scholarly journals Genome-wide sequence variations between wild and cultivated tomato species revisited by whole genome sequence mapping

BMC Genomics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Kamlesh Kumar Sahu ◽  
Debasis Chattopadhyay
Keyword(s):  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Sequence Mapping ◽  
Tomato Species ◽  
Genome Wide ◽  
Sequence Variations

scholarly journals Linkage disequilibrium maps for European and African populations constructed from whole genome sequence data

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Alejandra Vergara-Lope ◽  
M. Reza Jabalameli ◽  
Clare Horscroft ◽  
Sarah Ennis ◽  
Andrew Collins ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Genome Sequence ◽  
Sequence Data ◽  
Association Studies ◽  
Large Population ◽  
Whole Genome Sequence ◽  
European Ancestry ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Genome Wide

Abstract Quantification of linkage disequilibrium (LD) patterns in the human genome is essential for genome-wide association studies, selection signature mapping and studies of recombination. Whole genome sequence (WGS) data provides optimal source data for this quantification as it is free from biases introduced by the design of array genotyping platforms. The Malécot-Morton model of LD allows the creation of a cumulative map for each choromosome, analogous to an LD form of a linkage map. Here we report LD maps generated from WGS data for a large population of European ancestry, as well as populations of Baganda, Ethiopian and Zulu ancestry. We achieve high average genetic marker densities of 2.3–4.6/kb. These maps show good agreement with prior, low resolution maps and are consistent between populations. Files are provided in BED format to allow researchers to readily utilise this resource.

scholarly journals Imputation to whole-genome sequence using multiple pig populations and its use in genome-wide association studies

2019 ◽  
Vol 51 (1) ◽  
Author(s):  
Sanne van den Berg ◽  
Jérémie Vandenplas ◽  
Fred A. van Eeuwijk ◽  
Aniek C. Bouwman ◽  
Marcos S. Lopes ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Association Studies ◽  
Genome Wide Association ◽  
Whole Genome Sequence ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Genome Wide

scholarly journals CircosVCF: circos visualization of whole-genome sequence variations stored in VCF files

2017 ◽  
Vol 33 (9) ◽  
pp. 1392-1393 ◽  
Author(s):  
E Drori ◽  
D Levy ◽  
P Smirin-Yosef ◽  
O Rahimi ◽  
M Salmon-Divon
Keyword(s):  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Sequence Variations

A genome-wide resource of intron spanning primers compatible for quantitative PCR and intron length polymorphism in rice

2019 ◽  
Vol 79 (02) ◽  
Author(s):  
Humira Sonah ◽  
Hasthi Ram ◽  
Bikram Pratap Singh ◽  
Jawaharlal Katara ◽  
Radha Chopra ◽  
...  
Keyword(s):  
Quantitative Pcr ◽  
Genome Sequence ◽  
Sequence Variation ◽  
Whole Genome Sequence ◽  
Pcr Analysis ◽  
Sequence Information ◽  
Whole Genome ◽  
Intron Length Polymorphism ◽  
Genome Wide ◽  
A Genome

Whole genome sequence availability in rice has provided several advantages for genomics as well as other omics assisted applications. Genome-wide molecular markers are one of such availability that has exceptional importance in modern plant breeding. In the present study, a resource of intron-spanning primers (ISPs) was developed using whole genome sequence information of two rice subspecies, japonica (cv. Nipponbare) and indica (cv. 93-11). The ISPs were designed in a way that the PCR using a cDNA template will yield 60 to 100 base pair size amplicon ideal for the quantitative PCR analysis. Whereas, PCR using genomic DNA will amplify the introns, which are more prone to sequence variation. The sequence variation in the intron serves as an excellent marker resource. The application of ISPs was demonstrated by characterizing 12 diverse rice cultivars. A total of eight out of ten ISPs were found to be polymorphic. The resource will be helpful for the rice molecular biologist and breeder community.

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