Anchor Markers Research Articles

Comparative performance of marking of small-diameter peripheral lung neoplasms by preoperative transthoracic use of methylene blue preparations and placement of an anchor marker system

The study compared marking of small-diameter peripheral lung neoplasms by preoperative transthoracic use of 1% aqueous methylene blue solution and placement of an anchor marker system. The study evaluated the results of treatment of 36 patients with pulmonary nodules, including 27 men and 9 women aged 52 to 76 years, who were examined and treated at the Surgical Clinic of the S.M. Kirov Military Medical Academy in 2020-2023. Marking of small-diameter peripheral lung neoplasms by transthoracic use of 1% aqueous methylene blue solution made possible to detect abnormalities and lesions and perform a biopsy in 73.3% of cases. The duration of the diagnostic procedures was 30 [20-40] minutes. No postoperative complications were reported. The mean length of stay in this group of patients was 8 [6; 12] patient days. Placement of an anchor marker system allowed detection and verification of lung lesions in 95% of cases. In addition, the duration of videothoracoscopic biopsies was also 30 [20-40] minutes. No complications or deaths were reported. The mean length of stay was 7 [5; 11] patient days. The use of anchor markers to label small peripheral pulmonary nodules in the preoperative phase has some significant advantages compared with dye injection techniques, such as shorter duration of lesion mapping (p = 0.046) and less manipulation complications (p = 0.04), as well as a higher frequency of lesion detection during minimally invasive procedures. When comparing various techniques for marking pulmonary lesions, it was found that mapping of small-diameter peripheral pulmonary infiltrates using anchor markers is characterized by high performance, greater safety, facilitates intraoperative navigation for biopsy of small-diameter peripheral pulmonary neoplasms, and is superior than transthoracic use of 1% aqueous methylene blue in terms of rates of detection of pulmonary nodules during minimally invasive procedures, duration of manipulation, and complication rates.

A-157 Evaluation of Cellular Stability in Bone Marrow for Flow Cytometry Analysis

Abstract Background Plasma cells are sensitive and can rapidly deteriorate after sample collection or due to roughhandling. Delayed sample processing remains a common challenge due to logistical limitations.Specialized tests performed in central pathology laboratories are frequently located aconsiderable distance from healthcare providers. According to the Clinical Flow CytometricAnalysis of Neoplastic Hematolymphoid Cells; Approved Guideline-Second Edition, BM samplescollected in EDTA anticoagulant should be analyzed within 12 to 24 h. The objective of thisstudy was to define the stability of a bone marrow (BM) sample within 48 h through theevaluation of the main cell populations with a focus on plasma cells. Methods Nineteen bone marrow samples (without the use of preservative medium) were evaluated at 0, 24 h and 48 h, collected in EDTA anticoagulant and stored at 4°C before processing. To definethe stability of the samples, the MFI (mean fluorescence intensity) was evaluated. The samplepreparation protocol was performed based on the monoclonal gammopathy screening panel attime 0 (CD38 FITC, CD138V500; CD45V450; CD19PECY7, CD56PE, CD27PERCP and KAPPA APCand LAMBDAAPCH7), and at times 24 h and 48 h it was performed a panel with anchor markers (CD45V450, CD19PEcy7, CD38FITC, CD138V500, CD56PE), acquisition in FACS CANTO II and FACSLyric equipment and data analysis performed with Infinicyt software. To assess the impact ofsample storage and the MFIs of individual markers, positive reference populations wereanalyzed using the antigen CD38 for plasma cells, CD19 for B lymphocytes, CD56 for NK cells andCD45 for other populations. Statistical analysis was performed using the Paired t-test,considering statistically significant results those with P < 0.05. Results In the present study, the evaluation at 24 and 48 h showed that the populations ofgranulocytes, B lymphocytes and plasma cells did not present a significant difference betweenthe evaluated times. The monocyte population showed a decrease of P < 0.05 in the time 48 h an in the first 24 h it remains stable. In NK cells, despite P < 0.05 between 0–24 h and 0–48 h, it can be observed that between 24 h–48 h the population remained stable. Conclusion Evaluating these results, based on the cell type of interest, different delays are acceptable.Despite the greater sensitivity of plasma cells, it was concluded that the evaluation of CD38 asan anchor marker for plasma cells can be used in up to 48 h without significant change inthe MFI evaluation for analysis of this cell with this marker. The differences found in NK lymphoidcell may be due to methodological problems, considering that the analyzed panel is not ideal forevaluating this population. Therefore, it is necessary to carry out more detailed studies for othertypes of cell populations.

