Pakistani scientists develop DNA “barcode” to identify salt tolerant plants

Published January 21, 2015
The research is the doctorate thesis of Uzma Munir (r) under the supervision of Dr Qamarunnisa (l). — Photo by Suhail Yusuf
The research is the doctorate thesis of Uzma Munir (r) under the supervision of Dr Qamarunnisa (l). — Photo by Suhail Yusuf

KARACHI: Pakistani scientists have developed a “genetic barcode” system which could be used for accurate and quick identification of medicinally important halophytes (salt tolerant plants) across the world.

The method can be a valuable tool for plant taxonomists to find useful halophytes. The scientists from the Dr A Q Khan Institute of Biotechnology and Genetic Engineering (KIBGE) at Karachi University collected different species of genus, Suaeda or Sea Blite commonly found in Asia.

They also gathered different samples from across Pakistan and they targeted specific chloroplast gene with the hopes of finding a similar DNA sequence to develop a potential bar code common in halophytes.

The team examined Suaeda. fruticosa, S. monoica, S. acuminata, S. heterophylla and S. oluf species. They studied three chloroplast DNA (cpDNA) regions rbcL, matK and psbB, psbN, psbT and one nuclear DNA (nrDNA) region or Internal Transcribed Spacer (ITS) was tested for the identification of Suaeda species.

To develop the barcode, the scholars studied 11 fresh and herbarium samples of five different species of Suaeda. The samples were collected from Uthal and Hub, Balochistan and five different cities of Sindh and Punjab.

Different species of Suaeda. — Photo by Bilquees Gul
Different species of Suaeda. — Photo by Bilquees Gul

The results showed similarity in rbcl and ITS region of plants as they were conserved or common in all species of Suaeda and declared as DNA barcode for quick identification.

Halophytes like Suaeda grow in desert and saline areas but are often very difficult to identify as they change their appearance in response to climate and soil conditions.

Sometimes experts are even left puzzled by two plants of the same species.

“The plant DNA barcode has been developed for first time in Pakistan. It also showed promising results when the sequence was compared with the National Centre for Biotechnology Information databanks,” Dr. Syeda Qamarunnisa, one of the researchers at KIBGE, told Dawn.com.

Now, the team is studying the possibility of whether the barcode can be applied to halophytes other than Suaeda.

“The method can also be used to identify other important halophytes of different genus,” Qamarunnisa said.

Different species of Suaeda are used as medicine, fodder, fuel and other economically benefits. For instance, Suaeda fruticosa is used in baking soda and while its tree is used for fuel. Suaeda monoica is used for ointments for wounds and in traditional medicines for hepatitis.

In 2012, scientists from other than KIBGE noticed antibacterial, antioxidant and anti-cancerous properties in the leaves of Suaeda fruticosa, however, some other species of suaeda needs to be evaluated for healing properties.

The research by the scientists in Pakistan is the doctorate thesis of Uzma Munir under the supervision of Dr Qamarunnisa and Dr. Anjum Parveen. In their previous work, the researchers extensively worked on medicinal properties of Suaeda.

Dr. Bilquees Gul, the Head of the Institute of Sustainable Halophytes Utilization (ISHU) at Karachi University, agreed that identification of Suaeda was difficult and the DNA barcode developed by the scientists could play a very important role in recognising useful species of Suaeda.

“Suaeda is a highly variable species that lives in an extremely challenging and variable environment. DNA barcoding of this plant is a very interesting subject. It can be used for clear cut identification of a species which is not generally possible by classical taxonomy.

“Barcoding will not only help to speed up the identification process but also for phylogenetic conclusions. More work to be needs to done for application of this technique for practical purpose,” Gul told Dawn.com.

How DNA barcoding works

DNA barcoding is a comparatively new technique in which almost every plant or animal can be identified through matching genetic make up between species.

The other established technique is taxonomy, a study of physical appearance to identify animals, birds and plants.

By establishing a DNA region as a yardstick from the genome of an animals or plants, a barcode can be developed to identify other close species. It works in the same way as scanners and the black stripes on the products in super stores.

The one good example is 648 base-pair region in the mitochondrial cytochrome c oxidase 1 gene (“CO1”) that is being used for the identification of many birds, butterflies and fish.

The scenario is different in plants as rbcl and matK are being used as the barcode regions. However, the technique will produce more viable results if used with taxonomy.

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