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.