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5 results for “RAD capture”
Data from: Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs
<p><i><span>Background</span></i></p> <p><span>The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in <i>de-novo</i> genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (<i>Penaeus monodon</i>) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq).</span></p> <p><i><span>Results</span></i></p> <p><span>Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7,542 high-quality SNPs were retained. From these, 4,236 high-quality genome-wide loci were selected for bates-probe development and 4,194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 </span>± 14.7 to 93.0% ± 3.5%<span>), </span>increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7<span>), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches.</span></p> <p><i><span>Conclusion</span></i></p> <p><span>Importantly, this assay equips the <em>P. monodon</em> industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as <em>P. monodon</em> breeding programs transition to undertaking genomic selection.</span></p>
Data from: Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs
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Data from: HyRAD-X, a versatile method combining exome capture and RAD sequencing to extract genomic information from ancient DNA
Over the last decade, protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been widely developed. Their use is however limited to DNA of relatively high molecular weight. During the last year, several methods exploiting hybridization capture using probes based on RAD-sequencing loci have circumvented this limitation and opened avenues to the study of samples characterized by degraded DNA, such as historical specimens. Here, we present a major update to those methods, namely Hybridization capture from RAD-derived probes obtained from a reduced eXome template (hyRAD-X), a technique applying RAD-sequencing to messenger RNA from one or few fresh specimens to elaborate bench-top produced probes, i.e., a reduced representation of the exome, further used to capture homologous DNA from a samples set. In contrast to previous hybridization-capture methods, the reference catalog on which reads are aligned does not rely on de novo assembly of anonymous RAD-sequencing loci, but on an assembled transcriptome obtained from RNAseq data, thus increasing the accuracy of loci definition and Single-Nucleotide-Polmorphisms (SNP) call, and targeting, specifically, expressed genes. Finally, the capture step of hyRAD-X relies on RNA probes, increasing stringency of hybridization, making it well suited for low-content DNA samples. As a proof of concept, we applied hyRAD-X to subfossil needles from the coniferous tree Abies alba, collected in lake sediments (Origlio, Switzerland) and dating back from 7200-5800 years before present (BP). More specifically we investigated genetic variation before, during, and after an anthropogenic perturbation that caused an abrupt decrease in Abies alba population size, 6500-6200 years BP. HyRAD-X produced a matrix encompassing 524 exome-derived SNPs. Despite a lower observed heterozygosity was observed during the 6.500-6.200 years BP time slice, genetic composition was nearly identical before and after the perturbation, indicating that re-expansion of the population after the decline was driven by autochthonous specimens. To the best of our knowledge, this is the first time a population genomic study incorporating ancient DNA samples of tree subfossils is conducted at a moderate cost using reproducible exome-reduced complexity.
Data from: HyRAD-X, a versatile method combining exome capture and RAD sequencing to extract genomic information from ancient DNA
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Data from: Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens
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