Identification and validation of insertion–deletion polymorphisms in pigeonpeaS KSinghauthorS MKaleauthorR KSaxenaauthorPSinhaauthorSParupalliauthorVSuryanarayaauthorJObalaauthorC VSameer KumarauthorR KVarshneyauthorCompletely sequenced plant genomes provide scope for designing a large number of genome wide insertion–deletion (InDel) markers, which are useful in various aspects of crop breeding and genetic analysis. With the objective of developing InDel markers from pigeonpea genome, the re-sequencing data of eight MAGIC parental lines were used to identify InDels using Dindel software. As a result, a total of 102,181 InDels were identified. Of these 70158 InDels were found unique. The higher number of InDels were found in intergenic (43%) followed by upstream (26%) and downstream (24%) regions. A total of 6.93 % of Indels were found in the genic region. Out of 70158 InDels, 2,426 (1032 Insertions and 1394 deletions) with ≥20 bp size among different parental lines were selected. Average distribution of selected 2426 InDels was found 220 InDels/LG with maximum number of InDels on CcLG11 (385 InDels) and minimum number of In- Dels on CcLG05 (70 InDels). A set of 293 InDels could assess genetic diversity and establish phylogenetic relationships among 16 parental lines of different mapping populations. Validation of these primer pairs on parental lines of different mapping population resulted in higher amplification success rate (≥83%) with almost 52.04% polymorphism rate among parental lines on 3% agarose gel. The number of alleles per locus ranged from 2 to 9 with an average of 3.8 alleles. Further, to track the genome of parents in complex funnel crossing scheme of pigeonpea MAGIC population at 28-two way, 14-four way and 7-eigth way stages, we have identified unique InDel primers for each of the 8 MAGIC parents. The result showed that InDel markers with their high polymorphic potential in comparison to SSR markers would be preferred candidate markers in various marker-based applications in pigeonpea genetics and breeding.PigeonpeaGenetics and Genomics2017-02Conference or Workshop Item