Controversy over pigeonpea genome
Two separate groups of Indian scientists have laid claim on cracking the genome of the humble pigeonpea — called the poor man’s meat — sparking off a controversy on the prestigious genome projects.
Last week, the Indian media was abuzz with news of the complete genome sequencing of the protein-rich legume by a group of 31 scientists of the Indian Council of Agricultural Research (ICAR). Simultaneously, embargoed press releases of a paper on pigeaonpea genome sequencing by an international group of scientists, including those from Hyderabad-based International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), were also received by mediapersons.
The close proximity of these announcements was striking. The ICAR scientists reported their finding online1 on October 25, 2011 and posted a press statement on the ICAR website on November 2. The ICRISAT group, partnering with Chinese and American organisations, published their paper 12 days later on November 6, 20112 but an embargoed press release was doing the rounds on November 1.
The major difference between the two sequencing projects is that while the ICRISAT-led team has assembled 605.78 Mb out of the 833.07 Mb (about 72.5%) of the genome, the ICAR team has captured 511 Mb (about 61%). Both groups have submitted their data to the US-based National Centre for Biotechnology Information (NCBI) Genbank, an open access, annotated collection of all publicly available nucleotide sequences and their protein translations.
Nagendra Kumar Singh, leader of the ICAR team and a professor at the National Research Centre on Plant Biotechnology of the Indian Agricultural Research Institute, claimed that it was not a case of parallel efforts. Calling the incident ‘unfortunate and sad’, he said,”It is not a case of two parallel sequencing projects. ICAR started the Pigeonpea Genomics Initiative (PGI) coordinated by me under the Indo-US Agricultural Knowledge Initiative (AKI) about five years back when there was absolutely no genomic information on pigeonpea,” he told Nature India.
ICRISAT, he said, was made a partner in this proejct by ICAR with a funding of about Rs 2 crores over four years “hoping that, located in our own backyard for over 50 years, they can play the same role in improving legume productivity as IRRI and CIMMYT did for rice and wheat.” Later, ICRISAT got collaborators to do the sequencing at a much cheaper price and so did not continue with them, he contends.
However, lead researcher of the ICRISAT-led team Rajeev Varshney, who was also part of the Indo-US AKI project earlier, disagrees. “The AKI project was aimed at developing genomic resources and no genome sequencing was done. After the project ended, we and our global collaborators started to move towards sequencing the ‘Asha’ genotype of pigeonpea that was developed and released by ICRISAT,” he told Nature India. This work was funded by Washington-based Consultative Group on International Agricultural Research (CGIAR) Generation Challenge Programme and supported by the Chinese genome firm BGI-Shenzhen, ICRISAT and collaborating US and UK institutes.
Varshney says he presented the first glimpse of the pigeonpea genome in January 2011 at a conference in San Diego, USA followed by a workshop in Bali and an Indo-Irish scientist meeting in Bangalore in mid 2011.
The ICRISAT scientist further says that after completing and analysing the genome sequences, his team started discussions with all partners around mid June 2011. “N. K. Singh was also asked to join the author list. Two early versions of our manuscript were sent to him in late June and early July. He asked us to remove him from the author list and keep him in the acknowledgments,” Varshney says.
He says they had no knowledge that Singh and his team were planning to write another paper and so kept him updated with all communication with the journal as well as the acceptance of their paper. “Although our manuscript was accepted on October 3, 2011, we could not convey it to anyone because of the embargo from the journal”, he adds.
Varshney alleges that while Singh was part of the global team, he never told any member of the team about generating genome data. “After working for about two and half years in collaboration with more than 10 partner institutes, he (Singh) told us in mid June 2011 that they too had generated some sequence data. We were surprised to know this.”
Singh says that after the AKI project ended, they received additional funds from ICAR under another national project for pigeonpea sequencing and began generating data by outsourcing the sequencing runs to private service providers. “I wanted ICRISAT to allow us to merge the two assemblies and get a more complete coverage before rushing for publication but the response was in the negative,” he says.
Varshney explains that it was too late to include the ICAR data in the assembly and redo the analysis. So they went ahead with the manuscript in which Singh did not want co-authorship. “But he never told us that he is planning to submit a manuscript based on his data.”
Singh acknowledges that the “controversy will be there for some time to come” while urging that the situation called for objective assessment of facts.
Confusion and duplication of efforts apart, the genome sequencing brings a lot of cheer to plant scientists as it would enable them to identify the structure and function of more than 48000 genes of pigeonpea (called ‘arhar’ in Hindi). Incidentally, pigeon pea is the first ‘non-industrial crop’ and the second food legume (after soybean) to have been completely sequenced.
India is the largest producer of pigeonpea but crop productivity in the country is less than a ton per hectare. The sequence data would be crucial for crop improvement and sustainable food production, especially in economically backward regions of Asia and sub-Saharan Africa. “There are some unique genes that impart drought tolerance to pigeonpea. This trait can be transferred to similar crops like soybean, cowpea or common bean,” Varshney says.
Pigeonpea is grown on about 5 million hectares in Asia, sub-Saharan Africa and South-Central America. Because of their high protein content, legumes have been part of the daily diet of poor people in these regions. With the genome sequence as a reference, it would be faster and cheaper to screen ‘good genes’ from seed collections stored in genebanks. This would also help cut down on the time taken to breed new varieties from 6-10 years to just about 3 years.