309 The Korean Society of Crop Science J. Crop Sci. Biotech. 2015 (December) 18 (5) : 309 ~ 318 RESEARCH ARTICLE DOI No. 10.1007/s12892-015-0015-y Development and Utility of PCR-based Intron Polymorphism Markers in Sorghum [ Sorghum bicolor (L.) Moench] Inapakurti Jaikishan, Passoupathy Rajendrakumar * , Ragimasalawada Madhusudhana, Maruthamuthu Elangovan, Jagannath Vishnu Patil ICAR - Indian Institute of Millets Research, Rajendranagar, Hyderabad 500030, Telangana State, India Received: February 10, 2015 / Revised: July 21, 2015 / Accepted: July 28, 2015 Ⓒ Korean Society of Crop Science and Springer 2015 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 mark- ers 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, construc- tion of linkage maps and comparative genomics studies. Key words : genetic diversity, length polymorphism, PCR-based markers, potential introns, sorghum DNA sequence variations have been exploited for the development of molecular markers, which are employed in various genetics and breeding applications such as linkage map construction, QTL mapping, genetic diversity assess- ment, hybrid purity testing, and marker-assisted selection. Among the array of molecular markers available, PCR-based markers are mostly preferred by researchers due to their sim- plicity, easy assay, and lower costs as compared to other markers systems. Genic molecular markers are becoming more popular since an enormous number of genes as well as transcript sequences of some economically important crop species are available in the public domain (Varshney et al. 2009). These markers have several inherent advantages over random DNA markers (Varshney et al. 2007) as they help in the identification of ‘perfect marker’ for marker-assisted selection (MAS), estimation of functional genetic diversity among germplasm lines, comparative mapping among the related species, and identification of chromosomal duplica- tion events (Gujaria et al. 2011). The majority of eukaryotic genes possesses introns, which are widespread, abundant, and variable (Deutsch and Long 1999; Hawkins 1988). Introns are non-coding regions of a gene that are transcribed into mRNA but not translated since they are spliced out during pre-mRNA processing. Introns are less conserved and accumulate more number of mutations than exon regions (Kahl 2015). Such variations in intron sequences can be exploited as genetic markers (Presgraves 2006). Variations in introns occur as single nucleotide poly- morphisms and/or length polymorphisms, which can be Introduction Passoupathy Rajendrakumar ( ) Email: rajendra@millets.res.in Tel: +91-40-24599326 Fax: +91-040-24599304 Electronic supplementary material The online version of this article (DOI No. 10.1007/s12892-015-0015-y) contains supplemen- tary material, which is available to authorized users.