Functional Molecular Markers: Basic Concept
Authors: Rakesh Kumar Prajapat1, Ashish Marathe2, Deepak Pawar1
1 Ph.D scholar, NRCPB, IARI, New Delhi-110012
2 Ph.D scholar, Division of Biochemistry, IARI, New Delhi-110012



Molecular marker

Genetic markers are the centre for designing a genetic map which provide information regarding the order of genes along chromosomes. In 1913, Alfred H. Sturtevant generated the first genetic map using six morphological traits (termed 'factors') in the fruit fly (Drosophila melanogaster) and, soon after, Karl Sax produced evidence for genetic linkage between a qualitative and a Quantitative Trait Locus (seed color and seed size) in the common bean (Phaseolus vulgaris). Genetic markers are used in both basic plant research and plant breeding to characterize plant germplasm, for gene isolation, for marker-assisted introgression of favorable alleles and for variety protection. These molecular marker have been used for exploitation of DNA sequence variation(s) in and among the crop species and create new sources of genetic variation by introducing new and favourable traits from landraces and related crop species. Markers can aid selection for target alleles that are not easily assayed in individual plants, minimize linkage drag around the target gene, and reduce the number of generations required to recover a very high percentage of the recurrent parent genetic background. Improvements in marker detection systems and in the techniques used to identify markers linked to useful traits, has enabled great advances to be made in recent years.

A genetic marker is a gene or DNA sequence with a known location on a chromosome with distinguishable phenotype and associated with a particular gene or trait. It can be described as a variation, which may arise due to mutation or alteration in the genomic loci that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like minisatellites.

The restriction fragments length polymorphism (RFLP) markers put a plateform for most of the work in crop plants, valuable markers have been generated from random amplification polymorphic DNA (RAPD) and amplified fragments length polymorphism (AFLP). Simple sequence repeats (SSR) or microsatellite markers have been developed more recently for major crop plants and this marker system is predicted to lead to even more rapid advances in both marker development and implementation in breeding programs.

Functional Molecular Markers:

In the past few years, functional genes, ESTs and genome sequences have facilitated development of molecular markers from the transcribed regions of the genome. Among the important molecular markers that can be developed from ESTs are single-nucleotide polymorphisms (SNPs), simple sequence repeats (SSRs). Putative functions for the markers derived from ESTs or genes can be deduced using homology searches (BLASTX) with protein databases (e.g. NR-PEP and SWISSPROT). Therefore, molecular markers generated from expressed sequence data are known as 'functional markers' (FMs). A DNA marker is typically derived from a small region of DNA that shows sequence polymorphism between individuals within a species. Thousands of phenotypically neutral, random DNA markers (RDMs) can be generated for any species and have been successfully used in many studies to represent genomes in biodiversity studies or to map trait genes. FMs have been developed extensively for the plant species in which ESTs or gene sequence data are available. By screening the unigene consensus sequences from over 50 plant species, demonstrated the feasibility of predicting molecular markers (e.g. SSRs and SNPs) that can be used to develop FMs for several species. FMs have some advantages over random markers that are generated from anonymous region of the genome, because FMs are linked to the desired trait allele. Such markers are derived from the gene responsible for the trait of interest and target the functional polymorphism in the gene they allow selection in different genetic backgrounds without revalidating the marker-quantitative trait locus (QTL) allele relationship. An FM allows breeders to track specific alleles within pedigrees and populations, and to minimize linkage drag flanking the gene of interest.

As markers become more abundant, breeders can develop strategies that are compatible with financial resources and breeding goals. Markers are increasingly being applied for selection of parental materials and for accelerated selection of loci controlling traits that are difficult to select phenotypically. Such examples include pyramiding of genes for disease resistance, quality trait and those that interact with the environment. Linked deleterious alleles are potential problem as the number of selected loci increase, particularly if the donor parent is a related wild species. Therefore, closely linked markers are most desirable for reducing linkage drag, which require larger population size and more backcross generations to be developed.

About Author / Additional Info:
I am a Ph. D. Research Scholar at IARI, New Delhi