Biofortified » Cotton

The real success story of GM cotton and edible cotton oil in India 2002-2011

David Tribe — Fri, 15 Jul 2011 13:33:00 +0000

A wonderful colorful and readable booklet about the success of Bt cotton in India has been made available from the ISAAA website for India.
A sample table from this booklet tells the story of the massive expansion of cotton output over the last 10 years.

Indian cotton production statistics this last decade

“Amidst the oilseed crisis, cotton is the only oilseeds crop that has shown a remarkable progress after the introduction of Bt cotton hybrids in 2002. In the last nine years, cottonseed has become an important source of oilseeds in the country. The production of cotton oil registered a three-fold increase from 0.46 million tons in 2002-03 to 1.20 million tons in 2010-11 (Table 3). “

Summary.
In this decade, 2002 to 2011, Bt cotton has been successfully used as a multiple purpose crop in three ways: in the form of edible oil as food for human consumption; de-oiled cake as an animal feed; and kapas for fiber. The production of cotton seed, and its byproducts as oil and meal, has increased manifold from 0.46 million tons in 2002-03 to 1.20 million tons in 2010-11. As a result, Bt cotton meal (de-oiled cake) contributes one third of the country’s total demand for animal feed, whereas cotton oil contributes 13.7% of total edible oil production for human consumption in the country – a significant contribution which offsets more than half of the import bill for edible oil valued at US$6.5 billion annually. Increased production of Bt cotton oil could be one of the important strategies to substitute for edible oil imports which constitute more than 50% of the total edible oil consumption in the country. In 2009-10 India, for the first time ever, imported more edible oil, 8.80 million tons, than the 7.88 million tons it produced domestically. Due to the high nutritional content of cotton oil, Bt cotton oil is marketed after blending it with different edible oils. India is becoming increasingly dependent on expensive imports of vegetable oil, which is a valid strategic concern, and biotech Bt cotton and its second generation of stacked products, as a multipurpose crop for oil, fiber and feed, can play a critical role in Indian agriculture in the near, mid and long term future (James, 2010).

It is noteworthy that the by-products of Bt cotton, have been safely consumed as food and feed in India for nine years, without incident. Given this unblemished record, which is consistent with experience of more than 10 other countries world-wide, now maybe is the time for India to benefit from the application of the well-tested Bt technology in other crops.

Citation: Choudhary, B. and Gaur, K. (2011). Bt cotton in India: A multipurpose crop, ISAAA Biotech Information Centre, ISAAA, New Delhi, India

Update:

10 Years of Bt in India: Biotech Seeds Save Indian Market
By K.R. Kranthi May 1, 2011 Cotton 24-7
Part II: 10 Years of Bt in India
By K.R. Kranthi May 1, 2011 Cotton 24-7

Other relevant posts at GMO Pundit (see also the “Cotton” and “India” tags)

Fluffy revolution
Financial Chronicle, India Sep 23 2009

For several years before the introduction of the new variety, cotton exports from India fluctuated between few thousands bales and one lakh bales. Within three years, exports moved to 5.8 million bales, peaking at 8.5 million in 2007-08 and earning foreign exchange worth Rs 8,366 crore. Compared with the other two top producers of cotton in the world, India’s performance is even more impressive. In 2002, the United States produced 17.2 million bales and China 25.2 million bales, according to figures published by the US department of agriculture. The spurt in India’s cotton production took it to 29 million bales in 2008-09, while the US declined to 13.52 million bales, having peaked at 23.89 in 2005-06. China produced 36. 5 million. From producing around 40 per cent of what China did, India has now touched a level of almost 70 per cent. Against the US, India’s output was 61 per cent

Roundup of Indian cotton statistics

International Food Policy Research Institute study on the possible connection between Bt cotton and farmer suicides in India
We first show that there is no evidence in available data of a “resurgence” of farmer suicides in India in the last five years. Second, we find that Bt cotton technology has been very effective overall in India. However, the context in which Bt cotton was introduced has generated disappointing results in some particular districts and seasons. Third, our analysis clearly shows that Bt cotton is neither a necessary nor a sufficient condition for the occurrence of farmer suicides. In contrast, many other factors have likely played a prominent role.

Pollen defences used to protect corn and cotton against fungus damage

David Tribe — Sun, 08 May 2011 21:36:00 +0000

From GMO Pundit.

Flower power to help improve corn yield › News in Science (ABC Science)

Flower power to help improve corn yield

Wednesday, 4 May 2011 Anna Salleh

Reposted from ABC Radio Australia

Genes normally only active in the flowers of plants could be used to protect the whole plant from resist fungal disease, say Australian researchers.

Professor Marilyn Anderson of La Trobe University is presenting her work at an Australian Academy of Science seminar in Canberra today.

Anderson and colleagues in agricultural biotechnology company Hexima are working together with seed giant Pioneer to develop transgenic corn that is resistant to the major fungal diseases that decrease yield.

