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The study involved evaluation of 96 wheat genotypes for early maturity and related traits and molecular characterization of trait specific candidate genotypes using 26 (20 random and 6 genic) SSR markers. Trait characterization revealed significant variation for early maturity and other related traits. The analysis of genotypic data of 26 markers led to the detection of 166 alleles ranging from 2 to 8 alleles with an average of 3.8 alleles per locus. Separate analysis of genotypic data of 20 random and 06 trait specefic markers led to the identification of 118 and 51 alleles, respectively. Allelic diversity study in the two sub-populations i.e., early and late maturing populations detected a total of 167 and 144 alleles, respectively. Higher gene diversity was detected in early maturing sub-population (0.135) when compared to late maturing sub-population (0.071). Single marker analysis revealed significant association of 05 random (Xcfd31, Xcfd39, Xgwm148, Xgwm190 and Xgwm538) and 02 trait specific markers (Xwmc1 and Xgwm271) with early maturity. Therefore, two trait specific markers explaining 21.36% and 10.94% phenotypic variation (PVE%) respectively for early maturity are declared validated during the present study. Overall, the findings of the present study will prove useful in future wheat improvement programs aimed at developing early maturing wheat varieties.

Soybean seed size and concentrations of protein, oil, sucrose, stachyose, and raffinose are major breeding targets to improve quality. The objectives of this study were to quantify genetic, environment, and genotype-by-environment effects on the stated traits, and to identify and validate quantitative trait loci (QTL) associated with them. Recombinant inbred lines (RILs) derived from two crosses between high-performing food-grade soybeans and imported high-protein edamame (MF1 x OAC Ramsay, and MF1 x DH410) were grown in four Southern Ontario environments. Single nucleotide polymorphism (SNP) markers were generated for RILs using genotyping-by-sequencing. Construction of linkage groups and QTL analyses were done using IciMapping software. Significant genotype-by-environment interactions were found for seed size but no other traits. In total, 94 QTL were discovered underlying the traits of interest, 14 of which were identified in another population or environment. The findings of this study can assist breeders in developing cultivars with improved seed quality. Mackellar Farms; Grain Farmers of Ontario; Ontario Ministry of Agriculture, Food and Rural Affairs; University of Guelph; Ontario Agri-Food Innovation Alliance

Fruit juices are becoming more and more popular in the whole world. However, the increasing fruit juice fraud cases are undermining the healthy development of fruit juice industry. Fruit juice authenticity represents an important food quality and safety parameter. Many techniques have been applied in fruit juices authenticity assessment. The purpose of this review is to provide a research overview of the targeted and untargeted analyses of fruit authentication, and a method selection guide for fruit juice authenticity assessment. Targeted markers, such as stable isotopes, phenolics, carbohydrates, organic acids, volatile components, DNAs, amino acids and proteins, as well as carotenoids, will be discussed. And untargeted techniques, including liquid/gas chromatography-mass spectrometer, nuclear magnetic resonance, infrared spectroscopy, inductively-coupled plasma-mass spectrometry/optical emission spectrometer, fluorescence spectra, electronic sensors and others, will be reviewed. The emerging untargeted for novel targeted marker analysis will be also summarized.

Popcorn (Zea mays L.) is a special type of maize that pops up when heated leading to high flake volume. It is being used as a popular fiber-rich and nutritious snack all over the world. The genetic control of the popping rate and flake volume is not well understood. The cross made between high popping volume inbred line as the female parent and low popping volume composite as the male parent. The F2 population of 504 plants showed continuous variation for popping volume signifying that the popping volume is a quantitative trait governed by multiple genes. Only a set of 126 out of 313 maize SSR markers were successfully amplified using the standard PCR reaction and 66 among these were found polymorphic between the two parents. Bulk segregant analysis (BSA) of F2 plants based on F2:3 seeds were carried out for mapping popping volume QTL using the 66 polymorphic SSR markers. Only four markers showed an association with popping volume in BSA. Out of the four, three SSR markers (bnlg1331, bnlg1520, bnlg1144) showed high association with the popping volume data after de-bulking of the positive and negative plants used in the bulks. All the 504 F2 plants were genotyped using 3 SSR markers and the F2:3 seeds were phenotyped for popping volume. The single marker analysis of the F2 plants showed that the 3 SSR markers bnlg1331, bnlg1520, and bnlg1836 on chromosome 1, 2, and 5, respectively, were closely associated with the QTL for popping volume covering 78% of total phenotypic variance.

