Starchy matters

Despite being an important crop required for food security, the potato cannot be grown in most parts of southern India. Simply because, the crop requires soil temperature to stay below 20 degrees Celsius, which is not found in the Deccan.
Thousands of miles away, scientists sitting amidst picturesque hills in Shimla, plan to change the age-old practice.

Researchers from the Central Potato Research Institute (CPRI) are part of the global Potato Genome Sequencing Consortium (PGSC), which hopes to map the potato genome by the end of 2010.

Once the genome is complete, the CPRI team’s first priority would be to find out how this tuber crop can be genetically manipulated for growing in warmer regions.
The consortium began working in January 2006. After three-and-a-half years, the first draft of the potato genome was put up on the PGSC website in September, 2009. The scientists said at least one more year is required to complete the entire gene map of the ubiquitous potato.
Potato, a key member of the Solanaceae family, is a close relative of tomato, pepper, and eggplant. It is the world’s third most important food crop and most critical vegetable crop.

Improving yield, quality
Access to the genetic blueprint of how a potato plant grows and reproduces, is anticipated to assist potato scientists in improving yield, quality, nutritional value and disease resistance of potato varieties.
More importantly, the potato genome sequence will permit potato breeders to reduce the 10-12 years currently needed to breed new varieties.
In 2007-08, India produced 28.47 million tons of potato. The total area under potato cultivation is estimated to be about 1.55 million hectares. As potato requires a cooler climate, bulk of the potato in India is produced in Punjab, Uttar Pradesh, Bihar, West Bengal and Assam as a vital winter crop. It is also an important summer crop in Himachal Pradesh.  In fact, because of the temperature factor, in south India potato is grown only in pockets like Ooty, Chikmagalur, Hassan and Dharwad.
Crop scientists apprehend that because of increased temperature, potato production in north and east India may dip.
“That’s why we will be looking for genes which will help create a potato variety that can be grown even if soil temperature stands at 25 degrees,” CPRI biotechnologist Swarup Chakrabarti and one of the members of PGSC said.
Even though the official estimates for 2008-09 is still not out, according to CPRI estimates, it could be around 26 million tonnes because the crop suffered heavy damage in the eastern region due to late blight epidemic. Fighting the blight through genetic tinkering is another long-term objective of the scientists. To meet both objectives, the starting point would be to have a complete potato genome sequence.

The potato genome sequencing consortium was initiated in January 2006 by the Wageningen University in the Netherlands. Since then it has grown into a global research effort with contribution from scientists in 14 countries.

The CPRI represents India in the consortium which has three Latin American nations, Argentina, Peru and Chile, besides The Netherlands, China, Russia, New Zealand, USA, UK, Ireland and Poland.
Each copy of the potato genome consists of a dozen chromosomes and has a length of approximately 840 million base pairs, making it a medium-sized plant genome. Most lines of potato, such as the widely cultivated Solanum tuberosum, have four slightly different copies of the genome that can be traced to parents and grandparents, with some recombination occurring during sexual cycles.

Mapping chromosome-2
Because of the genome’s complexity, it was decided countries will split the burden. India’s responsibility was mapping the chromosome-2. The tedious mapping process began and then accelerated, thanks to two critical developments.  
The first breakthrough comes from Virginia Tech scientist Richard Veilleux who contributed a unique potato variety that puts sequencing on fast track.
Contrary to regular potato which carried four copies of the chromosome or a research version carrying two copies, Veilleux’s Solanum phureja line was unique because of only one copy of the genome (known as a “monoploid” in scientific parlance). This simplified the PGSC task.

The 12 chromosomes in monoploid version was artificially doubled to make the potato a double monoploid, which the consortium decided to sequence using whole genome sequencing technology, which provided the second big push to the project.
In 2008, the consortium initiated sequencing of the doubled monoploid (DM) potato to simplify and complement the original effort. In June 2009, PGSC members met in Carlow, Ireland to plan the final phases of the project and the first draft of the DM version was made public in September end.

“Sequencing the DM will act as a reference to the tuberosum genome. The genetic mapping of both lines is expected to be completed by 2010 end,” he said.
The Potato Genome Sequencing Consortium on its website, however, claimed that it hope to finish the work by 2009 end.
Thanks to a new computer programme developed by the Beijing Genomics Institute, the potato genome assembly, which is publicly available on the PGSC website covers 95 percent of potato genes.

Over the next six months, PGSC members will update the genome with an annotation of the genes, an analysis of when and where they are switched on and off, and a review of specific suites of genes critical to potato production. “Availability of whole genome sequencers in the last two years fast tracked the process. The potato research institute acquired one in August 2009,” Chakrabarti said.