Controversy over pigeonpea genome

Source: http://www.nature.com/nindia/2011/111107/full/nindia.2011.160.html

Subhra Priyadarshini

The humble legume at the heart of the controversy.©ICRISAT

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.

Nagendra Kumar Singh.

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.

Rajeev Varshney.

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.

  • References

    1. Singh, N. K. et al. The first draft of the pigeonpea genome sequence. J. Plant Biochem. Biot. doi: 10.1007/s13562-011-0088-8 (2011)
    2. Varshney, R. K. et al. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat. Biotechnol.doi: 10.1038/nbt.2022 (2011)

 

22 comments

  1. Anand Singh says:

    Rajeev Varshney is misleading the country, he is contradicting himself, he first admits that he sent a manuscript of paper as late as june to Dr. N.K. Singh, a MANUSCRIPT is prepared only when all the research is done. so he basically kept Dr. N.K.Singh in the dark all the while. Dr. Singh did the right thing by refusing to accept authorship in that paper as science ethics say that one should not claim authorship in what he has not contributed intellectiually (though it is sad that certain spin doctors resort to this kind of activity, to please people they try to lure them by offering to include their name in papers) …. anyways, Rajeev Varshney says that he expects the whole of ICAR to keep an eye on what presentations he is giving in IRELAND and other countries to know what research rajjev varshney is doing When Rajeev Varshney himself who says he is an INDIAN scientist does not know what research is going on in the real indian scientific community of ICAR.

    Dr N.K.Singh was very right in deciding to complete the work that they had started in the Indo-US AKI, and to sequence the pigeon pea genome, he had faith in Indian scientists and ICARs competence and was able to complete the same work earlier than ICRISAT who had probably had no faith in ICARs abilities and therefore neglected ICAR despite being funded by ICAR for the initial part of the project.

    Anyways controversy apart, i agree with Dr. N.K.Singh that the data would be beneficial for breeder who now would be able to bring a revolution in creating new varities of pigeon pea. and as an indian i am proud of ICARs indigenous achievement.

  2. Dr. Naresh Kumar says:

    I am viewing this controversy since I got mail from Dr. R.K. Varshney and his partner Rachit Saxena regarding sharing the news and paper in Nature Biotechnolgy.
    A few days after I saw this news flashing on ICAR website and claimed made by Dr. N.K.Singh.
    With due respect to both the great scientists I would like to opine that Perhaps Dr. R. K. Varshney is misleading the scientific society as I feel that the idea would have been originally concieved by Dr. N. K. Singh and copied and carried by Dr. Varshney. Although I would not like to claim but the later has done it with me also when I was doing my part of my PhD research with him in 2009 and I concieved the idea of sequencing mitochondrial genome of A, B, R, lines of pigeonpea in order to understand the switch on and swith off mechanism of male sterilty and I even delivered a seminar over this. At that time I was involved in isolation of Mitochondrial DNA but as soon as they (Dr. Varshney and Rachit Saxena)found it of worth potential I was just asked to keep away. The real drama started when he sent the DNA for sequencing to USA to get it sequenced through next generation sequencers and report it to be done first in India but the company asked them to reconfirm wether it was real Mitochondrail DNA and they could not do it. Later in a personnel communacation with Dr. Rajeev Varshney I was surprised to know that he even didn’t know that pigeonpea is a perennial species originally untill I told him while visiting the field with one scientist from USA. Although I had many issues on ethical grounds where I was actively involved in experimentation and the credit was denied. He has played with the time and emotions of many young researchers and used them as biorobots for his genomics industry while promoting favouritism. He even dared me to see me to my life and get me finished. Despite of all, I wish the genome information should be used for the betterment of science and development of resources.

  3. Dr. Ashish Kumar says:

    First of all my heartily congratulations to team ICRISAT who brought our Indian pigeonpea at the global platform by publishing this work in a dream journal of every scientist; Nature Biotechnology.

    I was fortunate enough to be associated with Rajeev’s group. Even it is not required but still I would like to tell the community that all the students working with him are getting all the due credit and as a result all of them are publishing good quality articles in high impact factor journals. Everybody from that lab is flourishing excellently and getting good opportunities ahead in their life in India as well as abroad.