Genetic purity is conventionally performed through grow-out-test (GOT) with morphological characters. Simple sequence repeat (SSR) markers are independent of G X E interaction. Herewith, 16 high yielding varieties of rice were analysed using 55 SSR markers for DNA fingerprinting and identification of genetic impurities: 14 were found to be polymorphic and amplified 48 alleles with an average of 3.43 alleles per each primer pair. The number of alleles amplified ranged from 2 to 6 and the size of the PCR products amplified from these 14 primer pairs ranged from 80 to 450 bp with polymorphic information content (PIC) from 0.14 (RM 346) to 0.99 (RM 5900). PICs at 0.5 or higher are highly informative SSR markers for genetic studies and the study reported (7/14) markers to be highly informative based on PIC values. Besides, the values of effective multiplex ratio, marker index and resolving power for the selected polymorphic primer pairs disclosed that the SSR markers used in the study are highly informative and could be potentially used for distinctness, uniformity and stability (DUS) testing, genetic purity analysis and DNA fingerprinting of rice varieties. Economic analysis of grow-out-test and SSR marker based genetic purity showed that the GOT process incurs Rs. 5.8 (INR) per seed (USD 0.07), while DNA-based marker analysis incurs Rs. 53.75 (INR) or $ 0.71 (USD).

The present investigation was undertaken to assess the genetic diversity in gamma rays irradiated mutants of four grape genotypes based on RAPD and SSR markers. There were 36 mutants selected from in vitro mutated four grape genotypes, namely Pusa Navrang, H-76-1, Pearl of Csaba and Julesky Muscat on the basis of morpho-physiological and biochemical traits. These mutants and non-irradiated individuals were subjected to RAPD and SSR marker analysis to detect the genetic variation amongst them. Six RAPD and eleven SSR primers were employed for PCR amplification and total 63 distinct and easily scoreable bands were generated which ranged between 110 (SSR) and 2500 (RAPD) bp. All the bands were found to be polymorphic in nature and identified 13 solid mutants, among the initially selected 36 putative mutants. The distribution of mutants by cluster analysis suggested existence of high degree of difference at the genetic level in the mutants and non-irradiated control individuals. The mutants were largely grouped into the four major clusters based on the doses of gamma irradiation except some mutants from Julesky Muscat and Pearl of Csaba genotypes. Minimum similarity coefficient (0.37) was noted in mutants of Pusa Navrang and maximum (0.70) in Hybrid-76-1. Unique banding patterns were amplified by both the types of markers (RAPD and SSR). It was suggested that Julesky Muscat was amplified uniquely by RAPD-OPA01, OPP02, SSR-VVMD14, VMCIB11, VMC8G9 primers, H-76-1 by RAPD- OPA01 and SSR- VVMD 14 primers, Pusa Navrang by RAPD-OPP02 and SSR-VVMD-21 primers and Pearl of Csaba by RAPD-OPA01, OPP04, SSR-VMC8G9 primers. The result from this study suggests that OPA01 (RAPD) and VVMD14 (SSR) were the most informative primers and generated maximum numbers of reproducible bands. The combination of these primers will be very useful for the identification of solid mutants which could be evaluated in the field.

Spot blotch (SB) caused by the fungus Cochliobolus sativus, is an economically important disease on barley worldwide. Molecular analysis of SB resistance using quantitative trait locus (QTL) analysis can improve the efficiency of the breeding process. In the current work, and to accelerate development of SB-resistant barley cultivars, AFLP markers linked to SB resistance have been identified by using F2 recombinant inbred lines derived from a cross between the resistant barley cv. Banteng and the susceptible cv. WI2291. Single marker analysis (SMA) based on t-test revealed that out of 82 AFLP markers; five AFLP markers AAC × CTG (700 bp), ACT × CAT (600 bp), ACT × CAT (400 bp), ACT × CTG (550 bp) and AGG × CAG (490 bp) were identified. The data showed that SMA-based t-test could be a useful analysis for dominant markers such AFLP in breeding programs, and that the AFLP detected markers can be employed in genomics-assisted breeding for selection of SB-resistant barley genotypes.

