Isolation and characteristics of eight novel polymorphic microsatellite loci from the genome of garlic (Allium sativum L.)

Here we characterized eight novel polymorphic SSR markers, developed from an enriched genomic library of garlic (Allium sativum L.). These SSRs produced a total of 64 alleles across 90 garlic accessions, with an average of 8 alleles per locus. Values for observed (H_O) and expected (H_E) heterozygosity ranged from 0.16 to 0.77 (mean = 0.44) and from 0.22 to 0.86 (mean = 0.65), respectively. Six loci deviated significantly (P < 0.05) from Hardy–Weinberg equilibrium (HWE). The averages of gene diversity and PIC values were 0.65 and 0.62, respectively. The mean genetic similarity coefficient was 0.4380, indicating that among garlic accessions existed wide genetic variation. Based on 64 alleles obtained by 8 SSRs, a phenogram was constructed to understand the relationships among the 90 accessions. These newly developed SSRs should prove very useful tools for genotypes identification, assessment of genetic diversity and population structure in garlic.     

Sesquiterpenoids from Carpesium divaricatum and their cytotoxic activity

In the course of searching for cytotoxic terpenoids from medicinal plants in China, two new eudesmane sesquiterpenoids, 5α-hydroxy-13-methoxy-7αH,11αH-eudesm-4(15)-en-12,8β-lactone (1) and 1β-hydroxy-7αH,11αH-eudesm-4(15)-en-12,8β-lactone (2), along with fourteen known sesquiterpenoids were isolated from the whole plant of Carpesium divaricatum. The structures of new compounds were determined using spectroscopic methods, including IR, HRESIMS, and 1D and 2D NMR spectroscopy. The cytotoxicity of selected sesquiterpene lactones against human oral epidermoid carcinoma (KB), human breast cancer (MCF-7) and human hepatoma (HepG-2) cells was also evaluated by MTT method.     

Association analysis of physicochemical traits on eating quality in rice (Oryza sativa L.)

Improvement of rice eating quality is an important objective in current breeding programs. In this study, 130 rice accessions of diverse origin were genotyped using 170 SSR markers to identify marker–trait associations with physicochemical traits on eating quality. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r ² value for all intrachromosomal loci pairs was 0.0940. LD between linked markers decreased with distance. Marker–trait associations were investigated using the unified mixed-model approach, considering both population structure (Q) and kinship (K). In total, 101 marker–trait associations (p < 0.05) were identified using 52 different SSR markers covering 12 chromosomes. The results suggest that association mapping in rice is a viable alternative to quantitative trait loci mapping, and detection of new marker–trait associations associated with rice eating quality will also provide important information for marker-assisted breeding and functional analysis of rice grain quality.     

Prolyl endopeptidase inhibitory activity of unsaturated fatty acids

Prolyl endopeptidase (PEP, EC 3.4.21.26) is widely distributed in various organs, particularly in the brains of amnestic patients. Evaluation of PEP levels in postmortem brains of Alzheimer's disease patients revealed significant increases in PEP activity, suggesting that a specific PEP inhibitor can be a good candidate for an antiamnestic drug. In this study, mono- and polyunsaturated fatty acids were investigated to determine their role as PEP inhibitors. Oleic, linoleic, and arachidonic acids, eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) showed PEP inhibitory activities (IC50 values of 23.6 +/- 0.4, 43.8 +/- 1.8, 53.4 +/- 1.2, 99.4 +/- 1.2, and 46.2 +/- 1.0 microM, respectively), indicating that they were effective PEP inhibitors, with inhibition constant (Ki) values of 26.7 +/- 0.3, 51.0 +/- 0.7, 91.3 +/- 3.1, 247.5 +/- 2.6, and 89.0 +/- 2.3 microM, respectively. Oleic acid showed the highest PEP inhibitory activity. Dixon plots of PEP inhibition showed oleic, linoleic, and arachidonic acids, EPA, and DHA are noncompetitive inhibitors; despite higher IC50 values of these unsaturated fatty acids than strong natural inhibitors, they may have potential use in preventing memory loss.     

Isolation and characterization of 28 polymorphic SSR loci from castor bean (<Emphasis Type="Italic">Ricinus communis</Emphasis> L.)

Castor bean (Ricinus communis) is cultivated for seed oil throughout tropical and subtropical regions but the understanding of its genetic variability is limited. Because applicable microsatellite markers are not sufficient, we isolated and characterized polymorphic simple sequence repeat (SSR) loci acquired from a microsatellite-enriched genomic DNA library of castor bean. Finally, 28 SSR loci revealed polymorphisms in a castor bean collection consisting of 72 accessions. A total of 73 alleles were detected, with an average of 3.18 alleles per locus, and the polymorphism information content (PIC) ranged from 0.03 to 0.47 (mean = 0.26). Values for observed (H_O) and expected (H_E) heterozygosity ranged from 0.00 to 0.19 (mean = 0.11) and from 0.04 to 0.54 (mean = 0.31), respectively. To understand genetic relationships within the castor bean collection, a dendrogram was constructed based on profiles of the 28 SSR loci. These newly developed SSRs will be useful tools for assessing genetic diversity and population structure in castor bean.     

