chromosome 10 and 55 candidate genes on chromosome 11 in the high peak SNP sites of associated loci for RGP and DMGT, respectively. By detecting highly associated variations located inside genic regions and performing functional annotation of the genes, we detected 23 candidate genes for RGP and 18 genes for DMGT for LTG. In addition, the haplotype and sequence analysis of the candidate gene (Os10g0371100) with RGP trait and the candidate gene (Os11t0104240-00) with DMGT revealed correlation between sequences of functional variations and phenotypes. Several novel LTG-related candidate genes previously were known for the function during rice germination and uncovered their substantial natural variations. These candidate genes represent valuable resources for molecular breeding and genetic improvement of cold tolerance during rice germination. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-018-1252-9) contains supplementary material, which is available to authorized users.

Pyruvate orthophosphate dikinase (PPDK) is a component of glycolysis to mediate endosperm energy charge by adjusting the ratio of ATP to ADP and AMP that proposed to balance the flow of carbon into starch, protein, fatty acid and amino acid biosynthesis. However, these were inconsistent with the first report of a T-DNA insertional knockout mutant of the rice PPDK gene (flo4) showed that rice with inactivated PPDK gene failed to produce a opaque seeds. Therefore, the PPDK might have multifaceted functions in grain filling stage, which in some ways might depend on the direction of the reversible catalysis. Suweon 542 is a rice (Oryza sativa L.) mutant developed from Oryza sativa ssp. japonica cv. Namil. Suweon 542 has a milky-white floury endosperm suitable for dry filling, with low starch damage, low grain hardness, and fine flour particle size. The mutant locus on chromosome 5 controls the floury endosperm phenotype of Suweon 542. Fine mapping of this locus is required for efficient breeding of rice germplasm suitable for dry milling. In this study, whole genome of Suweon 542 and Milyang 23 were re-sequenced using Illumina HiSeq 2500. Co-segregation analysis of F3:4 family populations derived from Suweon 542/Milyang 23 was performed using eight CAPS markers and phenotypic evaluation of the endosperm. The target region was mapped to a 33 kb region and identified to encode cytosolic pyruvate orthophosphate dikinase protein (cyOsPPDK). A G→A SNP in exon 8 of cyOsPPDK resulting in a missense mutation from Gly to Asp at amino acid position 404 was responsible for the floury endosperm of Suweon 542. qRT-PCR experiments revealed that FLO4-4 was expressed to a considerably higher level in Suweon 542 than in Namil during the grain filling stage. Overall, fine mapping of FLO4-4 and candidate gene analysis provided further insight into the floury endosperm of rice, and reveal a novel SNP in cyOsPPDK gene can affect the floury endosperm phenotype through active PPDK gene during grain filling stage.