Indeterminate Genotypes Research Articles

Screening Andean Diversity Panel Dry Bean Lines for Resistance to Bacterial Brown Spot Disease Under Field Conditions in South Africa.

Bacterial brown spot (BBS) disease caused by Pseudomonas syringae pv. syringae is an important disease of dry bean (Phaseolus vulgaris L.), with grain yield losses of 55% reported in South Africa. This study aimed to identify BBS disease-resistant genotypes from 415 Andean Diversity Panel (ADP) dry bean lines and 5 check cultivars under field conditions across three sites in South Africa: Warden and Middelburg under natural infestation and Potchefstroom under artificial inoculation. Plants at Potchefstroom were inoculated with P. syringae pv. syringae using three isolates at 21, 28, and 36 days after planting, and disease scoring was done at 7, 14, and 21 days after inoculation following a modified 1 to 9 International Centre for Tropical Agriculture (CIAT) scale. The BBS severity percentage and the area under the disease progress curve (AUDPC) were applied to quantify the reaction of bean genotypes to BBS disease. The study identified 17.2% of evaluated germplasm as resistant and 45.3% as moderately resistant. Genotypes ADP-0592, ADP-0790, ADP-0120, and ADP-0008 were selected for both resistance and high seed yield across the three environments. Genotypes ADP-0546, ADP-0630, ADP-0120, and ADP-0279 were selected for both high yield and resistance at Warden, whereas ADP-0038, ADP-0721, and ADP-0790 were selected for both traits at Middelburg, and lastly, ADP-0120 and ADP-0079 were selected for both traits at Potchefstroom. The best genotypes selected for both high yield and BBS resistance had grain yield >1.45 t ha-1 across sites and >1.85 t ha-1 at individual sites, and they out yielded the best-performing check cultivar (1.13 t ha-1) and the grand mean yield (0.87 t ha-1) across sites. The AUDPC had a strong negative correlation (r = -0.55, P < 0.001) with grain yield at Potchefstroom. Medium-seeded genotypes showed a lower AUDPC than the large-seeded genotypes, and indeterminate genotypes showed a lower AUDPC than determinate genotypes. The genotypes selected for resistance and yield can be utilized in future dry bean improvement efforts for the South African bean market.

Indeterminate Prediction of Hepatitis C Virus Genotype by Commercial Real-Time Polymerase Chain Reaction Assay Resolving by Sequencing to Avoid the Consequence of Inaccurate Typing.

Pakistan is ranked second highest after Egypt in hepatitis C virus (HCV) infection. Accurate typing is mandatory to be compliant with the World Health Organization strategy to eliminate HCV infection in 2030. We characterized the HCV genotypes using Abbott real-time polymerase chain reaction assay and indeterminate samples were sequenced. We also investigated the distribution of HCV genotype among different age groups and gender in chronic HCV patients. One thousand thirteen samples were tested for HCV genotyping using Abbott real-time HCV genotyping assay. RNA extraction from plasma was done using the m2000sp platform. The amplification and detection of genotypes was done on m2000rt instrument. The lower limit of detection assay is 500 IU/mL. The indeterminate genotypes were analyzed by sequencing of the NS5B region. We found genotype 1 in 1.68%, genotype 1b in 0.89%, genotype 1a in 0.79%, genotype 2 in 0.6, genotype 3 in 94.37%, genotype 4 in 0.4%, genotype 5 in 0.09%, and indeterminate genotype result were found in 1.18%. Abbott assay could not identify 12 samples of genotype 3 (1.18%) and gave the indeterminate result. It also fails to assign some of the samples of genotype 1 into 1a and 1b. The indeterminate genotypes were resolved by sequencing followed by phylogenetic analysis. Genotype 3 is the predominant genotype and significantly higher in females as compared with males. Genotype 1a is more common in males than in females. Indeterminate HCV genotypes on sequencing analysis identify as genotype 3a and likewise subtype of genotype1 as 1a.

