Biomarker
Nama : Arya Wira Wardhana
NPM : 21025010035
Class : A
Biomarker
Plants endure various
unfavorable climatic conditions during their growth cycle. Such conditions
consist of biotic stresses, including attack by herbivores and infection by
pathogens, and abiotic stresses, including heat and cold, drought, nutrient
scarcity, higher salt levels, and harmful metals and metalloids (arsenic,
cadmium, and aluminum) in the soil. Temperature (heat or frost), drought and
salt are the main and most commonly encountered climatic factors that reduce
agricultural yields. These impacts are a dangerous sign for food security and
also affect the geographical distribution of plants in nature. Climate change,
i.e. long-term changes in weather patterns, is a significant source of abiotic
stress. The plant's constitutive basal defense system is triggered upon
introduction of stress. Several signaling pathways are activated differently
depending on the type of stress. Typical defense pathways are regulated by
enzyme kinases and phytohormones. For example, ion channels are stimulated by
jasmonic acid, abscisic acid, ethylene, and salicylic acid and through the
generation of reactive oxygen species (ROS). These factors accumulate and
reprogram the genetic and metabolic machinery. Defense responses reduce
biological losses caused by stress; this process is the basis of plant
tolerance.
Plant production and
yield are mainly affected by abiotic stresses due to adverse changes in
environmental conditions. External factors that affect plant growth or
condition are usually labeled as stress in biological terms. Stress is
recognized as a major diversion from the normal plant life cycle. Plants
exposed to stress display three basic response phases: first is the alarm phase
(initiation of stress), the second is the resistance phase (activation of
defense systems), and the third is the exhaustion phase (loss due to stress).
The effect of stress on plant systems is observed in many crops, affecting
plant growth. Salinity is a major climatic factor that limits growth and
productivity. It affects biological characteristics by increasing water acquisition
and retention and altering the management of ion homeostasis. Furthermore,
drought stress (regular water scarcity) will lead to reduced plant survival,
development and growth. Drought is usually associated with a lack of available
water in the soil, but can also be exacerbated by excessive evapotranspiration.
Such stress can occur under humid conditions and with high air temperatures,
i.e. higher temperatures in the surrounding atmosphere. This stress is caused
by an imbalance between water uptake from the soil and water loss through
evapotranspiration fluxes.
Impact of abiotic stress
on agriculture
Changes in nutrients and
their management, along with variations in biosynthetic capacity, are major
factors that ultimately reduce or stop plant growth. Protective systems for
plant survival under abiotic stress are essential for maintaining plant growth
and production levels in the agricultural sector. Abiotic stress defenses can
be explored and understood using molecular genetics. Stress defense systems have
been well studied with such methods, focusing on stress tolerance. Salinity,
drought, heat, nutrient scarcity, heavy metal levels, water/air pollution,
light photoperiodicity and intensity can all cause abiotic stress. These
factors can affect plants individually or together and can ultimately alter
metabolic systems to reduce productivity, development and growth rates. Higher
levels of stress may not be tolerated and result in plant death. Freedom from
stress is not possible. Therefore, plants exhibit specific metabolic and
molecular responses to survive in stressful environments.
Abiotic stress may entail
changes in soil and plant environmental constituents and conditions that may
lead to reduced yields of primary agricultural crops worldwide. Currently, agricultural
land in unstressed areas accounts for only 10% of crop production. The
remaining 90% face one or more environmental stresses. Plants continue to adapt
to abiotic stresses biochemically, physiologically, molecularly and
phenotypically. However, a constant need exists for additional efforts to
improve stress tolerance by genetically enhancing plant defenses, promoting
technologies for resource conservation, and adopting other approaches
Application of DNA
Markers for Abiotic Stress Tolerance
RAPD Marker Analysis for
Salinity and Drought Stress
Random amplified
polymorphic DNA (RAPD) is a PCR-based marker. The initial sequence data of the
sample is not required in RAPD analysis. Many loci from many individuals can be
analyzed for screening purposes using limited resources. RAPD is widely used
due to its easy experimental methodology and excellent genetic screening of
intra- and interspecific hybrids.
These markers are useful
for identifying salinity stress tolerant genes in many crops. Various
mechanisms are available to plants for tolerance/resistance to salinity stress.
Such responses are genetically regulated. Therefore, improving salinity
tolerance in agricultural crops is very important, especially in
salinity-affected areas. DNA markers can help identify and categorize
salt-tolerant genotypes. Utilizing PCR for RAPD amplification of specific DNA
sequences is a basic approach to detect salt-tolerant genes. A study was
conducted in wheat to evaluate the genetic diversity of salt-resistant
genotypes using plants grown in salt-affected fields. These DNA markers
effectively distinguished salt-resistant genotypes from salt-sensitive
genotypes. Polymorphic primer pairs between tolerant and sensitive genotypes
confirmed genetic variation.
Various changes in DNA
can be caused by salinity stress, such as structural damage and rearrangements.
Such changes are caused by secondary stresses, such as oxidative damage
associated with the formation of ROS (hydroxyl radicals, singlet oxygen,
superoxide and hydrogen peroxide). RAPD markers help identify genetic instability
of salt-affected (NaCl-treated) cotton seedlings. RAPD markers showed missing
DNA bands on agarose gels, weak or strong band intensity, and the presence of
new bands compared to control plant DNA. Previous findings confirmed that the
application of RAPD can successfully investigate toxicological stress. The RAPD
primer OPA08 is informative and has significant potential to identify DNA
variation affected by NaCl (saline) stress. Unfortunately, some problems still
exist for the application of the RAPD technique
Identification of Genetic
Diversity under Heat and Freeze Stress
Screening for
heat-resistant varieties or genotypes under field conditions (morphological
screening) is not preferred due to uncontrollable climatic influences that
jeopardize the repeatability and precision of the experiment. In addition,
assurance of regularity of high temperatures (heat stress) in the growing area
is not possible. Genetic assessment of quantitative characteristics for
adaptive responses is mandatory. Molecular analysis enables the utilization of
specific genotypes in breeding strategies to improve yield stability and crop
sustainability under severe stress.
Heat resistance is a
multi-genetic characteristic with various resistance components regulated by
different sets of genes in different tissues or at different growth stages.
Sequence-related amplified polymorphism markers (SRAP) are PCR-type molecular
markers that retrieve DNA fragments in a single PCR reaction. These DNA markers
amplify multiple alleles and polymorphic loci and are reproducible. SRAP can
amplify specific active and efficient genes, as gene sequences are required for
this method. Due to their multiallelic and multilocus properties, these markers
are often favored for DNA fingerprinting, genetic diversity evaluation, and
gene mapping. Random distribution across the plant genome is not suitable for
the use of SRAP markers. Another DNA marker, target region amplified
polymorphism (TRAP), is an efficient and active PCR-type marker that works with
two 18-mer DNA primers. One primer is "fixed" from an EST (expressed
sequence tag), while the second primer is linked to one of the GC- or
AT-abundant nuclei to pair with an exon or intron.
These markers were
applied to wheat genotypes grown for heat resistance. Genetic analysis was
performed for SRAP and TRAP markers to evaluate genetic diversity in durum
wheat genotypes. Genetic diversity in agronomic characteristics under heat
stress was identified. Field performance data based on agronomic traits use
multi-genetic and complex forms. However, marker-assisted information from SRAP
and TRAP analyses is valuable for the identification of genetic diversity in an
impartial manner compared to agricultural morphological evaluation.
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