A method for discovery of genome-wide SNP between any two genotypes from whole-genome re-sequencing data.
Advances in sequencing technologies have aided the discovery of millions of genome-wide DNA polymorphisms such as single-nucleotide polymorphisms (SNPs) and insertion-deletions (InDels) which are an invaluable resource for marker-assisted breeding. Presently available bioinformatics tools assist the discovery of polymorphisms between target genotypes and the reference genome for a range of species. The discovery of polymorphisms between two genotypes within a breeding program is complicated by several factors such as bias in the number of reads from each genotype and residual heterozygosity within each genotype. In this chapter, we describe a novel approach where polymorphisms between a pair of genotypes are discovered from whole-genome re-sequencing data.
Division of Genetics, Indian Agricultural Research Institute, New Delhi, India.
S Gopala
SG
Krishnan
Daniel L E
DL
Waters
Robert J
RJ
Henry
D019295:Computational Biology / Q000379:methods*; D016678:Genome; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D054643:INDEL Mutation; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods