title: Development of new SNP derived cleaved amplified polymorphic sequence marker set and its successful utilization in the genetic analysis of seed color variation in barley.
abstract: The aim of the present study was to develop a new cost effective PCR based CAPS marker set using advantages of high-throughput SNP genotyping. Initially, SNP survey was made using 20 diverse barley genotypes via 9k iSelect array genotyping that resulted in 6334 polymorphic SNP markers. Principle component analysis using this marker data showed fine differentiation of barley diverse gene pool. Till this end, we developed 200 SNP derived CAPS markers distributed across the genome covering around 991cM with an average marker density of 5.09cM. Further, we genotyped 68 CAPS markers in an F2 population (Cheri×ICB181160) segregating for seed color variation in barley. Genetic mapping of seed color revealed putative linkage of single nuclear gene on chromosome 1H. These findings showed the proof of concept for the development and utility of a newer cost effective genomic tool kit to analyze broader genetic resources of barley worldwide.
authors.affiliation: University of Bonn, Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, Katzenburgweg 5, 53115 Bonn, Germany.
authors.forename: Annemarie
authors.initials: A
authors.lastname: Bungartz
authors.affiliation: University of Bonn, Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, Katzenburgweg 5, 53115 Bonn, Germany.
authors.forename: Marius
authors.initials: M
authors.lastname: Klaus
authors.affiliation: University of Bonn, Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, Katzenburgweg 5, 53115 Bonn, Germany.
authors.forename: Boby
authors.initials: B
authors.lastname: Mathew
authors.affiliation: University of Bonn, Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, Katzenburgweg 5, 53115 Bonn, Germany.
authors.forename: Jens
authors.initials: J
authors.lastname: Léon
authors.affiliation: University of Bonn, Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, Katzenburgweg 5, 53115 Bonn, Germany. Electronic address: a.naz@uni-bonn.de.
authors.forename: Ali Ahmad
authors.initials: AA
authors.lastname: Naz
mesh_terms: D054458:Amplified Fragment Length Polymorphism Analysis / Q000191:economics / Q000379:methods*; D032461:Chromosomes, Plant / Q000235:genetics; D008040:Genetic Linkage; D001467:Hordeum / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D012639:Seeds / Q000502:physiology
keywords: Barley; CAPS marker set; Molecular markers; SNP; Seed color