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

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• 作者：Annemarie Bungartz ; Marius Klaus ; Boby Mathew ; Jens Lé ; on ; Ali Ahmad Naz ; ^{a.naz@uni-bonn.de" class="auth_mail" title="E-mail the corresponding author}
• 关键词：SNP ; single nucleotide polymorphism ; CAPS ; cleaved amplified polymorphic sequence ; PCR ; polymerase chain reaction
• 刊名：Genomics
• 出版年：2016
• 出版时间：March 2016
• 年：2016
• 卷：107
• 期：2-3
• 页码：100-107
• 全文大小：1596 K

文摘

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 991 cM with an average marker density of 5.09 cM. 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.