Marker Associated Screening (MAS)

From past two decades there has been growth in the relatively new field of plant biotechnology and its associated techniques. These are not only for the manipulation of biological systems for the benefit of mankind, but also to undertake studies for better understanding of the fundamental and basic life processes. It has become the fastest and most rapidly growing technology in the world. Basically Biotechnology is defined as "any technique that uses living organisms (or parts of organisms) to make or modify products, to improve plants and animals or to develop microorganisms for specific uses". It provides best and cost-effective means to produce an array of novel, improvised products. It has the ability to increase food productivity, reduce chemical dependency of agriculture, lower the cost of raw materials and negative environmental impacts associated with traditional production methods.

Agriculture today is characterized by a sharp reduction in the diversity of cultivated plants. Out of total of 30,000 edible plant species only 30 'feed the world', with the three major crops being maize (Zea mays), wheat (Triticum aestivum) and rice (Oryza sativa). The lack of inter-specific and intra-specific genetic variability among cultivated crops could lead into lack of adaptation to increase abiotic stress with high ozone concentration and drought. Genetic resources can be defined as all materials that are available for improvement of a cultivated plant species. In classical plant breeding, genetic resources may be considered as those materials that, without selection for adaptation to the target environment, do not have any immediate use for the breeders. The importance of the different classes of genetic resources for crop improvement depends on the targeted crop species.

Many agriculturally important traits such as yield, quality and some forms of disease resistance are controlled by genes and are known as quantitative traits (also 'polygenic,' 'multifactorial' or 'complex' traits). The regions within genomes which contain genes associated with a particular quantitative trait are known as quantitative trait loci (QTLs). The QTLs is based only on conventional phenotypic evaluation is not possible. A major breakthrough in the characterization of quantitative traits which created opportunities to select for QTLs was by the development of DNA (or molecular) markers in the 1980s. The main use of DNA markers in agricultural research is the construction of linkage maps for diverse crop species. Linkage maps are used for identifying chromosomal regions that contain genes controlling simple traits (controlled by a single gene) and quantitative traits using QTL analysis. DNA markers are widely accepted as potentially valuable tools for crop improvement in rice, wheat, maize, barley, tuber crops, pulses, oilseeds, horticultural crop species and pasture species. Some studies suggest that DNA markers will play a vital role in enhancing global food production by improving the efficiency of conventional plant breeding programs.

Twenty-first century agriculture will face formidable challenges to provide mankind with a high and appropriate level of food security by enhancing the sustainability of agricultural practices, reducing environmental impact and preserving bio diversity. Many efforts were made to adapt the environment to the plant; new crops should be genetically manipulated for maximizing resource capture, yield and yield stability. To this end, genomics assisted crop improvement (GACI) offers a wide range of opportunities to identify major loci influencing the target traits and to select plants with the desirable combination of alleles with marker assisted selection (MAS), marker-assisted backcrossing (MABC) or marker-assisted recurrent selection (MARS).

Marker-assisted selection is based on marker information only (pure MAS) or on index of marker plus phenotypic data (combined MAS). In both methods, markers can only lead to gametic phase disequilibrium exists between the marker loci and their pertinent QTL. In generations derived from a cross between two homozygous lines, the disequilibrium is caused by linkage. At present MAS can significantly accelerate the improvement of quantitative traits in backcrossing programs. It may also be useful for selecting among progenies in advanced generations of a mapping population. The success of a marker-based breeding system depends on three main factors: a genetic map with an adequate number of uniformly-spaced polymorphic markers to accurately locate desired QTLs or major gene(s), Close linkage between the QTL or a major gene of interest and adjacent markers, Adequate recombination between the markers and rest of the genome and An ability to analyses a larger number of plants in a time and cost effective manner. The success of MAS depends on location of the markers with respect to genes of interest.

MAS is useful for traits that are difficult to select that is disease resistance, salt tolerance, drought tolerance, heat tolerance, quality traits (aroma of basmati rice, flavour of vegetables). The approach involves selecting plants at early generation with a fixed, favorable genetic background at specific loci, conducting a single large scale marker assisted selection while maintaining as much as possible the allelic segregation in the population and the screening of large populations to achieve the objectives. No selection is applied outside the target genomic regions, to maintain as much as possible the Mundelein allelic segregation among the selected genotypes. After selection with DNA markers, the genetic diversity at unselected loci may allow breeders to generate new varieties and hybrids through conventional breeding in response to targets that's set in breeding program. The important steps that's involved In Validation of molecular markers are Extraction of the DNA from test samples and find whether there is one to one relationship with marker and the trait. Extracting the DNA of breeding population at the seedling stage and apply to MAS. Select sample on the basis of presence of desired molecular markers for the concerned trait. For other traits, selection is based on classical breeding methods. Limitations of MAS are cost factor; requirement of technical skill, automated techniques for maximum.DNA marker has to be validated for each of the breeding population.

Marker-assisted backcrossing for a single gene

Marker-assisted backcrossing is the simplest form of MAS, in which the goal is to incorporate a major gene from an agronomically inferior source (donor parent) into an elite cultivar or breeding line (recurrent parent). The desired outcome is a line containing only the major gene from the donor parent, with the recurrent parent genotype present everywhere else in the genome. Two types of selection are recognized. Foreground selection, in which the breeder selects plants having the marker allele of the donor parent at the target locus. The objective is to maintain the target locus in a heterozygous state (one donor allele and one recurrent parent allele) until the final backcross is completed. Then, the selected plants are self-pollinated and progeny plants identified that are homozygous for the donor allele. Background selection, in which the breeder selects for recurrent parent marker alleles in all genomic regions except the target locus, and the target locus is selected based on phenotype. Background selection is important in order to eliminate potentially deleterious genes introduced from the donor. Soybean yields were increased by using marker-assisted backcrossing to introgress a yield QTL from a wild accession into commercial genetic backgrounds. Although the yield enhancement was observed in only two of six genetic backgrounds, the study demonstrates the potential of incorporating wild alleles with the assistance of markers.

Marker-assisted selection for multiple genes

Using markers to select for multiple genes is too complex, and less proven, than selection for a single gene. Population sizes required to recover individuals with the entire desired marker patterns increase exponentially with the number of genes involved. In a backcrossing, there may be little opportunity to select for the recurrent parent genome, because only few individuals will have the desired marker pattern at all the target loci. If some of the genes are QTLs, whose locations and effects are often imprecisely estimated, even then it is uncertainty that the results of MAS will meet expectations. MAS for multiple QTL markers was compared to phenotypic selection in maize QTLs had previously been identified for 2nd generation European corn borer (ECB) resistance in one population. For each trait and population, selection was carried out, with the 10 highest or 10 lowest families selected in each fraction. Each of the five selected sub-populations was recombined by random mating the selected families, followed by evaluation in field trials. Results showed that MAS was effective for both traits, but not always as effective as phenotypic selection. In some cases, MAS was effective in moving the population in one direction, but not in the other.


References

• Allard, R. W., Theory. Principles of Plant Breeding, Wiley, New York, 1960.

• Visscher, P. M. et al., Marker assisted introgression in back cross breeding programs. Genetics, 1996,

• Akkaya MS, Bhagwatt AA, Cregan PB: Length polymorphisms of simple sequence repeat DNA in soybean.

• Genetics132 Riday H (2011) Paternity testing a non-linkage based marker assisted selection scheme for out bred forage species. Crop Sci 51

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