Large‐scale GWAS in sorghum reveals common genetic control of grain size among cereals

Grain size is a key yield component of cereal crops and a major quality attribute. It is determined by a genotype’s genetic potential and its capacity to fill the grains. This study aims to dissect the genetic architecture of grain size in sorghum. An integrated genome‐wide association study (GWAS) was conducted using a diversity panel (n = 837) and a BC‐NAM population (n = 1421). To isolate genetic effects associated with genetic potential of grain size, rather than the genotype’s capacity to fill the grains, a treatment of removing half of the panicle was imposed during flowering. Extensive and highly heritable variation in grain size was observed in both populations in 5 field trials, and 81 grain size QTL were identified in subsequent GWAS. These QTL were enriched for orthologues of known grain size genes in rice and maize, and had significant overlap with SNPs associated with grain size in rice and maize, supporting common genetic control of this trait among cereals. Grain size genes with opposite effect on grain number were less likely to overlap with the grain size QTL from this study, indicating the treatment facilitated identification of genetic regions related to the genetic potential of grain size. These results enhance understanding of the genetic architecture of grain size in cereal, and pave the way for exploration of underlying molecular mechanisms and manipulation of this trait in breeding practices.     

IRAP,a retrotransposon-based marker system for the detection of somaclonal variation in barley

The retrotransposon-based marker system, inter-retrotransposon amplified polymorphism (IRAP), and inter-simple sequence repeats (ISSRs) were used to detect somaclonal variation induced by tissue culture. IRAPs use a single primer designed to amplify out from the 5′ LTR sequence of the BARE-1 retrotransposon combined with a degenerate 3′ anchor, similar to that of ISSR primers. We analysed DNA polymorphisms in 147 primary regenerants and parental controls from three cultivars of barley (Hordeum vulgare). The ISSR marker system generated an average of 218 bands per primer, with 29 polymorphisms of which 12 were novel non-parental bands. In comparison, the IRAP system generated an average of 121 bands per primer, with 15 polymorphisms of which nine were novel non-parental bands. Polymorphism detected for IRAP and ISSR markers was more than twofold higher in Golden Promise than Mackay and Tallon cultivars. However, there was no significant difference in the frequency of novel non-parental bands. Cluster analysis revealed that the level of polymorphism and genetic variability detected was comparable between IRAP and ISSR markers. This suggests that retrotransposon-based marker systems, such as IRAP, based on retrotransposons such as BARE-1, are valuable tools for the detailed characterisation of mutation profiles that arise during tissue culture. Their use should improve our understanding of processes influencing mutation and somaclonal variation and allow for the design of methods that yield fewer genome changes in applications where maintaining clonal integrity is important.     

Synthesis and fungicidal activity of tubulin polymerisation promoters. Part 3: Imidazoles

A novel class of experimental fungicides has been discovered, which consists of special tetrasubstituted imidazoles. They are highly active against important phytopathogens, such as Botrytis cinerea (grey mould), Uncinula necator (grape powdery mildew), Mycosphaerella graminicola (wheat leaf blotch) and Alternaria solani (potato and tomato early blight). Their fungicidal efficacy is due to their ability to promote fungal tubulin polymerization, which leads to a disruption of microtubule dynamics. These imidazoles are five-membered ring analogs of similar substituted triazolopyrimidines and pyridazines with the same mode of action. A concise four-step synthesis route has been used to prepare them from commercially available starting materials.     

Additive effects of three auxins and copper on sorghum in vitro root induction

A healthy root system is vital for tissue culture plantlet survival and rapid adaptation from the in vitro microenvironment to glasshouse conditions. Optimization of the root induction medium is an effective way to promote root induction and elongation. Levels of three auxins (α-naphthaleneacetic acid [NAA], 3-indoleacetic acid [IAA], and 3-indolebutyric acid [IBA]) and copper sulfate (CuSO₄) have been investigated in a series of experiments with a sorghum inbred line, Tx430. Significant improvement in root proliferation and shoot growth were observed on Murashige and Skoog (MS) medium supplemented with 1 μmol/L CuSO₄, 1 mg/L NAA, 1 mg/L IAA, and 1 mg/L IBA. On average, one explant (the original in vitro-derived shoot) of Tx430 regenerated 56.7 roots, which was 20-fold higher on the optimal medium than on MS control medium. Another tested genotype SA281 showed similar response patterns as Tx430 across media. In addition, 100% of Tx430 and SA281 plantlets originating from the optimized root induction medium all survived after being transferred to potting soil in the glasshouse. The results demonstrate that a combination of auxins (NAA, IAA, and IBA) and CuSO₄ together at optimal concentrations provide additive effects on promoting root proliferation and explant growth of in vitro sorghum in root induction medium, and subsequently resulted in 100% survival rate of plantlets ex tissue culture. Compared with two published and frequently used root induction media, the optimized medium significantly enhanced root induction and plantlet growth.     

High‐throughput detection and screening of plants modified by gene editing using quantitative real‐time polymerase chain reaction

Gene editing techniques are becoming powerful tools for modifying target genes in organisms. Although several methods have been developed to detect gene‐edited organisms, these techniques are time and labour intensive. Meanwhile, few studies have investigated high‐throughput detection and screening strategies for plants modified by gene editing. In this study, we developed a simple, sensitive and high‐throughput quantitative real‐time (qPCR)‐based method. The qPCR‐based method exploits two differently labelled probes that are placed within one amplicon at the gene editing target site to simultaneously detect the wild‐type and a gene‐edited mutant. We showed that the qPCR‐based method can accurately distinguish CRISPR/Cas9‐induced mutants from the wild‐type in several different plant species, such as Oryza sativa, Arabidopsis thaliana, Sorghum bicolor, and Zea mays. Moreover, the method can subsequently determine the mutation type by direct sequencing of the qPCR products of mutations due to gene editing. The qPCR‐based method is also sufficiently sensitive to distinguish between heterozygous and homozygous mutations in T₀ transgenic plants. In a 384‐well plate format, the method enabled the simultaneous analysis of up to 128 samples in three replicates without handling the post‐polymerase chain reaction (PCR) products. Thus, we propose that our method is an ideal choice for screening plants modified by gene editing from many candidates in T₀ transgenic plants, which will be widely used in the area of plant gene editing.     