Pranic agriculture is a newly emerging concept of sustainable and eco-friendly agriculture. Pranic agriculture techniques are applied to plants before sowing and at the time of plant development to improve growth and yield. The present study aimed to understand the influence of pranic agriculture on growth, yield, and genetic polymorphism of ridge gourd. An increase in root length by 38%, stem girth by 8%, and the number of days taken for the premier harvest was advanced and found to be significant (p

Screening of F2 population from cross WH711 (susceptible parent) and PBW698 (resistant parent) against stripe rust was done on the basis of field reaction of yellow rust and 12 morphlogical traits. The genotyping of parents was done by using 80 SSR markers out of which 11 were found polymorphic. These 11 markers were used to screen 250 individuals of F2 population. Mendelian inheritance was followed by five markers viz. Xgwm631, Cfa2040, Xsps3000, Barc76 and Xgwm 130 which segregated according to expected ratio of 1:2:1 with chisquare values 5.78, 4.23, 2.75, 9.2 and 7.6 respectively. Single marker analysis showed markers Xgwm631, Cfa2040 (Yr2, Yr6), Xsps3000 (Yr10), Xgwm130 (Yr7), Xwmc407 (Lr17), Barc46, Xgwm413 (Yr15), Barc187 (Yr27) and Xgwm273 (YrH52) were linked with yellow rust locus at 0.01% of significance hence these genes may be present in the breeding population. Cfa2040 was found linked with flag leaf area, number of spikelets and Barc181 with spike weight locus. Markers on chromosomes 7A and 1B showed LOD values 6.64 and 6.86 conferring tight linkage with yellow rust locus thus can be used for MAS.

Fennel (Family Apiaceeae) is one of those strategic medicinal and aromatic plants in Egypt with great value as an economical exported plant. Fennel undergoes propagation through breeding of some fennel cultivars from different world region in order to keep out of genetic deterioration in the native Egyptian cultivars, and enrich its favorable active ingredients. The advanced plant breeding programs depend on some markers such as morphological, cytological, biochemical and molecular markers to study its genetic diversity. In this work two molecular markers ISSR and SCoT markers were used to assessment of genetic diversity among six fennel cultivars (Foeniculum vulgare Mill.) planted in Egypt; three of Egyptian origin (Balady, Elalamy and Azoricum) and the other ones are of different origin (Holland, Indian and German). The analyzed data reveals that the ISSR marker is more discriminating, provides more informative data than SCoT marker and can be reliable to evaluate the genetic diversity among the six examined cultivars as it performs the highest percentage of polymorphism 61% and higher unique bands number (4). According to ISSR molecular marker German and Indian cultivars are close distant; can exchange gene in between them smoothly despite the ultimate change in the environmental and weather conditions of their origin land. In conclusion, according to Nie,s and li,s coefficient based on SCoT marker analysis between the cultivars; Indian cultivar was quite distant from Azoricum by the same time that Azoricum is close distant to Holland, as well as; Elalamy is close distant to Balady.

Obesity drives an imbalanced signature of specialized pro-resolving mediators (SPM). Herein, we investigated if high fat diet-induced obesity dysregulates the concentration of SPM intermediates in the brains of C57BL/6 J mice. Furthermore, given the benefits of EPA for cardiometabolic diseases, major depression, and cognition, we probed the effect of an EPA supplemented high fat diet on brain SPM intermediates. Mass spectrometry revealed no effect of the high fat diet on PUFA-derived brain metabolites. EPA also did not have an effect on most brain PUFA-derived metabolites except an increase of 12-hydroxyeicosapentaenoic acid (12-HEPE). In contrast, EPA dramatically increased serum HEPEs and lowered several PUFA-derived metabolites. Finally, untargeted mass spectrometry showed no effects of the high fat diet, with or without EPA, on the brain metabolome. Collectively, these results show the murine brain resists a deficiency in SPM pathway markers in response to a high fat diet and that EPA supplementation increases 12-HEPE levels.

