scholarly journals Adapting Genotyping-by-Sequencing for Rice F2 Populations

2016 ◽  
Author(s):  
Tomoyuki Furuta ◽  
Motoyuki Ashikari ◽  
Kshirod K. Jena ◽  
Kazuyuki Doi ◽  
Stefan Reuscher
Keyword(s):  
Low Cost ◽  
Genotyping By Sequencing ◽  
Cost Effective ◽  
Snp Markers ◽  
Reduced Representation ◽  
F2 Population ◽  
Wild Rice Species ◽  
Miseq Platform ◽  
Mapping Populations ◽  
Genotype A

ABSTRACTRapid and cost-effective genotyping of large mapping populations can be achieved by sequencing a reduced representation of the genome of every individual in a given population and using that information to generate genetic markers. A customized genotyping-by-sequencing (GBS) pipeline was developed to genotype a rice F2 population from a cross of Oryza sativa ssp. japonica cv. Nipponbare and the African wild rice species Oryza longistaminata. While most GBS pipelines aim to analyze mainly homozygous populations we attempted to genotype a highly heterozygous F2 population. We show how species-and population-specific improvements of established protocols can drastically increase sample throughput and genotype quality. Using as few as 50,000 reads for some individuals (134,000 reads on average) we were able to generate up to 8,154 informative SNP markers in 1,081 F2 individuals. Additionally, the effects of enzyme choice, read coverage and data post-processing are evaluated. Using GBS-derived markers we were able to assemble a genetic map of 1,536 cM. To demonstrate the usefulness of our GBS pipeline we determined QTL for the number of tillers. We were able to map four QTLs to chromosomes 1, 3, 4 and 8 and confirm their effects using introgression lines. We provide an example of how to successfully use GBS with heterozygous F2 populations. By using the comparatively low-cost MiSeq platform we show that the GBS method is flexible and cost-effective even for smaller laboratories

scholarly journals APPLICATIONS OF MOLECULAR MARKERS AND GENOMIC TOOLS IN PEARL MILLET [CENCHRUS AMERICANUS (L.) MORRONESYN. PENNISETUM GLAUCUM (L.) R. BR.]

2021 ◽  
Vol 9 (06) ◽  
pp. 681-690
Author(s):  
Bassirou Mbacke ◽  
◽  
Abdoulaye Dieng ◽  
Keyword(s):  
Pearl Millet ◽  
Pennisetum Glaucum ◽  
Draft Genome ◽  
Genotyping By Sequencing ◽  
Cost Effective ◽  
Reduced Representation ◽  
Phosphorus Absorption ◽  
Sequencing Method ◽  
Genetic Mechanisms ◽  
Pool Formation

Thisreviewsummarizesthemainmolecularmarkersandtheirapplicationson pearl milletaswellasasummaryof the discoveriesonitsreferencegenome.Molecularmarkers,unlikemorphologicalandbiochemicalmarkers,arehighlypolymorphicandneutral. Theirgreatliabilitycomesfromthefactthattheydirectlyconcern the DNA.Theyhavebeenwidelyusedonpearl millet,rangingfromlow andmedium-throughputtohigh-throughput markers, targetingspecificregionsorcharacterizinggermplasmat thegenomelevel. Many studiesrelatetomappingusingdifferentpopulationsandhaveidentifiedQTLslinkedtoimportantagronomictraits(floweringtime,tolerancetodrought,to mildew,phosphorus absorption),iron content...Studieshavealsobeenconductedondomesticationsyndromeandshowedtheir importance of genes flowfromwildmilletstocultivatedvarieties. Genotyping-by-Sequencing - a rapid, cost-effective and reduced representation sequencing method – has been used to assess genetic diversity, population structure, LD and heterotic pool formation in pearl millet. A draft genome sequence that can serve as a reference for further development of genomics-assisted breeding is now available. It is an important milestone in generating genomic resources for pearl millet. Annotation of 24,000 genes indicates that enrichment of wax biosynthesis genes providing potential genetic mechanisms for heat and drought tolerance. Althoughmolecularmarkersarewidelyappliedtomillet,geneticandgenomicresourcesarestilllimitedcomparedtootherimportantcereals.However,theavailabilityofacollectionofinbredlinesrepresentativeofgermplasmandareferencegenomeoffernewperspectivesintheimprovement of pearl millet.

