In a vast forest area, a majority of numerous species—from the tiniest fungus to the tallest human being—are benefitting from an important wealth of product and ecosystem services from forests. These products include wood, fruits, vegetables, and medicines. Forests and trees also provide shelter for insects, animals, and other living beings, which are very essential for the ecosystems. Forests hold various functions benefitting the human population in terms of livelihood, economy, ecotourism, and as well as biodiversity.

However, with the ever-changing environments and increase in global average temperatures, some species of forest trees fail to cope up to such changes while others (under the same species) succeed in adapting in order to survive. By assessing the genetic makeup of the forest trees through DNA analysis, the differences among similar trees can be distinguished with the aid of molecular tools that can scan through the genetic constitution of the trees.

The variation that is observed in the genetic makeup of species is called genetic diversity. With more genetic variations, it is more likely that some individuals possess alleles (alternative form of genes) that better suit the environment; and because of the success of these individuals, their population will continue for more generations.

Having less genetic diversity leads to uniformity, with population having individuals less likely to adapt and survive in the changing environment. For instance, modern agriculture employs the use of monoculture. This is beneficial in terms of growing and harvesting crops but in the long run, it will be a problem when a disease or parasites attack the field. Due to genetic uniformity, every plant is vulnerable.

The same is true for forest trees. Tree domestication tends to decrease genetic variability as limited plants are selected and propagated. Little genetic variation within a species impedes the process of healthy reproduction as evident by the expression of harmful traits in the offspring resulting from inbreeding (mating of genetically related organisms). Inbred trees grow that develop slowly, are often deformed and many die suddenly and inexplicably before reaching maturity. Few inbred trees survive and reproduce in natural forest setting.

With low genetic diversity comes increased susceptibility to disease and increase mortality of the population in environmental disturbances. In 1890, an epidemic had spread across Panama wiping out hectares of banana production. Being genetically identical, banana plants are susceptible to the fungal disease, providing little to no resistance against the disease. Such scenario ultimately leads to extinction of the population and eventually extinction of the species.

Genetic variations

In order for plant geneticists to tell apart genetic variations, they use segments of DNA (deoxyribonucleic acid) sequence of the individuals to mine them out despite the limited availability of whole genome sequences from forest trees species. These segments of DNA are called DNA-based molecular markers which are widely used in studying genetic diversity, as well as for identification of species.

Mr. Jordan Abellar, ERDB-based Biologist ensures proper collection on plant materials for the DNA analysis

Mr. Jordan Abellar, ERDB-based Biologist shared the processes involved in the genetic diversity study. According to Mr. Abellar, after collecting the plant material (leaf, stem, or root), careful optimization of protocols follows wherein the DNA of the material is isolated. This process is called DNA extraction. The process involves breaking the cell wall and cell membrane (cell lysis), removing the organelles, and destroying the nuclear membrane. After these processes, the “purest” DNA can be extracted.

Having a desirable amount of DNA with superior purity, molecular biologists then subject this DNA to a temperature sensitive process that produces millions of copies of it in a matter of an hour or two. This copying process is called DNA amplification or polymerase chain reaction (PCR) discovered by Nobel Prize winner Kary Mullis in 1985. It involves a series of heating-cooling-heating the DNA. These temperature changes allow the enzymes and other reagents to copy the target regions (molecular markers) of the DNA.

PCR is an indispensable technique known to be used in medical and clinical laboratory research including forensic science in crime scene investigations. It also holds a potential swing in improving forensic botany for higher productivity and survivability of forest trees species and for the trees to achieve superiority in growth parameters.

ERDB’s studies

The Ecosystems Research and Development Bureau of DENR has initiated genetic diversity studies of priority forest tree species in the Philippines. In its early year since the establishment of ERDB’s Forest Molecular Biology Laboratory, its researchers have been harnessing the potential of Random Amplified Polymorphic DNA (RAPD) markers to assess the levels of genetic variations of indigenous forest tree populations.

Schematic diagram of the laboratory procedures for genetic diversity analysis. Presented by JMAbellar

To cite a few, according to Dr. Maria Theresa delos Reyes, Supervising Science Research Specialist and ERDB’s project leader for genetic diversity study of indigenous forest tree species, the team had already assessed the genetic diversity of Limuran (Calamus ornatus Blume var. philippinensis Becc.) in different sampling populations across the Luzon Island. Thirty to fifty samples were collected from several provinces. The study found Bataan population holding the highest genetic diversity, therefore was rendered as a potential source of genes useful for tree improvement and breeding programs; while for Narra (Pterocarpus indicus Willd.), Ilocos was the most genetically diverse population.

Narra leaf samples ground in liquid nitrogen: the starting material for molecular analysis. Photo by JMAbellar

Because of the limitations presented by RAPD markers, ERDB utilized a new marker system called Simple Sequence Repeats (SSR). Using these molecular markers, the assessment of Kaway­­an tinik (Bambusa blumeana Schultes f.) was completed. Results revealed that the Pangasinan population was the most genetically diverse (Delos Reyes M.A., et al., 2015).

To date, Dr. de los Reyes mentioned that the diversity of five forest tree species (Narra, Benguet Pine, Bagalunga, Molave, and Ipil) are included in the study Assessment of Genetic Diversity of Priority Forest Tree Species through DNA Analysis of the Genetic Improvement of Priority Forest Tree Species for Quality Wood Production Project after being selected based on the criteria stated in DAO 2010-11 “Revised Regulations Governing Forest Tree Seed and Seedling Production, Collection and Disposition”. Moreover, transferability of these SSR markers to progenies planted in Progeny Test Plantation of the Progeny Tests Cum Seedling Seed Orchards study is being documented. The genetic diversity of these plantations is also being assessed.

Genetic variation is the basis of evolution and the catalyst for species to adapt to ever changing environment. Hence, “Assessment of genetic variation among and within populations is essential for the success of any tree breeding and selection programs for both in situ and ex situ conservation. It holds vast potentials for the preservation of the forest ecosystems in the Philippines” said Dr. Sofio B. Quintana, ERDB Director. He further stressed that “The implementation of efficient measures to conserve the genetic resources of forest tree species in the Philippines can be addressed by having a complete understanding on the patterns of genetic variation within species”.

As the country faces unceasing deforestation and its accompanying loss of genetic resources for its biodiversity, the necessity to study the genetic diversity and molecular characteristics of forest tree resources is very imperative and timely. Karol Josef Lucena, Jordan Abellar and Jorge Cyril Viray

Amplified! A thermal cycler unit for producing millions of copies of DNA. Photo by JMAbellar

 

Observing the genetic variations between two Molave individuals. Different banding patterns were generated using similar SSR markers. Photo by JMAbellar