Decoding the pigeonpea genome creates opportunities

Tuesday, 31 January 2012 14:11

Pigeon pea plant small "The timing's neat," says Dr Jean-Marcel Ribaut, Director of the Generation Challenge Programme (GCP) of the Consultative Group on International Agricultural Research (CGIAR). "We decoded the pigeonpea genome last November, which is a great way to start 2012!"

The collaborative project that sequenced the pigeonpea genome brought together 12 participating institutes operating under the umbrella of the International Initiative for Pigeonpea Genomics (IIPG). The initiative was led by Dr Rajeev K Varshney, the GCP Comparative and Applied Genomics Theme Leader. He is also Director of the Center of Excellence in Genomics (CEG) at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). Other participants in the Initiative included the Beijing Genomics Institute (BGI) in Shenzhen, China; four universities; and five other advanced research entities, both private and public. The Plant Genome Research Program of the National Science Foundation, USA, also funded part of this research.

"A crop of many virtues"
"Pigeonpea, the grains of which make a highly nutritious food, is a hardy and drought-resistant crop. It is grown in the semi-arid tropics and subtropics of Asia, Africa, the Americas, and the Caribbean," explains Dr Ribaut. "Now that the project has successfully captured almost 73 percent of this crop's genome and identified 48,680 genes, new varieties can be quickly developed. This will have significant impact on resource-poor communities in the semi-arid regions because they will then have the opportunity to improve their livelihoods and increase food availability."

Dr Ribaut describes pigeonpea (Cajanus cajan (L) Millsp) as "a crop of many virtues." This ancient crop was domesticated in southern Asia, probably 3,500 years ago. Today, it feeds about 1,000 million people, most of whom are poor. Current world production is 4 million tons - worth about USD 1,500 million - and produced on 5 million hectares. India, a major consumer of this legume, grows around 85 percent of the world's production. Eastern Africa and Central America are also major producers.

"Nutritionally, both people and livestock can significantly benefit from pigeonpeas," says Dr Larry Butler, the GCP Product Delivery Theme Leader. Their high protein and amino acid contents so effectively supplement starchy staples that pigeonpeas are sometimes called the ‘poor man's meat'. This crop's prolific seed production and resistance to drought help reduce farmers' vulnerability to potential food shortages during dry periods. Agronomically, the crop is used to improve soils, serves as an intercrop, and provides windbreaks, fencing, firewood, and thatching. It also has industrial potential for flour production, canning, and lac production. Lac is a scarlet resin used as dye. It is produced by scale insects, for which pigeonpea is a host plant.

Low yields – the poor farmer's burden
Dr Ribaut mentions the current challenges of dryland environments, rapidly increasing population growth, and threats of climate change and scarce natural resources. He adds, "We cannot help but agree with Dr William Dar, Director General of ICRISAT, who observed that the ‘mapping of the pigeonpea genome is a breakthrough that could not have come at a better time!'"

Dr Butler agrees, adding that "perhaps the most important problem faced by pigeonpea farmers is low yields." He explains, "As most of these farmers are smallholders, they have few resources with which to battle crop diseases and pests, drought, and poor soils."

As a result, average world yields have stagnated over the last 50 to 60 years at between 650 to 866 kilograms per hectare. Some countries must import to make up deficits. India, for example, imports about 3 million tons of pigeonpeas annually. Prices for pigeonpeas are therefore soaring. Yet, as Dr Butler points out, "under ideal conditions, the crop can produce about 2.5 tons per hectare."

"One way of assisting resource-poor farmers is to make available pigeonpea varieties that have been improved to cope with stresses," he suggests.

The treasure in the genome
If a variety is to successfully ward off a disease or other stress, then it must have the genes to do so, points out Dr Varshney. "Like all living organisms, pigeonpea plants vary in their ability to resist stress," he explains. "For example, some pigeonpea plants cope with drought better than others. The reason they can do so is because they have genes that direct them to have, for instance, deeper, water-seeking roots, whereas other pigeonpea individuals don't have these genes."

Dr Varshney goes on to explain, "Essentially, this is what breeding is about: it is the deliberate choosing of those plants that have adaptive characteristics such as longer roots." He expounds further: "Thus, through breeding, a drought-resistant pigeonpea variety is developed, the plants of which consistently possess those particular genes that tell them to grow deep roots. This long-rooted variety is thus more likely to survive droughts."

Dr Varshney points out that the size of the pigeonpea genome is about average for legume crops, comprising 22 pairs of chromosomes. These complex microscopic bodies carry thousands of genes each. So far, 48,680 genes have been identified for pigeonpea.

