title: Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.).
abstract: Food security is a global concern and substantial yield increases in cereal crops are required to feed the growing world population. Wheat is one of the three most important crops for human and livestock feed. However, the complexity of the genome coupled with a decline in genetic diversity within modern elite cultivars has hindered the application of marker-assisted selection (MAS) in breeding programmes. A crucial step in the successful application of MAS in breeding programmes is the development of cheap and easy to use molecular markers, such as single-nucleotide polymorphisms. To mine selected elite wheat germplasm for intervarietal single-nucleotide polymorphisms, we have used expressed sequence tags derived from public sequencing programmes and next-generation sequencing of normalized wheat complementary DNA libraries, in combination with a novel sequence alignment and assembly approach. Here, we describe the development and validation of a panel of 1114 single-nucleotide polymorphisms in hexaploid bread wheat using competitive allele-specific polymerase chain reaction genotyping technology. We report the genotyping results of these markers on 23 wheat varieties, selected to represent a broad cross-section of wheat germplasm including a number of elite UK varieties. Finally, we show that, using relatively simple technology, it is possible to rapidly generate a linkage map containing several hundred single-nucleotide polymorphism markers in the doubled haploid mapping population of Avalon × Cadenza.
authors.affiliation: School of Biological Sciences, University of Bristol, Bristol, UK.
authors.forename: Alexandra M
authors.initials: AM
authors.lastname: Allen
authors.forename: Gary L A
authors.initials: GL
authors.lastname: Barker
authors.forename: Simon T
authors.initials: ST
authors.lastname: Berry
authors.forename: Jane A
authors.initials: JA
authors.lastname: Coghill
authors.forename: Rhian
authors.initials: R
authors.lastname: Gwilliam
authors.forename: Susan
authors.initials: S
authors.lastname: Kirby
authors.forename: Phil
authors.initials: P
authors.lastname: Robinson
authors.forename: Rachel C
authors.initials: RC
authors.lastname: Brenchley
authors.forename: Rosalinda
authors.initials: R
authors.lastname: D'Amore
authors.forename: Neil
authors.initials: N
authors.lastname: McKenzie
authors.forename: Darren
authors.initials: D
authors.lastname: Waite
authors.forename: Anthony
authors.initials: A
authors.lastname: Hall
authors.forename: Michael
authors.initials: M
authors.lastname: Bevan
authors.forename: Neil
authors.initials: N
authors.lastname: Hall
authors.forename: Keith J
authors.initials: KJ
authors.lastname: Edwards
mesh_terms: D000483:Alleles; D015415:Biomarkers / Q000032:analysis; D002874:Chromosome Mapping; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D015723:Gene Library; D008040:Genetic Linkage; D005838:Genotype; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D011123:Polyploidy; D016415:Sequence Alignment; D014908:Triticum / Q000235:genetics*
chemical_list: D015415:Biomarkers