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Unlocking the genome of legumes

2016 is the international year of legumes! And for good reason: legumes have much to contribute to achieving a sustainable agriculture. The sequencing of the genome of a model legume plant in 2011 was a pivotal moment for tapping into the high potential of legume crops.

Green pods of Medicago truncatula. This plant is cultivated within the framework of an experimental project carried out by INRA in Montpellier (UMR 759 LEPSE) on the effects of environmental stress on the physiology of some model plants. © INRA, PROSPERI Jean-Marie
By Pascale Mollier, translated by Inge Laino
Updated on 07/03/2017
Published on 04/08/2016

Legumes, a family with great agricultural potential

Peas, horse beans, lentils, alfalfa, clover… Legumes have a trait that is unique in the plant world: they can store atmospheric nitrogen thanks to symbiosis with bacteria that settle into their roots.  This has many advantages. Used in crop rotations, legumes make nitrogen available to the crops that come after them, allowing growers to save on synthetic nitrogen fertilisers (1). They also boost biodiversity, and can curb the transmission of disease and pests. When it comes to food, legumes are an important source of protein for both humans and animals.

Despite these advantages, legume crops have been on the wane in France and Europe since the 1980s (2). They represent a mere 2% of land used for major crops in Europe, as opposed to more than 15% in North America and 26% in South America. Lacking in protein crops, Europe imports 75% of the plant protein it uses in animal feed, primarily in the form of soybean cakes.

Understanding the genome of legumes is key to improving them genetically. Once that is achieved, they can be harvested in earnest and successfully re-integrated into crop rotations.

INRA chooses a model: Medicago truncatula

INRA is part of an international consortium that has deciphered almost all of the eight chromosomes of the Medicago truncatula genome (3). Medicago truncatula, proposed as a model legume plant by INRA in the 1980s, is very similar to most legumes grown in Europe such as peas, horse beans, alfalfa and clover. Specifically, the order of their genes on chromosomes is the same across the board (4). That is why determining the sequence of the genome of Medicago truncatula has allowed science to order the majority of genes over the eight chromosomes for several species. This knowledge is expected to make it much easier to pinpoint key genes in legume crops.

The genetic origin of nitrogen-fixing symbiosis

The study also revealed that the genome of legume plants was duplicated about 60 million years ago. Thanks to this event, the genes involved in a much older symbiosis with mycorrhizal fungi evolved and gave rise to genes that play a part in nitrogen-fixing symbiosis.

 
 
(1) Savings in nitrogen fertiliser goes hand in hand with savings in fossil fuel, which is necessary for producing and transporting these fertilisers. They also lead to a cut-back in greenhouse gas emissions, since nitrogen fertilisers are at the root of nitrous oxide (N2O) emissions, which has a global warming effect 300 times greater than that of carbon dioxide.
(2) For different, sometimes historically-related, reasons: low cost of nitrogen fertilisers, greater economic support for cereal crops.
(3) France achieved the sequencing of both branches of chromosome 5, i.e. 45 million base pairs.
(4) So-called shared synteny.

Reference

Nevin D. Young, Frédéric Debellé, Giles E. D. Oldroyd, et al. The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses. Nature, 16 November 2011, DOI: 10.1038/nature10625

Participants in the consortium include, notably: University of Oklahoma; J. Craig Venter Institute; Genoscope (CEA Institut de Genomique); Wellcome Trust Sanger Institute; University of Minnesota; LIPM INRA/CNRS; John Innes Center; Noble Foundation; University of Wageningen; MIPS; Ghent University; National Center for Genome Resources (NCGR); BIA INRA; and CNRGV INRA.

The sequencing of 44 million base pairs that make up the DNA of chromosome 5 of Medicago truncatula was financed by the European Grain Legumes project (in equal parts between the EU and Genoscope - Institut de Génomique CEA), the ANR SEQMEDIC project, INRA and the CNRS.

Tychius aureolus, charancon des graines de Luzerne.. © INRA, CARRE Serge

Direct benefits of sequencing Medicago

Thanks to the sequencing of the Medicago truncatula genome, scientists have identified a family of insecticidal proteins in this model species. An albumin of the same family had already been found in peas. In Medicago, the variety of genes encoding these proteins is unparalleled, due to mechanisms of intense duplication over the course of evolution. By exploring this diversity, researchers found a peptide that acts as an insecticide and is ten times more potent than the albumin 1b peptide in peas. This discovery led to a patent in 2013. Read the article.