A-159 Role of TCRB1 Antibody in the Evaluation Panel of T Lymphoproliferative Diseases

Abstract Background The diagnosis of T lymphoproliferative diseases is usually a challenge due to the difficulty indifferentiating pathological T cells from reaction cells and also due to the limitation of clonalitytests currently available. TCRB1 is a monoclonal antibody specific for region 1 of the TCR T cellreceptor Beta chain constant, detecting clonal populations of TCRab positive T cells in caseswhere its expression is monotypic. Its application is similar to immunoglobulin light chainrestriction in the detection of B cell lymphoproliferations and in normal T CD3 + TCRab + cells, theexpression of this marker is polytypic. The objective of the present work is to report theexperience of including this antibody in the lymphoproliferative T panel in a private laboratoryin southern Brazil. Methods Samples received with indication of lymphoproliferative disease and lymphocytosis wereevaluated using the tube Lymphocyte Screnning Tube—LST (Euroflow) and were acquired usingFACS CANTO or FACS LYRIC cytometers. Analyzes were performed using Infinicyt software. After, all, samples that showed alteration in the CD4/CD8 ratio, or antigen alteration in the expressionof pan T markers were evaluated for the complete investigation panel according to Euroflowprotocol. This panel had the incorporation of the tube for the evaluation of clonality that hasthe TCRB1 antibody in the PE channel associated with the anchor markers CD45V500, CD3PerCpcy5, CD4V450 and CD8APCH7. The channels that were not used (FITC, APC, Pecy7) areused when necessary, to evaluate antigens that can help select the desired aberrant population,such as CD5, CD2, CD7 antibodies or to assess maturation, like CD45RA and CD27. Data werecollected from the beginning of the use of this antibody from February 2021 until the presentmoment. Results During this period, 2870 samples for immunophenotyping analysis were received, of which 17cases were T chronic lymphoproliferative diseases. Of the 17 cases found, 11 (65%) were caseswith the pathological population TCRab positive and the expression of TCRB1 could beevaluated. In these cases, the expression of the patologic cells was monotypic for the TCRB1antigen. The cases were: 4 large granular lymphocytic (LGL) leukemia, 4 Adult T-cellleukemia/lymphoma /Peripheral T-cell lymphoma, unspecified , 1 Sezary syndrome, 1 T-celllymphoblastic lymphoma in cortical/common thymocyte stage and 1 T-cell prolymphocyticleukemia (T-PLL). Recent studies have demonstrated the high specificity of this test for clonality, as long as it is associated with an expanded and standardized lymphoproliferative panel. Thepresent cases demonstrated good results for peripheral blood samples, bone marrow and lymphnode biopsy. Conclusion T-lymphoproliferative disorders remain a diagnostic challenge, due to the difficulty of a simpletest to assess clonality. The inclusion of the TCRB1 antibody in the lymphoproliferative panelincreased the specificity of the test for diagnosis, being a method of rapid execution and lowcost. Another advantage of using this marker is the possibility of evaluating small cell clonesthat may not be detected in molecular biology techniques due to the sensitivity of the test.

Carbon ion radiotherapy using fiducial markers for prostate cancer in Osaka HIMAK: Treatment planning.

