Natural magic to counter witchweed crop menace
SARID programme to benefit local farmers and enhance regional research capabilities
2 August 2012
Africa is the only continent that cannot feed itself: food production per person is about the same as it was in 1960 (ref 1, ref 2). One of the reasons is the prevalence of African witchweed, also known as Striga, a root parasite of staple cereal crops such as maize, sorghum, rice and millet.
Striga causes estimated global annual losses of US$7Bn and adversely affects food security for more than 100M people (ref 3) mostly in sub-Saharan Africa; in fact there is a near perfect overlap between areas of Striga infestation and subsistence agriculture where hunger prevails.
Striga is considered the major biological constraint to crop production in sub-Saharan Africa, and the prize for controlling it is progress for the food security, economic development and wellbeing of millions of people living on the African continent. So researchers in the UK, India and Africa have been collaborating through the SARID programme (see 'Sustainable agriculture overseas') to develop research capabilities in Africa and use new methods to look for Striga-resistant varieties of crops.
Two species of Striga, the purple-flowered Striga hermonthica and the red-flowered S. asiatica are the most destructive to host crop plants. Both are hardy enemies. Each Striga flower spike produces more than 50,000 seeds which can remain viable in soil for up to 20 years (ref 4). An estimated 100M hectares of land are infested with Striga seed and yield losses of 20-100% are common, leading some farmers to abandon cultivating infected crops.
The parasite invades crop roots and survives by siphoning off water and nutrients from the host plant, making it stunted and earning the parasite the fearful 'witchweed' moniker. Moreover, as a root parasite Striga hides underground for much of its life making it very difficult to control.
A counter strategy – as part of an integrated control programme – is to grow cultivars that have natural resistance to the parasite so local farmers can grow crops to harvest without using expensive herbicides that are not always effective and may damage the environment.
However, despite the recent development of several sorghum (ref 5) and maize (ref 6, ref 7) cultivars with improved resistance to Striga, scientists have yet to identify the genes responsible for resistance. Professor Julie Scholes from the University of Sheffield has been researching mechanisms underlying crop susceptibility and resistance to Striga for more than 10 years. She says that because the Striga seed bank is so genetically diverse (ref 8), long term success requires the identification and exploitation of multiple sources of host resistance.
Under the SARID programme, Scholes and collaborators aimed to identify witchweed-resistant varieties of crops and hunt down genes responsible for resistance in two important cereal crops: sorghum and rice.
Sorghum is the second most important cereal grain in Africa (by area harvested after maize) and rice production and consumption are increasing there at the fastest rate of any cereal (ref 9). Rice is the preferred staple food in the expanding cities in Africa and is a key strategic crop for attaining food security and poverty alleviation (ref 10). Rice is also a favoured crop to work on from an experimental point of view its genome has been sequenced and there are many genomic resources available to aid the identification of resistance genes.
Screen and select
The first part of the project was to screen a range of African rice cultivars, including 18 different Nerica (from 'New Rice for Africa') cultivars, to determine which showed the best resistance and tolerance to the Striga parasite.
The recent introduction of the Nerica cultivars, generated by crossing the African rice species Oryza glaberrima with the Asian rice species O. sativa (ref 11, ref 12), is one of the main reasons for the rapid expansion of rice in Africa – they are high yielding with good nutritional quality and have excellent drought tolerance and disease resistance. The development of the Nerica cultivars earned their creators Dr Monty Jones and Professor Yuan Longping the 2004 World Food Prize (ref 12).
Unfortunately, the Nerica cultivars have a highly variable resistance to Striga. So studies were carried out under both controlled laboratory conditions at the University of Sheffield and in field trials at Kyela in Tanzania – an area heavily infected by S. asiatica – and at Mbita Point in Kenya, where S. hermonthica is widespread. Field studies allow researchers to determine how durable resistance is in the field when cultivars are exposed to variable environmental factors such as soil conditions, water and light levels, and exposure to other pests and pathogens. In contrast, laboratories studies offer standardised conditions to determine the influence of genes alone.
Together, the field and laboratory studies showed that some Nerica cultivars possess broad spectrum resistance to a range of S. hermonthica and S. asiatica ecotypes (sub-populations of a species) whilst others are extremely susceptible (ref 13, ref 14). "This knowledge is important as it allows us to advise farmers on which cultivars to grow in their area," says Scholes.
Scholes' collaborator Dr Jonne Rodenburg from the Africa Rice Centre adds that since these adapted varieties are already available in many parts of Africa, dissemination of the research results to inform farmer organizations and extension services in the affected areas is likely to result in a quick shift from Striga susceptible to Striga resistant varieties. "This will obviously have great positive impact on the livelihoods of resource-poor farmers in Africa," he says.
The next step was to identify where on the rice chromosomes the Striga resistance genes are located, so that these genes can be transferred, via marker assisted breeding programmes, into high yielding varieties that the farmers want to grow. "We're using modern genomic resources but based on African germplasm which means that results will be immediately applicable," says Scholes.
Over the years, Scholes and colleagues at Sheffield have developed a novel and effective system to carefully control environmental parameters whilst observing and recording root and parasite growth. As this all takes place in soil it's no easy task. The solution is multiple chambers called 'rhizotrons' (after rhizome, a plant's root systems). "These systems allow us to monitor and quantify parasitism in real time," says Scholes.
