A step forward in rice research

Genomes of 186 Bangladeshi rice varieties have been sequenced in Beijing Genomics Institute, China as part of a global collaborative project, opening up new opportunities for varietal developments.

These include rice germplasms, high yielding varieties (HYV) and advanced lines. Germplasm is the living genetic resources such as seeds or tissue that is maintained for the purpose of animal and plant breeding, preservation and other research uses. 

Rice breeders and scientists are elated at the latest development of rice genomics. They believe this new understanding of rice gene pool would help them breed new generation rice varieties that are more productive, stress tolerant, less environmentally damaging and more climate-smart.

A genome is an organism's complete set of DNA that contains all of the information needed to build and maintain that organism. A genome sequence is like an inbuilt instruction book that tells living organisms how to grow and react to the environment.

Each rice plant has about 400 million "genetic letters" in its genome sequence while the human genome is made up of over 3 billion of such letters.

Md Sazzadur Rahman, a Bangladeshi rice scientist, who is working on developing carbon dioxide (CO2) efficient rice variety, told The Daily Star that genome mapping of so many rice breeding lines comes as a boon for the research he is carrying out.

He has been studying on CO2 responsiveness of rice varieties by randomly picking some 202 germplasms from the gene bank of Bangladesh Rice Research Institute (BRRI).

"Now that I'm getting complete genome sequences of some of these germplasms (24 to be precise), it'll be helpful for me to try developing the CO2 efficient rice in future," hoped Sazzad, a senior scientific officer (SSO) at BRRI Plant Physiology Division.

CO2 is a potent greenhouse gas and plays a vital role in regulating the earth's surface temperature, currently constituting about 0.04% or in other words, 400 parts per million (ppm) of the atmosphere.

"There are some projections that CO2 concentration may reach 600 ppm by 2050. So we've to prepare now for developing rice varieties that are able to withstand high temperature in future," said the BRRI scientist.

The genome sequencing of 186 Bangladeshi rice varieties comes as part of an international collaboration -- 3K RGP (3,000 Rice Genomes Project) -- that accomplished the decoding of 3,000 rice varieties of 89 countries.   

 Three research institutions -- the Chinese Academy of Agricultural Sciences (CAAS), the Beijing Genomics Institute (BGI) Shenzhen and the IRRI -- collaborated to sequence the genomes of 3,000 rice varieties and lines stored in the IRRI (82%) and the CAAS (18%) gene banks. 

Bill and Melinda Gates Foundation, and the Chinese Ministry of Science and Technology jointly funded the sequencing and the initial analysis.

Of the 186 decoded Bangladeshi rice breeds, seeds of 179 germplasms and four advanced breeding lines were taken from the IRRI gene bank while seeds of two high-yielding varieties (BR11 and BR24) and one advanced line were taken from the CAAS collection.

The homegrown traditional varieties include Binnaful, Hijol Digha, Jabor Sail, Kalabokri, Lal Moti, Pankhiraj, Badshabhog, Kushiara, Dhola Aman, Birui Sail and Sada Jira. 

BRRI has a collection of about 8,000 rice germplasms in its own gene depository and duplicate copies of this gene pool are also stored at the IRRI gene bank, Seed Storage Laboratory at Fort Collins, Colorado in USA and Svalbard Global Seed Vault in Norway.

With 127,000 rice accessions the IRRI maintains the biggest collection of rice genetic diversity in the world at the International Rice Genebank in the Philippines. Countries from all over the world send their rice to the IRRI for safe keeping and common public good.

Last week, the Philippines-based IRRI formally placed all the genome maps of 3,000 rice varieties with the UN FAO-based International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) in Rome in a move to set up a global data exchange system for crop genetic resources.

This new 3K RGP data analysis set is massive at 120 terabytes, which is well beyond the computing capacities of most research institutions. However, these new results are now publicly available online as an Amazon Web Services (AWS) Public Data Set. 

 BRRI sources said they have so far downloaded genome maps of 10 varieties and would access others gradually.  

Some BRRI scientists said they would not be able to make the best out of the huge genome resources unless they are equipped with powerful internet servers, computers and better trained manpower in bioinformatics.

Bioinformatics is an interdisciplinary field that combines computer science, statistics, mathematics and engineering to analyse and interpret biological data.

There is not a single bioinformatician at the BRRI at the moment.

Dr Zeba Islam Seraj, who teaches biochemistry and molecular biology at the University of Dhaka, told The Daily Star that her lab has got two bioinformaticians.

"Soon we're going to offer bioinformatics training from the newly set up Centre for Bioinformatics Learning Advancement and Systematic Training," she said.

Dr Zeba, the scientist behind developing the country's first transgenic salt-tolerant rice, said establishment of a genomic institute could help provide lab facilities for genome sequencing and data analysing of varied plants.     

On completion of 3,000 rice genome sequencing, CAAS President Jia-Yang Li, BGI Chief Executive Jun Wang and IRRI Director General Robert Stewart Zeigler wrote a joint commentary in the UK-based Giga Science journal.

They said, "For this ambitious effort to be meaningful beyond the scientific community, significant investments will have to be made in measuring plant performance under a wide range of conditions, as well as the development of data management approaches that can apply the genetic knowledge to practical uses."