Optimizing N Fertilization to Improve Yield, Technological and Nutritional Quality of Tomato Grown in High Fertility Soil Conditions.

Processing tomato is the second most important worldwide cash crop, generally produced in high-input systems. However, fruit yield and quality are affected by agronomic management, particularly nitrogen (N) fertilization, whose application to indeterminate growth genotypes for canning has yet to be investigated in depth. Hence, the objective of this work was to assess the effects of different N rates (0, 50, 125, 200, 275, and 350 kg ha−1) on fruit yield and quality characteristics of processing tomato ‘San Marzano’ landrace. The results of our study showed that 125 and 200 kg of N ha−1 are the most appropriate rates in soil with high fertility, ensuring the highest values of marketable yield and brix yield. However, plants fertilized with 125 kg of N ha−1 attained higher values of N efficiency and fruit K and P concentrations than plants fertilized with 200 kg of N ha−1. Our results suggest that overdoses of N supplies negatively affected fruit yield and quality of San Marzano landrace grown in high soil fertility conditions, also reducing the agricultural sustainability. Hence, specific agronomic protocol and extension services are required to optimally manage tomato crop systems.

Improved determination of Neisseria gonorrhoeae gyrase A genotype results in clinical specimens

The emergence of drug-resistant Neisseria gonorrhoeae has prompted the development of rapid molecular assays designed to determine antimicrobial susceptibility. One common assay uses high-resolution melt analysis to target codon 91 of the gyrase A gene (gyrA) to predict N. gonorrhoeae susceptibility to ciprofloxacin. We extracted DNA from remnant clinical specimens that had previously tested positive for N. gonorrhoeae using the Aptima Combo 2 for CT/NG assay (Hologic, San Diego, CA, USA). We selected DNA extracts from specimens with indeterminate, WT and mutant gyrA genotype results from a previous study using high-resolution melt analysis to detect the gyrA codon 91 mutation. We re-tested those specimens using the recently CE-marked ResistancePlus GC (beta) assay (SpeeDx, Sydney, Australia). Of 86 specimens with indeterminate gyrA genotypes on high-resolution melt analysis, the ResistancePlus GC (beta) assay (SpeeDx) identified 30 (35%) WT, 22 (26%) mutant and 34 (40%) indeterminate gyrA genotypes. The ResistancePlus GC (beta) assay showed improved N. gonorrhoeae gyrA genotype determination compared with a prior gyrA genotypic high-resolution melt assay.

Natural post-flowering photoperiod and photoperiod sensitivity: Roles in yield-determining processes in soybean

Promising yield-determining responses to artificial photoperiod manipulation during post-flowering phases have been identified in soybean [Glycine max (L.) Merrill]. These responses enhance resource capture as a result of changes in phase duration, and resource use efficiency as a result of changes in node production and pod development, alleviating intra-node pod interference. This work aims to evaluate the relevance of these responses under natural conditions and discriminate direct from indirect photoperiodic effects, that is, effects caused by changes in the capture of resources. Two field experiments were conducted with a combination of sowing dates, with similar pre- and different post-flowering photoperiod, indeterminate genotypes including near isogenic lines and commercial varieties with different photoperiod sensitivity, and shadings with different incident radiation during post-flowering. Longer post-flowering photoperiod and higher plant photoperiod sensitivity delayed crop development, particularly in lines with alleles E2, E3 or Clark background. This delay resulted in extra radiation capture and node production, which were positively related to yield. Direct photoperiodic effects on nodes per m2 were evidenced in response to changes in post-flowering photoperiod and plant photoperiod sensitivity. The distribution of available resources such as radiation in more nodes per m2 increased use efficiency. Longer post-flowering photoperiod and higher plant photoperiod sensitivity enhanced pod establishment on usually dominated positions such as lateral racemes, affecting pods per m2. Finding these relevant yield-determining effects under natural conditions suggests that processes related to post-flowering photoperiodic responses are a plausible way to enhance resource capture and use efficiency and yield in soybean production systems. In cropping systems in which the whole growing season is used to maximize yield, these post-flowering photoperiodic responses could be adopted at the expense of the pre-flowering phase duration.