Hence, with colleagues at Sheffield she is using their rhizotron systems to quantify resistance to Striga in a 'mapping' population of rice developed by Dr Mathias Lorieux at the International Center for Tropical Agriculture (CIAT), Columbia. "This population of rice lines is ideal for tracking down resistance genes," says Scholes. One of the parents of the mapping population is an O. glaberrima cultivar that shows very good resistance to Striga; the other is an O. sativa cultivar which is very susceptible to the parasite. Both the parents are adapted to drought prone conditions in Africa so results will be of immediate use for breeding Striga-resistant crops for African farmers.
Using a technique called quantitative trait loci (QTL) analysis, the researchers identified a small region of the O. glaberrima genome that contains the resistance genes. "We are now carrying out a set of rice crosses that will allow us to narrow down this region further to identify a small number of candidate genes," Scholes explains.
Scholes is also working with Dr Tom Hash and Dr Dan Kiambi from the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) and Professor Andy Greenland from the National Institute of Agricultural Botany (NIAB), UK, to see if the resistance QTL in rice correspond to similar areas in the sorghum genome. So far, early results indicate that some regions of DNA that code for resistance correspond between the species, while others are unique for each species. Identification of resistance genes in both species (and genes unique to each) will aid our understanding of resistance mechanisms and hopefully catalyse beneficial impacts from laboratory to farmers' fields.
Nurturing a knowledge base
An important part of the SARID programme is to develop research capacity in the countries that grow, consume and export the crops in question. This builds a knowledge base and expertise to develop local and regional economies.
Mr Boubacar Kountche, a PhD student at ICRISAT, Niger, spent three months with Scholes at the University of Sheffield learning to use the rhizotron system to investigate resistance in pearl millet. He says that the visit was "a great success" and he found that, like rice, natural resistance to Striga varies widely between the 16 millet cultivars he tested – meaning that as for rice, millet contains resistance genes that will be useful for breeding programmes.
As a result of this visit, Boubacar has taken this expertise back to Niger where the technology is now being used to enhance regional research capabilities. "Discussions are undergoing regarding the establishment of the rhizotron system at the ICRISAT-Center in Niger for further and deep screening of diverse millet populations for post-attachment resistance mechanisms," he says, adding that resistant varieties are being tested in farmers' fields under multi-location trials.
The University of Sheffield also hosted Dr Steven Runo, a lecturer from Kenyatta University, Kenya, to undertake a six-month fellowship. The aim of Steven's work was to test whether a novel high-throughput technology platform – known as the 'hairy root' system – which Steven has adapted for maize would be suitable for testing the function of candidate Striga-resistance genes. This work was very successful as Steven showed that hairy roots became infected with Striga.
"It's exciting as it will allow us, for the first time, to rapidly assess whether particular host genes alter susceptibility to Striga," says Scholes. "We are now working together to transfer this technology to rice and sorghum."
Finally, Scholes together with ICRISAT colleagues Dr Santie de Villiers and Dr Santosh Deshpande and Mamadou Cissoko, a SARID-funded PhD student, ran a training workshop in the application of molecular markers in crop improvement to 13 African scientists, plant breeders and PhD students. The participants came from seven different countries (Ethiopia, Kenya, Malawi, Sudan, South Sudan, Tanzania and Zambia), and the course was held at the Biosciences eastern and central Africa (BecA) Hub, an initiative developed within the framework of Centres of Excellence for Science and Technology in Africa, and hosted and managed by the International Livestock Research Institute (ILRI) in Nairobi, Kenya.
Students on the workshop said that the training was very informative. One student remarked "the choice of trainers was excellent and highly inspiring, especially in ease of understanding how to combine theory and practice". The aim of this workshop was to provide participants with theoretical background in the use of molecular markers in crop improvement, as well as practical experience in molecular laboratory procedures such as DNA extraction, DNA quantity and quality tests, electrophoresis and simple sequence repeat genotyping.
"The course was very well received" says Scholes. "The use of molecular markers in crop breeding is a rapidly expanding technology and I made many new friends and research collaborations."
Sustainable agriculture overseas
The Sustainable Agricultural Research for International Development (SARID) programme, jointly funded by the Department for International Development (DFID) and BBSRC, was set up to help poor farmers increase their agricultural output by supporting high-quality biological and biotechnological research in crop science and sustainable agriculture. The programme was also aims to establish productive partnerships between scientists in the UK and developing countries.
Twelve projects conducted over five years have been funded from a pot of £7.5M with DFID being the main co-funder. The programme has involved 32 collaborations between UK universities and institutions across the globe, and other research initiatives. They include reducing arsenic levels in rice, tackling pests and pathogens of bananas, coconuts, kale, cabbage and sweet potatoes, as well as efforts against pests such as invasive nematodes.
In January 2010, DFID provided extra funding to encourage additional research capacity building activities; 11 projects applied and nine supplementary grants were awarded in March 2010.
The SARID programme is due to end in March 2013.
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- Scientist wins prize for new African rice
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- Rodenburg J, Cissoko M, Kayeke J, Midega CAO, Khan ZR Kyalo G, Scjoles JD (2011) Field expression of resistance against Striga asiatica and S. hermonthica in the New Rice for Africa (NERICA) cultivars. In 11th World Congress on Parasitic Plants, edited by M. Vurro and H. Eizenberg. Martina-Franca, Italy. (Conference paper)