Proteome changes in ovarian epithelial cells derived from women with BRCA1 mutations and family histories of cancer

Malignant transformation of the ovarian surface epithelium (OSE) accounts for most ovarian carcinoma. Detection of preneoplastic changes in the OSE leading to overt malignancy is important in prevention and management of ovarian cancer. We identified OSE proteins with altered expression derived from women with a family history (FH) of ovarian and/or breast cancer and mutations in the BRCA1 tumor suppressor gene. Proteins from SV-40-transformed FH-OSE cell lines and control OSE lines derived from women without such histories (non-family history) were separated by two-dimensional PAGE. Gels were analyzed, a protein data base was created, and proteins were characterized according to their molecular weight, isoelectric point, and relative abundance. Mass spectrometry was performed on tryptic protein digests, and data bases were searched for known proteins with the same theoretical tryptic peptide masses. Several proteins showed altered expression in the FH-OSE cells. Beta-tubulin and to a lesser extent ubiquitin carboxyl-terminal hydrolase and glyoxalase 1 appeared to be up-regulated. In contrast, proteins suppressed in FH lines include the 27-kDa heat shock protein, translationally controlled tumor protein, and several proteins associated with actin modification such as actin prepeptide, F-actin capping protein alpha subunit, and cofilin. Sequencing of several cofilin gel spots revealed phosphorylation of serine 3, a post-translational modification associated with decreased actin binding and cytoskeletal reorganization. Two-dimensional Western blots probed with cofilin antibody showed multiple protein spots with isoelectric points of 6-9 pH units. Blots of one-dimensional gels showed a significant reduction in cofilin expression in three FH lines when compared with three non-family history lines (p < or = 0.05). Identification of these and other OSE proteins may be useful in detecting changes suggestive of increased risk of developing preneoplastic disease and defining the possible role(s) of the BRCA1 gene in regulation of OSE cell function.     

RAD51 135G-->C modifies breast cancer risk among BRCA2 mutation carriers: results from a combined analysis of 19 studies

RAD51 is an important component of double-stranded DNA–repair mechanisms that interacts with both BRCA1 and BRCA2. A single-nucleotide polymorphism (SNP) in the 5′ untranslated region (UTR) of RAD51, 135G→C, has been suggested as a possible modifier of breast cancer risk in BRCA1 and BRCA2 mutation carriers. We pooled genotype data for 8,512 female mutation carriers from 19 studies for the RAD51 135G→C SNP. We found evidence of an increased breast cancer risk in CC homozygotes (hazard ratio [HR] 1.92 [95% confidence interval {CI} 1.25–2.94) but not in heterozygotes (HR 0.95 [95% CI 0.83–1.07]; P=.002, by heterogeneity test with 2 degrees of freedom [df]). When BRCA1 and BRCA2 mutation carriers were analyzed separately, the increased risk was statistically significant only among BRCA2 mutation carriers, in whom we observed HRs of 1.17 (95% CI 0.91–1.51) among heterozygotes and 3.18 (95% CI 1.39–7.27) among rare homozygotes (P=.0007, by heterogeneity test with 2 df). In addition, we determined that the 135G→C variant affects RAD51 splicing within the 5′ UTR. Thus, 135G→C may modify the risk of breast cancer in BRCA2 mutation carriers by altering the expression of RAD51. RAD51 is the first gene to be reliably identified as a modifier of risk among BRCA1/2 mutation carriers.     

Predictive Factors of Patient Satisfaction with Pharmacy Services in South Korea: A Cross-Sectional Study of National Level Data

Objectives

Patient satisfaction has emerged as a prerequisite to improving patients’ health behaviors leading to better health care outcomes. This study was to identify predictive determinants for patient satisfaction with pharmacy services using national-level data.

Methods

A cross-sectional evaluation was conducted using 2008 Korean National Health and Nutrition Examination Survey (KNHANES) data. To assess the predictive factors for patient satisfaction with pharmacy services, an ordinal logistic regression model was conducted adjusting for patient characteristics, clinical comorbidities, and perception of health.

Results

A total of 9,744 people, a representative sample of 48.2 million Koreans, participated in the 2008 KNHANES, of whom 2,188 (23.6%) reported visits to pharmacy within the last 2 weeks prior to the survey. Of the patients who visited the pharmacy, 74.6% reported to be either “very satisfied” or “satisfied,” and 25.4% responded as being “neutral,” “dissatisfied,” or “very dissatisfied.” A multivariate ordinal logistic regression analysis with weighted observations revealed that patients with fair perception of health (adjusted OR 1.32; 95% CI 1.01–1.74; p<0.05) and those with middle to low family incomes (adjusted OR 1.34; 95% CI 1.02–1.76; p<0.05) were more likely to be satisfied with pharmacy services, and employment-based insurers were less likely to be satisfied with pharmacy services (adjusted OR 0.80; 95% CI 0.65–0.97; p<0.05).

Conclusion

Our findings indicated that three out of four patients expressed satisfaction toward pharmacy services. Middle to low family incomes, fair perception of health, and employee insured individuals were significant predictors of patient satisfaction with pharmacy services.