scholarly journals BAC Libraries from Wheat Chromosome 7D: Efficient Tool for Positional Cloning of Aphid Resistance Genes

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Hana Šimková ◽  
Jan Šafář ◽  
Marie Kubaláková ◽  
Pavla Suchánková ◽  
Jarmila Číhalíková ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Positional Cloning ◽  
Cost Effective ◽  
Wheat Chromosome ◽  
Aphid Resistance ◽  
Insert Size ◽  
High Coverage ◽  
Bac Libraries ◽  
Greenbug Resistance ◽  
Targeted Approach

Positional cloning in bread wheat is a tedious task due to its huge genome size and hexaploid character. BAC libraries represent an essential tool for positional cloning. However, wheat BAC libraries comprise more than million clones, which makes their screening very laborious. Here, we present a targeted approach based on chromosome-specific BAC libraries. Such libraries were constructed from flow-sorted arms of wheat chromosome 7D. A library from the short arm (7DS) consisting of 49,152 clones with 113 kb insert size represented 12.1 arm equivalents whereas a library from the long arm (7DL) comprised 50,304 clones of 116 kb providing 14.9x arm coverage. The 7DS library was PCR screened with markers linked to Russian wheat aphid resistance geneDnCI2401, the 7DL library was screened by hybridization with a probe linked to greenbug resistance geneGb3. The small number of clones combined with high coverage made the screening highly efficient and cost effective.

scholarly journals Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 899
Author(s):  
Fotis Pappas ◽  
Christos Palaiokostas
Keyword(s):  
Genetic Diversity ◽  
Salvelinus Alpinus ◽  
Arctic Charr ◽  
Cost Effective ◽  
Limiting Factors ◽  
Phenotypic Traits ◽  
Production Volume ◽  
High Coverage ◽  
Genomic Relationships ◽  
Low Coverage

Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding.

scholarly journals Is an integrated model of school eye health delivery more cost-effective than a vertical model? An implementation research in Zanzibar

2021 ◽  
Vol 6 (1) ◽  
pp. e000561
Author(s):  
Ving Fai Chan ◽  
Fatma Omar ◽  
Elodie Yard ◽  
Eden Mashayo ◽  
Damaris Mulewa ◽  
...  
Keyword(s):  
Implementation Research ◽  
Cost Savings ◽  
Cost Effective ◽  
Integrated Model ◽  
Health Screening ◽  
High Coverage ◽  
Health Delivery ◽  
Screening Cost ◽  
Eye Health ◽  
The Cost

ObjectiveTo review and compare the cost-effectiveness of the integrated model (IM) and vertical model (VM) of school eye health programme in Zanzibar.Methods and analysisThis 6-month implementation research was conducted in four districts in Zanzibar. Nine and ten schools were recruited into the IM and VM, respectively. In the VM, teachers conducted eye health screening and education only while these eye health components were added to the existing school feeding programme (IM). The number of children aged 6–13 years old screened and identified was collected monthly. A review of project account records was conducted with 19 key informants. The actual costs were calculated for each cost categories, and costs per child screened and cost per child identified were compared between the two models.ResultsScreening coverage was 96% and 90% in the IM and VM with 297 children (69.5%) from the IM and 130 children (30.5%) from VM failed eye health screening. The 6-month eye health screening cost for VM and IM was US$6 728 and US$7 355. The cost per child screened for IM and VM was US$1.23 and US$1.31, and the cost per child identified was US$24.76 and US$51.75, respectively.ConclusionBoth models achieved high coverage of eye health screening with the IM being a more cost-effective school eye health delivery screening compared with VM with great opportunities for cost savings.

