scholarly journals A diagnostic marker kit for Fusarium wilt and sterility mosaic diseases resistance in pigeonpea

2020 ◽  
Author(s):  
Rachit K. Saxena ◽  
Anil Hake ◽  
Abhishek Bohra ◽  
Aamir W. Khan ◽  
Anupama Hingane ◽  
...  
Keyword(s):  
Fusarium Wilt ◽  
Diagnostic Marker ◽  
Development Program ◽  
Cost Effective ◽  
Phenotypic Variance ◽  
Breeding Programs ◽  
Specific Pcr ◽  
Novel Approach ◽  
Resistant Varieties ◽  
Pathogen Variability

Abstract Fusarium wilt (FW) and sterility mosaic diseases (SMD) are key biotic constraints to pigeonpea production. Occurrence of these two diseases in congenial conditions is reported to cause complete yield loss in susceptible pigeonpea cultivars. Various studies to elucidate genomic architecture of the two traits have revealed significant marker–trait associations for use in breeding programs. However, these DNA markers could not be used effectively in genomics-assisted breeding for developing FW and SMD resistant varieties primarily due to pathogen variability, location or background specificity, lesser phenotypic variance explained by the reported QTL and cost-inefficiency of the genotyping assays. Therefore, in the present study, a novel approach has been used to develop a diagnostic kit for identification of suitable FW and SMD resistant lines. This kit was developed with 10 markers each for FW and SMD resistance. Investigation of the diversity of these loci has shown the role of different alleles in different resistant genotypes. Two genes (C.cajan_03691 and C.cajan_18888) for FW resistance and four genes (C.cajan_07858, C.cajan_20995, C.cajan_21801 and C.cajan_17341) for SMD resistance have been identified. More importantly, we developed a customized and cost-effective Kompetitive allele-specific PCR genotyping assay for the identified genes in order to encourage their downstream applications in pigeonpea breeding programs. The diagnostic marker kit developed here will offer great strength to pigeonpea varietal development program, since the resistance against these two diseases is essentially required for nominating an improved line in varietal release pipeline.

scholarly journals Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
João Vitor Maldonado dos Santos ◽  
Everton Geraldo Capote Ferreira ◽  
André Luiz de Lima Passianotto ◽  
Bruna Bley Brumer ◽  
Adriana Brombini Dos Santos ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Allelic Variation ◽  
Major Gene ◽  
Cost Effective ◽  
Stem Canker ◽  
Snp Marker ◽  
Phenotypic Variance ◽  
Breeding Programs ◽  
A Genome ◽  
Marker Assay

Abstract Background Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous), is an important soybean disease that has been responsible for severe losses in the past. The main strategy for controlling this fungus involves the introgression of resistance genes. Thus far, five main loci have been associated with resistance to SSC. However, there is a lack of information about useful allelic variation at these loci. In this work, a genome-wide association study (GWAS) was performed to identify allelic variation associated with resistance against Diaporthe aspalathi and to provide molecular markers that will be useful in breeding programs. Results We characterized the response to SSC infection in a panel of 295 accessions from different regions of the world, including important Brazilian elite cultivars. Using a GBS approach, the panel was genotyped, and we identified marker loci associated with Diaporthe aspalathi resistance through GWAS. We identified 19 SNPs associated with southern stem canker resistance, all on chromosome 14. The peak SNP showed an extremely high degree of association (p-value = 6.35E-27) and explained a large amount of the observed phenotypic variance (R2 = 70%). This strongly suggests that a single major gene is responsible for resistance to D. aspalathi in most of the lines constituting this panel. In resequenced soybean materials, we identified other SNPs in the region identified through GWAS in the same LD block that clearly differentiate resistant and susceptible accessions. The peak SNP was selected and used to develop a cost-effective molecular marker assay, which was validated in a subset of the initial panel. In an accuracy test, this SNP assay demonstrated 98% selection efficiency. Conclusions Our results suggest relevance of this locus to SSC resistance in soybean cultivars and accessions from different countries, and the SNP marker assay developed in this study can be directly applied in MAS studies in breeding programs to select materials that are resistant against this pathogen and support its introgression.

