Why Marker is any sign used to indicate position

Why study genetic diversity?

The
cultivation of lands dates back to thousands of years. Man has been raising
plants and animals to meet the daily needs of food, feed, clothing, shelter,
medicines and such. The ever increasing human population raises the necessity
of increased food production. Thousands of plants species have been
domesticated globally to suffice the livelihood. Availability of variations in
plant genetic resources facilitates the development of new and improved
varieties with desirable traits. Different approaches have been in use to
generate high yielding varieties. Few genotypes with important traits are being
cultivated over huge land coverage; this is leading to the loss of genetic
diversity and extinction of landraces. Protection of genetic diversity is
important towards its utilization in future breeding programs for crop
improvement and increased productivity to support the booming population
explosion.

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What are the tools available for studying genetic
diversity?

            The
diversity in plants and/or populations is widely characterized through:
morphological, biochemical and molecular markers. Marker is any sign used to
indicate position or presence of something. The physical appearances such as
plant height, seed colour, seed size, disease reaction which can be used to
differentiate plants by naked eyes are morphological markers. The use of
enzymes/proteins for variability studies is included in biochemical markers. Such
markers are limited in number and studies need large scale experiments.

DNA based markers assess
polymorphism at the level of DNA, the genetic material. Amongst the molecular
markers used, DNA markers are more suitable and ubiquitous to most of the
living organisms (Joshi et al.,
1999). DNA based molecular markers reveal neutral sites of variation at the DNA
sequence level. They represent genetic differences between individual organisms
or species. Generally DNA markers themselves do not affect the phenotype of the
trait of interest because they are located only near to or ‘linked’ to the
genes controlling the trait.  Use of
DNA-based molecular markers allows for the most efficient comparison between
two individuals, because they are detectable at all stages of development of
the organism (Mohan et al., 1994).
Molecular markers have several advantages over the traditional phenotypic
markers and thus offer great scope for improving the efficiency of conventional
plant breeding. Besides, these markers are practically unlimited in number and
are not environmentally regulated. DNA markers are used in assessing the level
of genetic diversity within germplasm, construction of linkage maps and marker
assisted breeding.

 

Common Molecular Markers and Genotyping Methods

            Restriction
Fragment Length Polymorphisms (RFLPs) were first hybridization based markers
developed for human genetic studies and later on used in plant analysis.

            The
limitations of hybridization based markers led to advent of Polymerase Chain
Reaction (PCR) based markers such as: Random Amplified Polymorphic DNA (RAPD),
Sequence Characterized Amplified Regions (SCAR), Amplified Fragment Length
Polymorphism (AFLP), Simple Sequence Repeats (SSR), Single Nucleotide
Polymorphisms (SNPs). RAPDs use arbitrary primers for random amplification of
genomic DNA; where differences in amplified products give information on
diversity in samples. RAPDs are quick, simple and inexpensive markers; but
results are non-reproducible. SSRs or microsatellites are markers based on
polymorphism in short tandem repeats. SNPs are DNA sequence variations
occurring when a single nucleotide differs among individuals/members of a
population/species. These are most abundant markers in genomes of most
organisms including plants and are the widely used markers in current plant
studies.     

 

The current
discovery of a sufficiently large number of polymorphic markers to achieve
genome coverage is slow because it is a sequential process. Once markers are
identified, the cost of scoring the markers (genotyping) is high and the
throughput low. We need tools that can support high-throughput genotyping at
reduced cost per data point.

 

Advances in molecular studies      

Illumina
Infinium Beadchips and Affymetrix Axiom GeneChip Arrays are the more recent arrays
developed for high throughput genotyping. Illumina Infinium assays with Bead Array technology
are based on a two-color single base extension from a single hybridization
probe per SNP marker with allele calls ranging from 3K to over 5 million per
sample (Steemers and Gunderson, 2007). Affymetrix Axiom technology based
on a two-color, ligation-based assay with 30-mer probes allowed simultaneous
genotyping of 384 samples with 50K SNPs, or 96 samples x 650K SNPs (Hoffmann et
al., 2011).

            Diversity Array Technology (DArT) is
sequence information and assay independence method that can be used for
high-throughput diversity analysis at low cost per data-point compared to
earlier markers. It was developed in rice and has been used in wheat, barley,
sorghum, chickpea, sugarcane, eucalyptus, Musa and others. These are
primarily dominant markers or based on differences in intensity; which limits
its use in certain applications.