    With due respect to Dr Naresh who is known to me from Pantnagar days and was working with this group for almost one and half year, also got a publication as a co-author in BMC Plant Biology despite of his unethical code of conduct in his PhD submission.

    Dr. Varshney has never harmed any student and I am having several examples who are having the papers in their credit even after leaving the lab. Dr Naresh should not mislead the scientific community for his personal grudges. Dr. Varshney is not only a great Scientist, but also a wonderful person who has always helped several students to achieve their dream goals in their career and writing such things about him is nothing but a foolish note. Regarding the Pigeonpea genome we should talk about betterment of science not who sequenced first who second! SCIENCE SHOULD NOT HAVE ANY BOUNDRIES OR LIMITS………………………

  4. Anand Singh says:

    Dr. Ashish Kumar.

    I respect your eternal loyalty towards Dr. Varshney, obviously according your own admission he has done alot for you so you must be indebted towards him, i respect that emotion, In todays world honesty and loyalty towards your seniors, teachers and country is difficult to find (you can discuss this with Dr. Varshney )

    But the allegation that Dr.. Naresh is levelling against Dr. Varshney is very grave. A GREAT scientist should never THREATEN any human being. If what Dr. Naresh is saying is true then this a even more serious crime than any crime of stealing credit or opportunism in science

  5. Anand Singh says:

    Now i personally feel this blame game should end. it does not give a good impression of the scientific commmunity,,, God is looking on the actions of every one he will ultimately decide who is right and who is wrong and write destiny of everyone….

  6. Dr. Ashish Kumar says:

    Mr Anand Singh!
    Your comments show that you are working for Dr NK Singh and Dr Naresh Kumar and therefore you are having full time job to write rubbish things on this site and other sites just to malign the image of Dr Varshney. First check your background and ask yourself whether you should really write scientifically incorrect and baseless comments here there. Ask Dr NK Singh- who did unethical thing that he was aware with everything about preparation, communication and acceptance of paper of the global team and without telling anything to them (read above main story), he communicated paper to the journal (chief editor is the last author on the paper and was the handling editor of the paper) which has just 0.5 impact factor. I don’t know your scientific background- but I am not aware with any genome paper which has been published in so low impact factor journal. Anyone who has any knowledge of genomics can clearly tell that either there is some issue with the quality of data or they wanted to get the cheap priority. As you said, I strongly believe that God knows everything- and He will write destiny of people who cheat and spread wrong things. Hope that you will not continue this chain response- if so, I too will continue- so it is upto you what you want! Best thing will be- you use your time in constructive things- and let others do the same – otherwise there is no end for such non-productive discussions!

  7. Anand Singh says:

    i do not work for anyone i am not even into science so that rubbishes your claim ,, anyway the way you are getting agitated and doing mud slinging tells alot about you and your scientific temperament.. first ask Varshney whether he knew about the sequencing going on @ NRCPB or not , ask him whether he was asked by Dr.N.K.Singh to merge the Sequences or not ,,, and ask varshney whether he tried to give the lure of authorship in Nature to Dr N.K.Singh or not ans ask him why did he refuse it ,,, If it is very clear to you that Nature is a very good paper and The one in which ICAR got its paper published was bad then it shows that Dr.N.K.Singh was not greedy of authorship , it was something else, he was loyal to his country by getting the work he had done by the indian taxpayers money published in Public domain in an indigenous effort unlike someone who is hungry for fame and Breaks away from Indian Initiatives despite being funded by the country just see his name in International journals… you tell me if the same could have been done in India as proved by ICAR what was the need for Varshney to run away to get associated with companies like Monsanto.. Now tell who ran away for cheap publicity, the one who broke away opportunistically from the AKI or the one who denied a CHARITY authorship offered by your master and preferred to continue the work which the country had entrusted on him..

