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Full Description
The ability to produce vast amounts of DNA sequence data has enabled the discovery of molecular markers in model organisms, crops, as well as orphan species making genotyping the rate limiting factor, and this volume focuses on the different markers available and the low to high throughput genotyping of these markers. Given the diverse nature of some of these systems, an overview is provided on the identification of markers from sequence data, as well as data analysis with example applications once the genotyping data has been generated. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls.
Authoritative and easily accessible, Plant Genotyping: Methods and Protocols is aimed at plant molecular biologists, geneticists, plant breeders and ecologists who have a target question and need to know the most suitable markers and genotyping system to use.
Contents
Advances in Plant Genotyping - Where the Future Will Take Us.- Molecular Marker Applications in Plants.- Bioinformatics: Identification of Markers from Next Generation Sequence Data.- Molecular Marker Databases.- Plant Genotyping Using Fluorescently Tagged Inter Simple Sequence Repeats (ISSRs): Basic Principles and Methodology.- SSR Genotyping.- Genotyping Analysis Using an RFLP Assay.- DNA Barcoding for Plants.= Multiplexed Digital Gene Expression Analysis for Genetical Genomics in Large Plant Populations.- SNP Genotyping by Heteroduplex Analysis.- Application of the High-Resolution Melting Technique for Gene Mapping and SNP Detection in Plants.- Challenges of Genotyping Polyploid Species.- Genomic Reduction Assisted Single Nucleotide Polymorphism Discovery using 454-Pyrosequencing.- Inter-SINE Amplified Polymorphism (ISAP) for Rapid and Robust Plant Genotyping.- Screening of Mutations by TILLING in Plants.- Gene Analysis Using Mass Spectrometric Cleaved Amplified Polymorphic Sequence (MS-CAPS) with Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALSI-TOF).- Quantitative SNP Genotyping of Polyploids with MassARRAY and Other Platforms.- SNP Genotyping using KASPar Assays.- Skim Based Genotyping by Sequencing.- The Restriction Enzyme Target Approach to Genotyping by Sequencing (GBS).- Methods for the Design, Implementation and Analysis of Illumina Infinium™ SNP Assays in Plants.- Use of the Illumina GoldenGate Assay for Single Nucleotide Polymorphism (SNP) Genotyping in Cereal Crops.
