Identification and validation of insertion?deletion polymorphisms in pigeonpea uri icon


  • Completely sequenced plant genomes provide scope for designinga large number of genome wide insertion?deletion (InDel)markers, which are useful in various aspects of crop breeding andgenetic analysis. With the objective of developing InDel markersfrom pigeonpea genome, the re-sequencing data of eight MAGICparental lines were used to identify InDels using Dindel software.As a result, a total of 102,181 InDels were identified. Of these70158 InDels were found unique. The higher number of InDelswere found in intergenic (43%) followed by upstream (26%)and downstream (24%) regions. A total of 6.93 % of Indels werefound in the genic region. Out of 70158 InDels, 2,426 (1032 Insertionsand 1394 deletions) with ?20 bp size among differentparental lines were selected. Average distribution of selected2426 InDels was found 220 InDels/LG with maximum numberof InDels on CcLG11 (385 InDels) and minimum number of In-Dels on CcLG05 (70 InDels). A set of 293 InDels could assessgenetic diversity and establish phylogenetic relationships among16 parental lines of different mapping populations. Validation ofthese primer pairs on parental lines of different mapping populationresulted in higher amplification success rate (?83%) withalmost 52.04% polymorphism rate among parental lines on 3%agarose gel. The number of alleles per locus ranged from 2 to9 with an average of 3.8 alleles. Further, to track the genomeof parents in complex funnel crossing scheme of pigeonpeaMAGIC population at 28-two way, 14-four way and 7-eigth waystages, we have identified unique InDel primers for each of the8 MAGIC parents. The result showed that InDel markers withtheir high polymorphic potential in comparison to SSR markerswould be preferred candidate markers in various marker-basedapplications in pigeonpea genetics and breeding

publication date

  • 2017