scholarly journals Cost-Effective and Time-Efficient Molecular Assisted Selection for Ppv Resistance in Apricot Based on ParPMC2 Allele-Specific PCR

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1292 ◽  
Author(s):  
Ángela Polo-Oltra ◽  
Carlos Romero ◽  
Inmaculada López ◽  
María Luisa Badenes ◽  
Elena Zuriaga
Keyword(s):  
Woody Species ◽  
Cost Effective ◽  
Prunus Armeniaca ◽  
Host Susceptibility ◽  
Limiting Factor ◽  
Plum Pox Virus ◽  
Breeding Programs ◽  
Specific Pcr ◽  
Allele Specific ◽  
Ppv Resistance

Plum pox virus (PPV) is the most important limiting factor for apricot (Prunus armeniaca L.) production worldwide, and development of resistant cultivars has been proven to be the best solution in the long-term. However, just like in other woody species, apricot breeding is highly time and space demanding, and this is particularly true for PPV resistance phenotyping. Therefore, marker-assisted selection (MAS) may be very helpful to speed up breeding programs. Tightly linked ParPMC1 and ParPMC2, meprin and TRAF-C homology (MATH)-domain-containing genes have been proposed as host susceptibility genes required for PPV infection. Contribution of additional genes to PPV resistance cannot be discarded, but all available studies undoubtedly show a strong correlation between ParPMC2-resistant alleles (ParPMC2res) and PPV resistance. The ParPMC2res allele was shown to carry a 5-bp deletion (ParPMC2-del) within the second exon that has been characterized as a molecular marker suitable for MAS (PMC2). Based on this finding, we propose here a method for PPV resistance selection in apricot by combining high-throughput DNA extraction of 384 samples in 2 working days and the allele-specific genotyping of PMC2 on agarose gel. Moreover, the PMC2 genotype has been determined by PCR or by using whole-genome sequences (WGS) in 175 apricot accessions. These results were complemented with phenotypic and/or genotypic data available in the literature to reach a total of 325 apricot accessions. As a whole, we conclude that this is a time-efficient, cost-effective and straightforward method for PPV resistance screening that can be highly useful for apricot breeding programs.

Genetic characterization of Meloidogyne incognita isolates from Turkey using sequence-related amplified polymorphism (SRAP)

Biologia ◽  
2012 ◽  
Vol 67 (3) ◽  
Author(s):  
Zübeyir Devran ◽  
Ömür Baysal
Keyword(s):  
Genetic Variation ◽  
Meloidogyne Incognita ◽  
Cost Effective ◽  
Nematode Species ◽  
Root Knot Nematode ◽  
Breeding Programs ◽  
Widespread Species ◽  
Resistant Varieties ◽  
Southern Root Knot Nematode

AbstractSouthern root knot nematode Meloidogyne incognita is the most widespread-species, causing serious yield losses in protected vegetables fields in the West Mediterranean region of Turkey. The knowledge of genetic variation within M. incognita is required for disease management and improvement of resistant varieties by breeding programs. In the present study, the isolates were classified into different groups based on sequence-related amplified polymorphism (SRAP) fingerprints. To our knowledge, this is the first study carried out on the characterization of M. incognita isolates using SRAP. The schematic diagram by tested primers to differentiate of M. incognita isolates was formed in discrimination of nematodes as an effective molecular tool since it is cost effective and easiness. Data presents a genetic variation on root-knot nematode species. These selected SRAP markers can be used to follow genetic structure and differentiation on M. incognita isolates in a certain region.

scholarly journals Association mapping of a locus that confers Southern stem canker resistance in soybean