“With climate change and growing population, we know that within the next couple of decades we’re going to have to increase cereal production by 70 per cent,” says Anderson. “So all companies are looking at ways to improve the yield of grains, especially rice, corn and wheat.”

Anderson’s earlier work focussed on the molecular mechanism underlying how flowers recognise pollen and decide whether to accept it or reject it.

During that time she discovered a family of molecules called defensins, which are potent anti-fungal molecules.

“We call them ancient immunity molecules because similar molecules are present in insects, and even in humans, and they are involved as the first barriers against disease,” says Anderson.

Tobacco flower chemical

She and colleagues have been focussing on one key defensin, called NaD1, found in only the flowers of ornamental tobacco.

“This molecule seems to attack all sorts of fungal diseases,” says Anderson.

Her team is now engineering transgenic crops to express anti-fungal chemicals throughout the whole plant.

Anderson and colleagues are also tweaking the tobacco defensin to make it more potent and able to kill an even broader range of fungi.

With the help of colleague Professor David Craik at the University of Queensland, the researchers analysed the structure of the defensin.

“Now that we know its structure in detail we can start changing little bits of it and tailoring it,” says Anderson.

The researchers have also developed new gene stacking technology and are testing combinations of defensins and other anti-fungal chemicals, which they hope will ward off fungal resistance to the chemicals in the field.

Trials of defensin-producing transgenic corn in glasshouse trials at La Trobe University are underway and still have several years to run, says Anderson.

Testing will continue until the team finds the best genes and best gene combinations, she says.

Anderson says her current research is aimed at the major fungal diseases of corn in North America. But the research could also be of interest to the Australian wheat industry, which shares some of the same fungal diseases.

Anderson’s early work was funded by Australian Research Council.

Together with Dr Robyn Heath and Professor Adrienne Clark, Anderson set up Hexima, which developed and tested transgenic cotton engineered to contain defensins.

The current partnership with Pioneer is a result of the success of cotton field trials, she says.

Anderson says her company’s philosophy is only to use genes from plants in developing transgenic crops.

“We feel the public will be much happier if they were natural genes that plants use anyway for protection against disease,” she says.

Tags: pest-management, biotechnology, pests

This post was syndicated from GMO Pundit. You may comment here or on the original entry.

Production-chain management is key issue in GM crop escapes

David Tribe — Sat, 18 Dec 2010 23:34:00 +0000

From GMO Pundit.

Sloppy seed-sorting main culprit in GM crop escapes
(Press release about a free access PLoS ONE article linked below)
María Elena Hurtado
17 December 2010
IMAGE: Honey bees transmit GM pollen to non-GM fields, but human error plays a bigger role in GM contamination

Careless handling of seeds may be the key reason for the unintended spread of genetically modified (GM) crops, a study has found.

The discovery challenges the widespread belief that the main source of GM contamination is the transfer of pollen by bees from GM crops to non-GM counterparts in neighbouring fields. Human error during seed production and handling is the more likely culprit, say the researchers.

Stands of non-GM crop plants are currently planted near or within fields of modified crops to provide refuges for pests. This technique helps prevent the pests developing resistance to the pesticides used on GM crops. But human error could undermine this widely used strategy, the paper says.

Shannon Heuberger, an entomologist at the University of Arizona, United States, and her colleagues measured the gene flow — the movement of genes between different populations that occurs when a plant from one population fertilises a plant from the other — in Bt (Bacillus thuringiensis) cotton, the widely planted GM crop, in 15 fields in Arizona.

They found that gene flow via the transmission of pollen by bees was rare. Fewer than one per cent of seeds produced by ordinary cotton plants contained genes from Bt cotton that had been transmitted in this way.

But poor seed-sorting resulted in some seed bags intended for planting in non-GM fields containing as much as 20 per cent GM seed. One non-GM field was found to have a large number of GM plants due to human error in planting.

“Our most important result is that growers can minimise gene flow by screening the seed before planting it in seed-production fields and by being more cautious in their planting process,” Heuberger told SciDev.Net.

“In comparison, designing strategies to minimise bee pollination between fields can be quite difficult because insect behaviour is hard to predict,” she added.

The study concludes that seed producers and decision makers should consider screening seeds to monitor the presence of GM seeds in the supply, and that they also need to communicate “the importance of segregating seed types at planting to reduce human error”.

María Isabel Manzur, head of biodiversity at the Sustainable Societies Foundation (FSS), a Chilean environmental non-governmental organisation, said: “This is a very interesting study because it helps elucidate at a greater depth how transgenic contamination takes place”.

“It corroborates once more that transgenic crops can contaminate surrounding crops, which is something that biotech companies frequently deny despite all the evidence to the contrary.”

The study was published in PLoS ONE last month (30 November).

