A flow diagram illustrating the marker development procedures in this study. The first stage was to make a cross to develop, then phenotype a genetic population. The second stage was to conduct NGS-based RAD sequencing on a small number (20) of plants representing the presence and absence of the gene of interest to generate large number of sequence reads, followed by bioinformatics analysis to identify SNP markers showing correlation between marker genotypes and plant phenotypes. The third stage was to convert SNP markers into simple PCR-based markers. Finally, the PCR-based markers were tested on a large segregating population to confirm the genetic linkage between the markers and the gene of interest before the markers were implemented in molecular plant breeding.
Yang et al. BMC Genomics 2012 13:318 doi:10.1186/1471-2164-13-318