Marker-assisted selection


Marker assisted selection or marker aided selection is an indirect selection process where a trait of interest is selected based on a marker linked to a trait of interest, rather than on the trait itself. This process has been extensively researched and proposed for plant and animal breeding, nevertheless, as of 2013 breeding programs based on DNA markers for improving quantitative traits in plants are rare.
For example, using MAS to select individuals with disease resistance involves identifying a marker allele that is linked with disease resistance rather than the level of disease resistance. The assumption is that the marker associates at high frequency with the gene or quantitative trait locus of interest, due to genetic linkage. MAS can be useful to select for traits that are difficult or expensive to measure, exhibit low heritability and/or are expressed late in development. At certain points in the breeding process the specimens are examined to ensure that they express the desired trait.

Marker types

The majority of MAS work in the present era uses DNA-based markers. However, the first markers that allowed indirect selection of a trait of interest were morphological markers. In 1923, Sax first reported association of a simply inherited genetic marker with a quantitative trait in plants when he observed segregation of seed size associated with segregation for a seed coat color marker in beans. In 1935, Rasmusson demonstrated linkage of flowering time in peas with a simply inherited gene for flower color.
Markers may be:
The following terms are generally less relevant to discussions of MAS in plant and animal breeding, but are highly relevant in molecular biology research:
A distinction can be made between selectable markers and screenable markers. Most MAS uses screenable markers rather than selectable markers.

Gene vs marker

The gene of interest directly causes production of protein or RNA that produce a desired trait or phenotype, whereas markers are genetically linked to the gene of interest. The gene of interest and the marker tend to move together during segregation of gametes due to their proximity on the same chromosome and concomitant reduction in recombination between the marker and gene of interest. For some traits, the gene of interest has been discovered and the presence of desirable alleles can be directly assayed with a high level of confidence. However, if the gene of interest is not known, markers linked to the gene of interest can still be used to select for individuals with desirable alleles of the gene of interest. When markers are used there may be some inaccurate results due to inaccurate tests for the marker. There also can be false positive results when markers are used, due to recombination between the marker of interest and gene. A perfect marker would elicit no false positive results. The term 'perfect marker' is sometimes used when tests are performed to detect a SNP or other DNA polymorphism in the gene of interest, if that SNP or other polymorphism is the direct cause of the trait of interest. The term 'marker' is still appropriate to use when directly assaying the gene of interest, because the test of genotype is an indirect test of the trait or phenotype of interest.

Important properties of ideal markers for MAS

An ideal marker:
Morphological markers are associated with several general deficits that reduce their usefulness including:
To avoid problems specific to morphological markers, DNA-based markers have been developed. They are highly polymorphic, exhibit simple inheritance, are abundant throughout the genome, are easy and fast to detect, exhibit minimum pleiotropic effects, and detection is not dependent on the developmental stage of the organism. Numerous markers have been mapped to different chromosomes in several crops including rice, wheat, maize, soybean and several others, and in livestock such as cattle, pigs and chickens. Those markers have been used in diversity analysis, parentage detection, DNA fingerprinting, and prediction of hybrid performance. Molecular markers are useful in indirect selection processes, enabling manual selection of individuals for further propagation.

Selection for major genes linked to markers

'Major genes' that are responsible for economically important characteristics are frequent in the plant kingdom. Such characteristics include disease resistance, male sterility, self-incompatibility, and others related to shape, color, and architecture of whole plants and are often of mono- or oligogenic in nature. The marker loci that are tightly linked to major genes can be used for selection and are sometimes more efficient than direct selection for the target gene. Such advantages in efficiency may be due for example, to higher expression of the marker mRNA in such cases that the marker is itself a gene. Alternatively, in such cases that the target gene of interest differs between two alleles by a difficult-to-detect single nucleotide polymorphism, an external marker may present as the most realistic option.

Situations that are favorable for molecular marker selection

There are several indications for the use of molecular markers in the selection of a genetic trait.
In such situations that:
The cost of genotyping is reducing while the cost of phenotyping is increasing particularly in developed countries thus increasing the attractiveness of MAS as the development of the technology continues.

Steps for MAS

Generally the first step is to map the gene or quantitative trait locus of interest first by using different techniques and then using this information for marker assisted selection. Generally, the markers to be used should be close to gene of interest in order to ensure that only minor fraction of the selected individuals will be recombinants. Generally, not only a single marker but rather two markers are used in order to reduce the chances of an error due to homologous recombination. For example, if two flanking markers are used at same time with an interval between them of approximately 20cM, there is higher probability for recovery of the target gene.

QTL mapping techniques

In plants QTL mapping is generally achieved using bi-parental cross populations; a cross between two parents which have a contrasting phenotype for the trait of interest are developed. Commonly used populations are near isogenic lines, recombinant inbred lines, doubled haploids, back cross and F2. Linkage between the phenotype and markers which have already been mapped is tested in these populations in order to determine the position of the QTL. Such techniques are based on linkage and are therefore referred to as "linkage mapping".A

Single step MAS and QTL mapping

In contrast to two-step QTL mapping and MAS, a single-step method for breeding typical plant populations has been developed.
In such an approach, in the first few breeding cycles, markers linked to the trait of interest are identified by QTL mapping and later the same information is used in the same population. In this approach, pedigree structure is created from families that are created by crossing number of parents. Both phenotyping and genotyping is done using molecular markers mapped the possible location of QTL of interest. This will identify markers and their favorable alleles. Once these favorable marker alleles are identified, the frequency of such alleles will be increased and response to marker assisted selection is estimated. Marker allele with desirable effect will be further used in next selection cycle or other experiments.

High-throughput genotyping techniques

Recently high-throughput genotyping techniques are developed which allows marker aided screening of many genotypes. This will help breeders in shifting traditional breeding to marker aided selection. One example of such automation is using DNA isolation robots, capillary electrophoresis and pipetting robots.
One recent example of capllilary system is Applied Biosystems 3130 Genetic Analyzer. This is the latest generation of 4-capillary electrophoresis instruments for the low to medium throughput laboratories.

Use of MAS for backcross breeding

A minimum of five or six-backcross generations are required to transfer a gene of interest from a donor to a recipient. The recovery of the recurrent genotype can be accelerated with the use of molecular markers. If the F1 is heterozygous for the marker locus, individuals with the recurrent parent allele at the marker locus in first or subsequent backcross generations will also carry a chromosome tagged by the marker.

Marker assisted gene pyramiding

Gene pyramiding has been proposed and applied to enhance resistance to disease and insects by selecting for two or more than two genes at a time. For example, in rice such pyramids have been developed against bacterial blight and blast. The advantage of use of markers in this case allows to select for QTL-allele-linked markers that have same phenotypic effect.
MAS has also been proved useful for livestock improvement.
A coordinated effort to implement wheat '' marker assisted selection in the U.S. as well as a resource for marker assisted selection exists at the .