    Use your head ,, think objectively, rather just spitting venom ,,

    and i had not even heard the name of Dr. Naresh Kumar earlier. all i had said is that if he has come out with allegation of someone threatening to FINSIH him ,, It is a matter of grave concern ,, now if you find something offensive in this also then i cant help it ,,

    We should end this discussion now,, i am sure the scientific community knows what each scientist stands for ,, it is futile for us to debate over here

  8. Dr. Ashish Kumar says:

    Mr Anand Singh,

    If you are not from the scientific community how do you know about both the scientists and science and who ran away from AKI, went to Monsanto, who is serving best on Indian tax and who is a real Indian (seems like you have good connections). The answers to your questions are already there in the editor’s review read it carefully and asking the same questions again and again does not change the reality that the article was published in a dark room by Dr NK Singh and his intelligent team.

    Very importantly, before you reply ask Dr NK Singh how was it possible for him to have handling editor of his article who is also last author of this manuscript also happens to be the chief editor of the same journal in which article has published. (Seems like the luring for authorship worked to get the article published unethically). I am pretty sure that your limited knowledge in the field of science will not be able to answer this because you may not understand the terms and conditions for publications in any journal, so better ask from Dr NK Singh or any other scientist in the world this time. I am keenly awaiting to hear the answer of this question !!!!!!! All the best!!!!!!!!!

  9. Dr. Ashok says:

    Many many congratulations to Dr Varshney for publication in prestigious journals. I completely agree with you Dr. Ashis. No doubt it’s only scientific jealous and nothing. Research quality of Dr. N.K. Singh anybody can access when he communicated his manuscript in 0.55 impact factor Journal. Dr. Varshney never cheated to scientific community and always helped to many students and scientific comunity. He is very cool and devoted to science. This is not fare because in many previous publications Dr. Varshney has given name of Dr. N.K. Singh. Dr. N.K. Singh should feel proud that one Nature Biotechnology paper published by an our Indian scientist.

  10. Siddanagouda Biradar says:

    Hope this is not the right platform to discuss about Dr N K Singh or Dr Varshney. Please stop discussion here. it’s not good

  11. Ramoo says:

    Dear Siddanagouda! why science and the misconduct in science has to be discussed only inside four walls when it has a bearing on the general society. In fact it is only the scientists who are discussing it. Still not reached to general public.
    ramoo

  12. Siddanagouda S Biradar says:

    Ramoo Sir

    Discussing science and misconduct in science need to be discussed but not the personal issues of any scientist. Let it be purely scientific instead of commenting like “he dared me to see me to my life and get me finished”. It spreads wrong message to public. Let’s respect both Dr M K Singh and Dr Rajeev Varshney for their achievement rather than pointing one and appraising another. Healthy discussion is needed instead of dragging personal issues into the discussion. Neither Dr N K Singh nor Dr Varshney are my teachers but in view of their achievements, capability, high profiled background,their reputation, i feel it’s not good to discuss about their personal issues linking to this Pigeonpea controversy!

  13. Ramoo says:

    I agree with you that the discussion should not fall to this level. But this is the status of the so called scientists in India today. I heard several such things on various platforms where we tried to discuss issues very scientifically on GM crops, Pesticides etc. all this shows the degeneration of science in India. Whatever comments are made are also made by other scientists in response to the article right. The people who never responded to any one of the posting on agrarian crisis, farmer suicides etc have all of a sudden became active to discuss this issue. It shows where their interest lies. We have not taken any position for or against Dr. MK Singh or Rajeev Varshney on this issue. We are only trying to understand the issue otherwise how do people know what is happening inside the four walls in the name science spending public money…

  14. Jai Prakash says:

    First of all i also agree that personal mud slinging should not happen in public domain and Dr. Naresh if Dr. Varshney has really threatened you or used the kind of language that you allege him to have used then you should rather report to the police or take protection of law rather than posting about it here, It wont help anyone by making such allegation here and also the young scientists should also refrain from using language which is unbecoming of a student of science, you should use more objective arguments in a discussion rather using language used in suspense novels and fairy tales, you guys are the future of scientists of tomorrow so kindly bear that in mind.

