Wheat genome unravelled: can help in dealing with climate change

It took the best scientific minds from 20 nations, including India, to scale what is considered as the “Mt. Everest of the genome world”.

After 13 years of painstaking effort, a global community of scientists has decoded the gigantic bread wheat genome (Chinese Spring variety), a feat that breeders hope will help address the productivity and climate resilience issues, especially in India, which is the world’s second-largest producer of the grain.

The group of scientists known as the International Wheat Genome Sequencing Consortium (IWGSC) published in August 2018 a detailed description of the genome of bread wheat, the world’s most widely cultivated crop.

Wheat is the staple food of more than a third of the global human population and accounts for almost 20 percent of the total calories and protein consumed by humans worldwide, more than any other single food source. It also serves as an important source of vitamins and minerals, according to a IWGSC press release.

The reference genome provides a roadmap to improve and innovate the crop just like the advances that rice (Oryza sativa L.) had witnessed, following the unravelling of its genome in 2005. Rice was the first crop genome that was sequenced.

“The high quality reference genome generated by the global community will help in better understanding of the basic biology of wheat plant and identifying genes underlying important traits,” Kuldeep Singh, senior molecular geneticist and director of National Bureau of Plant Genetic Resources, told Mongabay-India.

This achievement will enhance the wheat breeders’ toolbox and pave the way for development of wheat varieties with higher yields, enhanced nutritional quality, improved sustainability and varieties that are better adapted to climate challenges, said Singh. 

Singh (formerly with the Punjab Agricultural University), Nagendra Singh at ICAR-National Research Centre on Plant Biotechnology, New Delhi and JP Khurana at the University of Delhi, spearheaded the Indian effort (comprising 18 scientists) to sequence chromosome 2A of the genome.

Wheat cultivation in India has been traditionally dominated by the northern region of India.

Singh explained that the major challenges to wheat productivity in future in India will pertain to enhancing yields by 2050 and accelerating the breeding of climate-resilient wheat varieties.

“One challenge is to improve its yields by 60-70 percent in next 32 years (by 2050) when India’s population stabilises at 1.66 billion. This translates to roughly two percent per annum and our current rate of improvement is 1-1.5 percent,” Singh said.

The other aspect is developing varieties which, during their growth period, can tolerate higher and more erratic temperatures due to climate change, are resistant to emerging diseases and insects, require less water and other inputs including major and micronutrients and are nutritionally richer.

The challenge of ozone pollution

In addition, ozone pollution is also identified as a “significant challenge” to global food production, including wheat growth, in a recent multinational study led researchers from the UK-based Centre for Ecology & Hydrology (CEH).

Putting ozone into context with other crop stressors, including heat stress, pests and aridity, study results showed a predicted national mean wheat yield loss of 12.6 percent for India, which added up to an estimated 13 million tonnes of annual lost yield due to ozone (average for the period 2010-12).

For the state with the highest wheat production, Uttar Pradesh, predicted percentage yield losses due to ozone were in the range of 15 percent to 20 percent in most of the wheat‐producing areas.

“We show that the impact of ozone on wheat yield is at a comparable level to pressures from other stresses in some areas of India. Also, the area of highest ozone impacts on wheat production coincided with an area with high levels of heat stress too,” CEH’s Katrina Sharps and co-author of the study told Mongabay-India.

The authors identified practical, short-term actions such as breeding new varieties of crop that are more resilient to ozone, better timing of irrigation and the development of non-toxic agrochemicals, that farmers and growers can take to improve crop yields.

In this regard, Kent Burkey, of the United States Agricultural Research Service (USDA-ARS) and a co-author of the ozone pollution study, said, knowing the wheat genome sequence could contribute to breeding more ozone resilient varieties by helping to identify specific genes located in the genome near known DNA markers associated with ozone tolerance.

“Manipulating the function and regulation of these specific genes would be a targeted approach to enhance ozone tolerance. However, this may not be a straightforward process because the ozone-tolerance trait may involve more than one gene,” Burkey said.

