Marker Assisted Selection

K K Vinod

Primary objective of any plant breeding programme is selection of the best genotype from an array of breeding lines (genotypes). Conventionally, selection involves various traits that are expressed in plants (phenotypes) and the selection tools employed by the breeders involve qualitative (visual or perceivable traits) and/ or biometrical (quantitative) traits. However, since gene expression is always modified by the environment due to several adaptive reasons, selection of traits is not always as successful as it should be. This led to the thinking of selecting directly for the genes themselves, as the genes are coded on the DNA molecules that are free of environmental interference. However, selection of genes was not an easy job as it appeared to be, because of their obscure locations on the genome. Hence, this is achieved indirectly by selecting detectable DNA variations in the individual genomes, which are either associated or closely linked to the target genes, as detected by the co-segregation of these fragments with phenotype. Such detectable DNA fragments are called markers. Use of these molecular markers has opened a novel way for selection known as marker assisted selection or marker aided selection (MAS). Extensive use of molecular markers by the present day breeders has opened up a separate field of study, the molecular breeding.

Principles of MAS

As the name indicates, MAS is not a breeding method but markers are used as a selection aid. We consider that traits may be typically controlled by single or many genes. Although in strict sense no trait is controlled by a single gene but a group of genes, the practical consideration of mono, oligo and polygenes revolves around the number of genes that produce the perceivable quantum effect of the trait. Any detectable DNA fragment lying around or within these genes can report the presence of this gene in its carrier. This forms the fundamental idea behind MAS. MAS therefore can involve in selection for both qualitative and quantitative characters. However, MAS is not generally advocated for the selection of easily selectable traits, especially those qualitative traits with high heritability and penetrance, while for traits with low heritability and low expressivity MAS may be a good option.

Since markers tag for genes, MAS is useful mostly in transfer of genes from a donor to a recipient. Therefore the donor should have a distinguishable marker allele that is linked to the target gene. This marker allele should be distinctly different from the allele produced by the same marker in the recipient genotype. Now while crossing both donor and recipient it is easy to determine which progeny carry the gene by identifying the linked marker allele. The target allele of the gene may be either a dominant one or recessive. Most commonly used procedure in transfer of single gene from donor to recipient is backcross breeding. Since the recipient genotype is used repeatedly in crossing steps in the backcross process it is also called recurrent parent (RP). Using markers, the backcross breeding proceeds by selecting progenies that are carriers of the target allele until a stable homozygous genotype is obtained which has almost entirely of the recipient genome carrying the target allele. This is called marker assisted backcross breeding (MABB). Depending on the transfer of dominant or recessive allele backcross procedures may suitably vary.