Cost Effective Swath Bathymetry

2001 ◽  
Vol 35 (4) ◽  
pp. 33-45 ◽  
Author(s):  
Peter Hogarth
Keyword(s):  
Processing Time ◽  
Cost Effective ◽  
High Accuracy ◽  
High Coverage ◽  
Swath Bathymetry ◽  
World Survey ◽  
Set Up ◽  
Very High ◽  
Harbor Area ◽  
Wide Swath

Between 23rd and 25th July 2001 GeoSwath, a high specification shallow water wide swath bathymetry system, was used to survey the entire Portsmouth NH Harbor area. This paper deals with the results of this survey, illustrating the potential for significant reductions in the high costs, which have prevented widespread proliferation of Swath Bathymetry systems to date. Data, including a complete DTM gridded to 1 m resolution, will be presented and discussed in detail. These results show that the system is very easy to set up and use, requires greatly reduced boat and processing time, whilst offering high accuracy and very high coverage and resolution when used in a real-world survey of a dynamic harbor environment.

scholarly journals Aphid Resistance in Medicago truncatula Involves Antixenosis and Phloem-Specific, Inducible Antibiosis, and Maps to a Single Locus Flanked by NBS-LRR Resistance Gene Analogs

2005 ◽  
Vol 137 (4) ◽  
pp. 1445-1455 ◽  
Author(s):  
John Klingler ◽  
Robert Creasy ◽  
Lingling Gao ◽  
Ramakrishnan M. Nair ◽  
Alonso Suazo Calix ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Medicago Truncatula ◽  
Aphid Resistance ◽  
Single Locus ◽  
Resistance Gene Analogs

scholarly journals 230 Genome editing applications in plants: high-throughput CRISPR/Cas editing for crop improvement

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 56-56
Author(s):  
Michael Thomson
Keyword(s):  
Genome Editing ◽  
High Throughput ◽  
Positional Cloning ◽  
Gene Editing ◽  
Crop Improvement ◽  
Cost Effective ◽  
Gene Families ◽  
Ease Of Use ◽  
Plant Genome ◽  
Wide Range

Abstract The precision and ease of use of CRISPR nucleases, such as Cas9 and Cpf1, for plant genome editing has the potential to accelerate a wide range of applications for crop improvement. For upstream research on gene discovery and validation, rapid gene knock-outs can enable testing of single genes and multi-gene families for functional effects. Large chromosomal deletions can test the function of tandem gene arrays and assist with positional cloning of QTLs by helping to narrow down the target region. Nuclease-deactivated Cas9 fusion proteins with transcriptional activators and repressors can be used to up and down-regulate gene expression. Even more promising, gene insertions and allele replacements can provide the opportunity to rapidly test the effects of different alleles at key loci in the same genetic background, providing a more precise alternative to marker-assisted backcrossing. Recently, Texas A&M AgriLife Research has supported the development of a Crop Genome Editing Lab at Texas A&M working towards optimizing a high-throughput gene editing pipeline and providing an efficient and cost-effective gene editing service for research and breeding groups. The lab is using rice as a model to test and optimize new approaches aimed towards overcoming current bottlenecks. For example, a wealth of genomics data from the rice community enables the development of novel approaches to predict which genes and target modifications may be most beneficial for crop improvement, taking advantage of known major genes, high-resolution GWAS data, multiple high-quality reference genomes, transcriptomics data, and resequencing data from the 3,000 Rice Genomes Project. Current projects have now expanded to work across multiple crops to provide breeding and research groups with a rapid gene editing pipeline to test candidate genes in their programs, with the ultimate goal of developing nutritious, high-yielding, stress-tolerant crops for the future.

scholarly journals Accessing a Russian Wheat Aphid Resistance Gene in Bread Wheat by Long‐Read Technologies

2019 ◽  
Vol 12 (2) ◽  
pp. 180065 ◽  
Author(s):  
Zuzana Tulpová ◽  
Helena Toegelová ◽  
Nora L. V. Lapitan ◽  
Frank B. Peairs ◽  
Jiří Macas ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Bread Wheat ◽  
Russian Wheat Aphid ◽  
Aphid Resistance ◽  
Long Read
Sign in / Sign up

Export Citation Format

Share Document