Assessment of AFLP marker based genetic diversity in chilli <span style="mso-bidi-font-size:12.0pt" lang="EN-US">(<i style="mso-bidi-font-style: normal">Capsicum annuum</i><span style="mso-bidi-font-style:italic"> L. & <i style="mso-bidi-font-style:normal">C. baccatum</i><span style="mso-bidi-font-style: italic"> L.) </span></span></span>

49-54Chilli (Capsicum annuum L.) is a leading spice cum vegetable crop grown commercially in India. Selection of parents is one of the important steps in hybrid breeding programme. The efficiency of hybrid breeding programme could be increased if the inbred lines per se could be screened for genetic diversity using molecular markers. The present study was conducted to assess the amplified fragment length polymorphism (AFLP) marker based diversity in 59 (3 <i style="mso-bidi-font-style: normal">C. baccatum L. and 56 C. annuum) chilli genotypes during 2009 at University of Agricultural Sciences (UAS), Bangalore. The 8 AFLP primer combinations generated a total of 414 amplicons, of which 389 were polymorphic with an average of 48.62 bands. The primer combination, EcoRI+AGC and MseI+GCT was found to amplify a highest number of 81 scorable bands with 97.53 per cent polymorphic bands. The PIC (polymorphic information content) values ranged from 0.84 to 0.97 with a mean of 0.93. All C. baccatum species (PBC 1752, PBC 80 and susceptible baccutum) were grouped in cluster I and other 56 chilli genotypes (C. annuum) were grouped in nine different clusters. The variation range of genetic similarity (GS) coefficients in two groups differed only slightly, where the values varied from 0.19 to 0.85 in Taiwan and from 0.24 to 0.90 in Indian genotypes. This indicates potentially identical diversity in Indian and Taiwan chilli gene pools. Considering the high polymorphism and data frequency revealed by AFLP markers, the technique is recommended for chilli genetic studies and for the identification of chilli genotypes.