By Jacqueline Batley
ISBN-10: 1493919652
ISBN-13: 9781493919659
ISBN-10: 1493919660
ISBN-13: 9781493919666
The skill to supply tremendous quantities of DNA series info has enabled the invention of molecular markers in version organisms, vegetation, in addition to orphan species making genotyping the speed restricting issue, and this quantity makes a speciality of different markers on hand and the low to excessive throughput genotyping of those markers. Given the various nature of a few of those platforms, an outline is equipped at the id of markers from series facts, in addition to facts research with instance purposes as soon as the genotyping facts has been generated. Written within the profitable Methods in Molecular Biology sequence structure, chapters contain introductions to their respective issues, lists of the required fabrics and reagents, step by step, quite simply reproducible protocols, and notes on troubleshooting and averting identified pitfalls.
Authoritative and simply obtainable, Plant Genotyping: equipment and Protocols is geared toward plant molecular biologists, geneticists, plant breeders and ecologists who've a objective query and wish to understand the main compatible markers and genotyping approach to use.
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Additional info for Plant Genotyping: Methods and Protocols
Example text
NGS technology combined with new software tools enables the discovery, validation, and assessment of genetic markers on a large scale. Among different markers systems, simple sequence repeats (SSRs) and Single nucleotide polymorphisms (SNPs) are the markers of choice for genetics and plant breeding. SSR markers have been a choice for large-scale characterization of germplasm collections, construction of genetic maps, and QTL identification. Similarly, SNPs are the most abundant genetic variations with higher frequencies throughout the genome of plant species.
36 Pradeep Ruperao and David Edwards Slider II calls SNPs when the confidence accumulated from the aligned reads is higher than confidence of the base in the reference genome. For recalibration of per-base quality scores, programs such as GATK [85] or SOAPsnp [86] are recommended. Samtools is a package used to manipulate NGS alignment, which includes the computation of genotype likelihoods (samtools) and SNP and genotype calling (bcftools). GATK can be used for NGS data alignment, SNP and genotype calling (Unifed Genotyper), SNP filtering, and SNP quality recalibration (Variant Recalibrator).
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Plant Genotyping: Methods and Protocols by Jacqueline Batley
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