"To date, 72.7 percent of the genome has been assembled. This is sufficient to enable us to change breeding approaches for pigeonpea," says Dr Varshney. "That is, we can now combine conventional and molecular breeding methods - something we couldn't do as well before - and access enough genes to create many new pigeonpea varieties that will effectively help improve the food security and livelihoods of resource-poor communities."

An African farmer proudly stands beside a prolifically seeding pigeonpea plant growing on her farm. Throughout dryland Africa, farmers like her are adopting new pigeonpea varieties. In eastern Kenya, for example, about 20 percent of farmers now grow them. This durable crop often flourishes under climatic conditions that will destroy staple food crops such as maize. (Photo: ICRISAT)

The genome as an effective breeding tool
"This is where the GCP's investment in the IIPG project has paid off," Dr Ribaut suggests. "Most of these types of improvements can be made, using conventional breeding techniques," he says. However, with these techniques, desirable pigeonpea varieties normally take six to ten years to develop. "This is slow delivery, when you're hungry," Dr Ribaut points out. He adds, "Modern crop improvement technologies are therefore crucial for speeding up the development of improved varieties for smallholder crops like pigeonpeas."

Another major issue is that conventional breeding efforts to improve pigeonpea varieties have been stymied by the crop's own narrow genetic diversity and lack of genetic and genomic resources. For pigeonpea, the situation was sufficiently acute for modern science to neglect the crop, despite its importance to so many millions of people in the world's dry areas. As a result, it was often called an ‘orphan crop'.

Creating the capacity to access the pigeonpea's genome is therefore a significant breakthrough, affirms Dr Varshney. "The crop is immediately ushered into the ‘molecular breeding era'," he says. He lists examples of molecular breeding approaches that can now be incorporated into breeding programmes using conventional methods: the use of ‘markers' for genetic mapping and trait identification, marker-assisted selection, marker-assisted recurrent selection, and genomic selection.

Using the genome to develop new varieties and hybrids would "considerably cut breeding time by doing away with several cropping cycles. It would most certainly reduce costs!" observes Dr Varshney. "This means new varieties would reach dryland areas of Africa and Asia more quickly, thus improving and increasing the sustainability of food production systems in these regions."

Dr Varshney warns: "We should remember, however, that, if we are to develop improved varieties, molecular techniques are not sufficient on their own." He explains, "They are basically highly effective tools that are best used together with conventional breeding techniques."

An ICRISAT pigeonpea field trial in Andhra Pradesh, India.

The crop is of the widely grown arhar dhal variety, also known as ‘Asha' (Hindi for ‘hope'). Its genome was sequenced by 12 partners collaborating in the International Initiative for Pigeonpea Genomics (IIPG).

The six-year project was completed in November 2011.

Research implications
"Capturing the pigeonpea genome not only has immediate humanistic benefits, but it will also further several broader research areas," says Dr Xavier Delannay, the GCP Director of Research. Examples include:

Several genes, unique to pigeonpea, that have been identified for drought tolerance. Future research may find ways of transferring these genes to other legumes in the pigeonpea family such as soybean, cowpea, and common bean, so that these crops will also become drought resistant - a significant asset in view of the increasingly drier climates in these crops' production areas.
Genes for other agronomically important traits can also be identified and used to enhance not only pigeonpea but other legumes too.
Genomewide association studies can now be created to assess thousands of pigeonpea accessions held in collections around the world. The genebank at ICRISAT alone holds more than 13,600 accessions. The potential diversity of genes among these yet-to-be-studied accessions can now be explored at much lower cost and much more quickly. The chances are also higher of finding variant genes whose superiority is such that they can be used to improve not only pigeonpea but also other legumes.
Transferring genes from the crop's close relatives, and even other, more distant, legumes to pigeonpea varieties will become more practical, thus helping to broaden the crop's genetic diversity.
The decoding of the genome will also help clarify the roles that certain gene families have played in the evolution and domestication of pigeonpea and its ancestors and relatives.

‘Cracking the egg' twice-pigeonpea genome research by Indian scientists
The pigeonpea genome was, in fact, decoded twice. Two teams of biotechnologists working in India published their results at almost identical times. One project was the IIPG project, led by ICRISAT, and described here; and the other was led by Dr NK Singh, a senior scientist at the National Research Centre on Plant Biotechnology (NRCPB) of the Indian Council of Agriculture Research (ICAR) in New Delhi.

Speaking to the New Delhi environmental fortnightly, Down to Earth, Dr Varshney confirmed that talks, aimed at planning the use of the genome's data in breeding programmes, have already begun with ICAR and other institutes. He also expressed the hope that pigeonpea productivity will, in the very near future, improve significantly.