PurposeCarbon ion radiotherapy for prostate cancer was performed using two fine needle Gold Anchor (GA) markers for patient position verification in Osaka Heavy Ion Medical Accelerator in Kansai (Osaka HIMAK). The present study examined treatment plans for prostate cases using beam‐specific planning target volume (bsPTV) based on the effect of the markers on dose distribution and analysis of target movements.Materials and MethodsGafchromic EBT3 film was used to measure dose perturbations caused by markers. First, the relationships between the irradiated film density and absolute dose with different linear energy transfer distributions within a spread‐out Bragg peak (SOBP) were confirmed. Then, to derive the effect of markers, two types of markers, including GA, were placed at the proximal, center, and distal depths within the same SOBP, and dose distributions behind the markers were measured using the films. The amount of internal motion of prostate was derived from irradiation results and analyzed to determine the margins of the bsPTV.ResultsThe linearity of the film densities against absolute doses was constant within the SOBP and the amount of dose perturbations caused by the markers was quantitatively estimated from the film densities. The dose perturbation close behind the markers was smallest (<10% among depths within the SOBP regardless of types of markers) and increased with depth. The effect of two types of GAs on dose distributions was small and could be ignored in the treatment planning. Based on the analysis results of internal motions of prostate, required margins of the bsPTV were found to be 8, 7, and 7 mm in left–right (LR), anterior–posterior (AP), and superior–inferior (SI) directions, respectively.ConclusionWe evaluated the dose reductions caused by markers and determined the margins of the bsPTV, which was applied to the treatment using fiducial markers, using the analysis results of prostate movements.

Evaluation of tolerance to apple replant disease (ARD) inMalusgermplasm

Apple replant disease (ARD), also described as soil decline, is known for centuries; however, up to now the ultimate causes are unknown. After replanting plants of the same species, the plants are characterized by a poor vegetative development, stunted growth and reduced yield in terms of quantity and quality. For tree nurseries and orchards, replant disease is increasingly problematic and a sustainable and economically feasible solution would be the use of ARD-tolerant rootstocks. Up to now, only a few Malus genotypes with tolerance to ARD have been described and hardly any information is available about the genetic and physiological mechanisms underlying these tolerances. The discrimination of ARD tolerant and susceptible genotypes is a prerequisite for future rootstock breeding, but also for molecular studies aiming at improving the breeding efficiency. For this reason, 48 genotypes of wild apple species and rootstock cultivars were evaluated for their tolerance/susceptibility to ARD in a greenhouse bio-test. The susceptibility to ARD was classified by an ARD susceptibility index (ASI) calculated based on biomass and the increase in shoot length, respectively. The development of genetic linkage maps enables the detection of markers linked to agronomical important traits. Such associated markers can be used for an early and rapid selection of eligible plants during the breeding process. In order to map quantitative trait loci (QTL) for ARD tolerance a cross between the genotype Malus × robusta 5 (tolerant to ARD) and the rootstock M.9 (susceptible to ARD) was established and used for the construction of a first genetic linkage map including 78 SSR anchor markers. In addition, a comparative transcriptome study using mRNA from roots of M.9 and M.×robusta 5, which were cultivated on both ARD and disinfected ARD soil will provide information about potential candidate genes, which are related to ARD-tolerance.

Genetic Features of the Tomato Marker Line Мо938

In cultivated tomato hybrids (Marglobe × Mo938), the anthocyanin-free gene shows linked inheritance with the d (dwarf) gene on chromosome 2, but with a recombination frequency approximately three times higher than that according to the genetic map and in other hybrids with the Marglobe line. Cytological analysis of the mother pollen cells of the hybrids (Marglobe × Mo938) revealed no abnormalities of meiotic division and segregation of chromosomes, as well as no decrease in fertility. By means of the functional allelism test, it was established that, unlike Mo500, Mo504, and Mo755 marker tomato lines, in Mo938 the anthocyanin-free trait is not determined by the aw (anthocyanin without) or aa (anthocyanin absent) genes of chromosome 2. Using the F2 progeny of interspecies hybrids (Mo938 × Solanum pimpinellifolium), independent inheritance of the anthocyanin-free gene relative to the wv (white virescent) and d marker genes, as well as to six SSR anchor markers distributed at different sites of chromosome 2, was established. Thus, the Mo938 tomato line carries the d and wv markers on chromosome 2, as well as the anthocyanin-free gene not belonging to chromosome 2.

4D modeling in a gimbaled linear accelerator by using gold anchor markers.