Link to full paper in PLoS ONE

PLoS ONE doi: 10.1371/journal.pone.0014128 (2010)

Pollen- and Seed-Mediated Transgene Flow in Commercial Cotton Seed Production Fields

Characterizing the spatial patterns of gene flow from transgenic crops is challenging, making it difficult to design containment strategies for markets that regulate the adventitious presence of transgenes. Insecticidal Bacillus thuringiensis (Bt) cotton is planted on millions of hectares annually and is a potential source of transgene flow.

Here we monitored 15 non-Bt cotton (Gossypium hirsutum, L.) seed production fields (some transgenic for herbicide resistance, some not) for gene flow of the Bt cotton cry1Ac transgene. We investigated seed-mediated gene flow, which yields adventitious Bt cotton plants, and pollen-mediated gene flow, which generates outcrossed seeds. A spatially-explicit statistical analysis was used to quantify the effects of nearby Bt and non-Bt cotton fields at various spatial scales, along with the effects of pollinator abundance and adventitious Bt plants in fields, on pollen-mediated gene flow. Adventitious Bt cotton plants, resulting from seed bags and planting error, comprised over 15% of plants sampled from the edges of three seed production fields. In contrast, pollen-mediated gene flow affected less than 1% of the seed sampled from field edges. Variation in outcrossing was better explained by the area of Bt cotton fields within 750 m of the seed production fields than by the area of Bt cotton within larger or smaller spatial scales. Variation in outcrossing was also positively associated with the abundance of honey bees.

A comparison of statistical methods showed that our spatially-explicit analysis was more powerful for understanding the effects of surrounding fields than customary models based on distance. Given the low rates of pollen-mediated gene flow observed in this study, we conclude that careful planting and screening of seeds could be more important than field spacing for limiting gene flow.

Shannon Heuberger *, Christa Ellers-Kirk, Bruce E. Tabashnik, Yves Carrière

Department of Entomology, University of Arizona, Tucson, Arizona, United States of America
Abstract
Background

Characterizing the spatial patterns of gene flow from transgenic crops is challenging, making it difficult to design containment strategies for markets that regulate the adventitious presence of transgenes. Insecticidal Bacillus thuringiensis (Bt) cotton is planted on millions of hectares annually and is a potential source of transgene flow.

Methodology/Principal Findings

Here we monitored 15 non-Bt cotton (Gossypium hirsutum, L.) seed production fields (some transgenic for herbicide resistance, some not) for gene flow of the Bt cotton cry1Ac transgene. We investigated seed-mediated gene flow, which yields adventitious Bt cotton plants, and pollen-mediated gene flow, which generates outcrossed seeds. A spatially-explicit statistical analysis was used to quantify the effects of nearby Bt and non-Bt cotton fields at various spatial scales, along with the effects of pollinator abundance and adventitious Bt plants in fields, on pollen-mediated gene flow. Adventitious Bt cotton plants, resulting from seed bags and planting error, comprised over 15% of plants sampled from the edges of three seed production fields. In contrast, pollen-mediated gene flow affected less than 1% of the seed sampled from field edges. Variation in outcrossing was better explained by the area of Bt cotton fields within 750 m of the seed production fields than by the area of Bt cotton within larger or smaller spatial scales. Variation in outcrossing was also positively associated with the abundance of honey bees.
Conclusions/Significance

Citation: Heuberger S, Ellers-Kirk C, Tabashnik BE, Carrière Y (2010) Pollen- and Seed-Mediated Transgene Flow in Commercial Cotton Seed Production Fields. PLoS ONE 5(11): e14128. doi:10.1371/journal.pone.0014128

Editor: Haibing Yang, Purdue University, United States of America

Received: June 18, 2010; Accepted: October 24, 2010; Published: November 30, 2010

Copyright: © 2010 Heuberger et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

This post was syndicated from GMO Pundit. You may comment here or on the original entry.

Movement of genes via cross pollination from cotton fields subject of a scientific study.

David Tribe — Fri, 03 Dec 2010 22:12:00 +0000

From GMO Pundit.

SCIENCE DAILY
Transgenic Crops: How Genes Jump from Crop to Crop
1st December 2010
A new data-driven statistical model that incorporates the surrounding landscape in unprecedented detail describes the transfer of an inserted bacterial gene via pollen and seed dispersal in cotton plants more accurately than previously available methods.

Shannon Heuberger, a graduate student at the University of Arizona’s College of Agriculture and Life Sciences, and her co-workers will publish their findings in PLoS ONE on Nov. 30.

The transfer of genes from genetically modified crop plants is a hotly debated issue. Many consumers are concerned about the possibility of genetic material from transgenic plants mixing with non-transgenic plants on nearby fields. Producers, on the other side, have a strong interest in knowing whether the varieties they are growing are free from unwanted genetic traits.

Up until now, realistic models were lacking that could help growers and legislators assess and predict gene flow between genetically modified and non-genetically modified crops with satisfactory detail.

