Computational assessment of polymorphism with linkage disequilibrium and hotspots of recombination in pathogenic genes of Fusarium oxysporum f. sp. lycopersici

Abstract

Linkage disequilibrium and recombination rate analysis are the major aspects to study association between nucleotide variations. Species of Fusarium oxysporum includes extensive group of soil and plant pathogens which causes vascular wilt and root diseases to wide range of agricultural crops. Further F. oxysporum is divided into more than 120 formea species (f.sp.) depending upon their hosts. Among all formea species, Fusarium oxysporum f. sp. lycopersici (Fol) is well known pathogen which infects tomato plants and leads towards a destructive disease i.e. “Fusarium wilt”. Our study is focused to analyse association based linkage disequilibrium pattern and recombination rate in five genes of interest for causing pathogenicity in both, plants as well as humans. The fmk1 gene has the highest average nucleotide diversity (ð) value (0.66) and lowest was found in fpr1 (0.54) whereas calculation of average number of nucleotide variation per site showed that gene fpr1 (765) to be highly variating gene and fmk1 (121) to be lowest variating gene. Further, LD analysis all polymorphic sites were considered except those sites which were segregating for three or four nucleotides. LD was calculated in terms of ZnS and variations indicate the success of linkage study and minimum number of recombination event identified in terms of Rm. Through observation it is concluded that the low nucleotide diversity was there, due to the presence of high number of repeated variable nucleotides in sequence because the current estimated LD suggests that it does not extend beyond a few hundreds of base pair.