The purpose of this study was to verify whether the dynamic tumor tracking (DTT) feature of a Vero4DRT system performs with 10-mm-long and 0.28mm diameter gold anchor markers. Gold anchor markers with a length of 10mm and a diameter of 0.28mm were used. Gold anchor markers were injected with short and long types into bolus material. These markers were sandwiched by a Tough Water (TW) phantom in the bolus material. For the investigation of 4-dimensional (4D) modeling feasibility under various phantom thicknesses, the TW phantom was added at 2cm intervals (in upper and lower each by 1cm). A programmable respiratory motion table was used to simulate breathing-induced organ motion, with an amplitude of 30mm and a breathing cycle of 3s. X-ray imaging parameters of 80kV and 125kV (320mA and 5ms) were used. The least detection error of the fiducial marker was defined as the 4D-modeling limitation. The 4D modeling process was attempted using short and long marker types and its limitation with the short and long types was with phantom thicknesses of 6 and 10cm at 80kV and 125kV, respectively. However, the loss in detectability of the gold anchor because of 4D-modeling errors was found to be approximately 6% (2/31) with a phantom thickness of 2cm under 125kV. 4D-modeling could be performed except under the described conditions. This work showed that a 10-mm-long gold anchor marker in short and long types can be used with DTT for short water equivalent path length site, such as lung cancer patients, in the Vero4DRT system.

Percutaneous ultrasound-guided fiducial marker placement for liver cancer robotic stereotactic radio-surgery treatment: A comparative analysis of three types of markers and needles

Background and study aimsPercutaneous placement of fiducial markers is required to perform stereotactic body radiation therapy (SBRT) for liver neoplastic lesions. This prospective trial was designed to evaluate the feasibility and safety of percutaneous ultrasound-guided placement of three different types of markers in patients with liver cancer referred for SBRT. Patients and methodsFifty patients underwent percutaneous ultrasound-guided implantation of a fiducial marker in the liver. Three sizes of needles were used: 25 gauge (G), 22G, and 17G. The 25G and 22G needles contained gold anchor markers of 0.28×10mm and 0.4 ×10mm size, respectively. In contrast, the 17G needle contained a gold grain marker of 1×4mm. Each patient received 1–6 markers, depending on lesion size and numbers. Technical feasibility and the occurrence of adverse events were registered. Computed tomography scans were acquired prior to SBRT to evaluate the location, visibility, or complications related to the markers. ResultsA total of 163 needles were used to deliver 163 markers in 50 patients. No major complications occurred. Minor complication occurrence rate was 12%. The total complication occurrence for all type of markers was 8.5%. No complications were observed with the use of the gold anchor marker of 0.4 ×10mm size. Variance analysis of the three markers showed a significant difference in the frequency of complications amongst the three markers (p<0.01). ConclusionPercutaneous ultrasound-guided placement of fiducial markers for SBRT of liver neoplastic lesions is safe and feasible. In our series, the 22G needle showed some advantage in terms of handling and safety when compared with the 25G and 17G needles. In addition, the gold anchor marker of 0.4 ×10mm size displayed a lower percentage of displacement.

Abstract 2259: Comprehensive evaluation of promising biomarkers for lung cancer risk prediction

Abstract Introductory sentence indicating the purposes of the study: Lung cancer will remain the number one cancer killer worldwide for the foreseeable future (Globocan 2012). Although low-dose CT screening has been shown to reduce mortality, there is an urgent need to improve risk prediction models to identify those subjects at high risk and most likely to benefit from screening in order its improve the screening efficacy (PMID: 23697514, 25372087). Brief description of pertinent experimental procedures: We have assembled a compendium of promising blood-based risk biomarkers for lung cancer that are currently being validated in order to identify a panel of validated risk markers for use in lung cancer risk assessment. Using pre-diagnostic serum samples from CARET cohort participants (current or former heavy smokers) we have recently validated pro-surfactant protein B (Pro-SFTPB) and Diacetyl spermine (DAS) as risk markers for non-small cell lung cancer (PMID: 26282655). Validation of additional markers from the compendium using Pro-SFTPB and DAS as anchor markers with further refinement of the risk prediction models is currently being performed in two large independent cohort studies (EPIC and NSHDS). Biospecimens from these cohorts include pre-diagnostic plasma from 550 former and current smoking lung cancer cases that were diagnosed within 5 years of blood draw, along with 1,100 matched controls. Summary of the new, unpublished data and conclusion: Preliminary data indicate that blood-based biomarkers of lung cancer risk have a strong potential to improve on questionnaire-based risk prediction models for lung cancer (PMID: 26282655). During the meeting we will present detailed results of the individual risk biomarkers and their associations with lung cancer risk up to 2 years prior to diagnosis, as well as an assessment of the extent to which they can improve traditional risk prediction models. Citation Format: Mattias A. Johansson, Ayumu Taguchi, David Muller, Samir Hanash, Paul Brennan. Comprehensive evaluation of promising biomarkers for lung cancer risk prediction. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2259.

