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Wheat ready for harvest. © INRA, COCHARD Hervé

First reference sequence of a bread wheat chromosome revealed

Scientists announced the publication of the first reference sequence1 of the biggest bread wheat chromosome. Thanks to an international collaboration, coordinated by INRA jointly with CEA (Genoscope), CNRS and Université d’Evry in France, this major achievement will allow the identification of numerous genes of agronomic interest, and accelerate wheat improvement. Scientists estimate that following this approach, a full reference genome sequence can be produced within three years. Results are published in Science on July 18th, 2014.

Updated on 07/18/2014
Published on 07/18/2014

Bread wheat (Triticum aestivum L.) is the most important crop in the world in terms of land use and is the staple food for over a third of the world population. Current bread wheat varieties are the result of continuous selection conducted by human for thousands of years. Wheat holds a complex genome (polyploid) comprised of three sub-genomes; altogether it is five-fold bigger than the human genome. “Although this complexity makes wheat a good model for studying large polyploid genomes, deciphering its sequence represented a great methodological challenge that delayed the advances in wheat genomics and particularly the sequencing”, says Frédéric Choulet, main author of the article published in Science.

A worldwide first

In the framework of a project called 3BSEQ, funded by ANR (French National Research Agency) and France Agrimer, scientists from INRA, CEA (Genoscope), CNRS, Université d’Evry, and international partners, produced the first reference sequence of the bread wheat chromosome 3B. To achieve this, several next generation sequencing technologies were combined, specific bioinformatic tools were developed and thousands of molecular markers were used. The result is a single sequence of 774 million nucleotides, gathering 8,500 long DNA fragments ordered along the chromosome.

Scientists compared this sequence with genomic data from related species such as rice or sorghum, and they discovered that 35% of the 7,700 genes identified on chromosome 3B were located on other chromosomes in the other cereals. This suggests that these genes currently found on chromosome 3B are the result of massive genomic rearrangements which are relatively recent from an evolutionary point of view and specific to wheat.

Recent and specialized genes at chromosome ends

By analyzing the sequence, researchers discovered a marked partitioning of the chromosome with contrasted patterns of organization, expression level and evolution rate between the extremities and the central region. While the extremities are significantly enriched in genes related to adaptation of the plant, expressed at a generally low level and specifically in certain tissues or stages of development, the central region is mainly composed of conserved genes involved in the basic metabolism of the plant.

The higher level of gene density at the ends can be explained by recent duplications, an evolutionary force stronger in wheat than in the other cereals. Thus, the massive expansion of the wheat genome was accompanied by a structural and functional partitioning and by the acquisition of new genes with adaptive functions.

A unique resource for the improvement of wheat breeding

“The reference sequence of chromosome 3B is a unique resource worldwide and it offers new opportunities for the identification of important genes of agronomic interest”, comments Catherine Feuillet, who led the project. As an example, some genomic regions of chromosome 3B are involved in the resistance to pathogens, in the tolerance to drought, and in yield; the specific genes controlling these traits are currently being identified. “A better understanding of the bread wheat genome will have two major impacts: from a basic science point of view, it will help understanding mechanisms impacting its organization, functioning and evolution; it will also pave the way to the development of the necessary tools and methodologies to improve the efficiency of selection programs” adds Choulet.

Buoyed by this success, the International Wheat Genome Sequencing Consortium (IWGSC, www.wheatgenome.org), in which INRA holds a leadership position, aims to finish sequencing the twenty other chromosomes within three years. French scientists from INRA and CEA (Genoscope) have already begun the sequencing of 2 other chromosomes.

Reference

Frédéric Choulet, Adriana Alberti, Sébastien Theil, Natasha Glover, Valérie Barbe, Josquin Daron, Lise Pingault, Pierre Sourdille, Arnaud Couloux, Etienne Paux, Philippe Leroy, Sophie Mangenot, Nicolas Guilhot, Jacques Le Gouis, Francois Balfourier, Michael Alaux, Véronique Jamilloux, Julie Poulain, Céline Durand, Arnaud Bellec, Christine Gaspin, Jan Safar, Jaroslav Dolezel, Jane Rogers, Klaas Vandepoele, Jean-Marc Aury, Klaus Mayer, Hélène Berges, Hadi Quesneville, Patrick Wincker, Catherine Feuillet. Structural and Functional Partitioning of Bread Wheat Chromosome 3B. Science, 18 July 2014. DOI: 10.1126/science.1249721

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Plant Biology and Breeding
Associated Centre(s):
Auvergne Rhône-Alpes

A pioneer wheat research laboratory

Since 2005 and the foundation of IWGSC, in which it plays a major role, the research unit “Genetics, Diversity, Ecophysiology of Cereals-GDEC”, based in Clermont-Ferrand, France, pioneered major advances in wheat genomics. It has established the first physical map of the giant chromosome 3B (Paux et al. Science 2008), and has acquired an international leadership in this field. Today, with the publication of the first reference sequence of this chromosome, the research unit’s leadership in bread wheat genomics is reinforced, and INRA confirms its major role in plant genomics at the international scale. This work sets future standards and paves the way to the production of the reference sequence of the entire genome.