Wheat is one of the major sources of food for much of the world. Since bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consortium now presents in the first transcription atlas of all wheat an annotated reference genome with a detailed analysis of gene content among sub-genomes and the structural organisation for all the chromosomes.
According to a press release of the German Helmholtz Centre in Munich/Germany, this sequence is the “anchor genome” for capturing the complete genetic diversity of bread wheat.
Knowledge of the function of the genes, if possible all genes, in an organism is crucial. The expression of genes at various points in time, in various organs and under different environmental influences is a starting point for acquiring this knowledge.
The transcription atlas now published for the wheat genome shows the direction in which research is developing, the Helmholtz Centre notes.
Under the leadership of the John Innes Centre in Norwich/UK, 200 scientists from seven countries and 17 research institutes took part in the study. The German researchers were from the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Gatersleben and the Helmholtz Centre in Munich.
For their study, the scientists analysed over 800 hundred expression data sets from 28 studies. They combined these with the fully annotated genome sequence to create a transcription atlas. The challenge here was not only the size but also the particular structure of the wheat genome, which is polyploid and comprises three individual genomes with different antecedents.
In their study, the scientists give a very comprehensive insight into the spatiotemporal transcription landscape of polyploid wheat. “For the first time, we are in a position to assign the proportions in the expression of characteristics to individual sub-genomes and to analyse the gene expression with the help of regulatory networks,” says Andrea Bräutigam, who participated in the project at the Leibniz Institute for Plant Genetics and Crop Plant Research. “What is striking is that major differences in gene expression exist particularly at the ends of the chromosomes, coding for agronomically important traits,” Bräutigam explains.
The study required an exact annotation of sequences, which was carried out at the Helmholtz Centre in Munich. “Annotation of the genes and the creation of family trees is the basis for clarifying structure and function. We were able to precisely identify the gene loci with specially developed algorithms,” Daniel Lang of the Helmholtz Centre in Munich states.
Cristobal Uauy, Principal Investigator of the study at the John Innes Centre, says: “Our understanding of genomes has enabled to dramatic progress in breeding and cultivation practices for other crops such as maize or rice. With the complete wheat genome now available, and follow-up work, it will be possible to identify genes in wheat more precisely and faster. This knowledge will help researchers and growers to use the allelic variations of polyploid wheat to improve targeted characteristics.”
R. H. Ramírez-González et al. (2018): The transcriptional landscape of polyploid wheat. Science,
The Helmholtz Centre, Munich, Germany
The Leibniz Institute, Gatersleben, Germany
The John Inns Centre, Norwich,UK