DNA markers improved the productivity and accuracy of classical plant breeding by means of marker-assisted selection (MAS). The enormous number of quantitative trait loci (QTLs) mapping read for different plant species have given a plenitude of molecular marker-gene associations. In this review, we have discussed the positive aspects of molecular marker-assisted selection and its precise applications in plant breeding programmes. Molecular marker-assisted selection has considerably shortened the time for new crop varieties to be brought to the market. To explore the information about DNA markers, many reviews have been published in the last few decades; all these reviews were intended by plant breeders to obtain information on molecular genetics. In this review, we intended to be a synopsis of recent developments of DNA markers and their application in plant breeding programmes and devoted to early breeders with little or no knowledge about the DNA markers. The progress made in molecular plant breeding, plant genetics, genomics selection, and editing of genome contributed to the comprehensive understanding of DNA markers and provides several proofs on the genetic diversity available in crop plants and greatly complemented plant breeding devices. MAS has revolutionized the process of plant breeding with acceleration and accuracy, which is continuously empowering plant breeders around the world.

Identification and characterization of crop mutants through molecular marker analysis are imperious to develop desirable traits in mutation breeding programs. In the present study, macromolecular variations with altered morphological, quantitative, and biochemical traits were generated through chemically induced mutagenesis via alkylating agents and heavy metals. Statistical analysis based on quantitative traits indicating enhanced mean value in mutant lines selected from the M₄ generation as compared to previous generations. Identification and characterization of morphology in selected mutant lines are based on altered phenotypes (e.g. tall and dwarf mutant with high yield, fruits with thick texture and bold seeds, etc.) in comparison to control populations. The useful mutations were recorded in phytochemicals (e.g. capsaicin and dihydrocapsaicin) and macro and micro nutrients profile (e.g. protein, iron, copper, cadmium and zinc) in selected mutant lines of Capsicum annuum L. Single Sequence Repeats (SSRs) markers analysis in selected mutant lines revealed genetic diversity in Capsicum. annuum L. The total of 44 alleles were observed with average number of allele 4.00. The Unweighted Pair Group Arithmetic Mean Method (UPGMA) showed maximum dissimilarity was recorded between mutant A-III and F-III followed by mutant G-III and C-III, while mutant B-III and G-III showed the lowest dissimilarity to each other followed by mutant L-III and mutant J-III. Correlation and Principal Component Analysis (PCA) revealed genetic diversity among mutant lines indicating their prioritization over other traits in indirect selection and also revealed that mutants treated with lower and medium concentrations were divergent. These mutant lines could be suitable in crop improvement programs for the broadening the genetic base of C. annuum L. Hierarchical Cluster Analysis (HCA) grouped the mutants into two clusters with variable euclidean distance indicated heterogeneous mutant lines developed from induced mutagenic treatments. Thus beneficial mutations could be induced in chilli genotypes via mutation breeding to enhance genetic variability in limited resources, period, and efforts.

Chemical mutagenesis is a pivotal tool for enhancing genetic diversity in horticultural crops. This study evaluates the mutagenic effects of EMS and MMS on Capsicum annuum L. var. NS1101 to enhance genetic variability for yield-related traits. Seeds of the M₀ generation were treated with EMS and MMS at concentrations of 0.10–1.00% for 6 h, and consequent induced genetic variations were evaluated in the M₁ and M₂ generations. A detailed analysis of the M₂ generation revealed chromosomal abnormalities, including chromosome fragmentation and micronuclei formation, although these were less frequent compared to the M₁ generation. Physio-morphological mutations, particularly leaf chlorophyll variants, were observed during seedling stages. The effects of EMS and MMS on yield and yield-related traits were also evaluated. The results demonstrated that EMS was a more effective mutagen than MMS, especially in the M₂ populations, although its efficiency decreased at higher concentrations. This study underscores the potential of EMS as a more potent mutagen for inducing beneficial mutations in chilli, offering insights into genetic mechanisms that could support future breeding programs focused on improving the production and yield of this important crop.