Genomic-assisted crop breeding – unlocking and unleashing the pigeonpea

Legume crops provide the vast majority of the world’s food, feed and oil, but climate change and population growth mean that the yields of these crucial crops are not what they could be. Science-based agriculture solutions, such as genomic-assisted breeding, have, therefore, become absolutely essential to bring crop productivity up to acceptable levels, particularly in marginal environments.

Yet, while some popular legumes, such as soybean and several cereal crops, have received attention from genomics-assisted breeding programmes, many have been left on the sidelines, despite their importance to food security in poor regions. Until recently, pigeonpea was one such crop.

Also known as ‘poor man’s protein’, pigeonpea is a crop grown on about five million hectares of semi-arid land in Asia, sub-Saharan Africa and South-Central America, which provides a well-balanced diet for millions and maintains the livelihoods of many smallholder farmers in semi-arid tropic (SAT) regions.

Little scientific research had been carried out on this orphan crop until the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) formed a global research partnership to map its genome sequence, bringing this marginal legume under the scientific spotlight and potentially positioning it as a major food crop for the future.

Indeed, in November 2011 the completed genome sequence of pigeonpea was featured in Nature Biotechnology, complete with valuable clues on how this groundbreaking research could be useful to crop improvement, resulting in sustainable food production in Asia and sub-Saharan Africa.

Three years in the sequencing: how the pigeonpea genome was mapped

The identification of 48,680 pigeonpea genes hasn’t been an easy process. "It’s taken three years to complete the draft assembly of pigeonpea," says Rajeev Varshney, lead scientist and coordinator for the pigeonpea genome sequencing project, which used basic genomic tools, such as molecular markers and genetic maps, to give the pigeonpea community access to the crop’s gene repertoire. "The team faced several challenges while working on this genome project.

"The first one was to start sequencing a genome without having a funded project. To overcome this, we developed an informal consortium and requested consortium members to contribute towards sequencing costs or analysis of data. BGI-Shenzhen played an important role in getting the genome sequence completed.

"Of course, there were also several technical challenges; for instance, assembling smaller sequence reads to scaffold level proved to be an enormous task."

Yet the project’s challenges – both funding and science-related – have been more than matched by the benefits the final genome sequence is set to bring to both smallholder farmers and the food production industry as a whole.

Unlocked potential – benefits of making genome sequences available

Due to biotic (pests and diseases) and abiotic (water logging and salinity) stresses, there is a huge gap between potential yield (2,500 kg/ha) and the yields actually obtained on farmers’ fields (750 kg/ha), but the availability of pigeonpea’s genome sequence could potentially change all that."

"For example, ‘good’ genes can be identified for enhancing yield in harsh environments where crop production is challenged due to biotic and abiotic stresses," Varshney explains. "These genes can be introgressed by using modern breeding (non-transgenic or non-GMO) approaches. As a result, it is now possible to develop superior varieties or hybrids with enhanced tolerance to abiotic stresses and resistance to biotic stresses."

Moreover, having the pigeonpea genome sequence as a reference will significantly speed up and reduce the cost of developing new and improved crop varieties for farmers. "As pigeonpea is an annual crop, only one crop can be harvested in a single year," Varshney notes. "The normal course of developing new varieties through conventional breeding takes eight to ten years."

This process could be sped up to around three years with the genome sequence information on hand. "It enables scientists to transfer or select important genes or genome segments from one genotype to another in a more guided way in a relatively shorter time frame," Varshney confirms.

Not only will the sequencing of the pigeonpea genome affect the productivity of the crop itself, but this breakthrough could also have a significant impact on other legume crops, such as soybean and cowpea. Many of the genes discovered were found unique to pigeonpea in terms of drought tolerance, a trait that can be transferred to other similar crops.

"Yield losses due to drought are increasing every year and in this quest for improved and more sustainable plant production, drought tolerant genes offer the possibility to combat this stress at the molecular level," Varshney remarks.

"With the global population increasing and the environment in which we live changing, producing improved crop varieties is essential for our long-term survival."

Scientific solutions: the only way forward

For ICRISAT Director General, Dr William Dar, the situation we currently find ourselves in is essentially ‘a perfect storm’. "In addition to hunger and famine, climate change and population growth worsen the situation further, mostly in developing countries," Varshney explains.

"In such circumstances, science-based development solutions are very important to global agriculture.

"Genomics-based approaches, for instance, can help identify the candidate genes to develop improved crop varieties with enhanced crop productivity in marginal environments. They will also help reduce the use of artificial fertilisers and, in turn, help the environment."

Genomics-assisted breeding also has the advantage of being acceptable to the general public. "There are still several groups and individuals who are not ready for GMO products," Varshney notes. "Therefore, molecular breeding products generated after genomics research applications in breeding are expected to have much better public acceptance.

"We are using the genome sequence to identify the ‘good’ genes and we don’t introgress any genes from outside; rather, we select the plant from a population that has good genes and will lead to a better product."

Looking further to the future, ICRISAT hopes to use the knowledge it has gained to develop genome sequences for other ICRISAT mandate crops such as chickpea, peanut and pearl millet, to further enhance crop varieties and therefore sustainable food production worldwide.

"We hope to have genome sequences not only for all five of our mandate crops, but for hundreds of thousands of lines of each of these species," he forecasts. "In that scenario, we will be able to identify better lines for use in breeding programmes and we can start deploying and promoting the use of ‘knowledge-based breeding’ rather than ‘chance breeding’."