Aegilops sharonensis, a wild relative of wheat, harbors diverse disease and insect resistance genes, making it a potentially excellent gene source for wheat improvement. In this study, we characterized and evaluated six wheat-A. sharonensis derivatives, which included three disomic additions, one disomic substitution + monotelosomic addition and two disomic substitution + disomic additions. A total of 51 PLUG markers were developed and used to allocate the A. sharonensis chromosomes in each of the six derivatives to Triticeae homoeologous groups. A set of cytogenetic markers specific for A. sharonensis chromosomes was established based on FISH using oligonucleotides as probes. Molecular cytogenetic marker analysis confirmed that these lines were a CS-A. sharonensis 2Ssh disomic addition, a 4Ssh disomic addition, a 4Ssh (4D) substitution + 5SshL monotelosomic addition, a 6Ssh disomic addition, a 4Ssh (4D) substitution + 6Ssh disomic addition and a 4Ssh (4D) substitution + 7Ssh disomic addition line, respectively. Disease resistance investigations showed that chromosome 7Ssh of A. sharonensis might harbor a new powdery mildew resistance gene, and therefore it has potential for use as resistance source for wheat breeding.

Objectives. The biological markers that can indicate specifically and sensitively the absence or presence of a certain condition or its state can be used for diagnostic support and disease monitoring. Thus, this research set out to study the changes in neuropeptides (substance P and calcitonin gene-related peptide) pro-inflammatory (TNFα, IL-1β and IL-6) and anti-inflammatory (IL-10) cytokine levels in the blood of patients with CRPS. Material and methods. Sixty patients were enlisted from the local Rheumatology Clinic of the Emergency County Hospital of Craiova and split into two groups (acute and chronic). CRPS related symptoms were estimated by means of the Neuropathic Pain Questionnaire. The quantification of cytokines and neuropeptides in blood was achieved using the high sensitivity colorimetric ELISA method. Outcomes. Cytokine analysis led to statistically insignificant results, while for the neuropeptides we obtained significantly increased values in the patient groups. ROC curves were used to assess the diagnostic accuracy of the neuropeptides both returning good AUC values. Conclusions. Our results indicate that the neuropeptide (substance P and calcitonin gene-related peptide) profile has a good diagnostic sensitivity. A limitation of the study is the low number of patients in the acute group, including more patients in this phase might offer more insights on the cytokines’ role, as they could be increased in comparison to chronic patients, due to their short half-life and low acting concentrations.

The wine sector is one of the most active and profitable in Italy; Italy is the largest wine producer in the world, followed by Spain and France. For this reason, it is subject to extensive legislative discipline. Calabria ranks sixteenth among Italian regions for wine production; however, in recent years, much effort has been made to promote the wine sector in this region. Nine Calabrian wines are designated as PDO (protected designation of origin) and ten wines as PGI (protected geographical indication). Among the PDO wines, Terre di Cosenza and Cirò are the most famous. Fraud prevention is necessary for consumer protection and for product valorization and promotion. Microsatellite marker analysis represents a reliable and effective tool for varietal characterization, allowing the detection of adulteration in the winemaking process. We sampled 20 grapevine cultivars from different areas of Calabria commonly used for production of the PDO wine Terre di Cosenza and 20 cultivars from other Italian regions in order to carry out a molecular characterization. The analysis was performed through six simple sequence repeat (SSR) markers proposed by the International Organization of Vine and Wine (OIV), VVSS2, VVMD5, VVMD7, VVMD27, VrZAG62, and VrZAG79. Some of the cultivars showed the same molecular profile, revealing the presence of synonymies and incorrect name assignment.

Doubled haploid technology is a valuable tool in plant breeding as it shortens the breeding cycle, fixes agronomic traits in homozygous state and enhances selection efficiency of useful recessive agronomic traits. However, successful adoption of doubled haploid (DH) technology for generating useful breeding material depends on intra-line uniformity and inter-line variability for agro-morphological traits. Therefore, the major emphasis of this study has been to assess these two aspects in DH population developed from F1 anthers of KRH4 rice hybrid. The developed DH lines were evaluated for agro-morphological traits to assess the uniformity of traits within and variability between the DH lines based on Z value and on the analysis of variance test respectively. The results of the experiment indicated that, the agronomic traits were indeed uniform within but different across DH lines. A wide and significant variation was observed among the DH lines for several growth and yield attributing traits. To confirm the uniformity and stability of the traits, selected DH lines were characterized in different seasons and growing conditions. The results showed a strong positive correlation in the agronomic traits within the lines under different seasons and also in contrasting environments. Further, the SSR marker analysis revealed that the DH lines are homozygous and stable across generations. From the study, it can be inferred that the DH technology forms an important tool in generating completely homozygous lines that are stable across seasons, environments and over generations.