scholarly journals Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Arnaud Comlan Gouda ◽  
Marilyn L. Warburton ◽  
Gustave L. Djedatin ◽  
Sèdjro Bienvenu Kpeki ◽  
Peterson W. Wambugu ◽  
...  
Keyword(s):  
Quality Control ◽  
Low Cost ◽  
Cost Effective ◽  
Snp Markers ◽  
Morphological Identification ◽  
Validation Data ◽  
Next Generation Sequencing Technology ◽  
Specific Pcr ◽  
Aa Genome ◽  
Diagnostic Snps

AbstractMorphological identification of closely related rice species, particularly those in the Oryza AA genome group, presents major challenges and often results in cases of misidentification. Recent work by this group identified diagnostic single nucleotide polymorphic (SNP) markers specific for several rice species and subspecies based on DArTseq next-generation sequencing technology (“DArTseq”). These SNPs can be used for quality control (QC) analysis in rice breeding and germplasm maintenance programs. Here, we present the DArTseq-based diagnostic SNPs converted into Kompetitive allele-specific PCR (KASPar or KASP) assays and validation data for a subset of them; these can be used for low-cost routine genotyping quality control (QC) analysis. Of the 224 species/subspecies’ diagnostic SNPs tested, 158 of them produced working KASP assays, a conversion success rate of 70%. Two validation experiments were run with 87 of the 158 SNP markers to ensure that the assays amplified, were polymorphic, and distinguished the five species/subspecies tested. Based on these validation test results, we recommend a panel of 36 SNP markers that clearly delineate O. barthii, O. glaberrima, O. longistaminata, O. sativa spp. indica and japonica. The KASP assays provide a flexible, rapid turnaround and cost-effective tool to facilitate germplasm curation and management of these four Oryza AA genome species across multiple genebanks.

scholarly journals A Robust DNA Isolation Protocol from Filtered Commercial Olive Oil for PCR-Based Fingerprinting

Foods ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 462 ◽  
Author(s):  
Piarulli ◽  
Savoia ◽  
Taranto ◽  
D’Agostino ◽  
Sardaro ◽  
...  
Keyword(s):  
Olive Oil ◽  
Dna Extraction ◽  
Dna Isolation ◽  
Low Cost ◽  
Virgin Olive Oil ◽  
Genotyping By Sequencing ◽  
Extra Virgin Olive Oil ◽  
Snp Markers ◽  
Dna Isolation Protocol ◽  
Fingerprinting Methods

Extra virgin olive oil (EVOO) has elevated commercial value due to its health appeal, desirable characteristics and quantitatively limited production, and thus it has become an object of intentional adulteration. As EVOOs on the market might consist of a blend of olive varieties or sometimes even of a mixture of oils from different botanical species, an array of DNA-fingerprinting methods have been developed to check the varietal composition of the blend. Starting from a comparison between publicly available DNA extraction protocols, we set up a timely, low-cost, reproducible and effective DNA isolation protocol, which allows an adequate amount of DNA to be recovered even from commercial filtered EVOOs. Then, in order to verify the effectiveness of the DNA extraction protocol herein proposed, we applied PCR-based fingerprinting methods starting from the DNA extracted from three EVOO samples of unknown composition. In particular, genomic regions harboring nine simple sequence repeats (SSRs) and eight genotyping-by-sequencing-derived single nucleotide polymorphism (SNP) markers were amplified for authentication and traceability of the three EVOO samples. The whole investigation strategy herein described might favor producers in terms of higher revenues and consumers in terms of price transparency and food safety.

scholarly journals Ancestry informative alleles captured with reduced representation library sequencing in Theobroma cacao