2019 ◽  
Author(s):  
João Vitor Maldonado dos Santos ◽  
Everton Geraldo Capote Ferreira ◽  
André Luiz de Lima Passianotto ◽  
Bruna Bley Brumer ◽  
Adriana Brombini Dos Santos ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Allelic Variation ◽  
Major Gene ◽  
Cost Effective ◽  
Stem Canker ◽  
P Value ◽  
Phenotypic Variance ◽  
Breeding Programs ◽  
A Genome ◽  
Marker Assay

Abstract Background Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous) is an important soybean disease, which has been responsible for severe losses in the past. The main strategy to control this fungus is through the introgression of resistance genes. So far, five main loci have been associated with resistance to Southern stem canker. However, there is a lack of information about useful allelic variation at these loci. In this work, a genome-wide association study (GWAS) was performed to identify allelic variation associated with resistance against Diaporthe aspalathi and to provide molecular markers useful in breeding programs. Results We characterized the response to Southern stem canker infection in a panel of 295 accessions from different regions of the world including important Brazilian elite cultivars. Using a GBS approach, the panel was genotyped and we identified marker loci associated with Diaporthe aspalathi resistance using GWAS analysis. We identified 19 SNPs associated with Southern stem canker resistance, all on chromosome 14. The peak SNP showed an extremely high degree of association (p-value = 6.35E-27) and explained a high level of the phenotypic variance (R2 = 70%). This strongly suggests that a single major gene is responsible for resistance to D. aspalathi present inn most of the lines comprising this panel. We also identified in resequenced soybean materials other SNPs in the region identified by GWAS in the same LD block that clearly differentiate resistance and susceptible accessions. The peak SNP was selected and used to develop a cost-effective molecular marker assay, which was validated in a subset of the initial panel. In an accuracy test, this SNP assay demonstrated 98% of selection efficiency. Conclusions Our results suggest a relevant importance of this locus in SSC resistance in soybean cultivars and accessions from different countries and the SNP marker assay developed in this study can be directly applied in MAS studies in breeding programs to select resistance materials against this pathogen and support its introgression.

scholarly journals Universal probe-based intermediate primer-triggered qPCR (UPIP-qPCR) for SNP genotyping

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Baowei Li ◽  
Yanran Liu ◽  
Xiaodan Hao ◽  
Jinhua Dong ◽  
Limei Chen ◽  
...  
Keyword(s):  
Dna Microarrays ◽  
Quantitative Polymerase Chain Reaction ◽  
Cost Effective ◽  
Snp Genotyping ◽  
Taqman Probe ◽  
Amplification Refractory Mutation System ◽  
Specific Pcr ◽  
Detection And Identification ◽  
Novel Approach ◽  
The Individual

Abstract Background The detection and identification of single nucleotide polymorphism (SNP) is essential for determining patient disease susceptibility and the delivery of medicines targeted to the individual. At present, SNP genotyping technology includes Sanger sequencing, TaqMan-probe quantitative polymerase chain reaction (qPCR), amplification-refractory mutation system (ARMS)-PCR, and Kompetitive Allele-Specific PCR (KASP). However, these technologies have some disadvantages: the high cost of development and detection, long and time consuming protocols, and high false positive rates. Focusing on these limitations, we proposed a new SNP detection method named universal probe-based intermediate primer-triggered qPCR (UPIP-qPCR). In this method, only two types of fluorescence-labeled probes were used for SNP genotyping, thus greatly reducing the cost of development and detection for SNP genotyping. Results In the amplification process of UPIP-qPCR, unlabeled intermediate primers with template-specific recognition functions could trigger probe hydrolysis and specific signal release. UPIP-qPCR can be used successfully and widely for SNP genotyping. The sensitivity of UPIP-qPCR in SNP genotyping was 0.01 ng, the call rate was more than 99.1%, and the accuracy was more than 99.9%. High-throughput DNA microarrays based on intermediate primers can be used for SNP genotyping. Conclusion This novel approach is both cost effective and highly accurate; it is a reliable SNP genotyping method that would serve the needs of the clinician in the provision of targeted medicine.

