By Saiful Bahri Kamaruddin
Pix Ismail Ibrahim, Penerbit UKM

BANGI, 9 Oct 2012 – Agriculture in Malaysia needs to be given a boost through research using the latest gene sequencing techniques that have now just being made available in the country, according to two scientists from the private sector.

Dubbed The Next Generation Techniques, they said the new techniques will allow smaller institutions with smaller budgets to do genetic research at affordable costs.

Dr Vahid Omidvar and Chan Wei Hseng from a Shah Alam-based biotechnology company Bioeasy were addressing a one-day seminar on Application of RNA and RAD-Tag Sequencing in Agriculture at The National University of Malaysia’s (UKM) Institute of Systems Biology (INBIOSIS) here today.

Dr Omidvar said, as new methods of sequencing genetic material of plants are offered to researchers, it would be easier to improve crop production in comparatively shorter periods.

RNA-sequencing (RNA-seq) of DNA is the process of reading the nucleotide bases in a DNA molecule, the information that determines the characters of every living thing. Nucleotide bases are basic proteins that are the building blocks of DNA and RNA.

DNA and RNA sequencing includes any method or technology that is used to determine the order of the four bases—adenine, guanine, cytosine, and thymine—in a strand of DNA.

Dr Omidvar said such applications can be used in the palm oil industry to propagate breeds of trees which can produce more fruit.

He explained that RNA-seq is particularly helpful in finding out which gene makes the oil palm fruit ripe, so that scientists can modify the gene to produce a variety of faster ripening fruit.

He cited the example of European scientists in Italy who successfully produced a wide variety of egg-plants or brinjals, to cater to rising consumer demand in the Mediterranean market. Other European researchers are now using RNA-seq to determine the genetic makeup of tomatoes and potatoes – all of them important cash crops on that continent.

He also proposed that researchers examine rice seeds more closely, as RNA-seq can be applied to further examine the DNA sequence of the very important food crop in Asia. He explained that traditional methods of sequencing takes years compared to RNA-seq that might only take months to complete.

One example of RNA-seq suitable for rice is Exome sequencing, which targets only the protein-coding regions, is currently a favored approach. It is less expensive than sequencing the whole genome.

He said our ignorance of genome function makes it difficult, if not impossible, to assess the impact of non-coding variants. RNA-seq provides a more comprehensive view of the transcriptome with one experiment.

Dr Omidvar listed out its advantages over other methods as: not dependent on prior knowledge, no design work required, increased dynamic range and sensitivity due to its ‘digital nature’, informative for splicing variation, lower cost, scalable in proportion to depth of sequencing and facilitates downstream applications such as mutation detection or RNA editing.

His colleague, Chan Wei Hseng, a UKM alumni and also a researcher in the company proposed Restriction Site Associated DNA (RAD) markers or RAD-Seq, which are actually a type of genetic marker that can be used for genetic mapping. The use of RAD markers for genetic mapping is often called RAD mapping.

Chan said RAD-Seq can be used to carry out population genetic studies on species with no, or limited, existing sequence data and has several advantages over previous methods for marker discovery. It is cheaper to carry out and yet more comprehensive compared to other techniques, which are more complex.

He said there is a huge catalogue of crop species to be researched, it would be better for agricultural scientists to save time by using the The Next Generation Techniques.