Genetic Markers

cDr. KOKO TAMPUBOLON, S.P., M.P.

Group of genetic markers

Genetic markers can be grouped as follows:

(1) Visible/morphological markers

(2) Protein markers, and
(3) DNA markers.
 Visible / Morphological Markers
Parameter Karakter
Permukaan batang Sangat Kasar
Pola pertumbuhan batang Lurus
Bentuk tajuk Tidak beraturan
Warna batang Abu-abu

Some examples Susunan daun

Lebar helaian daun
Berseling
Sedang
of such markers Bentuk helaian daun Bulat panjang
Bentuk pangkal daun Lancip
are shape and Tepi helaian daun Rata
Bentuk ujung buah cembung
color of Panjang tangkai buah sedang
flowers, color Warna tangkai buah
Panjang buah (cm)
Cokelat
17
and shape of Diameter buah (cm) 9,57
Warna kulit buah Hijau kekuningan
fruits and seeds, Warna daging buah Putih krem
Panjang biji (cm) 5
etc. Lebar biji (cm) 3
Berat biji (g) 16,87
Bentuk biji lonjong
Warna biji cokelat
 Limitations of morphological
markers
(1) The number of good visible / morphological
markers in a species is rather limited.
(2) Typically, only a few of these markers can be
analyzed in a single cross/mapping population
mainly due to difficulties in determining
phenotypes of different traits in a single plant.
(3) Generally, they can be scored only on whole plants
and that too during specific developmental stages.
(4) Many traits, e.g., disease resistance, may have a
threshold requirement for their expression.
Limitations of morphological markers

(5) Some genes governing the marker traits may

have pleiotropic effect on the trait of interest, i.e.,
the trait with which marker association is to be
tested. This would distort the segregation ratio and
cause error in gene mapping.

(6) Finally, maintenance of suitable genetic stocks

expressing the various marker traits would be
necessary.
 Protein-Based Markers
Protein-based markers are detected as electrophoretic
variants of proteins, including enzymes.

A schematic representation of the isozyme banding patterns seen in F1 generation

and their interpretations.
The enzyme molecule may be (1) monomer, (2) homodimer, (3) homotrimer, or
(4) homotetramer. A and a are the polypeptides encoded by the alleles A and a
 Advantages of Protein-based
markers

(1) They reflect differences in gene sequences more directly

than visible/morphological markers,
(2) only a small amount of tissue is needed for their detection,
(3) they can often be detected at seedling stage or even from
seeds,
(4) analysis of one marker usually does not interfere with that
for other protein-based markers.
(5) Therefore, many different marker loci can be analyzed in
the same cross.
(6) their analysis is relatively easy.
Limitation of Protein-based
markers
(1) Any two parents may be polymorphic for only a
relatively small number of protein-based markers.
(2) Isozymes represent only a small, nonrandom sample
of the structural genes of an organism.
(3) They detect only such mutations that produce a
functional enzyme with changed electrophoretic
mobility.
(4) A single band may represent two different isozymes
having identical mobility.
(5) They may vary with the tissue, the developmental
stage, and the environment
 DNA
Markers

The DNA-based
markers represent
variation in genomic
DNA sequences of
different individuals.
DNA Markers

Marker systems detect the following

three types of DNA sequence
polymorphisms:
(1) Variation at single nucleotides,
(2) Insertion/deletion (InDel) of one
to several bases, and
(3) Variation in the number of tandem
repeats of few to several
nucleotides.
 Advantages of DNA markers
(1) They represent polymorphism in the actual base
sequence of DNA distributed over the entire genome.
(2) The number of different marker loci is very large so that
all the genomic regions can be mapped at very high
marker densities.
(3) The sequence variation detected by these markers is
generally neutral, except when it is located in coding
sequences and affects the functions of concerned genes.
(4) Scoring for one DNA marker usually has no effect on
that of the others, so that multiple markers can be
evaluated simultaneously.
(5) Molecular markers show simple Mendelian inheritance.
Advantages of DNA markers
(6) Marker genotyping is independent of the prevailing
environment,
(7) The developmental stage of the plant,
(8) The marker assays are nondestructive.
(9) Marker-assisted selection (MAS) can also be used for an
allele that is not expressed in the available genotypes,
e.g., a recessive allele in heterozygotes.
(10) The DNA samples can be stored for future use,
(11) Specific marker stocks are not required.
Types of DNA Markers
(1) Restriction fragment length polymorphism (RFLP),
(2) Randomly amplified polymorphic DNAs (RAPDs),
(3) Arbitrary-primed PCR,
(4) DNA amplification fingerprinting (DAF),
(5) Amplified fragment length polymorphism (AFLP),
(6) Sequence-characterized amplified regions (SCAR),
(7) Sequence-tagged sites (STS),
(8) Allele-specific associated primers (ASAP),
(9) Single primer amplification reactions (SPARs),
(10) Simple sequence repeat (SSR) polymorphisms,
(11) SSR-anchored PCR,
Types of DNA Markers
(12) Cleaved amplified polymorphic sequences (CAPSs),
(13) Allele-specific PCR,
(14) Allele-specific ligation
(15) Single-strand conformation polymorphism (SSCP),
(16) Diversity array technology (DArT),
(17) Inter-SSR (ISSR) markers,
(18) Amplicon length polymorphism (ALP),
(19) Sequence-related amplified polymorphism (SRAP),
(20) Target region amplification polymorphism (TRAP),
(21) Transposable elementbased markers, and
(22) Single-nucleotide polymorphism (SNP).
 Applications of DNA Markers
Molecular markers have a variety of applications, including
(1) Fingerprinting of strains / varieties for unequivocal
identification;
(2) Mapping of genes and quantitative trait loci (QTLs);
(3) Efficient MAS for tightly linked QTLs and such oligogenes,
direct selection for which may be costly or problematic;
(4) Positional cloning of genes/QTLs;
(5) Identification of chromosome segments that would
contribute to improvements in the target traits;
(6) Establishing phylogenetic relationships among different
strains/species;
(7) Selection of parents for hybridization;
 Applications of DNA Markers
(8) Assessing the basis of somaclonal variation;
(9) Identification of pathogen races and biotypes;
(10) Prediction of heterotic cross combinations;
(11) Identification of wide hybrids;
(12) Gene pyramiding;
(13) Management and utilization of genetic resources.
(14) MAS allows the use of off-season nursery and
greenhouse facilities to reduce the time needed for
variety development
 Categories of DNA Markers
 On this basis, the markers are grouped as (1)
random, (2) gene-based, and (3) functional
markers.

 Chronology of their development, markers are

classified as
(1) First-generation/low (RFLP, RAPD, and their
modifications),
(2) Second-generation/medium (SSRs, AFLPs, and
their modifications), and
(3) Third-generation/high (ESTs and SNPs) markers
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