2018 ◽  
Author(s):  
Jaime A. Osorio-Guarín ◽  
Corey R. Quackenbush ◽  
Omar E. Cornejo
Keyword(s):  
Large Scale ◽  
Demographic History ◽  
Genotyping By Sequencing ◽  
Cost Effective ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Reduced Representation ◽  
Reduced Representation Library

AbstractAs the source of chocolate, cacao has become one of the most important crops in the world. The identification of molecular markers to understand the demographic history, genetic diversity and population structure plays a pivotal role in cacao breeding programs. Here, we report the use of a modified genotyping-by-sequencing (GBS) approach for large-scale single nucleotide polymorphism (SNP) discovery and allele ancestry mapping. We identified 12,357 bi-allelic SNPs after filtering, of which, 7,009 variants were ancestry informative. The GBS approach proved to be rapid, cost-effective, and highly informative for ancestry assignment in this species.

scholarly journals Genetic Diversity and Population Structure of Asian and European Common Wheat Accessions Based on Genotyping-By-Sequencing

2019 ◽  
Author(s):  
Xiu Yang ◽  
Ling Xi ◽  
Binwen Tan ◽  
Wei Zhu ◽  
Lili Xu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Common Wheat ◽  
Diversity Index ◽  
Genotyping By Sequencing ◽  
Cost Effective ◽  
Wheat Breeding ◽  
Snp Markers ◽  
Next Generation Sequencing Technology

Abstract Background Availability of information on the genetic diversity and population structure of germplasm facilitates its use in wheat breeding programs. Recently, with the development of next-generation sequencing technology, genotyping-by-sequencing (GBS) has been used as a high-throughput and cost-effective molecular tool for examination of the genetic diversity of wheat breeding lines. In this study, GBS was used to characterize a population of 180 accessions of common wheat originating from Asia and Europe between the latitudes 30° and 45°N.Results In total, 24,767 high-quality single-nucleotide polymorphism (SNP) markers were used for analysis of genetic diversity and population structure. The B genome contained the highest number of SNPs, followed by the A and D genomes. The polymorphism information content ranged from 0.1 to 0.4, with an average of 0.26. The distribution of SNPs markers on the 21 chromosomes ranged from 243 on chromosome 4D to 2,337 on chromosome 3B. Structure and cluster analyses divided the panel of accessions into two subgroups (G1 and G2). G1 principally consisted of European and partial Asian accessions, and G2 comprised mainly accessions from the Middle East and partial Asia. Molecular analysis of variance showed that the genetic variation was greater within groups (99%) than between groups (1%). Comparison of the two subgroups indicated that G1 and G2 contained a high level of genetic diversity. The genetic diversity of G2 was higher as indicated by the Shannon’s information index ( I ) = 0.512, diversity index ( h ) = 0.334, observed heterozygosity ( H o ) = 0.226, and unbiased diversity index (uh) = 0.338.Conclusion The present results will not only help breeders to understand the genetic diversity of wheat germplasm on the Eurasian continent between the latitudes of 30° and 45°N, but also provide valuable information for wheat genetic improvement through introgression of novel genetic variation in this region.

scholarly journals A Novel QTL for Resistance to Phytophthora Crown Rot in Squash

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2115
Author(s):  
Vincent Njung’e Michael ◽  
Yuqing Fu ◽  
Swati Shrestha ◽  
Geoffrey Meru
Keyword(s):  
Management Practices ◽  
Virulent Strain ◽  
Integrated Management ◽  
Genotyping By Sequencing ◽  
Average Density ◽  
Snp Markers ◽  
Crown Rot ◽  
Disease Resistance Gene ◽  
Resistant Cultivars ◽  
F2 Population

