Construction of interspecific genetic linkage map of pigeonpea using SCoT, RAPD, ISSR markers and simple inherited trait loci

An interspecific genetic linkage map of pigeonpea (2n=2x=22) has been constructed with 31 SCoT (start codon targeted polymorphism), 148 RAPD (random amplified polymorphic DNA), six ISSR (inter simple sequence repeat) and six trait loci controlling plant habit (PTY), seed hilum (SHM), density of non glandular short trichome (NGST), resistance to pod borer (PPB1), resistance to plume moth (PPM1), resistance to blue butterfly (PBB1) using 116 interspecific F-2 progenies derived from a cross of Cajanus cajan (cv. ICP-26) and C. scarabaeoides (acc. ICPW-94). These 191 markers were mapped into 11 linkage groups (LGs), varying between 320.63 and 43.38 cM and covering 1624.71 cM of the genome with an average marker interval of 8.51 cM. Four loci (PBB1, PPB1, NGST, PPM1) contributing resistance to pod borer complex were mapped to LG-2 as cluster and were flanked by OPB07(860) (12.9 cM) and OPA09(910) (12.5 cM). Likewise, the loci PTY and SHM were mapped to LG-1, and LG-7, respectively. The locus PTY flanked by OPB01(1580) (3.1 cM) and OPF02(1095) (3.5 cM), and the locus SHM was linked to OPE09(1110) with recombination fraction 0.258 (28.5 cM).