Therapeutic usability of two different fiducial gold markers for robotic stereotactic radiosurgery of liver malignancies: A pilot study.

To assess how the application of different types of markers affects the tracking accuracy of CyberKnife's. Fifteen patients were recruited and subjected to the ultrasound-guided placement of markers. Two different type of needles 25 gauge (G) and 17 G containing two different fiducial marker, gold notched flexible anchor wire 0.28 mm × 10 mm (25 G needle) and gold cylindrical grain 1 mm × 4 mm (17 G), were used. Seven days after the procedure, a CyberKnife planning computed tomography (CT) for the simulation of radiation treatment was performed on all patients. A binary CT score was assigned to the fiducial markers visualization. Also, the CT number was calculated for each fiducial and the values compared with a specific threshold. For each patient from 1 to 5, intra-hepatic markers were placed (one in 2 patients, three in 8 patients, four in 3 patients, and five in 2 patients). A total of 48 needles were used (thirty-two 17 G and sixteen 25 G) and 48 gold markers were placed (32 Grain shaped markers and 16 Gold Anchor). The result showed that the CT visualization of the grain markers was better than the anchor markers (P = 5 × 10(-9)). Furthermore, the grain markers were shown to present minor late complications (P = 3 × 10(-6)), and the best CT threshold number (P = 0.0005). The study revealed that the Gold Anchor fiducial marker is correlated with a greater number of late minor complications and low visualization by the CT.

Agronomic and Genetic Evaluation on a Dull Mutant Line Derived from the Sodium Azide Treated ‘Namil’, a Non-Glutinous Japonica Rice

Developing rice lines with various amylose contents is necessary to diverse usages of rice in terms of raw materials for processed food production, and thereby to promote rice consumption in Korea. A rice mutant line, 'Namil(SA)-dull1' was established through sodium azide mutagenesis on 'Namil', a non-glutinous Korean Japonica rice cultivar. Namil(SA)-dull1' had dull endosperm characteristics and the evaluated amylose content was 12.2%. A total of 94 F2 progenies from a cross between 'Namil(SA)-dull1' and 'Milyang23', a non-glutinous Tongil-type rice cultivar, was used for genetic studies on the endosperm amylose content. Association analyses, between marker genotypes of 53 SSR anchor markers and evaluated amylose contents of each 94 F2:3 seeds, initially localized rice chromosome 6 as the harboring place for the modified allele(s) directing low amylose content of 'Namil(SA)-dull1'. By increasing SSR marker density on the putative chromosomal region followed by association analyses, the target region was narrowed down 0.94 Mbp segment, expanding from 28.95 Mbp to 29.89 Mbp, on rice chromosome 6 pseu- domolecule. Among the SSR loci, RM7555 explained 84.2% of total variation of amylose contents in the F2 population. Further physical mapping on the target region directing low amylose content of 'Namil(SA)-dull1' would increase the breeding efficiency in developing promising rice cultivars with various endosperm characteristics.

Characterization and mapping of LanrBo: a locus conferring anthracnose resistance in narrow-leafed lupin (Lupinus angustifolius L.).