Climbing Mt. Everest

Cracking the genome itself came with its own set of hurdles: the enormity of the genome and its complexity. At 17 Giga bases, the bread wheat genome is five times as large as the human genome and 40 fold larger than the rice genome.

This is because bread wheat essentially is three species rolled into one, said Singh.

Bread wheat is an allopolyploid — which means it has evolved in nature by the natural crossing of three different but very closely related species, each contributing seven pairs of chromosomes which are referred to as A, B and D genomes, making a total of 21 pairs of chromosomes.

“Hence major challenges were to bring together larger number of countries and resources for undertaking this gigantic task. However, technological advances in flow cytometry-based sorting of individual chromosomes, high throughput DNA sequencing techniques and improved algorithms made it possible for the international community to achieve this task at a cost much lower than it was achieved for in human or rice genomes,” Singh explained.

“A lot of genetic and cytogenetic information was available in Chinese Spring line and hence this was used as the reference line,” Singh said.

Researchers also believe that using the genome map, gene editing techniques such as CRISPR can be deployed to modify genes with high precision.

This would be boosted by the genome map as it provides precise location of 107,891 genes and of more than 4 million DNA markers, as well as sequence information between the genes and markers containing the regulatory elements influencing the expression of genes.

“Insight into duplication of genes and expression of homologous genes are important contributions of this study. In future, it will help in gene editing which requires precise structural and functional details of a gene,” Singh informed.

Adding precision to India’s wheat breeding programme

For India, which has a robust wheat breeding programme and more than 500 varieties, the genome sequence adds precision to the breeding programme.

Singh highlighted that India has different agroecological zones and different climatic conditions and therefore varieties suited to specific zones and climate.

“For example, we have northwestern plains (Punjab, Haryana, parts of Rajasthan) that have a different variety, for eastern India we have a different variety and so on and so forth,” Singh noted.

“Because of the agroecological zones and climate and our robust wheat breeding programme we have all sorts of varieties such as high input irrigation condition, rain fed conditions. So far we have more than 500 varieties. With the genome sequence, use of new technologies would add precision to the breeding programme and it makes it possible to bring together genes which was not possible with conventional breeding,” Singh elaborated.

Wheat breeding in India dates to the early 1900s but the Green Revolution in the 1960s is credited for being a gamechanger.

The Green Revolution in wheat refers specifically to the rapid adoption of varieties with semi‐dwarf stature (shorter plant with a stronger stalk) during the late‐1960s and early‐1970s. These plants could productively utilise greater amounts of fertiliser.

“Due to the dwarf gene we could have a jump during the Green Revolution. Thereafter, we have seen a consistent increase otherwise we would not have met the major requirements of our population. Though there has been a consistent increase in productivity, there are years where productivity has gone down. As we go from here every step will become difficult,” Singh emphasised.

For example, earlier increasing productivity by one quintal (100 kg) per acre was relatively easier. Now when we have an average yield of 3.2 tonne per hectare (or in Punjab it is 5.5 tonne per hectare), going up from there will be very, very tough, he observed.

“As you scale Mount Everest, the initial steps are easier but as you climb higher and higher it gets difficult so we do realise that productivity will be a challenge and genomic data will aid us to address that challenge,” Singh said.

However, he cautioned against viewing the genome sequence as a magic wand.

“We have to be very, very careful that it (genome sequence data) is not a magic wand that it can do everything. The country has to be very careful. I still think the country would need to think of population control as well. Science alone may not be able to feed our population of 1.66 billion people in 2050,” he said.

CITATION

Appels, R., Eversole, K., Feuillet, C., Keller, B., Rogers, J., Stein, N., … & Ronen, G. (2018). Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science, 361(6403), eaar7191.

Mills, G., Sharps, K., Simpson, D., Pleijel, H., Frei, M., Burkey, K., … & Kobayashi, K. (2018). Closing the global ozone yield gap: Quantification and cobenefits for multistress tolerance. Global change biology.

Banner image: A field of wheat in Germany. Photo by Max Ronnersjo/Wikimedia Commons.