Novel Side Effect of a Novel Medication

Introduction Glecaprevir/pibrentasvir (Mavyret) is a combination drug containing glecaprevir (100 mg) and pibrentasvir (40 mg). In the United States, it was approved by the Food and Drug Administration in August 2017 for treatment of hepatitis C. In Europe, it was also approved in August 2017 for the same indication. Here we report a new side effect of reversible hand tremors associated with the use of this drug. Case presentation This case involves a 45-year-old female with 1-year history of treatment naive chronic hepatitis C secondary to intravenous drug abuse. She had HCV viral load of 6.98 IU/ml, indeterminate genotype and ultrasound liver elastography showed mild to moderate fibrosis. She was started on 3 daily tablets glecaprevir/pibrentasvir for 8 weeks. 2 weeks into the treatment, she developed hand tremors, epigastric pain and gastroesophageal reflux. ON examination, she had fine resting tremors involving the fingers. She denied taking any other prescription or over the counter medication. Medication was stopped, and all symptoms improved in 3-4 days. Discussion Glecaprevir/pibrentasvir (MAVYRET) is a fixed-dose combination of glecaprevir, a hepatitis C virus (HCV) NS3/4A protease inhibitor, and pibrentasvir, an HCV NS5A inhibitor, and is indicated for the treatment of patients with chronic HCV genotype (GT) 1, 2, 3, 4, 5 or 6 infections without cirrhosis and with compensated cirrhosis (Child-Pugh A). Known side effects include hepatitis B reactivation, and more commonly increased serum bilirubin, headache, nausea, tiredness, and diarrhea. Our patient with Hepatitis C was started on glecaprevir/pibrentasvir and developed fine hand tremors after 2 weeks of treatment. This side effect was reversible and completely went away after stopping the medication.

HBV genotyping based on key epitopes of PreS1 antigen and its correlation with genotyping by full-length PreS1 sequencing

Objective: The aim was to investigate the genotype distribution of two major epitopes of large surface protein (PreS1) of hepatitis B in Chinese patients and to explore the association between the genotypes of these two epitopes, and to determine whether PreS1 full-length genotype could be revealed according to the polypeptide sequence of key epitopes. Methods: HBV DNA was extracted from the serum of patients for PCR amplification. 278 samples amplified successfully were sequenced and compared with the known HBV sequences in Genbank to determine the two key epitopes of HBV PreS1 genotype (amino acid epitope 21-47 and 94-117, abbreviated as P21 and P94) and PreS1 full-length genotypes. The correlation among three genotyping approaches was analyzed by Cohen's kappa coefficient to verify the consistency between the key-epitope genotyping and the full-length preS1 genotyping. Results: 232 samples were successfully sequenced. The genotyping based on the kind of P21 epitope protein sequence, 201 cases for genotype C, 23 cases for genotype B and 8 cases for uncertain genotypes and genotyping based on the form of P94 epitope protein sequence, 199 cases for genotype C, 25 cases for genotype B and 8 cases for indeterminate genotypes. Lastly, the genotyping based on sequence of the full-length PreS1 sequence, 207 and 25 cases for genotype C and B. P21 or P94 epitope genotyping and PreS1 full length genotyping were highly consistent, respectively, 96.55% and 96.12%, and the two epitopes (P21and P94) genotyping have parallel consistency (93.10%). Conclusion: In this study, an innovatively genotyping method based on the amino acid sequence of key epitopes was proposed. The genotypes of HBV in china were mainly B and C genotypes, and the genotypes of key conserved epitopes of HBV PreS1 were highly consistent with the full-length genotyping ( > 96%). Moreover, genotyping with one or two key epitopes can be used in place of the full-length genotyping.

