The International Wheat Genome Sequencing Consortium (IWGSC) published this week the first fully annotated reference genome of the bread wheat (Triticum aestivum), one of the world’s most important crops.
Wheat field. Image credit: Pezibear.
Wheat is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans.
It also has a large and complex genome with 16 billion base pairs — the building blocks of DNA — which is more than five times larger than the human genome.
But wheat is susceptible to drought and flood, and swathes of the crop are damaged each year by diseases such as wheat rust. The sequencing of its genome paves the way for much faster production of wheat varieties adapted to climate challenges, with higher yields, enhanced nutritional quality and improved sustainability.
Sequencing the wheat genome has long been a huge challenge. As well as its enormity, it has three sub-genomes and a large part of it is composed of repetitive elements. This means that vast parts of the genome are very similar, if not identical, to each other. This has made it difficult, until now, to distinguish each sub-genome and to put together the genome into its correct order.
A new paper published in the journal Science presents the fully annotated reference genome of the bread wheat variety Chinese Spring.
It details the sequence of the 21 chromosomes, the precise location of 107,891 genes and more than 4 million molecular markers, as well as sequence information between the genes containing the regulatory elements influencing the expression of genes.
“The publication of the wheat reference genome is the culmination of the work of many individuals who came together under the banner of the IWGSC to do what was considered impossible,” said Dr. Kellye Eversole, Executive Director of the IWGSC.
“The method of producing the reference sequence and the principles and policies of the consortium provide a model for sequencing large, complex plant genomes and reaffirms the importance of international collaborations for advancing food security.”
“The wheat genome sequence lets us look inside the wheat engine. What we see is beautifully put-together to allow for variation and adaptation to different environments through selection, as well as sufficient stability to maintain basic structures for survival under various climatic conditions,” said Professor Rudi Appels, from the University of Melbourne and Murdoch University.
It is expected that the availability of a high-quality reference genome sequence will boost wheat improvement over the next decades, with benefits similar to those observed with maize and rice after their reference sequences were produced.
“How do you thank a team of scientists who persevered and succeeded in sequencing the wheat genome and changed wheat breeding forever? Perhaps it is not with the words of a scientist, but with the smiles of well-nourished children and their families whose lives have been changed for the better,” said University of Nebraska-Lincoln’s Professor Stephen Baenziger.
Wheat genome deciphered, assembled, and ordered. Seeds, or grains, are what counts with respect to wheat yields (left panel), but all parts of the plant contribute to crop performance. With complete access to the ordered sequence of all 21 wheat chromosomes, the context of regulatory sequences, and the interaction network of expressed genes — all shown here as a circular plot (right panel) with concentric tracks for diverse aspects of wheat genome composition — breeders and researchers now have the ability to rewrite the story of wheat crop improvement. Details on value ranges underlying the concentric heatmaps of the right panel are provided in the full article online. Image credit: Appels et al, doi: 10.1126/science.aar7191.
The impact of the wheat reference sequence has already been significant in the scientific community, as exemplified by the publication on the same date of six additional publications describing and using the reference sequence resource, one in the same issue of the journal Science, one in the journal Science Advances and four in the journal Genome Biology.
The second Science paper provides annotation and resources to support researchers and breeders in understanding how wheat genes affect traits.
It uses the new reference genome to perform a genome-wide analysis of the expression of homeologs, or gene copies that are similar but originate in different ancestral genomes.
Pinpointing these in bread wheat will help scientists better understand the fundamental biology of polyploid wheat.
By combining gene expression datasets with the wheat genome sequence, John Innes Centre scientist Ricardo Humberto Ramirez-Gonzalez and co-authors revealed the balance of gene expression among homeologs across the various tissues, developmental stages and cultivars of wheat.
They identified tissue-specific biases in gene expression and co-expression networks during development and exposure to stress.
“Our work provides a framework to target key genes that underpin valuable agricultural traits in wheat,” they said.
Finally, in the Science Advances study leveraging the new reference sequence, Dr. Angéla Juhász of Murdoch University and the Centre for Agricultural Research at the Hungarian Academy of Sciences and colleagues closely examined the proteins contributing to various wheat-immune diseases and allergies, like celiac, baker’s asthma and wheat-dependent exercise-induced anaphylaxis (WDEIA).
“Exposure to specific proteins in wheat can cause severe allergic reactions in some people. Celiac disease, for example — a globally prevalent chronic inflammatory disorder — is triggered by prolamin proteins gliadin and glutenin, both common in wheat,” they said.
“In addition, respiratory or skin exposure to other types of proteins have also been implicated in adverse immune responses. However, due to the complexity of the wheat genome and the lack of complete genome information for this crop, a detailed understanding of the nature of these proteins has remained elusive.”
The researchers used the wheat genome to search for the genes that encode known allergy-inducing wheat proteins and mapped each across the entire sequence.
Their analysis identified 828 known and previously unknown genes potentially related to immune-responsive proteins.
The results show that the genes related to celiac and WDEIA are expressed in the starchy endosperm (the source of baking flour), while various lipid transfer proteins and alpha-amylase trypsin inhibitor gene families are involved in baker’s asthma.
Furthermore, the study revealed that temperature stress during flowering can increase the levels of major celiac and WDEIA proteins.
“Our analysis offers important insights into the role of environment and growing conditions on the levels of proteins problematic for human consumers,” the study authors said.
“This work will also inform production of low allergy wheat varieties, among others useful to the food industry.”
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Rudi Appels et al (The International Wheat Genome Sequencing Consortium). 2018. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361 (6403); doi: 10.1126/science.aar7191
R.H. Ramírez-González et al. 2018. The transcriptional landscape of polyploid wheat. Science 361 (6403); doi: 10.1126/science.aar6089
Angéla Juhász et al. 2018. Genome mapping of seed-borne allergens and immunoresponsive proteins in wheat. Science Advances 4 (8); doi: 10.1126/sciadv.aar8602
