SNP Discovery through Next-Generation Sequencing and Its Applications

Kumar, Santosh; Banks, Travis; Cloutier, Sylvie

doi:10.1155/2012/831460

Cited by 250 publications

(166 citation statements)

References 146 publications

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“…deer [16]. However, most of the current studies assessing phylogeny or population genetics of wild animals require only a reduced set of SNPs that are spread across the genome [7,17,18]. The commercially developed genotyping array for cattle were successfully applied in relation to the novel SNPs detection and validation on two genera from the families Cervidae; Odocoileus [19] and Rangifer [20].…”

Section: Introductionmentioning

confidence: 99%

Genomic variation across cervid species in respect to the estimation of red deer diversity

et al. 2017

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The aim of this study was to assess the genetic variations and relationships across evolutionary related cervid species in order to estimate the genetic diversity of the Red deer population that inhabits the forest area in the south-western part of Slovakia. The study was based on the application of cross-species SNP genotyping. The genomic data were obtained from a total of 86 individuals representing six genera (Axis, Dama, Cervus, Alces, Rangifer, and Odocoileus) using Illumina BovineSNP50 BeadChip. From 38.85% of successfully genotyped loci up to 1,532 SNPs showed polymorphism and were informative for subsequent analyses of the diversity and interspecifi c genetic relationships. Generally, a good level of observed heterozygosity was found across all species. The value of F IS (0.23±0.13) signalised the increase of a homozygous proportion within them. The application of molecular variance analysis to the hierarchical population structure showed that most of the variation was conserved within separate species (96%). The performed diversity analysis of Slovak Red deer population and comparative analysis of their phylogenic relationships among subspecies from genus Cervus did not identify a remarkable loss of genetic variability. Also, were not identifi ed any degree of admixture that could be due to the historical background of deer farming in Slovakia or reintroduction and hybridisation by other species from genus Cervus (C.canadensis, and C. nippon) which are the major risk of loss of autochthonous Red deer populations in many areas of Central Europe. The analysis of individual's ancestry showed consistent results with patterns of evaluated group differentiations which means low migration rates among all species.

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Section: Introductionmentioning

confidence: 99%

Genomic variation across cervid species in respect to the estimation of red deer diversity

et al. 2017

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“…Genotyping by sequencing (GBS) is a highthroughput and practical SNP discovery approach which involves sequencing of a plant population using multiplexing (bar coding) and next-generation sequencing (NGS) technologies (Kumar et al 2012). GBS can be used for SNP discovery and genotyping of plants by mapping the sequence reads of individual plants on a reference genome (Elshire et al 2011;Huang and Han 2013).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide SNP discovery and genetic linkage map construction in sunflower (Helianthus annuus L.) using a genotyping by sequencing (GBS) approach

Çelik

Bodur²,

Frary

et al. 2016

Mol Breeding

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Recently developed plant genomics approaches (LD mapping and genome-wide selection) require many molecular markers distributed throughout the plant genome. As a result, the availability of an increasing number of markers is essential for maintaining highly efficient and accurate plant breeding programs. In this study, we identified SNP loci in sunflower using a genotyping by sequencing (GBS) approach in an intraspecific F 2 mapping population. A total of 271,445,770 reads were generated by the Genome Analyzer II next-generation sequencing platform and 29.2 % of the reads were aligned to unique locations in the genome. A total of 46,278 SNP loci were identified and 7646 SNP loci were validated in an F 2 population. In addition, a SNP-based linkage map was constructed. This is the first report of SNP discovery in sunflower by GBS. The SNP markers and SNP-based linkage map will be valuable molecular genetics tools for sunflower breeding.

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“…Recently the high-throughput SNP genotyping techniques based on NGS method are used to analyze the genetic diversity (Kumar et al 2012;Shirasawa et al 2016). The NGS based advanced techniques such as genotyping-by-sequencing (GBS) (Elshire et al 2011;Poland and Rife 2012) and restriction site-associated DNA sequencing (RAD-Seq) have become popular choice for genetic analysis because they are low cost and flexible (Davey et al 2011) in experiment design.…”

Section: Introductionmentioning

confidence: 99%

Assessment of genetic diversity among four orchids based on ddRAD sequencing data for conservation purposes

Roy

Moitra

Sarker

2016

Physiol Mol Biol Plants

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SNP Discovery through Next-Generation Sequencing and Its Applications

Cited by 250 publications

References 146 publications

Genomic variation across cervid species in respect to the estimation of red deer diversity

Genomic variation across cervid species in respect to the estimation of red deer diversity

Genome-wide SNP discovery and genetic linkage map construction in sunflower (Helianthus annuus L.) using a genotyping by sequencing (GBS) approach

Assessment of genetic diversity among four orchids based on ddRAD sequencing data for conservation purposes

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