Indeterminate genotypes of hepatitis C virus by the Abbott RealTime HCV Genotype II assay in Morocco. About eight cases resolved by a sequencing method.

The early detection and genotyping of the hepatitis C virus (HCV) are important in the management of this infection. The genotype is the major factor influencing treatment decisions. That's why it is necessary to use fast and accurate methods in its determination. This study reports, over a period of 3 years (from May 2012 to July 2015), the percentage of indeterminate genotypes by the Abbott RealTime HCV Genotype II test and their results using a sequencing technique. Of 309 samples of 309 patients tested, 11 were indeterminate (4.4%). There were three cases of cross-reactivity (1b/4 in one case, 2/5 in two cases) and a possible co-infection 1 + 4. Among those indeterminate genotypes, cross-reactivities and co-infections, ten samples were tested by sequencing. The results were for four of them a 1d subtype, five were a 2i subtype and one was a 2l subtype. These results support the thesis of complementarity between the two methods: genotyping for the detection of mixed reactions and sequencing for resolving indeterminate cases by genotyping.

Direct Acting Antiviral Treatment Response in Chronic Hepatitis C Infection: Data From Tertiary Care Center in South India

Background and Aim: To assess the prevalence of HCV genotypes in southern India and the response to treatment with directly acting antivirals (DAA). Methods: The study was conducted between June 2015 and December 2016. 82 patients with chronic HCV infection visiting PSG Hospital, Coimbatore in southern India were treated as per EASL HCV treatment recommendations 2015 with available DAAs in India as follows: (1) Sofosbuvir(SOF) + Ribavirin(RBV) ± pegylated Interferon α(PEG-IFNα), (2) Ledipasvir(LDV) + SOF ± RBV, (3) Daclatasvir(DCV) + SOF ± RBV. Treatment was decided as per the patient's HCV genotype, extent of liver disease, previous treatment exposure status and contraindications. Results: HCV genotype 4 (58%) was the most prevalent, followed by genotypes 3 (21%), 1 (18%) and 2 (1%). One case was of indeterminate genotype. The overall response to Sofosbuvir (SOF)/Ribavirin (RBV) ± pegylated interferon (PEG-IFNα), Ledipasvir (LDV)/SOF ± RBV and Daclatasvir (DCV)/SOF ± RBV treatment across all genotypes showed SVR12 of 88.6% (n = 44), 96.6% (n = 29) and 100% (n = 9), respectively. SOF/RBV ± PEG-IFNα has shown better results in treating GT-1 and GT-4 infections in non-cirrhotics in south India than what most western studies have observed. The response to SOF/RBV ± PEG-IFNα in compensated and decompensated cirrhotics across all genotypes was 86.9% (n = 23) and 60% (n = 5) respectively, which was poor compared to LDV/SOF ± RBV or DCV/SOF ± RBV treatment. In one case of GT-3 infection treated with DAA, patient progressed to HCC 1 year after achieving SVR with persistent undetectable HCV RNA. Conclusion: GT-4 was the most prevalent HCV genotype in southern India. SOF + RBV ± PEG-IFNα may still have a role in treating GT-1 and GT-4 non-cirrhotics, but LDV + SOF ± RBV in GT-1 and GT-4 infections, and pan-genotypic DCV + SOF ± RBV have the best response in chronic HCV infection in southern India. The authors have none to declare.

Mineral nitrogen impairs the biological nitrogen fixation in soybean of determinate and indeterminate growth types

ABSTRACTSoybean (Glycine max Merrill) crop production in Brazil relies mainly on biological nitrogen fixation (BNF) for nitrogen (N) supply. Recent adoption of indeterminate growth-type genotypes has raised doubts on the need for supplemental mineral N that might negatively affect the BNF. We assessed the effects of mineral N on BNF attributes of soybean genotypes grown in central and southern Brazil. Genotypes were inoculated with Bradyrhizobium sp. and/or received mineral N in three sets of experiments. In the first set, two genotypes received increasing rates of mineral N in nutrient solution, which consistently reduced the BNF. In the second set, mineral N applied at sowing and/or topdressing reduced nodulation and ureides-N in determinate and indeterminate growth-type genotypes. In the third set, mineral N applied at R5.3 stage, foliar or as topdressing, did not increase grain yield in four field experiments. Mineral N impaired BNF irrespective of the growth type and had no effect on grain yield.