Phytophthora capsici Leonian causes significant yield losses in commercial squash (Cucurbita pepo) production worldwide. The deployment of resistant cultivars can complement integrated management practices for P. capsici, but resistant cultivars are currently unavailable for growers. Moderate resistance to Phytophthora crown rot in a selection of accession PI 181761 (C. pepo) (designated line #181761-36P) is controlled by three dominant genes (R4, R5 and R6). Introgression of these loci into elite germplasm through marker-assisted selection (MAS) can accelerate the release of new C. pepo cultivars resistant to crown rot, but these tools are currently unavailable. Here we describe the identification of a quantitative trait locus (QTL), molecular markers and candidate genes associated with crown rot resistance in #181761-36P. Five hundred and twenty-three SNP markers were genotyped in an F2 (n = 83) population derived from a cross between #181761-36P (R) and Table Queen (S) using targeted genotyping by sequencing. A linkage map (2068.96 cM) consisting of twenty-one linkage groups and an average density of 8.1 markers/cM was developed for the F2 population. The F2:3 families were phenotyped in the greenhouse with a virulent strain of P. capsica, using the spore-spray method. A single QTL (QtlPC-C13) was consistently detected on LG 13 (chromosome 13) across three experiments and explained 17.92–21.47% of phenotypic variation observed in the population. Nine candidate disease resistance gene homologs were found within the confidence interval of QtlPC-C13. Single nucleotide polymorphism (SNP) markers within these genes were converted into Kompetitive Allele Specific PCR (KASP) assays and tested for association with resistance in the F2 population. One SNP marker (C002686) was significantly associated with resistance to crown rot in the F2 population (p < 0.05). This marker is a potential target for MAS for crown rot resistance in C. pepo.

scholarly journals Development of a Panel of Genotyping-in-Thousands by Sequencing in Capsicum

2021 ◽  
Vol 12 ◽  
Author(s):  
Jinkwan Jo ◽  
Youngin Kim ◽  
Geon Woo Kim ◽  
Jin-Kyung Kwon ◽  
Byoung-Cheorl Kang
Keyword(s):  
Multiplex Pcr ◽  
Low Cost ◽  
Genotyping By Sequencing ◽  
Illumina Miseq ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Multiple Loci ◽  
Sequencing Method ◽  
Pcr Conditions

Genotyping by sequencing (GBS) enables genotyping of multiple loci at low cost. However, the single nucleotide polymorphisms (SNPs) revealed by GBS tend to be randomly distributed between individuals, limiting their direct comparisons without applying the various filter options to obtain a comparable dataset of SNPs. Here, we developed a panel of a multiplex targeted sequencing method, genotyping-in-thousands by sequencing (GT-seq), to genotype SNPs in Capsicum spp. Previously developed Fluidigm® SNP markers were converted to GT-seq markers and combined with new GT-seq markers developed using SNP information obtained through GBS. We then optimized multiplex PCR conditions: we obtained the highest genotyping rate when the first PCR consisted of 25 cycles. In addition, we determined that 101 primer pairs performed best when amplifying target sequences of 79 bp. We minimized interference of multiplex PCR by primer dimer formation using the PrimerPooler program. Using our GT-seq pipeline on Illumina Miseq and Nextseq platforms, we genotyped up to 1,500 (Miseq) and 1,300 (Nextseq) samples for the optimum panel size of 100 loci. To allow the genotyping of Capsicum species, we designed 332 informative GT-seq markers from Fluidigm SNP markers and GBS-derived SNPs. This study illustrates the first application of GT-seq in crop plants. The GT-seq marker set developed here will be a useful tool for molecular breeding of peppers in the future.

ASSESSMENT OF THE PLATELET COUNT IN THE PREGNANT WOMEN IN IGIMS, PATNA, BIHAR

2020 ◽  
Vol 4 (2) ◽  
Author(s):  
Tanwi Singh ◽  
Anshuman Sinha
Keyword(s):  
Platelet Count ◽  
Pregnant Women ◽  
Screening Test ◽  
Low Cost ◽  
Medical Science ◽  
Cost Effective ◽  
Platelet Indices ◽  
Increased Risk ◽  
Low Platelet Count ◽  
Severity Of The Disease