The article examines the relevance of creating a national repository of biological samples collected from Russian citizens. International practices in the introduction and application of proactive DNA-based human identification are analyzed. Information is provided about existing molecular genetic databanks, including one of the largest in the world – the UK National DNA Database containing over 6 million genetic profiles. Availability of reference samples for comparison helps in the identification of evidence found at the scene and thus contributes to effective crime detection. Authors point out the lack of uniform standards for human DNA marker analysis both in Russia and abroad, which significantly complicates DNA identification of biological material. Once a national databank of biological samples is established, the absence of a universally recognized DNA profiling system would be rendered irrelevant. Successful achievement of this objective relies on the use of the most effective and affordable method for collection and long-term storage of genetic material in dry form, i.e. collection paper cards (DNA cards).

Genetic epidemiology is a growing area of interest in the past years due to the availability of genetic data with the decreasing cost of sequencing. Machine learning (ML) algorithms can be a very useful tool to study the genetic factors on disease incidence or on different traits characterizing a population. There are many challenges that plagues the field of genetic epidemiology including the unbalanced case-control data sets, fallibility of standard genome wide association studies with single marker analysis, heavily underdetermined systems with millions of markers in contrast of a few thousands of samples, to name a few. Ensemble ML methods can be a very useful tool to tackle many of these challenges and thus we propose RubricOE, a pipeline of ML algorithms with error bar computations to obtain interpretable genetic and non-genetic features from genomic or transcriptomic data combined with clinical factors in the form of electronic health records. RubricOE is shown to be robust in simulation studies, detecting true associations with traits of interest in arbitrarily structured multi-ethnic populations.

Introduction and Aims The optimum volume of pleural fluid submitted for cytological analysis to detect and categorise suspected malignant pleural effusions has not been identified. A handful of studies have investigated the minimum fluid volume size to maintain sensitivity in identifying the presence of malignant cells and concluded 50–75mls pleural fluid is required. To date no study has formally assessed if varying sample sizes has any bearing on providing additional clinically relevant information beyond simply identifying malignant cells. We aimed to test the hypothesis that larger pleural samples sent for analysis increases the cellular material available for immunohistochemistry (to accurately diagnose the tumour type) and presence or absence of therapeutic tumour markers. Thereby avoiding repeated invasive diagnostic tests and delays to diagnosis and treatment options. Methods We undertook an observational single centre retrospective analysis of pleural fluid samples sent in patients with a suspected malignant pleural effusion. Samples were grouped according to volume sent. We evaluated the sensitivity rates for identifying malignant cells between volumes as has been investigated previously. Additionally, in cases where malignant cells were identified we assessed the proportion between groups where immunocytochemistry and tumour marker analysis could be performed. Results See table 1. Our results reveal comparable sensitivity in identifying malignant cells between groups. The proportion of samples where successful immunocytochemistry and tumour marker analysis could be performed tended to be higher in larger volumes with fewer instances where tests could not be performed due to insufficient cellular material. Conclusion and Future Considerations Our results need to be interpreted with caution as our case number was small. However, there were trends towards greater yields of more clinically useful data in larger volumes. Ours was an exploratory pilot study to assess whether our hypothesis warrants more formal investigation. A larger, prospective study where for each suspected malignant effusion different volumes of pleural fluid are submitted. Each sample volume would be analysed separately by a blinded pathologist. The proportions of positive yields could be compared with the lower volume acting as a control to establish if larger pleural volumes yield greater and more comprehensive cytological diagnoses.

Background: Aflatoxin contamination in groundnut is a serious health concern for both humans and ruminants. Genetic resistance is a viable, cost-effective and eco-friendly approach to manage aflatoxin contamination. Molecular markers particularly SSRs have been proved to be very effective in Marker Assisted Selection.Methods: In this study, single marker analysis using 30 SSR markers in 66 groundnut genotypes was executed to know if any selected SSRs were linked to in vitro seed colonization by Aspergillus flavus (IVSCAF) and/or aflatoxin contamination.Result: Single marker analysis revealed significant association of few SSR markers with tolerance to IVSCAF and/or aflatoxin contamination. Four markers viz., GM-1954, GM-1883, pPGPseq-2F05 and S-03 were found to be associated with in vitro seed colonization by A. flavus. The marker GM-1954 has shown a maximum R2 value of 14.07 indicating that 14.07 per cent phenotypic variation for IVSCAF has been explained by this marker (F=0.002**). Further, three markers viz., S-21, S-80 and GM-1954 were found to be associated with tolerance to aflatoxin contamination. It is evident from the results that, the marker GM 1954 has shown association with both IVSCAF as well as aflatoxin contamination. However, the R2 value of GM 1954, which explains the phenotypic variation for aflatoxin contamination, was less (6.21) as compared to that of IVSCAF (14.07).