Major Contribution of Flowering Time and Vegetative Growth to Plant Production in Common Bean As Deduced from a Comparative Genetic Mapping.

Determinacy growth habit and accelerated flowering traits were selected during or after domestication in common bean. Both processes affect several presumed adaptive traits such as the rate of plant production. There is a close association between flowering initiation and vegetative growth; however, interactions among these two crucial developmental processes and their genetic bases remain unexplored. In this study, with the aim to establish the genetic relationships between these complex processes, a multi-environment quantitative trait locus (QTL) mapping approach was performed in two recombinant inbred line populations derived from inter-gene pool crosses between determinate and indeterminate genotypes. Additive and epistatic QTLs were found to regulate flowering time, vegetative growth, and rate of plant production. Moreover, the pleiotropic patterns of the identified QTLs evidenced that regions controlling time to flowering traits, directly or indirectly, are also involved in the regulation of plant production traits. Further QTL analysis highlighted one QTL, on the lower arm of the linkage group Pv01, harboring the Phvul.001G189200 gene, homologous to the Arabidopsis thaliana TERMINAL FLOWER1 (TFL1) gene, which explained up to 32% of phenotypic variation for time to flowering, 66% for vegetative growth, and 19% for rate of plant production. This finding was consistent with previous results, which have also suggested Phvul.001G189200 (PvTFL1y) as a candidate gene for determinacy locus. The information here reported can also be applied in breeding programs seeking to optimize key agronomic traits, such as time to flowering, plant height and an improved reproductive biomass, pods, and seed size, as well as yield.

Chronic hepatitis C infection and liver disease in HIV-coinfected patients in Asia.

Data on markers of hepatitis C virus (HCV) disease in HIV-HCV-coinfected patients in resource-limited settings are scarce. We assessed HCV RNA, HCV genotype (GT), IL28B GT and liver fibrosis (FibroScan® ) in 480 HIV-infected patients with positive HCV antibody in four HIV treatment centres in South-East Asia. We enrolled 165 (34.4%) patients in Jakarta, 158 (32.9%) in Bangkok, 110 (22.9%) in Hanoi and 47 (9.8%) in Kuala Lumpur. Overall, 426 (88.8%) were male, the median (IQR) age was 38.1 (34.7-42.5) years, 365 (76.0%) reported HCV exposure through injecting drug use, and 453 (94.4%) were on combination antiretroviral therapy. The median (IQR) CD4 count was 446 (325-614) cells/mm3 and 208 (94.1%) of 221 patients tested had HIV-1 RNA <400 copies/mL. A total of 412 (85.8%) had detectable HCV RNA, at a median (IQR) of 6.2 (5.4-6.6) log10 IU/mL. Among 380 patients with HCV GT, 223 (58.7%) had GT1, 97 (25.5%) had GT3, 43 (11.3%) had GT6, eight (2.1%) had GT4, two (0.5%) had GT2, and seven (1.8%) had indeterminate GT. Of 222 patients with IL28B testing, 189 (85.1%) had rs12979860 CC genotype, and 199 (89.6%) had rs8099917 TT genotype. Of 380 patients with FibroScan® , 143 (37.6%) had no/mild liver fibrosis (F0-F1), 83 (21.8%) had moderate fibrosis (F2), 74 (19.5%) had severe fibrosis (F3), and 79 (20.8%) had cirrhosis (F4). One patient (0.3%) had FibroScan® failure. In conclusion, a high proportion of HIV-HCV-coinfected patients had chronic HCV infection. HCV GT1 was predominant, and 62% of patients had liver disease warranting prompt treatment (≥F2).