A novel and highly effective source of anthracnose resistance in narrow-leafed lupin was identified. Resistance was shown to be governed by a single dominant locus. Molecular markers have been developed, which can be used for selecting resistant genotypes in lupin breeding. A screening for anthracnose resistance of a set of plant genetic resources of narrow-leafed lupin (Lupinus angustifolius L.) identified the breeding line Bo7212 as being highly resistant to anthracnose (Colletotrichum lupini). Segregation analysis indicated that the resistance of Bo7212 is inherited by a single dominant locus. The corresponding resistance gene was given the designation LanrBo. Previously published molecular anchor markers allowed us to locate LanrBo on linkage group NLL-11 of narrow-leafed lupin. Using information from RNAseq data obtained with inoculated resistant vs. susceptible lupin entries as well as EST-sequence information from the model genome Lotus japonicus, additional SNP and EST markers linked to LanrBo were derived. A bracket of two LanrBo-flanking markers allows for precise marker-assisted selection of the novel resistance gene in narrow-leafed lupin breeding programs.

Genetic analysis of seedling resistance to crown rust in five diploid oat (Avena strigosa) accessions.

Crown rust, caused by Puccinia coronata Corda f. sp. avenae Eriks., is a serious menace in oats, for which resistance is an effective means of control. Wild diploid oat accessions are a source of novel resistances that first need to be characterised prior to introgression into locally adapted oat cultivars. A genetic analysis of resistance to crown rust was carried out in three diverse diploid oat accessions (CIav6956, CIav9020, PI292226) and two cultivars (Saia and Glabrota) of A. strigosa. A single major gene conditioning resistance to Australian crown rust pathotype (Pt) 0000-2 was identified in each of the three accessions. Allelism tests suggested that these genes are either the same, allelic, or tightly linked with less than 1 % recombination. Similarly, a single gene was identified in Glabrota, and possibly two genes in Saia; both cultivars previously reported to carry two and three crown rust resistance genes, respectively. The identified seedling resistance genes could be deployed in combination with other resistance gene(s) to enhance durability of resistance to crown rust in hexaploid oat. Current diploid and hexaploid linkage maps and molecular anchor markers (simple sequence repeat [SSR] and diversity array technology [DArT] markers) should facilitate their mapping and introgression into hexaploid oat.

Linkage of an ABCC transporter to a single QTL that controls Ostrinia nubilalis larval resistance to the Bacillus thuringiensis Cry1Fa toxin

Field evolved resistance of insect populations to Bacillus thuringiensis (Bt) crystalline (Cry) toxins expressed by crop plants has resulted in reduced control of insect feeding damage to field crops, and threatens the sustainability of Bt transgenic technologies. A single quantitative trait locus (QTL) that determines resistance in Ostrinia nubilalis larvae capable of surviving on reproductive stage transgenic corn that express the Bt Cry1Fa toxin was previously mapped to linkage group 12 (LG12) in a backcross pedigree. Fine mapping with high-throughput single nucleotide polymorphism (SNP) anchor markers, a candidate ABC transporter (abcc2) marker, and de novo mutations predicted from a genotyping-by-sequencing (GBS) data redefined a 268.8 cM LG12. The single QTL on LG12 spanned an approximate 46.1 cM region, in which marker 02302.286 and abcc2 were ≤2.81 cM, and the GBS marker 697 was an estimated 1.89 cM distant from the causal genetic factor. This positional mapping data showed that an O. nubilalis genome region encoding an abcc2 transporter is in proximity to a single QTL involved in the inheritance of Cry1F resistance, and will assist in the future identification the mutation(s) involved with this phenotype.

A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes.

