Chilli, is spice cum vegetable crop having various nutritious, medicinal and industrial application values in it. It consists of many species of which only five are cultivated. Among these, Capsicum annuum is widely cultivated across the world followed by Capsicum frutescens. Many of the biotic and abiotic stress also effect the crop production. Molecular markers usage in this crop has hasten the crop breeding programme to select diverse parental line, screening for biotic stress, transfer of recessive alleles, identifying and mapping, introgression of these beneficial genes and helps in marker assisted selection (MAS). Now most advanced next generation sequencing and genotyping technologies have also been generating more genomic resources which have to be used efficiently for crop improvement in future.

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