AMP-PCR-based assay for detection and quantification of genome wide natural methylation in rice

Natural and artificial selection efforts combined several favorable alleles of economically important traits in crop plants. However, the progress made is insufficient to meet the future food requirements. Hence, exploring new genetic resources and breeding strategies is important for sustainable improvement in production. The epigenetic variation that alters the phenotype expression without altering the gene sequence has played a crucial role in the process of evolution of modern-day crop plants. The methylation-based epigenetic variations are known to inherit more consistently than other types of epigenetic variation. However, detection and quantification of methylation in the plant genome is costly, hence limiting its utility in crop improvement. In the present investigation, we demonstrated the low-cost but effective approach for detecting and quantification of natural DNA methylation variation in the rice genome by employing custom-designed markers called amplified methylation polymorphism polymerase chain reaction markers (AMP-PCR markers). The methylation detected was scored in an effective method which was further used for quantification. The natural methylation in the diverse population of rice was used to showcase the methylation diversity.Furthermore, the methylation in germplasm accessions, breeding lines, and released varieties indicated the significant influence of artificial selection efforts on methylation in the rice genome. The genotypes cultivated in different ecologies exhibited different types of methylations. The results ensure the utility of the AMP-PCR assay approach in the detection and utilization of methylation variation at lower costs in crop improvement programs for complex economic traits.