Development and use of molecular markers: past and present

Abstract

Molecular markers, due to their stability, cost-effectiveness and ease of use provide an immensely popular tool for a variety of applications including genome mapping, gene tagging, genetic diversity diversity, phylogenetic analysis and forensic investigations. In the last three decades, a number of molecular marker techniques have been developed and exploited worldwide in different systems. However, only a handful of these techniques, namely RFLPs, RAPDs, AFLPs, ISSRs, SSRs and SNPs have received global acceptance. A recent revolution in DNA sequencing techniques has taken the discovery and application of molecular markers to high-throughput and ultrahigh-throughput levels. Although, the choice of marker will obviously depend on the targeted use, microsatellites, SNPs and genotyping by sequencing (GBS) largely fulfill most of the user requirements. Further, modern transcriptomic and functional markers will lead the ventures onto high-density genetic map construction, identification of QTLs, breeding and conservation strategies in times to come in combination with other high throughput techniques. This review presents an overview of different marker technologies and their variants with a comparative account of their characteristic features and applications.

Detection of a Subset of Posttranscriptional Transfer RNA Modifications in Vivo with a Restriction Fragment Length Polymorphism-Based Method

“…It has been widely used in the past as a medium-to highthroughput technique to detect genetic polymorphisms, define DNA marker loci, perform genome mapping or gene tagging, and to construct genomic linkage relationships in human pedigrees 11 .…”

High-Throughput Development of Polymorphic Simple Sequence Repeat Markers Using Two Whole Genome Sequence Data in Peucedanum japonicum

“…SSR markers are further universally implemented for intraspecies variation and population genetic studies such as parentage analysis, fingerprinting, genetic structure analysis and genetic mapping (Mittal et al 2009;Meng et al 2014;Grover et al 2016) due to variable polymorphic features and high reproducibility. Because of the utility and advantage of SSR markers, various programs have been developed to identify SSR motifs and primer design such as MISA (http://pgrc.ipk-gatersleben.de/misa/), SSR Locator, Primer3, and FullSSR (Rozen et al 2000;da Maia et al 2008;Abdelkrim et al 2009;Untergasser et al 2012;Metz et al 2016).…”

Biodiversity Studies in Key Species from the African Mopane and Miombo Woodlands

“…Altogether, these studies [70][71][72][73][74][75][76][77][78][79][80][81][82][83][84][85][86][87] reveal that the response of tropical trees to environmental and anthropogenic pressure is highly variable and that, in general, most of the species are resilient to extreme soil and climate conditions, being able to retain high levels of genetic diversity. This in turn highlights the relevance of integrative molecular analyses at a regional scale, to understand the mechanisms of species adaptation and evolution within the context of climate changes.…”

“…Polymerase chain reaction (PCR)-based markers, like random ampliied polymorphic DNA (RAPD), Ampliied fragment length polymorphism (AFLPs), inter-simple sequence repeats (ISSRs), simple sequence repeats (SSRs), or single-nucleotide polymorphisms (SNPs), are commonly used in plant science for a wide variety of purposes such as genome mapping, gene tagging, phylogenetic analysis, taxonomy, marked-assisted selection, and genetic diversity studies [64][65][66][67][68][69][70][71][72][73]. However, the analysis of the genetic variation and structure is an incipient issue in Miombo and Mopane research.…”