


2013 Accessing complex crop genomes with next-generation sequencing. 2010 Plant genome sequencing: applications for crop improvement. 2017 NOVOPlasty: de novo assembly of organelle genomes from whole genome data. 2011 A framework for variation discovery and genotyping using next-generation DNA sequencing data. 2011 Genome‐wide genetic marker discovery and genotyping using next‐generation sequencing. 2008 Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Methods 5, 887.Ĭronn R., Liston A., Parks M., Gernandt D. 2008 Identification of genetic variants using bar-coded multiplexed sequencing. V., Szelinger S., Sekar A., Redman M., Corneveaux J. 2018 The sequenced angiosperm genomes and genome databases. 2011 Stacks: building and genotyping Loci de novo from short-read sequences. 2009 A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. 2007 Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. 2016 SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RILs population. A., Falque M., Peterlongo P., Lhuillier E., Bouchez O. 2015 High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. 2008 Rapid SNP discovery and genetic mapping using sequenced RAD markers. 21, 961–973.Īrabidopsis Genome Initiative 2000 Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. 2011 Dindel: accurate indel calls from short-read data. The article summarizes the protocol, uses, bioinformatics tools, its application, and future prospects of skim sequencing in crop improvement.Īlbers C. The cost-effectiveness, simplicity, and genomewide coverage will increase the application of skims sequencing-based genotyping. Skim sequencing is being extensively used for genotyping in diverse plant species and has a wide range of applications, particularly in quantitative trait loci (QTL) mapping, genomewide association studies (GWAS), fine genetic map construction, and identification of recombination and gene conversion events in various breeding programmes. In the present review, we have discussed recent technological advancements, applicability, and challenges of skim sequencing-based genotypic approaches for crop improvement programmes. In this regard, skim sequencing, where low coverage whole-genome sequencing is used for the identification of large numbers of polymorphic markers cost-effectively. However, continuously lowering the cost of sequencing makes it more convenient to use whole genome-based approaches. Most of these methods are based on the reduced representation of the genome, which ultimately reduces the cost of sequencing by many folds. Numerous approaches exploring sequencing advances for genotyping have been developed over the past decade, which includes different variants of genotyping-by-sequencing (GBS), and restriction-site associated DNA sequencing (RAD-seq). High-throughput genotyping has become more convenient and cost-effective due to recent advancements in next-generation sequencing (NGS) techniques.