This study is the first to analyze gene flow of a genetically modified trait at such a comprehensive level. The new approach is likely to improve assessment of the transfer of genes between plants other than cotton as well.
“The most important finding was that gene flow in an agricultural landscape is complex and influenced by many factors that previous field studies have not measured,” said Heuberger. “Our goal was to put a tool in the hands of growers, managers and legislators that allows them to realistically assess the factors that affect gene flow rates and then be able to extrapolate from that and decide how they can manage gene flow.”

The researchers measured many factors in the field and developed a geographic information system-based analysis that takes into account the whole landscape surrounding a field to evaluate how it influences the transfer of genes between fields. Genes can be transferred in several ways, for example by pollinators such as bees, or through accidental seed mixing during farming operations.

Surprisingly, the team found that pollinating insects, widely believed to be the key factor in moving transgenic pollen into neighboring crop fields, had a small impact on gene flow compared to human farming activity, with less than one percent of seeds collected around the edges of non-Bt cotton fields resulting from bee pollination between Bt and non-Bt cotton.

Most previous studies focused on the distance between the non-transgenic crop field and the nearest source of transgenic plants.

“Although this approach is simple, it is potentially less useful for understanding gene flow in commercial agriculture where there can be many sources of transgenic plants,” Heuberger said.

Heuberger and her co-workers broadened the scope to include flower-pollinating bees, humans moving seeds around and the area of all cotton fields in a three-kilometer (1.9 mile) radius. This approach turned out to be more powerful in understanding the effect of surrounding fields than using the customary model based solely on distance.

For the study, the scientists chose 15 fields across the state of Arizona planted with cotton that did not have the transgenic protein encoded by a gene from the bacterium Bacillus thuringiensis, or Bt. They assessed the number of pollinators visiting cotton flowers through field observations and determined the transfer of genes by collecting samples of cotton bolls and determining their genetic identity.

“We saw a need for a spatially explicit model that would account for the whole surrounding landscape,” Heuberger said. “Our model takes into account the distance and area of all relevant neighboring fields, the effect of pollinators like bees and human factors that can result in the mixing of seed types.”

Heuberger’s findings have implications not just for genetically engineered traits but also more generally for seed production.

“When you grow a crop and want the variety to be pure, just being able to know how far gene flow will occur and how it is affected by pollinators and human farming activity in the area is very valuable.”

The research was funded by Western Region Sustainable Agriculture Research and Education and an Environmental Protection Agency STAR Fellowship.

Link to the full scientific paper with open access at PLOS ONE (key items represented here)

Pollen- and seed-mediated transgene flow in commercial cotton seed production fields
PLOS ONE, vol. 5(11)
Shannon Heuberger, Christa Ellers-Kirk, Bruce E. Tabashnik, Yves Carrière
Novermber 2010

Background

Methodology/Principal Findings

Conclusions/Significance

This post was syndicated from GMO Pundit. You may comment here or on the original entry.

Release of sterilised moths avoids the need for refuges in cotton growing

David Tribe — Thu, 18 Nov 2010 01:09:00 +0000

From GMO Pundit.

Success in integrated pest management of pink boll worm in Arizona provides encouraging news for both the environment and for cotton growers. A two-pronged strategy involving insect protected cotton and biological control with wide scale release of sterile moths virtually eliminates resistance to the genetically inbuilt cotton insect protection system in pink boll worm pests.

Summary of the original scientific publication:
Suppressing resistance to Bt cotton with sterile insect releases

Bruce E Tabashnik, Mark S Sisterson , Peter C Ellsworth, Timothy J Dennehy, Larry Antilla, Leighton Liesner, Mike Whitlow, Robert T Staten, Jeffrey A Fabrick, Gopalan C Unnithan, Alex J Yelich, Christa Ellers-Kirk, Virginia S Harpold, Xianchun Li & Yves Carrière

Abstract

Genetically engineered crops that produce insecticidal toxins from Bacillus thuringiensis (Bt) are grown widely for pest control. However, insect adaptation can reduce the toxins’ efficacy. The predominant strategy for delaying pest resistance to Bt crops requires refuges of non-Bt host plants to provide susceptible insects to mate with resistant insects. Variable farmer compliance is one of the limitations of this approach. Here we report the benefits of an alternative strategy where sterile insects are released to mate with resistant insects and refuges are scarce or absent. Computer simulations show that this approach works in principle against pests with recessive or dominant inheritance of resistance. During a large-scale, four-year field deployment of this strategy in Arizona, resistance of pink bollworm (Pectinophora gossypiella) to Bt cotton did not increase. A multitactic eradication program that included the release of sterile moths reduced pink bollworm abundance by >99%, while eliminating insecticide sprays against this key invasive pest.

Nature Biotechnology
Published online: 7 November 2010 | doi:10.1038/nbt.1704

This post was syndicated from GMO Pundit. You may comment here or on the original entry.

Community Contest #1 and more!