OBJECTIVES: To assess the prevalence of sarcopenic obesity and its association with functionality, lifestyle, biomarkers, and morbidities in older adults. METHODS: The study analyzed cross-sectional data from 270 older adults who participated in phase III of the Frailty in Brazilian Older People Study (Fragilidade em Idosos Brasileiros—Rio de Janeiro, FIBRA-RJ study-2013). They took part in a home interview surveying socioeconomic, demographic, lifestyle, morbidities, and functional data. Blood was collected for biochemical marker analysis and participants’ body composition was determined by dual-energy X-ray absorptiometry. For women, the diagnosis of sarcopenic obesity was defined at a body fat percentage ≥38% and appendicular skeletal muscle mass index (ASMMI)

In Ghana, the encapsulated blend of the powdered stem and root bark of Cassia sieberiana is prescribed and dispensed to patients at the Centre for Plant Medicine Research (CPMR), for the management of dysmenorrhea and gastric ulcer pain. This current formulation has significant challenges in manufacturing and optimization of therapeutic outcomes due to lack of standardization of actual quantities of the extracts obtained from ingestion of the product. The study sought to formulate and evaluate capsules of Cassia sieberiana using the stem and root bark. Extraction was undertaken with different solvents: absolute ethanol (F1) and 70% ethanol (F2). These 2 formulations were compared to the existing product (MP1) by CPMR. Granules for encapsulation were prepared by wet granulation and their flow properties compared with MP1. Drug-excipient compatibility was studied using FT-IR, TLC and UV. Quality control tests on MP1, F1 and F2 capsules were conducted using pharmacopoieal methods. From the results obtained, organoleptic and physicochemical properties of the extracts demonstrated its suitability for use in oral capsule formulation. MP1, F1 and F2 recorded a λmax of 278 nm, 278 nm and 276 nm, respectively. The extract per dose of capsules was found to be 27.84 ± 0.11 mg and 36.65 ± 0.03 mg for F1 and F2, respectively. Granules of F1 and F2 had good flow properties whereas MP1 demonstrated a fair flow property. FT-IR spectra showed possible interaction between extracts and excipients. However, TLC results indicated similar compounds present in the extracts and granules. The UV marker analysis also indicated no interaction since the percentage drug contents in F1 and F2 capsules were found to be 98.0% ± 1.40 and 98.90% ± 2.80 respectively. All 3 formulations passed the disintegration and uniformity of weight tests except MP1 which failed the latter. F1 capsules recorded the highest dissolution efficiency (99%) while MP1 recorded the lowest (22%). There was significant difference (p < 0.0001) in the release of Cassia sieberiana among the three formulations. This study has demonstrated the potential replacement of Cassia sieberiana capsules on the market with capsules developed from its extract with F1 capsules being the most desirable.

