Whole-genome resequencing: changing the paradigms of SNP detection, molecular mapping and gene discovery

2015 ◽  
Vol 35 (1) ◽  
Author(s):  
Xiangyang Xu ◽  
Guihua Bai
Keyword(s):  
Molecular Mapping ◽  
Gene Discovery ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Snp Detection ◽  
Whole Genome Resequencing

scholarly journals High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut

2018 ◽  
Vol 16 (11) ◽  
pp. 1954-1967 ◽  
Author(s):  
Gaurav Agarwal ◽  
Josh Clevenger ◽  
Manish K. Pandey ◽  
Hui Wang ◽  
Yaduru Shasidhar ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Candidate Gene ◽  
Genetic Map ◽  
Fine Mapping ◽  
Gene Discovery ◽  
High Density ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Whole Genome Resequencing

scholarly journals SNP detection for massively parallel whole-genome resequencing

2009 ◽  
Vol 19 (6) ◽  
pp. 1124-1132 ◽  
Author(s):  
R. Li ◽  
Y. Li ◽  
X. Fang ◽  
H. Yang ◽  
J. Wang ◽  
...  
Keyword(s):  
Massively Parallel ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Snp Detection ◽  
Whole Genome Resequencing

Genetic diversity and population structure of Tibetan sheep breeds determined by whole genome resequencing

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Lei-Lei Li ◽  
Shi-Ke Ma ◽  
Wei Peng ◽  
You-Gui Fang ◽  
Hai-Rui Duo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Sheep Breeds ◽  
Tibetan Sheep ◽  
Whole Genome Resequencing

scholarly journals Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Luciano Calderón ◽  
Nuria Mauri ◽  
Claudio Muñoz ◽  
Pablo Carbonell-Bejerano ◽  
Laura Bree ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Somatic Mutations ◽  
Clonal Propagation ◽  
Variant Calling ◽  
Vitis Vinifera L ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
Genome Resequencing ◽  
Diversity Pattern ◽  
Whole Genome Resequencing

AbstractGrapevine cultivars are clonally propagated to preserve their varietal attributes. However, genetic variations accumulate due to the occurrence of somatic mutations. This process is anthropically influenced through plant transportation, clonal propagation and selection. Malbec is a cultivar that is well-appreciated for the elaboration of red wine. It originated in Southwestern France and was introduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbec grapevines, we generated whole-genome resequencing data for four accessions with different clonal propagation records. A stringent variant calling procedure was established to identify reliable polymorphisms among the analyzed accessions. The latter procedure retrieved 941 single nucleotide variants (SNVs). A reduced set of the detected SNVs was corroborated through Sanger sequencing, and employed to custom-design a genotyping experiment. We successfully genotyped 214 Malbec accessions using 41 SNVs, and identified 14 genotypes that clustered in two genetically divergent clonal lineages. These lineages were associated with the time span of clonal propagation of the analyzed accessions in Argentina and Europe. Our results show the usefulness of this approach for the study of the scarce intra-cultivar genetic diversity in grapevines. We also provide evidence on how human actions might have driven the accumulation of different somatic mutations, ultimately shaping the Malbec genetic diversity pattern.

scholarly journals Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery

BMC Genomics ◽  
2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Paul Stothard ◽  
Jung-Woo Choi ◽  
Urmila Basu ◽  
Jennifer M Sumner-Thomson ◽  
Yan Meng ◽  
...  
Keyword(s):  
Holstein Cattle ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Whole Genome Resequencing

scholarly journals Genetic dissection of natural variation in oilseed traits of camelina by whole‐genome resequencing and QTL mapping

2021 ◽  
Author(s):  
Huang Li ◽  
Xiao Hu ◽  
John T. Lovell ◽  
Paul P. Grabowski ◽  
Sujan Mamidi ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Natural Variation ◽  
Whole Genome ◽  
Genetic Dissection ◽  
Genome Resequencing ◽  
Whole Genome Resequencing

scholarly journals Whole-Genome Resequencing Points to Candidate DNA Loci Affecting Body Temperature under Cold Stress in Siberian Cattle Populations

Life ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 959
Author(s):  
Alexander Igoshin ◽  
Nikolay Yudin ◽  
Ruslan Aitnazarov ◽  
Andrey A. Yurchenko ◽  
Denis M. Larkin
Keyword(s):  
Body Temperature ◽  
Cold Stress ◽  
Candidate Snps ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Functional Annotations ◽  
Cold Environments ◽  
Cold Tolerant ◽  
Cold Sensitive ◽  
Whole Genome Resequencing

Despite the economic importance of creating cold resilient cattle breeds, our knowledge of the genetic basis of adaptation to cold environments in cattle is still scarce compared to information on other economically important traits. Herein, using whole-genome resequencing of animals showing contrasting phenotypes on temperature maintenance under acute cold stress combined with the existing SNP (single nucleotide polymorphism) functional annotations, we report chromosomal regions and candidate SNPs controlling body temperature in the Siberian cattle populations. The SNP ranking procedure based on regional FST calculations, functional annotations, and the allele frequency difference between cold-tolerant and cold-sensitive groups of animals pointed to multiple candidate genes. Among these, GRIA4, COX17, MAATS1, UPK1B, IFNGR1, DDX23, PPT1, THBS1, CCL5, ATF1, PLA1A, PRKAG1, and NR1I2 were previously related to thermal adaptations in cattle. Other genes, for example KMT2D and SNRPA1, are known to be related to thermogenesis in mice and cold adaptation in common carp, respectively. This work could be useful for cattle breeding strategies in countries with harsh climates, including the Russian Federation.

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