Frank N. Foode — Mon, 11 Oct 2010 01:21:29 +0000

Hi everybody! Frank N. Foode here. Biofortified is workin’ on building its community of editors, contributors, and readers with the new profile system. We’re also coming up on our first Biennial celebration on the 31st of the month, making this an exciting month for talking about plant genetics. Plus we’ll have more to say about our own Rally to Restore Sanity in the debate over genetic engineering, and if that was not enough, there will be opportunities for everyone to be able to win fabulous prizes – and I’m going to tell you about your first chance!

The first Biofortified Community Contest is on, and it will be a contest for the best comment or comments. That’s right, just by writing just one awesome comment that contributes to the discussion here, you can win a prize! It could be about some of the many things we talk about on the blog such as the science, politics, social and philosophical issues, personal beliefs, or a collection of helpful links that you have scoured the internet for.

Here are the rules:

Anyone can nominate someone for this contest, but must link to at least one comment (can be several) by that author.
You may nominate yourself!
Editors (and me) are ineligible for the contest – but contributing authors can get in on the action.
Comments can be from any date in the past, present, or future. They can be comments on posts or in the forum.
In order to accept the award, comment author must be registered, fill out at least some of their profile, and have a picture uploaded for their avatar. (Profile can be done after the winner is announced. Picture need not be a human photo – how about a cool plant?)
The winner(s) will be judged on how awesomely smart, cool, funny, and productive their comments are. We want to reward people that help elevate the discussion and give them a special status in the community.
Nominations will close on Friday October 15th at midnight Pacific Standard Time. (End of the day, not the beginning!)
Winner(s) will be decided by Biofortified’s editors, and will be announced on the 17th of October.

What do you win, aside from eternal glory? Why, some genetically engineered blog schwag. Get your farmer’s market groove on with your very own Biofortified Canvas Tote!

Let's see, celery, kale, parsley... um what's this stick of butter for?

It comes complete with an embroidered shopping list pocket with an elastic pen loop so you can check things off as you shop. (Note: Veggies, shopping list, pen, and Frank not included.) Be the first to own it, and take it down to your local Whole Foods to show off that you are a part of the discussion. (While we do not know for sure if the cotton bags are made from genetically engineered varieties, it is more likely than not.)

If you don’t win this time around, don’t despair because as soon as it is over we will have a second one, with a special twist. And finally, if the debate about genetic engineering makes you feel like wielding a knife, we will also have the first annual Frankenfood Carving Contest coming up later this month as well!

Nominate your entries in the comments below. (Due to the fact that multiple links can get your comment caught up in our voluminous spam queue, we recommend making nominations while logged in.) If you have been nominated, filling out your profile right away will help your chances of winning. And you can also second nominations and root for those whom you think really deserve to win! Good Luck, and remember it’s not too late to make a winning comment!

Genome sequence of Peruvian wild cotton enters the public domain through corporate donation to databases

David Tribe — Wed, 22 Sep 2010 23:46:00 +0000

From GMO Pundit.

MONSANTO AND ILLUMINA REACH KEY MILESTONE IN SEQUENCING OF COTTON GENOME. Press release

Companies Will Donate Info to the Public Domain; Texas A&M Professor to Lead Effort on Cotton Genome Sequencing

ST. LOUIS and SAN DIEGO (Sept. 22, 2010) – The complicated cotton genome is one step closer to having its genetic threads unraveled, thanks to a key research milestone completed and announced today by Monsanto Company (NYSE:MON) and San Diego-based Ilumina Inc. (NASDAQ: ILMN). Combining Monsanto’s knowledge of cotton genomics and Illumina’s next generation sequencing technology, a critical landmark has been achieved that could lead to the development of cotton crops with higher yields, better fiber quality, and greater resistance to diseases and pests.
The two companies have completed sequencing a wild Peruvian cotton species, Gossypium raimondii, and will donate their findings to the public. The completion of G. raimondii will aid public and private researchers in their quest to sequence the more elusive genome of domesticated cotton, G. hirsutum.