    Now as far as the debate of the sequencing and science is involved, i agree with Mr.Ramoo that in a country where farmers suicides is such a big issue rather than discussing credit of research what is more important is how does india benefit from this research. As far as i understand that both ICAR and ICRISAT have used the words “Indian Scientists” and the indian government has funded both organizations in sequencing at some stage. so the question which really concern us Indians is that

    on which sequence can india claim intellectual property? Has the sequence been submitted by ICRISAT been submitted in the name of India (the newsreports that we get to read says “Indian Scientists at ICRISAT Decode Pigeon Pea”), Scientists are here today and will in future they wont, what will really benefit this country is the Intellectual Property they leave behind for their country. So can anyone of the above gentlemen please answer this question ? who owns intellectual property of the sequence? in whose name is it submitted ? Will india have to become a slave in front of someone for a research which could have well been done in India?

    Who published first, Who got a paper published in a top journal, what impact factor it has, Which group of scientists sacrificed a lure of authorship in the top journal by the other…. all this is immaterial what really matters is how does our country india benefit, As Dr. APJ Abdul Kalam says an Individuals can never be above the nation, specially in one where the community which feeds the whole of the nation, the farmers finds it difficult to feed himself and his own family.

  15. zack says:

    I can neither vouch for the ICRISAT-led or ICAR-led efforts nor am I interested in knowing who did it first but can certainly say how genome sequencing and the follow up publication works.

    For those of you who are new to this game of genome sequencing, a few facts:

    1. ICRISAT’s effort is v misleading, it’s not an Indian effort, they have outsourced science and analysis to BGI, the factory or A Sequencing BPO, a term that can be easily understood by all Indians.

    2. Publication in Nature Biotechnology has nothing to do with the quality of science but because of the lobby and ICRISAT’s association with folks from the US and BGI. BGI itself lobbies and licks a**es of US/European scientists to get their papers accepted in top-ranking journals. At times, BGI entirely funds the research in some US/European institutions and get authorships for BGI’s scientists in return. This is not science but Political Science.

    3. The ICAR team must make sure that their paper is freely available. In fact, it’s outrageous to even think that the journal, which is primarily Indian (although published by Springer, one of the money-making publishing sharks), publishes papers paid by Indian tax payer’s money is asking the same taxpayers to pay money to see the paper. Not acceptable. Pl post the full paper online free on the ICAR/department site.

    Varshney or whosever, stop playing games. If you have guts and scientific integrity, come to India, establish a lab here, do science here, train students here and then publish your second genome sequencing paper from India with Indian students and scientists in Nature Biotechnology (without any pseudo collaborators from outside of India). If that happens, we shall all bow in front of you.

    Thank you.
    Norman

  16. Raman says:

    @Ashok Kumar.

    What you are saying is very silly, as far as norms of papers go a scientist should not “Giv”e name of scientists in the author list based on their whims and fancies they are supposed to give names of scientists and researchers only who work, if one does not work then it is unethical for a scientist to give his name. So if Rajeev Varshney does this business of giving names of scientist based on his Whims and Fancies (which you said he does) then i would say it is unethical.

  17. SRF says:

    I agree with Anand Singh, for the statement- One should not claim authorship in what he has not contributed intellectually. In case where someone get funding (for eg. ICAR) and just used that public money to sequence genome with outsourcing (Multi national Companies) for a plant species which is already being sequenced by other group (may by any nation or pvt company). Is this good thing to accept just for Fame. And who should be Author of such work, the person who has authority to use (or west) gov money. Is the genome sequencing is great research to claim both of Heros as great scientists and what matter who thought before to sequence the plant species. what great idea sirji.

  18. Rakesh Singh says:

    It is unfortunate that Rajeev Varshney of ICRISAT broke away from ICARs initiative of Pigeonpea genome that led to wastage of money by redundant research. Rajeev Varshney was given funding by ICAR under Indo US AKI. It is very funny and surprising if Rajeev Varshney say he did not know about what work was going on in ICAR on pigeonpea genome, everyone knew about it, it was in public domain. Another interesting fact is that Rajeev Varsheny too is on the Editorial Board of the journal in which ICARs team has got their published and it is said that a journal is only as good as its editor.

  19. conventional plant breeder says:

    Dear all stupid biotechnologists…all this is useless.
    We will do better with conventional plant breeding with cheaper rate.

  20. Robert says:

    CGIAR Institutes according to several reports on the internet are acting agencies where private companies outsource their research.

    http://www.etcgroup.org/content/taking-care-business-cgiar-and-gm-contamination

    They are misusing public fund for self glorification of individuals

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