Comparison of eating quality and seed storage protein among Korean rice landraces

Improving eating quality and nutrition is one of the most important objectives in rice breeding program. Palatability factors and seed protein patterns of 69 Korean rice landraces were compared in this study. Of seven palatability factors, setback viscosity (SBV) had the largest variance, ranging from -144 to 45. Water content (WC) had the lowest variance, ranging from 11.0 to 13.0. In correlation analysis, eating quality was positively correlated with all palatability factors except gelatinization temperature (GT). In principal component analyses (PCA), the first PC with Eigen value of 5.06 explained 42.2% of the total variance. Cool paste viscosity (CPV) was the variable that had the largest positive loading. The second PC with Eigen value of 2.09 explained an additional 17.4% of the total variance. SBV was a variable that had the highest negative loading. Peak viscosity (PKV) had positive variance between PC1 and PC2. The 69 Korean rice landraces were clustered into four groups based on physicochemical properties and palatability factors, with groups I and II showing higher EQ than other groups. SDS-PAGE analyses revealed five seed storage patterns in the 69 Korean rice landraces. Among them, 84% (58 landraces) had pattern I. These results indicate that it is possible to develop high palatability cultivars using Korean rice landraces. In addition, screening of landraces based on variation in seed storage protein profile using SDS-PAGE could be highly effective for the identification of valuable rice genetic resources.     

Selection and Molecular Characterization of Soybeans with High Oleic Acid from Plant Germplasm of Genebank

Journal of Crop Science and Biotechnology - Altering soybean fatty acid profiles to improve soybean oil quality has long been time goal of soybean researchers. Soybean oil with elevated oleic acid...     

A study on relative abundance,composition and length variation of microsatellites in 18 underutilized crop species

In the present work, genomic DNA libraries for 18 underutilized crop species (including 11 dicot and 7 monocot species) were enriched for several di- and tri- nucleotide microsatellites by using an optimized procedure. About 500–960 clones from each library were sequenced and all the sequences were characterized to have a comparative look on relative abundance, composition and length variations of perfect microsatellites among different crops. Sequence analysis revealed contrasting differences in the abundance of di- and tri-nucleotide microsatellites with the predominance of tri-nucleotide microsatellites in 11 crops and that of di-nucleotides in other 8 crops. Among di-nucleotide microsatellites, AG/GA class was the most abundant in all the crops except for four crops in which AC/CA class was predominant. Among tri-nucleotide repeats, AGC/GCA/CAG class was the most abundant in eight crops followed by AGG/GGA/GAG class in four crops, whereas in the remaining six crops, the most abundant class was highly variable. The longest di- and tri-nucleotide repeats were observed in Chinese cabbage and mungbean with the average lengths of 70 and 57 base pairs, respectively. These observations revealed species-specific in the distributions of microsatellite repeat motifs. The present study provides highly valuable information that can be useful in targeted development of specific microsatellites markers for genetic analysis of these underutilized crops.     

Phytochemical distribution and antioxidant activities of Korean adzuki bean (<Emphasis Type="Italic">Vigna angularis</Emphasis>) landraces

Total polyphenol content (TPC), total phenolic acid content (TPA), and total flavonoid content (TFC) in 209 Korean adzuki bean landraces were determined by colorimetric methods. Antioxidant effects were evaluated with the DPPH, ABTS, ferric reducing antioxidant power (FRAP), reducing power (RP), and SOD assays. TPC, TPA, and TFC in the 209 Korean adzuki bean landraces ranged from 1.1 to 11.7 mg gallic acid equivalents/g, 0.37 to 5.03 mg caffeic acid equivalents/g, and 0.17 to 0.91 mg quercetin equivalents/g, respectively. Antioxidant activities as assessed by the DPPH, ABTS, FRAP, PR, and SOD assays showed wide variation, ranging from 12.2 to 86.3 (IC₅₀), 0.85 to 5.25 mg ascorbic acid equivalents (ASC)/g, 0.41 to 5.44 mg ASC/g, 0.54 to 1.83 mg ASC/g, and 60.4 to 142.8 (IC₅₀), respectively. Using the relative antioxidant capacity index (RACI), we found that the IT189394 had the highest antioxidant activity. In clustering analysis, 209 Korean adzuki bean landraces were classified into three clusters. Among them, cluster I contained 22 landraces with higher antioxidant activities, TPC, TFC, and TPA and smaller seed sizes than the other clusters. We anticipate that these results will provide useful information for the development of adzuki bean-based functional foods.     

Cross-amplification of SSR markers developed from Allium sativum to other Allium species

For genetic analysis of the genus Allium, which is composed of diverse species, we acquired 50 transferable and polymorphic microsatellite markers from A. sativum and tested them for transferability in five Allium species. Among the 50 simple sequence repeat (SSR) loci, the dinucleotide motif was the most prevalent, with a ratio of 50% (25/50), and (GT)n was more frequent than (GA)n within the dinucleotide motif. The average number of amplified alleles ranged from 1.452 to 1.910 and the accessions of A. tuberosum had a maximum of 4.8 alleles per accession with the GB-AS-104 SSR marker. Whereas A. porrum belonging to the Allium section revealed 73.0% transferability, A. altaicum and A. fistulosum appertaining to different sections showed low transferability, with a ratio of 47.6% and 48.0%, respectively. The phylogenetic results for these SSR markers did not deviate from previous classifications of the genus Allium. As the rate of successful amplification of SSR markers generally correlates with genetic distance, these SSR markers are potentially useful in the analysis of genetic relationships between or within Allium species.