Bioinformatics: identification of markers from next-generation sequence data.
With the advent of sequencing technology, next-generation sequencing (NGS) technology has dramatically revolutionized plant genomics. 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. This chapter discusses various tools available for genome assembly and widely focuses on SSR and SNP marker discovery.
School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia.
Pradeep
P
Ruperao
David
D
Edwards
D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D005819:Genetic Markers; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D018895:Microsatellite Repeats / Q000235:genetics; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D014908:Triticum / Q000235:genetics
D005819:Genetic Markers