BackgroundCassava, Manihot esculenta Crantz, is one of the most important crops world-wide representing the staple security for more than one billion of people. The development of dense genetic and physical maps, as the basis for implementing genetic and molecular approaches to accelerate the rate of genetic gains in breeding program represents a significant challenge. A reference genome sequence for cassava has been made recently available and community efforts are underway for improving its quality. Cassava is threatened by several pathogens, but the mechanisms of defense are far from being understood. Besides, there has been a lack of information about the number of genes related to immunity as well as their distribution and genomic organization in the cassava genome.ResultsA high dense genetic map of cassava containing 2,141 SNPs has been constructed. Eighteen linkage groups were resolved with an overall size of 2,571 cM and an average distance of 1.26 cM between markers. More than half of mapped SNPs (57.4%) are located in coding sequences. Physical mapping of scaffolds of cassava whole genome sequence draft using the mapped markers as anchors resulted in the orientation of 687 scaffolds covering 45.6% of the genome. One hundred eighty nine new scaffolds are anchored to the genetic cassava map leading to an extension of the present cassava physical map with 30.7 Mb. Comparative analysis using anchor markers showed strong co-linearity to previously reported cassava genetic and physical maps. In silico based searching for conserved domains allowed the annotation of a repertory of 1,061 cassava genes coding for immunity-related proteins (IRPs). Based on physical map of the corresponding sequencing scaffolds, unambiguous genetic localization was possible for 569 IRPs.ConclusionsThis is the first study reported so far of an integrated high density genetic map using SNPs with integrated genetic and physical localization of newly annotated immunity related genes in cassava. These data build a solid basis for future studies to map and associate markers with single loci or quantitative trait loci for agronomical important traits. The enrichment of the physical map with novel scaffolds is in line with the efforts of the cassava genome sequencing consortium.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1397-4) contains supplementary material, which is available to authorized users.

The genetic and molecular origin of natural variation for the fragrance trait in an elite Malaysian aromatic rice through quantitative trait loci mapping using SSR and gene-based markers

MRQ74, a popular aromatic Malaysian landrace, allows for charging considerably higher prices than non-aromatic landraces. Thus, breeding this profitable trait has become a priority for Malaysian rice breeding. Despite many studies on aroma genetics, ambiguities considering its genetic basis remain. It has been observed that identifying quantitative trait loci (QTLs) based on anchor markers, particularly candidate genes controlling a trait of interest, can increase the power of QTL detection. Hence, this study aimed to locate QTLs that influence natural variations in rice scent using microsatellites and candidate gene-based sequence polymorphisms. For this purpose, an F2 mapping population including 189 individual plants was developed by MRQ74 crosses with ‘MR84’, a non-scented Malaysian accession. Additionally, qualitative and quantitative approaches were applied to obtain a phenotype data framework. Consequently, we identified two QTLs on chromosomes 4 and 8. These QTLs explained from 3.2% to 39.3% of the total fragrance phenotypic variance. In addition, we could resolve linkage group 8 by adding six gene-based primers in the interval harboring the most robust QTL. Hence, we could locate a putative fgr allele in the QTL found on chromosome 8 in the interval RM223–SCU015RM (1.63cM). The identified QTLs represent an important step toward recognition of the rice flavor genetic control mechanism. In addition, this identification will likely accelerate the progress of the use of molecular markers for gene isolation, gene-based cloning, and marker-assisted selection breeding programs aimed at improving rice cultivars.

Gene-based SNP discovery and genetic mapping in pea.

Key message Gene-based SNPs were identified and mapped in pea using five recombinant inbred line populations segregating for traits of agronomic importance. Pea (Pisum sativum L.) is one of the world’s oldest domesticated crops and has been a model system in plant biology and genetics since the work of Gregor Mendel. Pea is the second most widely grown pulse crop in the world following common bean. The importance of pea as a food crop is growing due to its combination of moderate protein concentration, slowly digestible starch, high dietary fiber concentration, and its richness in micronutrients; however, pea has lagged behind other major crops in harnessing recent advances in molecular biology, genomics and bioinformatics, partly due to its large genome size with a large proportion of repetitive sequence, and to the relatively limited investment in research in this crop globally. The objective of this research was the development of a genome-wide transcriptome-based pea single-nucleotide polymorphism (SNP) marker platform using next-generation sequencing technology. A total of 1,536 polymorphic SNP loci selected from over 20,000 non-redundant SNPs identified using deep transcriptome sequencing of eight diverse Pisum accessions were used for genotyping in five RIL populations using an Illumina GoldenGate assay. The first high-density pea SNP map defining all seven linkage groups was generated by integrating with previously published anchor markers. Syntenic relationships of this map with the model legume Medicago truncatula and lentil (Lens culinaris Medik.) maps were established. The genic SNP map establishes a foundation for future molecular breeding efforts by enabling both the identification and tracking of introgression of genomic regions harbouring QTLs related to agronomic and seed quality traits.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-014-2375-y) contains supplementary material, which is available to authorized users.

