Marker-Assisted Selection in Crop Plants

Abstract

Plant kingdom, the base for every ecological pyramid, serves as a key source for food and evolution. Individualisation and analysis of genetic diversity and relatedness between or within different species, genera and population are the central task for many disciplines of biological science. Till recently, only the morphological traits/markers have been extensively used for this purpose. However, these morphological markers are often influenced by environment, which require special experimental designs to distinguish genotypic and phenotypic variation in a population. Later, the developments in biochemistry and molecular biology complemented many markers like protein, isozyme and DNA markers, which enable the breeders to overcome the limitations faced in the use of morphological markers. They show co-dominance (with exception of Random Amplified Polymorphic DNA (RAPD), mostly a dominant marker) so that all the genotypes can be classified, a large number of samples can be analysed, require only a limited quantity of plant tissue for analysing, thus eliminating the need for raising a large population in the field and one need not wait for the maturity of the plant. All living organisms are made up of cells that are programmed by genetic material called DNA. This molecule is made up of a long chain of nitrogen-containing bases (there are four different bases: adenine (A), cytosine (C), guanine (G) and thymine (T). Only a small fraction of the DNA sequence typically makes up genes, i.e., that code for protein, while the remaining and major share of the DNA represents non-coding sequences, the role of which is not yet clearly understood. The genetic material is organised into sets of chromosomes (e.g., five pairs in Arabidopsis thaliana; 30 pairs in Bos taurus (cow), and the entire set is called the genome. In a diploid individual (i.e., where chromosomes are organised in pairs), there are two alleles of every gene, one from each parent. Marker-assisted selection (MAS) is the breeding strategy in which selection for a gene is based on molecular markers closely linked to the gene of interest, rather than gene itself and the markers are used to monitor the incorporation of desirable allele from the donor source. Molecular markers should not be considered as normal genes as they usually do not have any biological effect. Instead, they can be thought of as constant landmarks in the genome. They are identifiable DNA sequences, found at specific locations of the genome and transmitted by the standard laws of inheritance from one generation to the next. They rely on a DNA assay in contrast to morphological markers that are based on visible traits, and biochemical markers that are based on proteins produced by genes. Different kinds of molecular markers exist, such as restriction fragment length polymorphisms, RAPDs markers, amplified fragment length polymorphisms, microsatellites and single-nucleotide polymorphisms (SNPs). Thus, MAS is the breeding strategy in which selection for a gene is based on molecular markers closely linked to the gene of interest, rather than gene itself and the markers are used to monitor the incorporation of desirable allele from the donor source.