Genome-wide identification of candidate phosphate starvation responsive genes and the development of intron length polymorphism markers in maize

To develop genetic markers associated with tolerance to low phosphorus, we identified candidate phosphate starvation responsive (PSR) genes and developed their intron length polymorphism (ILP) markers in maize on a genome-wide scale. Based on the known plant PSR genes, 161 candidate PSR genes were identified. Of these genes, 138 genes contained at least one intron and were then used to develop 606 PSR-ILP markers by designing PCR primers to the intron-flanking exonic regions. PCR evaluation was performed on 43 randomly selected PSR-ILP markers in 30 maize inbred lines. Of the primers, 88.4% amplified stable and pure products in all maize inbred lines, and 53.5% of the markers showed ILP, with PIC values ranging from 0.06 to 0.80. The result of clustering analysis of the 30 maize inbred lines, based on the polymorphism of 23 ILP markers, suggests that the ILP markers developed in this study are not only efficient for genetic diversity analysis but also potentially useful for marker assisted selection for tolerance to low phosphorus.