A Novel Approach for the Treatment of Sialolithiasis that Preserves Salivary Duct Anatomy

2021 ◽  
pp. 000348942110189
Author(s):  
Gani Atilla Şengör ◽  
Ahmet Mert Bilgili
Keyword(s):  
Salivary Gland ◽  
Success Rate ◽  
Cost Effective ◽  
Complete Removal ◽  
Level Of Evidence ◽  
Invasive Approach ◽  
Pneumatic Lithotripsy ◽  
Novel Approach ◽  
Surgical Methods ◽  
Salivary Gland Stones

Objective: The sialendoscopy era in the treatment of salivary gland stones has reduced the use of classical surgical methods. However, the miniature ducts and tools may cause difficulties in removing large sialoliths. Therefore, invasive combined oral surgeries or gland resection may be considered. We searched for the most suitable method in order to stay in line with the minimally invasive approach that preserves the ductus anatomy, and that can reduce the surgical fears of patients. Materials and Methods: The study included 84 cases (23 parotid and 61 submandibular) in whom stones were fragmented by pneumatic lithotripsy and removed between January 2015 and January 2020. The parotid cases comprised 7 females and 16 males, and the submandibular cases comprised 25 females and 36 males. Intraductal lithotripsy was performed using pneumatic lithotripter. This study has fourth level of evidence. Results: Based on total number of cases (n = 84), success rate was 67/84 (79.7%) immediately after sialendoscopy, and overall success rate was 77/84 (91.6%). Based on number of stones treated (n = 111), our immediate success rate was 94/111 (84.6%), and overall success rate was 104/111 (93.7%). The success criteria were complete removal of the stone and fragments in a single sialendoscopy procedure and resolution of symptoms. Conclusions: We successfully treated salivary gland stones, including L3b stones, in our patient cohort with sialendoscopy combined with pneumatic lithotripsy. The lithotripsy method that we have adapted seems to be more useful and cost-effective compared to its alternatives. We were also able to preserve the ductus anatomy and relieve patients’ concerns. Level of Evidence: Level IV

scholarly journals QTL Mapping of Seedling and Adult Plant Resistance to Septoria Tritici Blotch in Winter Wheat cv. Mandub (Triticum aestivum L.)

Agronomy ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1108
Author(s):  
Dominika Piaskowska ◽  
Urszula Piechota ◽  
Magdalena Radecka-Janusik ◽  
Paweł Czembor
Keyword(s):  
Mapping Population ◽  
Triticum Aestivum L ◽  
Seedling Stage ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Adult Plant ◽  
Resistance Locus ◽  
Phenotypic Variance ◽  
Breeding Programs ◽  
Plant Stage

Septoria tritici blotch (STB) is one of the most devastating foliar diseases of wheat worldwide. Host resistance is the most economical and safest method of controlling the disease, and information on resistance loci is crucial for effective breeding for resistance programs. In this study we used a mapping population consisting of 126 doubled-haploid lines developed from a cross between the resistant cultivar Mandub and the susceptible cultivar Begra. Three monopycnidiospore isolates of Z. tritici with diverse pathogenicity were used to test the mapping population and parents’ STB resistance at the seedling stage (under a controlled environment) and adult plant stage (polytunnel). For both types of environments, the percentage leaf area covered by necrosis (NEC) and pycnidia (PYC) was determined. A linkage map comprising 5899 DArTSNP and silicoDArT markers was used for the quantitative trait loci (QTL) analysis. The analysis showed five resistance loci on chromosomes 1B, 2B and 5B, four of which were derived from cv. Mandub. The location of QTL detected in our study on chromosomes 1B and 5B may suggest a possible identity or close linkage with Stb2/Stb11/StbWW and Stb1 loci, respectively. QStb.ihar-2B.4 and QStb.ihar-2B.5 detected on chromosome 2B do not co-localize with any known Stb genes. QStb.ihar-2B.4 seems to be a new resistance locus with a moderate effect (explaining 29.3% of NEC and 31.4% of PYC), conferring resistance at the seedling stage. The phenotypic variance explained by QTL detected in cv. Mandub ranged from 11.9% to 70.0%, thus proving that it is a good STB resistance source and can potentially be utilized in breeding programs.