Morphological and genetic characterization of indeterminate green bean genotypes having different seed coat color collected from Turkey

Morphological and genetic characterization of indeterminate green bean genotypes having different seed coat color collected from Turkey

English

The present study was aimed to investigate the yield and its contributing traits among indeterminate tomato genotypes in order to generate information regarding the extent of genetic variability, heritability and genetic advance. The experiment was conducted using a randomized complete block design with three replications at Vegetable Research Farm, Department of Horticulture, SHIATS, Allahabad during 2012-2013 cropping season. The analysis of variance revealed highly significant differences among all genotypes for the characters. Analysis of coefficient of variation revealed that the magnitude of phenotypic coefficient of variation was higher than genotypic coefficient of variation for all traits under study. The leaf curl incidence (39.73 and 39.74) and ascorbic acid (27.62 and 27.67) recorded high genotypic and phenotypic coefficients of variation, indicating higher magnitude of variability for these characters, thus the scope for improvement of these characters through simple selection would be better. The estimates of heritability were high for all the traits and ranged from 95 to 100 percent, suggested that selection based on phenotypic expression could be relied upon as there is major role of genetic constitution in the expression of these characters. High heritability accompanied with high genetic advance were noted for fruit yield per plant (1129.78), plant height (43.37), number of flowers per plant (40.35), number of leaves per plant (25.48) and ascorbic acid (21.68) indicating that these characters are under additive gene effects and that these traits could be considered as reliable indices for selection and higher responses of this trait could be expected from selection. Key words: Genetic variability, heritability, genetic advance, Solanum lycopersicum L., yield, yield traits.

Seed and fruit yield of indeterminate tomato genotypes grown on four nodes

This paper presents the impact of floral branches on the production of seeds and fruit The first and second nodes were the most important for yield. 1000 seed mass ranged from 2.82 g in variety Dunavski rubin, to 3.27 g in variety Novosadski jabucar. All genotypes showed significant differences in 1000 seed mass on I node. Mass of 1000 seeds in Novosadski jabucar and line V14 decreased from I to IV node, while in Dunavski rubin and Pegaz highest mass were on III node. Seed yield per plant ranged from 5.2 - 6.6 g. Total seed yield/ha ranged from 147 kg/ha (Pegaz) to 186 kg/ha (Novosadski jabucar). Very important parameter in tomato seed production is mass of fruit needed for 1 kilogram of dry seeds. Novosadski jabucar requires 247 kg of fruit, Pegaz 324 kg, line V14 332 kg, and Dunavski rubin 430 kg.

Discovery and mapping of Brassica juncea Sdt 1 gene associated with determinate plant growth habit.

Newly discovered determinate plant growth habit in Brassica juncea is simply inherited and can help in architectural restructuring of Brassica oilseeds. Brassica juncea is naturally indeterminate. This growth habit tends to accentuate intra-plant competition for resources within the plant canopy, leading to unfilled seeds, immature pods and tip sterility. Recent identification of plants with determinate growth habit is expected to open up new avenues for plant architectural modifications in crop Brassicas. Plants with determinate plant growth habit were identified in progenies of resynthesized B. juncea as a de novo variation. F1 plants, developed from crosses of determinate mustard with natural indeterminate genotypes were indeterminate, indicating the dominance of indeterminacy. F2 and F3 segregation revealed monogenic recessive inheritance in the progenies studied. Gene for determinacy (Sdt 1 ) was mapped to the linkage group 15 of B. juncea. Sdt 1 was flanked by SSR markers SJ6842 and Ni4-A10 at distances of 15.9 cM and 14.0 cM, respectively. Determinate progenies showed significant variation for plant height, flowering time and productivity. There appeared to be no adverse association in terms of lower pod density, productivity or oil content. Determinacy was under control of single recessive gene, mapped to the linkage group 15 of B. juncea. Determinate progenies with high agronomic performance were identified.