Sorghum (Sorghum bicolor (L.) Moench) is one of the most promising bio-energy crops with the ability to produce high biomass with low input. Plant height that has a significant contribution to gain in bio-ethanol production is among the most important biomass yield components. In the present study, sorghum genotypes were screened with four SSR markers which are associated with plant height QTLs. The molecular assays were confirmed with two different environments in two consecutive years. In the first year of the study, molecular analyses were performed with a sorghum collection consisting of 551 accessions as well as plant height measurements were performed under field condition. In the second year, 53 out of 551 accessions were selected and further tests with nine controls were performed in Antalya (a lowland province) and Konya (a highland province) locations along with molecular marker analyses. The results indicated that four SSR markers efficiency were assessed as 38% at lowland and 39% at highland. Markers 40-9187 and 37-1740 were of more powerful to explain plant height QTLs than the other two markers at two environments. This study reported the successful application of the association between markers and plant height in two environments to identify valuable genetic resources for bio-energy production in sweet sorghum., Sorgum (Sorghum bicolor (L.) Moench), düşük girdi ile yüksek biyokütle üretebilme yeteneğine sahip umut verici biyo-enerji bitkilerinden biridir. Biyoetanol üretiminde kayda değer katkıları olan bitki boyu, biyokütle verimini oluşturan en önemli bileşenler arasındadır. Bu çalışmada, sorgum genotipleri bitki boyu QTL'leri ile ilişkili dört SSR marker ile taranmıştır. Moleküler analizler, ardışık 2 yıl ve 2 farklı ortamda doğrulanmıştır. Çalışmanın ilk yılında 551 genotipten oluşan sorgum koleksiyonunda moleküler analizler ve tarla koşullarında bitki boyu ölçümleri yapılmıştır. İkinci yılda ise 551 genotipten 53'ü seçilerek, dokuz kontrol çeşit kullanılarak moleküler analizler ile birlikte Antalya (ova) ve Konya (yayla) lokasyonlarında ileri testler gerçekleştirildi. Sonuçlara göre; dört SSR markerin verimliliği ovada %38 ve yaylada %39’dur. 40-9187 ve 37-1740 markerleri, iki ortamda da diğer iki marköre göre bitki yüksekliği ile ilişkili QTL'lerin açıklanmasında daha güçlü olarak belirlenmiştir. Bu çalışma, şeker sorgumda biyo-enerji üretimi için değerli genetik kaynakları belirlemek adına iki ortamda da markerler ve bitki boyu arasındaki ilişkinin belirlenmesinde başarılı bir şekilde uygulandığının bildirilmesidir.

Living organisms require complex signaling interactions and proper regulation of these interactions to influence biological processes. Of these complex networks, one of the most distinguished is the Notch pathway. Dysregulation of this pathway often results in defects during organismal development and can be a causative mechanism for initiation and progression of cancer. Despite previous research entailing the importance of this signaling pathway and the organismal processes that it is involved in, less is known concerning the major Notch downstream targets, especially the onset and sequence in which they are modulated during normal development. As timing of regulation may be linked to many biological processes, we investigated and established a model of temporal patterning of major Notch downstream targets including broad, cut, and hindsight during Drosophila melanogaster egg chamber development. We confirmed the sequential order of Broad upregulation, Hindsight upregulation, and Cut downregulation. In addition, we showed that Notch signaling could be activated at stage 4, one stage earlier than the stage 5, a previously long-held belief. However, our further mitotic marker analysis re-stated that mitotic cycle continues until stage 5. Through our study, we once again validated the effectiveness and reliability of our MATLAB toolbox designed to systematically identify egg chamber stages based on area size, ratio, and additional morphological characteristics.

A total of 60 genotypes of peanut comprising 46 genotypes selected from ICRISAT mini core collection and 14 elite cultivars with differing kernel color and size were used to profile the nutritional parameters such as proximates (moisture, fat, ash, crude protein, crude fiber, carbohydrate content) and nutraceuticals (total polyphenol content and total antioxidant activity). The genotypes showed varied kernel color ranging from white to purple. Kernel skin color was quantified using colorimetry, and the color parameters were expressed as CIELAB color parameters. In total, nine morphological traits, six yield related traits, eight nutritional traits and eleven color parameters were observed across 60 genotypes. The sixty genotypes were grouped into ten clusters based on the color strength. Among them, Cluster-III with dark red seeds had the maximum fat content and total polyphenol content (TPC). Cluster-VI with light pink colored seeds had high antioxidant activity (AOA) and Cluster-X with white colored seeds had highest moisture and crude protein content. Color strength (K/S) was found to be positively correlated with TPC. Another color parameter, redness/greenness (a*) was found to be positively correlated with AOA. However, seed size was positively correlated with the crude protein content, but not with any other nutritional traits under study. The population studies based on the genotypic data indicated two distinct groups pertaining to botanical types of peanut. The marker-trait association (MTA) using single marker analysis indicated 75 major MTAs for most of the nutritional traits except for moisture content. The markers associated with nutritional parameters and other important yield related traits can further be utilized for genomics-assisted breeding for nutrient-rich peanuts.

