Friday, February 8, 2013

First ever genome of chickpea

By Dr P K Mukherjee

India is the largest producer of chana
A landmark breakthrough has been achieved by sequencing the genome of Chickpea (चना) by a team of 49 scientists of 10 labs across the world thanks to the dynamic leadership of Dr Rajeev Varshney. The significance of the research is immense as it would be possible in future to develop new varieties of chana which would be able to grow faster with more yields taking care of diseases, global warming and drought conditions. The research has not been patented but has been kept in open domain so that farmers in chickpea growing regions of India and rest of the world can be benefitted.

Dr Rajeev Varshney, Director, Center of Excellence in Genomics (CEG)
A global agricultural research team of 49 scientists successfully mapped the genome sequence of chickpea (चना ) which is the world’s second most widely grown legume crop after soyabean. There are two main types of chickpeas: small-seeded desi and larger-seeded Kabuli.While the consumption of desi is restricted primarily to Middle East and Southeast Asia, Kabuli is a popular and valuable global commodity. The highly nutritious chickpea contributes to income generation and improved livelihoods of smallholder farmers in African countries and is crucial to the food security in India.

Chickpea–a nutritious and agro-ecological legume crop

Domesticated in the ancient Mediterranean region over 700 years ago, chickpea is a major legume crop grown globally on 11.5 million hectares with India being the largest producer (70 percent of global production) and consumer. It is a highly nutritious, rich in protein, energy, vitamins and minerals. Its protein content is between 20-30 percent which is two to three times more than cereals like wheat and rice. Moreover, chickpea is the highest source of dietary fibre, a vital part of healthy diet, as it facilitates digestion.

Chickpea is cooked in many ways including chana dal (desi variety) and curries and its flour (besan) is used in making pakoras and many cuisines. It is also crucial for the nutrition of the poor. In India, roasted chickpea flour, called sattu, is the main meal for the poor, hard-working manual labourers because it is energising, nutritious and affordable. In fact, the World Food Program is currently exploring chickpea paste in a ready-to-use food to address malnutrition.

Genome mapping of chickpea

The global team succeeded in identifying an estimated 28,259 genes of chickpea after sequencing a Canadian Kabuli chickpea variety, called CDC Frontier. The team also carried out resequencing of additional 90 cultivated and wild varieties from ten different countries.

The chickpea genome sequencing project was undertaken by the International Chickpea Genome Sequencing Consortium (ICGSC) led by the International Crops Research Institute for the Semi-Arid Tropics ICRISAT), a member of the CGIAR Consortium. This was made possible, thanks to the collaborative efforts of Rajeev Varshney, who is the coordinator of ICGSC and Director of Centre of Excellence in Genomics at ICRISAT, and his 48 colleagues spread across the world. In all, 23 organisations from 10 countries have been involved in this global research. The collaborating countries are India, USA, Germany, Canada, Australia, China, Czech Republic, Denmark and Mexico. The team could successfully assemble 74 percent of the chickpea genome within record two years. This time span is relatively fast compared to the other grain genome sequencing like maize, rice and wheat attempted earlier.

Also, by analysing the genome, scientists have identified candidate genes for disease resistance, drought and heat tolerance and early maturity. The latter types have the advantage that the plants growing more quickly can be harvested earlier before the dry spells. This research was published in the highly ranked scientific journal, Nature Biotechnology on Jan 27, 2013.
This is the second time (after sequencing the pigeon pea genome in 2011, see December, 2011 issue of Lokayat) that an Indian scientist (Dr Rajeev Varshney, both the times) led genome sequencing of a crop species and published findings in the highest respected scientific journal.

What are the potential benefits of the genome sequencing of chickpea? India, being the largest producer and consumer of chickpea, will directly benefit from this research. The farming of this legume crop in India covers around 8 million hectares of land. It is the most dominating legume crop of India and is widely cultivated in Madhya Pradesh, Andhra Pradesh, Maharashtra and Uttar Pradesh. Chickpea is also an important component of the pulse industry in Australia, Canada and USA and so these countries are also expected to reap benefit from the chickpea mapping.
According to scientists, genome sequencing of chickpea would facilitate the development of improved varieties with higher yields. The chickpea genome sequencing is also expected to help development of superior varieties with enhanced drought tolerance and more resistance to damaging pests and diseases, such as the pod borer insects which cause nearly 20-30 percent annual yield losses in India alone.

Most climate scenarios foresee a 2 degrees warmer world. Against this backdrop of climate change, the genome mapping will help chickpea breeders developing more resilient varieties that are essential to adapt to a drier and warmer climate. An important prerequisite for crop improvement is genetic diversity. However, chickpea has a narrow genetic diversity which means that the cultivated varieties have very similar genes. This has basically resulted from domestication of the crop because, over the years, breeders and growers have continually chosen only a handful of chickpea varieties for breeding and cultivation. According to Rajeev Varshney, genome sequencing of 90 chickpea lines will help bringing lost genetic diversity from wild species to the varieties being cultivated. Thus, the new study can prove valuable for enhancing the genetic diversity of cultivated chickpea gene pool.
‘It may take 4-8 years to breed a new chickpea variety. Armed with genome sequencing this time could be almost halved’, said Rajeev Varshney.

The chickpea genome sequencing is publicly accessible with no intellectual property rights (IPR) involved. Thus, with open access to the chickpea genome, the breeders can develop improved crop varieties with market-preferred traits.

What are genome and genome sequencing?

Dr Rajeev Varshney
Genome represents the entire genetic information of an organism which, for plants and animals, is encoded in their deoxyribonucleic acid (DNA). Through genome sequencing, the scientists identify the genes responsible for various functions within the body of the organism. However, the genome sequence doesn’t immediately lay open the genetic secrets of an organism. Even when a draft of the genome sequence is in hand, much work still remains to be done. The scientists have to figure out how a genome works; what genes, making up the genome, are responsible for a characteristic trait; how different genes are related; and how various parts of the genome are coordinated