Domesticated cotton, more commonly known as American Upland cotton, accounts for more than 95 percent of U.S. production. Its genome has proven difficult to sequence and assemble because of its large size as well as the large quantity of repetitive DNA. The cotton genome, at about 2.7 billion nucleotides, is roughly comparable to the human genome at 3.2 billion. Additionally, most organisms—including humans—have two sets of chromosomes. However, domesticated cotton has four sets.
“Imagine you have four puzzles and all of their numerous pieces to put together in order,” says Ty Vaughn, Monsanto global cotton technology lead. “On top of that, many of the puzzle pieces are identical. The cotton genome presents the same unique challenge to researchers.”
Researchers chose a strategy to study related cotton species that closely represent the more complex domesticated cotton genome. The genetic structure of the G. raimondii species represents one part, and the G. arboretum species, more commonly known as tree cotton, represents the other. Additionally, previous molecular studies have shown that the G. raimondii and G. arboreum genomes have a great deal of similarity in the way that genes are arranged on chromosomes. This could allow the G. raimondii genomic sequence to serve as a base to assemble the even larger and more complicated G. arboreum genome. Having those two sequences together is expected to provide a path toward sequencing and understanding the genome of domesticated cotton.
“Today’s announcement will bring everyone closer to assembling the entire cotton genetic puzzle. Sequencing helps cotton breeders and researchers identify which genes are responsible for which characteristics in the crop,” says Vaughn. “A high-quality genome map can help us get where we need to go faster and the more detailed that map the faster we can get there.”
“The G. raimondii genome sequencing project is a great example of Illumina’s commitment to deep collaborations that leverage the quality, throughput and utility of our industry-leading technology,” said Michael Thompson, Ph.D., Global Sales Manager of Agrigenomics at Illumina. “We are pleased that this work will enable a thorough understanding of gene content and organization, and lay the ground work for unraveling and harnessing the diversity among the Gossypium genome types. These advancements will ultimately benefit both producers and consumers.”
Monsanto and Illumina will deposit the genetic data into the public domain through entry in the GenBank database, hosted by the National Center for Biotechnology Information. Monsanto has a history of donating its genomic knowledge to the public sector. In previous years, the company has made its sequencing of the Arabidopsis genome public and contributed significant genomic data to help complete the rice and corn genomes.
In cotton, Monsanto previously donated 4,000 cotton molecular markers and associated information to Texas AgriLife Research, an agency of the Texas A&M System, in April 2009. These types of public donations should help cotton research continue to move forward.
“As a leader in the cotton industry, we have the resources, expertise, and partners such as Illumina to conduct this type of work, and believe it’s important to share this knowledge with both public and private researchers so we can all benefit,” says Vaughn. “We can achieve the ultimate goal of a complete sequence of the cotton genome faster by sharing what we’ve learned and enabling others in the cotton community to continue and build upon this research.”
Once the information is publicly available, David Stelly a molecular breeder and cotton genomicist with Texas A&M University, is expected to lead the effort to pull together a group of researchers in the public sector to conduct further analysis of the G. raimondii genome and the role it plays in key functions such as fiber development.
“A public reference genome sequence is essential to efficient use of modern genomic technologies for both non-GE and GE approaches to genetic improvement,” says Stelly. “The lack of a good public reference genome for cotton has been among the most serious constraints on development of cotton genomics. The ongoing efforts by Monsanto and Illumina will lead to a good public reference genome for cotton, and help stimulate the creation of new and more efficient research paradigms in cotton research and improvement. These will be needed if society is to meet additional demands of the future, when we’ll have to produce more, yet use fewer resources.”

About Monsanto Company
Monsanto Company is a leading global provider of technology-based solutions and agricultural products that improve farm productivity and food quality. Monsanto remains focused on enabling both small-holder and large-scale farmers to produce more from their land while conserving more of our world’s natural resources such as water and energy. To learn more about our business and our commitments, please visit: www.monsanto.com. Follow our business on Twitter at www.twitter.com/MonsantoCo, on the company blog, Beyond the Rows at www.monsantoblog.com, or subscribe to our News Release RSS Feed.

About Illumina
Illumina (http://www.illumina.com) is a leading developer, manufacturer, and marketer of life science tools and integrated systems for large-scale analysis of genetic variation and function. We provide innovative sequencing and array-based solutions for genotyping, copy number variation analysis, methylation studies, gene expression profiling, and low-multiplex analysis of DNA, RNA and protein. We also provide tools and services that are fueling advances in consumer genomics and diagnostics. Our technology and products accelerate genetic analysis research and its application, paving the way for molecular medicine and ultimately transforming healthcare.

This post was syndicated from GMO Pundit. You may comment here or on the original entry.

Cotton like Candy

Karl Haro von Mogel — Sun, 06 Sep 2009 05:44:46 +0000

Or Cottonseed you can Eat thanks to Genetic Engineering.

A few years ago, I read about a research group that had used genetic engineering to remove a poisonous compound from cotton seed. Now, it seems, they are one step closer to making a positive impact on the availability of food for people in developing countries and beyond. Time Magazine reports that Dr. Keerti Rathore and his team, who made the development years ago have now moved on to field trials, a necessary step to test the resilience and effectiveness of the trait in real-world conditions.

RNA that Interferes

Let me tell you how this works. They used a technique called RNA interference, or RNAi. When plants (and other organisms we are finding) are infected with a virus that uses RNA as its genetic material, they defend themselves by chopping up the offending molecule. Cells use the double-stranded DNA as genetic material, and use the very similar single-stranded RNA to carry information from the genes to the rest of the cell for making proteins. But the RNA that these viruses use is double-stranded, like DNA. Since plants don’t use RNA as a double-strand, this gives them something different to detect and destroy, and that’s what they do.

An enzyme called Dicer detects double-stranded RNA and chops it up into little pieces, about 20 bases long, and a complex of enzymes called the RNA Induced Silencing Complex (RISC) uses those short pieces to destroy any other RNA molecules that come along that match the sequence of those short pieces. These short pieces of RNA are called Small Interfering RNA or siRNA.