Work area monitoring in dynamic environments using multiple auto-aligning 3-D sensors

Abstract. Compared to current industry standards future production systems will be more flexible and robust and will adapt to unforeseen states and events. Industrial robots will interact with each other as well as with human coworkers. To be able to act in such a dynamic environment, each acting entity ideally needs complete knowledge of its surroundings, concerning working materials as well as other working entities. Therefore new monitoring methods providing complete coverage for complex and changing working areas are needed. While single 3-D sensors already provide detailed information within their field of view, complete coverage of a complete work area can only be achieved by relying on a multitude of these sensors. However, to provide useful information all data of each sensor must be aligned to each other and fused into an overall world picture. To be able to align the data correctly, the position and orientation of each sensor must be known with sufficient exactness. In a quickly changing dynamic environment, the positions of sensors are not fixed, but must be adjusted to maintain optimal coverage. Therefore, the sensors need to autonomously align themselves in real time. This can be achieved by adding defined markers with given geometrical patterns to the environment which can be used for calibration and localization of each sensor. As soon as two sensors detect the same markers, their relative position to each other can be calculated. Additional anchor markers at fixed positions serve as global reference points for the base coordinate system. In this paper we present a prototype for a self-aligning monitoring system based on a robot operating system (ROS) and Microsoft Kinect. This system is capable of autonomous real-time calibration relative to and with respect to a global coordinate system as well as to detect and track defined objects within the working area.

An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus)

BackgroundModern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus.ResultsUnder the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent mapping experiments using a genetically diverse array of parental lines, which included three subspecies of watermelon. The 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel), 36 structure variation (SV) and 386 SNP markers from the four maps were used to construct an integrated map. This integrated map contained 1339 markers, spanning 798 cM with an average marker interval of 0.6 cM. Fifty-eight previously reported quantitative trait loci (QTL) for 12 traits in these populations were also integrated into the map. In addition, new QTL identified for brix, fructose, glucose and sucrose were added. Some QTL associated with economically important traits detected in different genetic backgrounds mapped to similar genomic regions of the integrated map, suggesting that such QTL are responsible for the phenotypic variability observed in a broad array of watermelon germplasm.ConclusionsThe integrated map described herein enhances the utility of genomic tools over previous watermelon genetic maps. A large proportion of the markers in the integrated map are SSRs, InDels and SNPs, which are easily transferable across laboratories. Moreover, the populations used to construct the integrated map include all three watermelon subspecies, making this integrated map useful for the selection of breeding traits, identification of QTL, MAS, analysis of germplasm and commercial hybrid seed detection.

A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping

BackgroundDurum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. Genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits (e.g. resilience to environmental and biotic stresses). A dense and accurate consensus map specific for T. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement.ResultsHigh quality genotypic data from six core recombinant inbred line populations were used to obtain a consensus framework map of 598 simple sequence repeats (SSR) and Diversity Array Technology® (DArT) anchor markers (common across populations). Interpolation of unique markers from 14 maps allowed us to position a total of 2,575 markers in a consensus map of 2,463 cM. The T. durum A and B genomes were covered in their near totality based on the reference SSR hexaploid wheat map. The consensus locus order compared to those of the single component maps showed good correspondence, (average Spearman’s rank correlation rho ρ value of 0.96). Differences in marker order and local recombination rate were observed between the durum and hexaploid wheat consensus maps. The consensus map was used to carry out a whole-genome search for genetic differentiation signatures and association to heading date in a panel of 183 accessions adapted to the Mediterranean areas. Linkage disequilibrium was found to decay below the r2 threshold = 0.3 within 2.20 cM, on average. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. A genome-wide association scan for heading date from 27 field trials in the Mediterranean Basin and in Mexico yielded 50 chromosome regions with evidences of association in multiple environments.ConclusionsThe consensus map presented here was used as a reference for genetic diversity and mapping analyses in T. durum, providing nearly complete genome coverage and even marker density. Markers previously mapped in hexaploid wheat constitute a strong link between the two species. The consensus map provides the basis for high-density single nucleotide polymorphic (SNP) marker implementation in durum wheat.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-873) contains supplementary material, which is available to authorized users.