A method for discovery of genome-wide SNP between any two genotypes from whole-genome re-sequencing data

S. Gopala Krishnan, Daniel L.E. Waters, Robert J. Henry

Research output: Book chapter/Published conference paperChapter in textbook/reference book

Abstract

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.
Original languageEnglish
Title of host publicationCereal genomics
Subtitle of host publicationMethods and protocols
EditorsR. Henry, A. Furtado
Place of PublicationTotowa, NJ
PublisherHumana Press Inc.
Chapter24
Pages287-294
Number of pages8
Volume1099
ISBN (Electronic)9781627037150
ISBN (Print)9781627037143
DOIs
Publication statusPublished - 2014

Publication series

NameMethods in Molecular Biology
Volume1099
ISSN (Print)1064-3745

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    Gopala Krishnan, S., Waters, D. L. E., & Henry, R. J. (2014). A method for discovery of genome-wide SNP between any two genotypes from whole-genome re-sequencing data. In R. Henry, & A. Furtado (Eds.), Cereal genomics: Methods and protocols (Vol. 1099, pp. 287-294). (Methods in Molecular Biology; Vol. 1099). Humana Press Inc.. https://doi.org/10.1007/978-1-62703-715-0_24