Radish (Raphanus sativus) is an economically important crop grown for its edible roots and leaves. It is a self-incompatible, outcrossing species, making the production of homozygous lines and the development of breeding populations difficult. However, this can be overcome with haploids production techniques using isolated microspores, providing the rapid production of homozygous lines for breeding. Thus, it would be useful to identify radishes with a high regeneration rate from microspore culture. In the current study, 96 radish cultivars or germplasms were evaluated for high regeneration rates. Also, a single-marker analysis (SMA) was applied to detect single nucleotide polymorphisms (SNPs) potentially associated with this trait using genotype-by-sequencing (GBS) technology. The regeneration rate from microspore culture of 96 lines showed a wide range, from 0% to 269.5%. From the SMA, 52 markers were detected at a p value of 0.001 and a total of 11 physically nearby genes with high levels of similarity in various species were identified as candidates for high regeneration rates. This result could be used for clarifying the genetic basis underlying these traits and developing molecular markers associated with regeneration rates and would be beneficial for generating homozygous inbred lines.

Date palm (Phoenix dactylifera L.) is an economically important fruit crop in hot arid regions. It is cultivated in many regions of Thailand. However, during the establishment of plantations, male and female trees cannot be clearly distinguished until about five years after planting when the palms first flower. The objective of this research was to differentiate gender (male / female) at seedling stage in the Thai date palm cultivar KL1 by using a specially developed DNA marker technique. A PCR based method, which included the use of specific tetra-primers, was found to be successful using extracts from young leaf samples. With these markers, flowering male date palms were represented with two amplicons (430 bp and 320 bp) while the female date palms were represented with only one amplicon (430 bp). When 100 non-flowering seedling of cv. KL1 were screened, 50 were identified as male and 50 as being female. This ratio of 1:1 between male and female is consistent with the principle of gender distribution in dioecious plants. When the tetra-primer method was used with other cultivars, including Deglet nour, Barhi, Hayani, Medjool and Tunisia, the same DNA banding patterns were determined. This method has potential to be used for the differentiation of gender in other date palm cultivars at the seedling stage. It would reduce the time required for gender determination from five years to a few hours.

Utilizing the available molecular markers for Nax1 and Nax2, the present study was aimed at validating these markers for salt tolerance in Kharchia 65 and then to introgress these loci from Kharchia 65 to HD 2851. F2 lines (grown under saline conditions) containing the Nax loci were selected using a combination of morpho-physiological information and linked molecular markers. Net house evaluation data showed enormous variation among Kharchia 65 × HD 2851 F2 plants including plant height, no. of tillers per plant, ear length, no. of grains/ear, no. of spikelets/spike, grain yield per plant, 1000 grain weight, biological yield/plant and harvest index. Out of 85SSR primers used, 22 SSRs showed polymorphism between Kharchia 65 and HD 2851 parental genotypes. From the net house evaluation data 100 F2 plants were selected. These plants were checked for the presence of Nax loci. Nine plants showed the presence of both the Nax loci. An assessment of distribution of Kharchia 65 and HD 2851 specific alleles for 22 polymorphic SSRs in 9 F2 plants showed that on an average, 71% alleles were from Kharchia 65 and 87.5% alleles were from HD2851.

Background Circulating inflammation markers are being increasingly measured in prospective cohorts to investigate cancer etiology. However, it is unclear how the measurements are affected by the freeze-thaw cycles of the specimens prior to marker analysis. Methods We compared concentrations of 45 inflammation markers between paired serum vials of 55 participants in the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial that have undergone one (T1), two (T2), and three (T3) freeze-thaw cycles at the time of assay. We computed the difference of analyte concentrations across paired vials (T1 vs. T2, T2 vs. T3) and tested whether the difference deviated from zero using the Wilcoxon signed-rank test. We also calculated Spearman rank correlation and weighted kappa statistics for T1 vs. T2 and T2 vs. T3 comparisons to assess agreement in rank ordering of subjects. Results Measurements between paired T1 and T2 samples were largely similar, with the difference not statistically deviating from zero for 36 of the 45 markers. In contrast, tests of the difference between paired T2 and T3 samples were statistically significant for 36 markers. However, the rank ordering of participants by marker concentration remained largely consistent across T2 and T3 samples, with Spearman correlation coefficients >0.8 for 42 markers and weighted kappas >0.7 for 37 markers. Conclusion We recommend that studies measuring inflammation markers use previously unthawed specimens to the extent possible, or match on the number of prior freeze-thaw cycles in nested case-control studies.