The major risk associated with low platelet count in pregnancy is the increased risk of bleeding during the childbirth or post that. There is an increased blood supply to the uterus during pregnancy and the surgical procedure requires cutting of major blood vessels. Women with thrombocytopenia are at increased risk of losing excessive blood. The risk is more in case of caesarean delivery as compared to vaginal delivery. Hence based on above findings the present study was planned for Assessment of the Platelet Count in the Pregnant Women in IGIMS, Patna, Bihar. The present study was planned in Department of Pathology, Indira Gandhi Institute of Medical Science, Patna, Bihar, India. The present study was planned from duration of January 2019 to June 2019. In the present study 200 pregnant females samples received for the platelet estimation were enrolled in the present study. Clinically platelet indices can be a useful screening test for early identification of preeclampsia and eclampsia. Also platelet indices can assess the prognosis of this disease in pregnant women and can be used as an effective prognostic marker because it correlates with severity of the disease. Platelet count is a simple, low cost, and rapid routine screening test. Hence the data generated from the present study concludes that platelet count can be used as a simple and cost effective tool to monitor the progression of preeclampsia, thereby preventing complications to develop during the gestational period. Keywords: Platelet Count, Pregnant Women, IGIMS, Patna, Bihar, etc.

Janus – A New Approach to Air Combat Pilot Training

2019 ◽  
Vol 2019 (4) ◽  
pp. 7-22
Author(s):  
Georges Bridel ◽  
Zdobyslaw Goraj ◽  
Lukasz Kiszkowiak ◽  
Jean-Georges Brévot ◽  
Jean-Pierre Devaux ◽  
...  
Keyword(s):  
Low Cost ◽  
Cost Effective ◽  
High Energy ◽  
Training System ◽  
Embedded Sensors ◽  
Pilot Training ◽  
New Approach ◽  
Combat Aircraft ◽  
Air Combat ◽  
The Cost

Abstract Advanced jet training still relies on old concepts and solutions that are no longer efficient when considering the current and forthcoming changes in air combat. The cost of those old solutions to develop and maintain combat pilot skills are important, adding even more constraints to the training limitations. The requirement of having a trainer aircraft able to perform also light combat aircraft operational mission is adding unnecessary complexity and cost without any real operational advantages to air combat mission training. Thanks to emerging technologies, the JANUS project will study the feasibility of a brand-new concept of agile manoeuvrable training aircraft and an integrated training system, able to provide a live, virtual and constructive environment. The JANUS concept is based on a lightweight, low-cost, high energy aircraft associated to a ground based Integrated Training System providing simulated and emulated signals, simulated and real opponents, combined with real-time feedback on pilot’s physiological characteristics: traditionally embedded sensors are replaced with emulated signals, simulated opponents are proposed to the pilot, enabling out of sight engagement. JANUS is also providing new cost effective and more realistic solutions for “Red air aircraft” missions, organised in so-called “Aggressor Squadrons”.

Motivating Compliance: Firm Response to Mandatory Disclosure Policies

2018 ◽  
Vol 32 (2) ◽  
pp. 103-119
Author(s):  
Colleen M. Boland ◽  
Chris E. Hogan ◽  
Marilyn F. Johnson
Keyword(s):  
Conflict Of Interest ◽  
Low Cost ◽  
Cost Effective ◽  
Data Availability ◽  
Policy Adoption ◽  
Future Research ◽  
Regulated Firms ◽  
Firm Response ◽  
Disclosure Rules ◽  
The Impact

SYNOPSIS Mandatory existence disclosure rules require an organization to disclose a policy's existence, but not its content. We examine policy adoption frequencies in the year immediately after the IRS required mandatory existence disclosure by nonprofits of various governance policies. We also examine adoption frequencies in the year of the subsequent change from mandatory existence disclosure to a disclose-and-explain regime that required supplemental disclosures about the content and implementation of conflict of interest policies. Our results suggest that in areas where there is unclear regulatory authority, mandatory existence disclosure is an effective and low cost regulatory device for encouraging the adoption of policies desired by regulators, provided those policies are cost-effective for regulated firms to implement. In addition, we find that disclose-and-explain regulatory regimes provide stronger incentives for policy adoption than do mandatory existence disclosure regimes and also discourage “check the box” behavior. Future research should examine the impact of mandatory existence disclosure rules in the year that the regulation is implemented. Data Availability: Data are available from sources cited in the text.

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