The goal of RNA-based viruses, or retroviruses, is to make DNA from their RNA genomes, and insert this DNA into the host cell where it can be used to make more viruses. So in addition to knocking out similar genes, a similar complex of enzymes called RITS (RNA-induced Transcriptional Silencing) can also find any genes in the cell’s DNA that match the siRNAs and ‘silence’ them by attaching small molecules called methyl groups to the DNA. This tells the cell’s enzymes to skip over the likely viral gene, protecting the cell from becoming a virus factory.

Once cells evolved this amazing defense mechanism, they put it to good use in their own evolution. (This is assuming the defense mechanism evolved first.) Now cells had a way to silence their own genes if need be. So if a gene produces an RNA molecule that doubles-back on itself, along comes Dicer to chop it up. The small pieces of RNA that are made in this fashion are called Micro RNAs, or miRNA. Any genes that match the sequence of this miRNA are doomed to be turned off.

In general, all it takes to get this silencing effect is to have an otherwise normal-looking gene with part of the gene duplicated and turned the other way around. This forms a ‘hairpin loop’ (looks like a bobby pin) in the RNA that gene produces, because the reversed part of the sequence can come back around and hook up with the forward part of the seqeunce. Now people with experience in RNAi will say, hey, it’s not that easy, but that’s the basic idea.

Micro RNAs are very cool, and they are rising in importance in genetics. When I was touring grad schools in 2007, one professor in Illinois showed me a picture of two soybeans, one green and one yellow, and asked me whether I thought the yellow soybean was caused by a dominant or recessive gene.

I answered, “Well, my first thought is that since the soybean lacks pigment, that it has a mutation in one of the genes in the pigment pathway that prevents the pigment from being formed, which is usually recessive.”

But I continued, “However if it is caused by a Micro RNA silencing one of those genes, then it would be dominant.” I was right, the yellow mutant was caused by a Micro RNA, that turned off one of the pigment genes in the way I described above.

“Ah, I tried to trick you!” She said. I forget whether she was holding her fist in the air as if to say, ‘foiled again,’ but it felt like that.

RNAi makes things just as if the gene it silences isn’t even there, kind of like if the gene was mutated so that it didn’t work anymore. But cells usually have two copies of every gene, one on each paired chromosome. Some plants have more than two of each chromosome, so they can have more. Usually, if you mutate a gene so that it doesn’t work anymore, the normal working copy or copies will still do the job in its absence. Such “knockouts” are therefore recessive, and you have to have every copy of the gene be non-functional to get your desired trait. Not with RNAi.

With RNAi, you usually only need one copy of the silencing gene, and it will turn off every copy of the target gene, and sometimes even similar genes in the same ‘gene family.’ Thus, MicroRNAs, whether natural or human-made, are dominant genes. One drop of miRNA does it.

The Gossypol Wall

Now let’s talk about the cotton. Cotton is grown for fiber, in fact every piece of clothing I am wearing right now is made from it. But sometimes, also, cottonseed is fed to ruminant cattle which can manage to digest it. But the rest of our farm animals, and us especially, cannot stomach it. That is because it contains a compound called Gossypol, which can cause low potassium levels and paralysis. (It can also apparently work as an effective male contraceptive… if you ignore the paralysis part.)

In the 1950s, researchers knew that cottonseed could be painstakingly processed to remove the poisonous gossypol, it made a suitable edible food. Cottonseed oil also finds its way into some foods today. So they decided that they would try to breed a gossypol-free cottonseed. By stacking up recessive nonfunctional or deleted gossypol genes in a cotton plant, they successfully made an edible cottonseed. The trouble was, it made a cotton plant that was itself quite edible for pests! Gossypol was necessary for plant defense througout the plant, so by knocking out the genes entirely it made a newly edible food that couldn’t be grown.

Fast forward fifty years to the work of Rathore et al. They realized that we have the technology to turn off the gossypol-making genes only in the seed, leaving the genes still working in the rest of the plant. Every gene has at least one promoter, a piece of DNA in front of it (or inside, and sometimes somewhere else), that tells the cell that there’s a gene there to express, and it also tells the cell when to express it. There are promoters that turn the gene on all the time, promoters that tell it to turn on only when a signal like an infection or insect attack is happening, promoters for stresses like drought, and promoters that turn the gene on only in certain tissues. Since all cells of the same plant have the same genes, the difference between each cell arises from which genes are being used and at what time.

Dr. Rathore and co. found a seed-specific promoter, one that turns on a gene only in the seed, and attached it to their RNAi construct that makes Micro RNAs. When they inserted it into a cotton plant and grew it, they found gossypol being produced in the leaves and stems as normal, and the compound was drastically reduced in the seeds. Success!

