3. MARKER ASSISTED SELECTION
Marker assisted selection or marker aided selection (MAS) is an indirect selection process where a
trait of interest is selected based on a marker (morphological, biochemical or DNA/RNA variation)
linked to a trait of interest (e.g. productivity, disease resistance, abiotic stress tolerance, and
quality), rather than on the trait itself. This process has been extensively researched and proposed
for plant and animal breeding.
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 (QTL) of interest, due to genetic linkage (close proximity, on the chromosome, of the marker
locus and the disease resistance-determining locus). 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.
4. 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, Karl 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 (Phaseolus vulgaris L.).
In 1935, J. Rasmusson demonstrated linkage of flowering time (a quantitative trait) in peas with a
simply inherited gene for flower color.[7]
Markers may be:
Morphological – These were the first markers loci available that have an obvious impact on the
morphology of plants. These markers are often detectable by eye, by simple visual inspection.
Examples of this type of marker include the presence or absence of an awn, leaf sheath coloration,
height, grain color, aroma of rice etc. In well-characterized crops like maize, tomato, pea, barley
or wheat, tens or hundreds of genes that determine morphological traits have been mapped to
specific chromosome locations.
Biochemical – A protein that can be extracted and observed; for example, isozymes and storage
proteins.
5. • Cytological – Cytological markers are chromosomal features that can be identified through
microscopy. These generally take the form of chromosome bands, regions of chromatin that
become impregnated with specific dyes used in cytology. The presence or absence of a
chromosome band can be correlated with a particular trait, indicating that the locus responsible
for the trait is located within or near (tightly linked) to the banded region.
• Morphological and cytological markers formed the backbone of early genetic studies in crops such
as wheat and maize.
• DNA-based- Including microsatellites (also known as short tandem repeats, STRs, or simple
sequence repeats, SSRs), restriction fragment length polymorphism (RFLP), random amplification
of polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and single
nucleotide polymorphisms (SNPs)
6. Important properties of ideal markers for MAS
• An ideal marker: Has easy recognition of phenotypes - ideally all possible phenotypes (homo-
and heterozygotes) from all possible alleles
• Demonstrates measurable differences in expression between trait types or gene of interest
alleles, early in the development of the organism
• Testing for the marker does not have variable success depending on the allele at the marker
locus or the allele at the target locus (the gene of interest that determines the trait of interest).
• Low or null interaction among the markers allowing the use of many at the same time in a
segregating population
• Abundant in number
• Polymorphic
7. Steps for MAS
Generally the first step is to map the gene or quantitative trait locus (QTL) 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 (<5 recombination
unit or cM) 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 (99%) for recovery of the target gene.
QTL mapping techniques.
Quantitative_trait_locus § QTL_mapping
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 (NILs), recombinant
inbred lines (RILs), doubled haploids (DH), 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".
