An international team of researchers have constructed the pangenome for chickpea (chana), one of the most economically important crops, and the third most common legume cultivated in the world. India is the world's largest producer of chickpea, responsible for 70 per cent of global production in 2019. It is a staple of Indian and Mediterranean diets and is grown in 60 countries around the world, particularly in south Asia and subsaharan Africa. The demand for chickpea is expected to track the increase in global population.
The pulses are a source of carbs, proteins, fibre, Vitamin B, folate, iron, phosphorus among other minerals and essential nutrients, and can potentially be used to counter malnutrition. When consumed as a part of a well balanced diet, the chickpea can fend off diabetes, heart disease and obesity. Additionally, the crop is great at nitrogen fixation, and cultivation improves the quality of the soil. It is an important source of protein, especially in the Global South.
We asked Dr Rajeev Varshney, lead author of the study if the chickpea can be considered a superfood, and if it can address the food security situation in the future. Varshney tells us, "The name tags notwithstanding, it can certainly be said that chickpea is a very rich source of protein, at over 20 g per 100 g. That apart, it is also rich in fiber. Chickpeas already are instrumental in contributing to food security in many nations. They are expected to play an increasingly greater role as the global population rises and the demand for protein, particularly plant-based protein, increases."
There are two main varieties of chickpea, the smaller, darker Desi-type, and the larger, lighter Kabuli-type. There are also intermediate and wild varieties. While traditional breeding approaches have increased yield, climate change has introduced new challenges, with draught or heat reducing yield by 70 per cent. The timely research allows for new breeding programs to develop crops that are resistant to climate change, as well as meet the health requirements of future populations.
Researchers from 41 organisations have worked together to assemble the pangenome, sequencing the genomes of 3,366 chickpea lines from 60 countries.
While pangenomes for bacteria and archaea have been constructed, there are only a few pangenomes for plants. The effort was led by researchers from the International Crops Research Institute for Semi-Arid Tropics (ICRISAT). A total of 29,870 new genes were identified along with 1,582 novel ones, which were previously unreported.
The effort is the largest pangenome study conducted for any plant. The pangenome consists of the core genome, shared by all the genomes studied, while the dispensable genome is shared by only a subset of the genomes studied. The pangenome allows researchers to see how the plant spread across the globe, with two paths of diffusion from the lands between the Persian Gulf, the Red Sea and the Mediterranean Sea, known as the Cradle of Civilisation or the Fertile Crescent.
Varshney says, "By employing whole genome sequencing, we have been able to affirm the history of chickpea's origin in the Fertile Crescent and identify two paths of diffusion or migration of chickpea to rest of the world. One path indicates diffusion to South Asia and East Africa, and the other suggests diffusion to the Mediterranean region (probably through Turkey) as well as to the Black Sea and Central Asia (up to Afghanistan)"
The genes also hide within them the history of the species. The study indicates that the cultivated species, known as Cicer arietinum diverged from the wild progenitor species, Cicer reticulatum around 12,600 years ago. There was a genetic bottleneck beginning around 10,000 years ago, with the population size reaching its minimum around 1,000 years ago. From around 400 years ago, there was a strong expansion, which indicates that there was a renewal in the interest of chickpea cultivation around the world at that time.
Despite the extent of cultivation and the importance of the crop, it has not been studied very well, earning it the tag of an 'orphan' crop. This is particularly true considering how well studied other legume crops are, such as beans and peas. The construction of the pangenome is the latest in a series of genomic studies on the chickpea conducted by the scientists at ICRISAT, providing the tools necessary to bring better crops to the market. In 2013, ICRISAT led the sequencing of a Kabuli-type chickpea, which was the first chickpea genome to be sequenced.
The research over years means that the chickpea can finally drop its 'orphan' tag. Dr Jacqueline Hughes, Director General of ICRISAT says, "By developing many genomic resources for chickpea over the last decade, ICRISAT has helped the crop shed its 'orphan' tag. With our partners in agricultural research for development, we will continue to research chickpea and translate findings into crop varieties that benefit farmers, consumers and nations."
The comparison of the domestic species to its wild progenitor allowed the researchers to identify detrimental genes that are responsible for reduced crop performance, that have not been bred out yet. These deleterious genes are more common in the wild progenitor species, and have been bred out to some extent by traditional and conventional breeding approaches, through selection and recombination. The identified deleterious genes can be targets for gene editing, or genomics assisted breeding programs.
Seven improved chickpea varieties have been introduced in India and Ethiopia over the last three years, because ICRISAT and other organisations have been using genomics assisted approaches targeting one or at most two genes.
The study also haplotypes, or blocks of genes in the domesticated varieties developed by farmers (known as landraces), that can increase the performance of the crop by improving traits such as yield, resilience to climate, and seed characteristics. Crop breeders strive to bring these haplotypes into cultivars, and now can be guided with the additional genomics information available. The research also shows the deployment of these haplotypes in the varieties using historical data of all chickpea varieties released between 1948 and 2012.
Dr Manish Roorkiwal, a senior scientist in Genomics and Molecular Breeding at ICRISAT and author of the study explains, "We examined 129 varieties released in the past. Though a few superior haplotypes were detected in some of these varieties, we found that most varieties lacked many beneficial haplotypes. We have arrived at 56 promising lines that can bring these haplotypes into breeding programs to develop enhanced varieties."
Dr Arvind Kumar, Deputy Director General-Research, ICRISAT says, "Genomic resources are crucial for accelerating the rate of genetic gains in crop improvement programs. It is hoped that the knowledge and resources made available through this study will help breeders across the world revolutionise chickpea breeding without eroding its genetic diversity."
The authors of the study, which has been published in Nature, have proposed three breeding approaches, that aim at 16 traits to enhance chickpea productivity, to take the science to the farms.
When asked what are the desirable traits to be bred into chickpeas apart from resilience to climate and an increased yield, Varshney explains, "From a purely scientific perspective, there are numerous traits that can be introduced. However, all breeding efforts are driven by real-world needs/requirements. Yield and climate-resilience are actually umbrella terms for a lot of traits and are not mutually exclusive. They encompass traits that include tolerance to disease or resistance to pests, or traits that involve changes to the plant's reproduction time, like early maturity, to help it escape from certain stresses."
The genomics driven breeding programs can extend beyond the farm, with the benefits even extending to the kitchens.
Varshney says, "Then there are traits that are influenced by cooking preferences, like the need for lowering cooking time, and there are also traits that may be targeted to enhance nutrition profile if consumption requirements are to be considered. Crop breeding strives to bring in as many beneficial traits as possible to meet the requirements and a resource like pan-genome is the first step towards doing it."
When asked about the next steps for practical applications of the study, Varshney says, "The next step involves deploying the information and resources in crop breeding programs. This study has identified beneficial genes for some key traits and the lines that have them. These lines can be crossed with existing elite cultivars to develop new varieties that are further enhanced. Subsequently, any such new lines developed will have to be tested for multiple years to determine real-world performance before they can be released as varieties."
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