Usefulness of selected weather indices to evaluation of yellow lupine yielding possibility

The aim of the undertaken research was an evaluation of the weather condition effect on growth and development as well as the yielding of yellow lupine plants. Weather conditions were characterized on the basis of the amount and distribution of precipitation, Sielianinov's index (K) and climatic water balance index (CWB). Genotypes of yellow lupine: Polo – an indeterminate and Legat – a determinate genotype were included into the research. An experiment was established by using the split-plot–split-block method at four replications on good rye complex soil. It founded on dependencies among values of Sielianinov's index, climatic water balance index (CWB), dynamic of mass increase and physiological indicator of plant growth (RGR). It was found that an unprofitable effect of the precipitation deficit is dependent on the developmental phase of lupine and a genotype. A shortage in precipitation which occurred after sowing caused a prolongation of emergence; however, it did not significantly decrease the plant's density because seedlings were able to use water accumulated in soil during the winter. Whereas, a long period of water shortage in the soil occurred from the beginning of flowering (BBCH 60) to pod setting (BBCH 75) had great effects on morphological features and yellow lupine yield. Unsuitable weather in this period caused a decrease in the plant's height, reduction of leaf area, inhibition of relative growth rate (RGR) and a reduction of pods and seeds number per plant. Polo (an indeterminate genotype), appeared less sensitive on periodic water deficit in the soil than Legat (a determined genotype). This was also confirmed by the values of R index (a ratio of dry mass of root system to the aboveground part mass), which is generally admitted as an indicator of the plant's resistance to drought stress.

US-1136, US-1137, and US-1138 Cowpea Lines for Cover Crop Use

US-1136, US-1137, and US-1138 are new cowpea lines with vigorous, indeterminate growth habits that were released by the Agricultural Research Service of the U.S. Department of Agriculture in 2010 and are recommended for use as a cover crop. Cowpeas are valued as a summer cover crop (Clark, 2007), because they thrive in hot moist environments, grow well in low-fertility soils, and their vigorous growth smothers weeds. They can fix up to 220 kg·ha nitrogen and are an excellent source of nitrogen for fallplanted crops. Resistance of cover crop cultivars to soilborne diseases is necessary to avoid increasing populations of pathogens and plant–parasitic nematodes that induce disease in rotational crops. Many indeterminate cowpea genotypes produce seeds with impermeable seedcoats (hard seeds). The major attributes of lines US-1136, US-1137, and US-1138 have rapid growth, high biomass production, a long vegetative growth period, and southern root knot nematode [Meloidogyne incognita (Chitwood) Kofoid and White] resistance, and they do not produce seeds with impermeable seedcoats.

Accuracy of a commercially available assay for HCV genotyping and subtyping in the clinical practice

BackgroundHepatitis C virus (HCV) genotyping is mandatory for tailoring dose and duration of pegylated interferon-α plus ribavirin treatment and for deciding on triple therapy eligibility. Additionally, subtyping may play a role in helping to select future treatment regimens that include directly-acting antivirals. However, commercial assays for HCV genotyping fail to identify the genotype/subtype in some cases. ObjectiveOur aims were (i) to determine the success rate of the commercial genotyping assay Abbott RealTime HCV Genotype II at identifying the genotype and the HCV-1 subtype; and (ii) to phylogenetically characterise the obtained indeterminate results. Study designHCV genotyping results obtained between 2009 and 2012 in a Spanish reference hospital were reviewed. A total of 896 people were genotyped with the Abbott RealTime HCV Genotype II assay. Specimens with an indeterminate result were retrospectively genotyped using the reference method based on the phylogenetic analysis of HCV NS5B sequences. ResultsUsing the commercially available assay, an indeterminate HCV genotype result was obtained in 20 of 896 patients (2.2%); these corresponded to genotypes 3a, 3k and 4d. Importantly, 8.6% of all cases where genotype 3 was detected were indeterminate. In addition, the HCV-1 subtype was not assigned in 29 of 533 cases (5.4%). ConclusionsThe implementation in the clinical microbiology laboratory of the reference method for HCV genotyping allows indeterminate genotype/subtype results to be interpreted and may lead to the identification of previously uncharacterised subtypes.

