Development and utility of PCR-based intron polymorphism markers in sorghum [Sorghum bicolor (L.) Moench]

Abstract

Sequence variations involving DNA insertions and deletions within introns provide suitable targets for the development of PCR-based markers. In this study, 37861 potential introns were identified in sorghum and primers were designed to develop intron length polymorphism (ILP) markers. Drastic variation was observed in the number of ILP markers on each chromosome with a range of 1498 (chr. 5) - 7290 (chr. 1), which was also reflected in the fluctuations in their density. About 200 ILP markers were assessed for their potential as PCR-based markers in 24 sorghum genotypes representing different races. Of these, 172 gave clear and robust amplification without multiple amplicons. Forty-eight of these markers were polymorphic yielding 122 alleles with an average of 2.5 alleles per marker. The number of alleles ranged from 2 to 6 while the PIC value ranged from 0.14 to 0.69. Cluster analysis grouped the genotypes into two major clusters. These markers would form an important addition to the existing DNA marker resources in sorghum and could be highly useful for genetic diversity analysis, construction of linkage maps and comparative genomics studies.