44 Million Metric Tons of Fun

What are the potential implications for this development? First, it opens up a huge potential source of food, particularly protein. From the 2006 article:

“Very few people realize that for every pound of cotton fiber, the plant produces 1.6 pounds of seed,” Rathore pointed out. “The world produces 44 million metric tons of cottonseed each year. Cottonseed typically contains about 22 percent protein, and it’s a very high-quality protein.”

In all, about 10 million metric tons of protein are contained in that amount of seed, he said.

They did the math, and calculated that this is enough protein to meet the daily requirements of 500,000,000 people. Half a billion.

That’s almost 1/13th of the human population. Yeah, this could be a big deal someday.

Next, since cottonseed was considered mostly a waste product of farms, it now becomes a thing of value to the farmer. This means that cotton farming from the Third World to the New World can be more profitable.

Finally, this could also reduce the costs of processing cottonseed for oil and animal feed, which is fairly costly. Looks like this patent is going to be worth some money someday.

But the most important part in my opinion is what this means for farmers and other people in developing countries who will be able to directly benefit from additional food on the market. As cottonseed will compete against other commodities, it could also lower the cost of other foods at the same time.

The new development reported by Time Magazine is that since the research on this RNAi gossypol first came out, it has progressed from the greenhouse to full-fledged field trials. They found that it worked just as well in the field as in the greenhouse. There doesn’t appear to be a paper in publication yet, according to a Pubmed search, but when that happens I will be interested to find out more about how well it did.

The fact that they used RNAi also has other implications. If somehow, a mutant cotton plant was found that doesn’t produce gossypol in its seeds, chances are it would be a recessive mutation, as I explained above. If this was bred into a cotton variety and grown in a field it should work just fine, just like the genetically engineered one does. But if someone plants a normal, wild-type cotton field next to it, it could cross-pollinate the recessive gossypol-free plants. Since the genetics of seeds depend on both of their parents and not just one, some of the seeds on the recessive plants could have dominant genes in them, thus restoring the poisonous gossypol.

RNAi cotton would not have this problem. It would already have the same gossypol-producing genes as every other cotton, and would silence them all the same. Farmers could be confident that their cotton will produce edible seeds no matter what their neighbors grow.

Imagine a farmer in India with only a few acres that can now sell their once almost-worthless piles of cotton seed as a food commodity… or maybe cook and eat them!

Failure Repealed

This news reminds me about The Union of Concerned Scientists’ recent report, ‘Failure to Yield.‘ Rather, it reminds me about how limited in scope the report was, excluding everything but transgenic soybeans and corn from consideration. The author, Doug Gurian-Sherman, explained that cotton was excluded from the report because it was not enough of a food crop since it was grown for fiber and animal feed.

Failure to Yield was motivated in large part by the “global food crisis” of the past few years. So we wanted to examine the ability of GE to address the challenges for food production given a growing global population, changing consumption patterns, and climate change impacts. For this reason, we decided to look at major GE food or feed crops in the United States, and this means soybeans and corn. We didn’t include canola, an oilseed crop, because the acreage devoted to canola, about a million acres, is only 0.6 percent of the acreage devoted to corn and soybeans in 2008.

Cotton was excluded because it is primarily a fiber crop. Cotton seed meal may also be used as animal feed, and the plant itself as fodder in some places, but these uses are secondary to fiber production. In other words, we did not look at GE cotton because the report is intended to inform the solution of the global food crisis, not a global clothing crisis.

Har har. The first thing I thought of when I read this explanation was the 2006 paper, written long before the UCS report. I had no idea how far along the research was at the time, so this news brings the UCS report to the forefront again. Here we have a report purporting to analyze genetic engineering’s potential to aid in the global food crisis, yet totally ignoring the ways that genetic engineering can help people obtain more food (and protein in this case!) other than increases in yield. The above passage also makes several tenuous arguments to justify excluding increases in cotton (and canola) yield that Gurian-Sherman admits elsewhere are indeed real.

Bt cotton has been studied in developing-country settings but there’s been less study of Bt corn. Yield increases can often vary from about 10 to 40%, and sometimes more.

So therefore, if this RNAi trait is included in Bt cotton, those 10-40% (to 80% according to one study, mentioned here by Pam Ronald) yield increases in cotton can indeed contribute to the rising global demand for food. That is, yield increases after this genetically-engineered trait could already provide enough protein to feed half a billion people per year.

Nutty with a crunch?

This is a fascinating development, not only from a genetics perspective, or a food production standpoint, but also from the point of view of cuisines. According to Dr. Keerti Rathore, cottonseed “tastes like chickpeas.” I wonder what kind of foods cottonseed will lend itself well to? Could we find a cottonseed masala, or see it one day floating in chicken soup instead of barley? Or would a cottonseed pilaf be more in order, with orzo, pecans, mushrooms, and sage?

Since cotton is also widely grown in the US, perhaps I might soon get to find out how toasted “TAMU nuts“* taste.

*TAMU stands for Texas A&M University. Cute.