Risk Alleles Identified in Genome-Wide Association Studies Are Associated with Expression Quantitative Trait Loci in Chronic Lymphocytic Leukemia.

Abstract 2875Genome wide association studies (GWAS) in chronic lymphocytic leukemia (CLL) have identified thirteen single nucleotide polymorphisms (SNPs) that are associated with the risk of developing CLL but do not affect the coding regions of genes. The functional targets of these SNPs remain largely unknown although they are thought to potentially serve as regulatory elements for nearby genes. We have previously published the results of a high resolution integrated genomic analysis of 161 CLLs with matched normal DNAs using Affymetrix 6.0 SNP arrays and Affymetrix U133 Plus 2.0 arrays run on the CLL lymphocytes. In this analysis, we sought to exploit this dataset to investigate whether SNP genotype at loci implicated in CLL risk by GWAS was associated with altered expression of genes in the CLL lymphocyte expression arrays. We therefore investigated 19 SNPs previously described in GWAS studies, either the SNP itself if present on the Affymetrix 6.0 SNP array, or one or more proxy SNPs for those not present on the array, chosen based on their high linkage disequilibrium (r2 > 0.7, usually > 0.9) with the GWAS SNP. Regions studied included 2q13 (1 SNP), 2q37.1 (1 SNP), 2q37.3 (1 SNP), 6p21.3 (1 SNP), 6p25.3 (2 SNPs), 8q24.2 (6 proxy SNPs), 11q24.1 (1 SNP), 15q21.3 (1 SNP), 15q23 (1 proxy SNP), 15q25.2 (1 SNP), 18q21.1 (1 proxy SNP), and 19q13.32 (2 proxy SNPs). We hypothesized that the genes most likely to be regulated by these loci would be located nearby, and therefore explored associations between SNP genotypes and the expression of genes located within 2 Mb of the relevant SNP using the Kruskal-Wallis test. The number of genes evaluated ranged from 11–22 depending on the locus. The analysis was performed independently for SNP genotypes derived from the tumor / lymphocyte samples (n=143) and from the normal / saliva samples (n=70–80). Discordant genotypes between tumor and normal samples were manually reviewed for reconciliation or excluded in the case of poor quality, indeterminate genotype or altered genomic copy number at the locus. Using the SNP genotypes from the tumor samples, we identified 13 genes with expression significantly associated with a risk SNP (using p value < 0.05). Using the SNP genotypes from the normal samples, we identified 15 genes using the same criteria. In both the tumor and normal analyses, eight SNPs were associated with a total of seven genes. The most significant associations were found between the risk allele of rs674313 on 6p21 and higher expression of HLA-DQA1 (p<0.0001), and between the risk allele of rs4802322 on 19q13 and higher expression of FKRP (p<0.0001), although the latter did not show a wide range of gene expression. IRF4 expression on 6p25 was also significantly associated with rs872071 (p=0.01), as we and others have previously shown. MYC expression was associated with two of the proxy SNPs at 8q24, rs17762878 (p=0.03) and rs7823764 (p<0.04). Additional significant associations were seen for rs4777184 on chromosome 15 with TLE3 expression (p<0.02), for rs783540 on chromosome 15 with CPEB1 expression (p<0.01), and for rs305088 on chromosome 16 with COX4NB expression (p<0.04). The regulation of IRF4 and MYC by GWAS SNP alleles is unsurprising; current work is focused on validating the associations with the other genes in an extension cohort and exploring their possible functions in CLL. Disclosures:No relevant conflicts of interest to declare.