scholarly journals Gas Detection and Identification Using Multimodal Artificial Intelligence Based Sensor Fusion

2021 ◽  
Vol 4 (1) ◽  
pp. 3
Author(s):  
Parag Narkhede ◽  
Rahee Walambe ◽  
Shruti Mandaokar ◽  
Pulkit Chandel ◽  
Ketan Kotecha ◽  
...  
Keyword(s):  
Sensor Fusion ◽  
Network Architecture ◽  
Cost Effective ◽  
Sensor Data ◽  
Dense Layer ◽  
Gaseous Emissions ◽  
Multiple Sensors ◽  
Single Output ◽  
Novel Approach ◽  
Single Sensor

With the rapid industrialization and technological advancements, innovative engineering technologies which are cost effective, faster and easier to implement are essential. One such area of concern is the rising number of accidents happening due to gas leaks at coal mines, chemical industries, home appliances etc. In this paper we propose a novel approach to detect and identify the gaseous emissions using the multimodal AI fusion techniques. Most of the gases and their fumes are colorless, odorless, and tasteless, thereby challenging our normal human senses. Sensing based on a single sensor may not be accurate, and sensor fusion is essential for robust and reliable detection in several real-world applications. We manually collected 6400 gas samples (1600 samples per class for four classes) using two specific sensors: the 7-semiconductor gas sensors array, and a thermal camera. The early fusion method of multimodal AI, is applied The network architecture consists of a feature extraction module for individual modality, which is then fused using a merged layer followed by a dense layer, which provides a single output for identifying the gas. We obtained the testing accuracy of 96% (for fused model) as opposed to individual model accuracies of 82% (based on Gas Sensor data using LSTM) and 93% (based on thermal images data using CNN model). Results demonstrate that the fusion of multiple sensors and modalities outperforms the outcome of a single sensor.

scholarly journals Implementation of Fused Filament Fabrication in Dentistry

2021 ◽  
Vol 11 (14) ◽  
pp. 6444
Author(s):  
Jörg Lüchtenborg ◽  
Felix Burkhardt ◽  
Julian Nold ◽  
Severin Rothlauf ◽  
Christian Wesemann ◽  
...  
Keyword(s):  
Fused Deposition Modeling ◽  
Present Report ◽  
Cost Effective ◽  
Great Promise ◽  
Temperature Sensitive ◽  
Fused Filament Fabrication ◽  
Digital Light Processing ◽  
Fused Deposition ◽  
Surgical Guides ◽  
Novel Approach

Additive manufacturing is becoming an increasingly important technique for the production of dental restorations and assistive devices. The most commonly used systems are based on vat polymerization, e.g., stereolithography (SLA) and digital light processing (DLP). In contrast, fused filament fabrication (FFF), also known under the brand name fused deposition modeling (FDM), is rarely applied in the dental field. This might be due to the reduced accuracy and resolution of FFF compared to vat polymerization. However, the use of FFF in the dental sector seems very promising for in-house production since it presents a cost-effective and straight forward method. The manufacturing of nearly ready-to-use parts with only minimal post-processing can be considered highly advantageous. Therefore, the objective was to implement FFF in a digital dental workflow. The present report demonstrates the production of surgical guides for implant insertion by FFF. Furthermore, a novel approach using a temperature-sensitive filament for bite registration plates holds great promise for a simplified workflow. In combination with a medical-grade filament, a multi-material impression tray was printed for optimized impression taking of edentulous patients. Compared to the conventional way, the printed thermoplastic material is pleasant to model and can allow clean and fast work on the patient.

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