Genomic Tools for Assessing Plant Diversity in the 2020s: From PCR-Based Markers to High-Throughput Sequencing and eDNA

A comprehensive understanding of plant diversity is essential for ecological research, conservation planning, and sustainable resource management. Advances in genetic technologies have transformed the assessment of plant biodiversity, enabling more precise and efficient characterization of genetic variation. Early molecular markers, widely used in the late 2000s, have largely been replaced by polymerase chain reaction (PCR)-based tools that require less DNA, are easier to use, and are supported by accessible commercial kits. The 2020s have seen the emergence of new, more accessible tools driven by cost reduction and efficiency improvements. High-throughput sequencing (HTS) technologies have further revolutionized the field by providing genome-wide insights into allelic diversity, structural polymorphisms, and epigenetic modifications. These innovations enhance the detection of adaptive variation, improve understanding of spatial genetic structure, and support the evaluation of environmental impacts on plant populations. Marker-assisted selection, now common in modern breeding, leverages genomic data to develop cultivars with enhanced resistance and desirable agronomic traits. Emerging tools such as environmental DNA (eDNA) analysis, high-throughput phenotyping, and advanced bioinformatics workflows expand the capacity to monitor species, assess population viability, and identify key traits linked to adaptation. The present review aims to highlight these technological advancements and the more recent and useful tools available from Next-Generation Sequencing to genotyping-by-sequencing, discussing their role for conserving plant genetic resources, improving breeding programs, and deepening knowledge of plant biodiversity within changing ecosystems.