Open AccessMultiplex single nucleotide polymorphism (SNP)‐based genotyping in allohexaploid wheat using padlock probes
Author(s) -
Edwards Keith J.,
Reid Alex L.,
Coghill Jane A.,
Berry Simon T.,
Barker Gary L. A.
Publication year - 2009
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/j.1467-7652.2009.00413.x
Subject(s) - biology , polyploid , genetics , genotyping , single nucleotide polymorphism , genome , snp genotyping , multiplex , snp , genotype , computational biology , gene
Summary Single nucleotide polymorphisms are the most common polymorphism in plant and animal genomes and, as such, are the logical choice for marker‐assisted selection. However, many plants are also polyploid, and marker‐assisted selection can be complicated by the presence of highly similar, but non‐allelic, homoeologous sequences. Despite this, there is practical and academic demand for high‐throughput genotyping in several polyploid crop species, such as allohexaploid wheat. In this paper, we present such a system, which utilizes public single nucleotide polymorphisms previously identified in both agronomically important genes and in randomly selected, mapped, expressed sequence tags developed by the wheat community. To achieve relatively high levels of multiplexing, we used non‐amplified genomic DNA and padlock probe pairs, together with high annealing temperatures, to differentiate between similar sequences in the wheat genome. Our results suggest that padlock probes are capable of discriminating between homoeologous sequences and hence can be used to efficiently genotype wheat varieties.