Czech scientists participated in decoding the bread wheat genome

Czech scientists participated in decoding the bread wheat genome
After thirteen years of intensive international collaboration, two hundred scientists from twenty countries managed to obtain a reference genome sequence of the most widespread agricultural crop, bread wheat. The International Consortium for Wheat Genome Sequencing (IWGSC) informed about the important advance in an article published in prestigious scientific journal Science. The discovery will help scientists and breeders to develop improved varieties of bread wheat in a shorter time. The researchers from the Institute of Experimental Botany of the Academy of Sciences of the Czech Republic in Olomouc (IEB ASCR), whose workplace is one of the three partners of the Centre of the Region Haná Biotechnological and Agricultural Research (CRH), contributed to this success.
Reading the genetic information of bread wheat has been considered impossible due to its enormous size, which comprises nearly seventeen billion letters of the genetic code. The genome of bread wheat is five times larger than that of humans because it consists of three mutually similar subgenomes and also because most of the genome is made up of various types of repetitive DNA sequences. According to the Head of the Centre for Plant Structural and Functional Genomics of IEB ASCR professor Jaroslav Doležel, this, together with the fact that scientists have read genomes by short pieces, made it very difficult to assemble the complete genome: "We may compare it to a situation when the text of three editions of the same book published in local dialects of the same language is cut to very short pieces, which are mixed. It is a daunting task to assemble correctly the three books from the short segments of the text. I am very happy that the project was successful. This would of course not be possible without extensive international cooperation. The research involved 73 research teams that used different methods, shared results and exchanged experiences "said plant geneticist Jaroslav Doležel.

Decoding the wheat genome will serve the breeders and future research

The finished reference genome sequence of wheat provides breeders with an important resource to address major food safety issues. Wheat is a staple food for about one third of the world's population. In 2050, the population will reach 9.6 billion and wheat yields need to rise 1.6 percent each year to ensure enough food. However, as the area of arable land decreases and the global climate has been changing, it will not be possible to produce enough food without planting improved varieties. With a detailed knowledge of genetic information of wheat, breeders can identify genes controlling yield, grain quality, resistance to diseases and pests and also drought-resistant genes. In future, this result will allow efficient use of new genome editing methods.
Obtaining the reference genome sequence of wheat is also important for fundamental research to elucidate the function of individual parts of the hereditary information and their effect on the growth and development of wheat. The first results obtained with the help of the reference sequence were published in six articles that were published on the same day as the main article; one in the same issue of the Science magazine, one in Science Advances and four in Genome Biology.

A significant contribution of researchers from Olomouc

The research Centre of IEB AS CR in Olomouc is one of the founding members of the IWGSC in 2003 and played an important role in the huge international project. The initial genome sequencing strategy was based on the method of chromosome sorting using flow cytometry, which was developed by the Olomouc team that remains the only one in the world to use the method routinely. This approach enables dissecting the large and complex plant genomes into smaller parts - chromosomes, and this greatly simplifies DNA sequencing and assembly of the short reads into large contigs. The Olomouc team was supplying DNA from individual chromosomes of wheat to collaborating laboratories in different parts of the world.
Another important contribution of the Czech science was the preparation of Bacterial Artificial Chromosome (BAC) libraries. These genomic resources provided the opportunity to sequence longer parts of the genome, which in turn facilitated the genome assembly. The team has been world leader in the preparation of BAC libraries from isolated chromosomes. A total of about 2.5 million BAC clones from individual wheat chromosomes are stored at IEB ASCR premises in special freezers at -80°C. Last but not least, the Olomouc research team participated in sequencing three out of twenty-one wheat chromosomes and recently supported the genome assembly by applying advanced methods, such as optical mapping.

The model cultivar was bread wheat "Chinese Spring"

The aim of the long-term project was to obtain entire, so-called reference genome sequence of bread wheat cultivar "Chinese Spring". The new results helped to closed numerous gaps in the wheat genome, which chromosome-based draft was published in 2014. Now the scientists know the sequences of all 21 wheat chromosomes as well as the location of 107,891 genes and more than 4 million molecular markers. Professor Jaroslav Doležel considers the recent findings of the international scientific community an extraordinary success: "We have obtained the complete text of the genetic information of bread wheat. We have a high quality genome sequence of one cultivar, with which we can easily compare genome sequences of the other cultivars. Thus, we do not have to build them again painstakingly from scratch and the differences can be identified much easier."

Nevertheless, scientists are facing new challenges. So far, the genome has been examined as a linearly ordered sequence of letters. In reality, the genetic information is carried in the linear sequence of nucleotides in DNA molecules, which are arranged in a three-dimensional space of cell nuclei with a diameter of a few micrometers, and their parts may interact, affecting plant growth, development and response to environmental stimuli. In wheat, this arrangement can be compared to a ball made of 42 ten inch-long fibers. Finding the interacting regions of DNA molecules is difficult, but scientists have already developed methods to identify and characterize them more closely.
  • The Science article is entitled "Shifting the limits in wheat research and breeding using a fully annotated reference genome" and can be read here.
  • All IWGSC reference sequence resources are publicly available at the IWGSC data repository at URGI-INRA Versailles and at other international scientific databases such as GrainGenes and Ensembl Plant.
International consortium for wheat genome sequencing (IWGSC)

IWGSC with 2400 members in 68 countries is an international consortium founded in 2005 by a group of wheat growers, scientists and breeders. The aim of the IWGSC is to obtain and publish a quality sequence of the wheat genome set and to provide background material for basic research, the results of which will enable breeders to obtain new varieties with the desired properties. IWGSC is a non-profit organization registered in the US

The Centre for Plant Structural and Functional Genomics, Institute of Experimental Botany of the Academy of Sciences of the Czech Republic

Is one of the three partners of the Centre of the Region Haná for Biotechnological and Agricultural Research in Olomouc, Czech Republic, and focuses on the analysis of the structure and function of genetic information of plants, in particular cereals, banana and grasses. The Centre uses the state-of-the-art methods of cytogenetics, molecular biology and genomics, and has been one of the pioneers in using flow cytometry in plant biology. The team participates in major international projects aimed at sequencing genomes of important crops and isolation of important genes. Under the guidance of professor Jaroslav Doležel the Centre has been developing unique methods and materials to support breeding of new cultivars of agricultural crops.