Identification of a non-redundant set of 202 in silico SSR markers and applicability of a select set in chickpea (Cicer arietinum L.) Gaurav AgarwalMurali M. SabbavarapuVikas K. SinghMahendar Thudi • S. SheelamaryPooran M. GaurRajeev K. Varshney

The paucity of sequence information flanking the simple sequence repeat (SSR) motifs identified especially in the transcript sequences has been limiting factor in the development of SSR markers for plant genome analysis as well as breeding applications. To overcome this and enhance the genic SSR marker repertoire in chickpea, the draft genome sequence of kabuli chickpea (CDC Frontier) and publicly available transcript sequences consisting of in silico identified SSR motifs were deployed in the present study. In this direction, the 300 bp sequence flankingtheSSRmotifswereretrieved byaligning566 SSR containing transcripts of ICCV 2 available in publicdomainonthereferencechickpeagenome.Aset of 202 novel genic SSRs were developed from a set of 507 primer pairs designed, based on in silico amplifi- cation of single locus and having no similarity to the publiclyavailableSSRmarkers.Further,40genicSSRs equally distributed on chickpea genome were validated on a select set of 44 chickpea genotypes (including 41 Cicer arietinum and 3 Cicer reticulatum), out of which 25werereportedtobepolymorphic.Thepolymorphism information content (PIC) value of 25 polymorphic genic SSRs ranged from 0.11 to 0.77 and number of alleles varied from 2 to 9. Clear demarcation among founder lines of multi-parent advanced generation inter-cross(MAGIC)populationdevelopedatICRISAT and near-isogenic nature of JG 11 and JG11 ? demon- strates the usefulness of these markers in chickpea diversity analysis and breeding studies. Further, genic polymorphicSSRsreportedbetweenparentallinesof16 different mapping populations along with the novel SSRs can be deployed for trait mapping and breeding applications in chickpea.