A higher proportion of locally produced plant protein in the current meat-rich diet could significantly reduce greenhouse gas emissions and biodiversity loss. However, plant protein production is hampered by the lack of a legume for cooler climates with agronomic value equivalent to that of soybean. Field bean (Vicia faba L.) has high yield potential and is well suited for cultivation in temperate regions, but genomic resources have been lacking. An international team of researchers, including scientists from the IPK Leibniz Institute, has assembled the field bean genome in high quality on a chromosome-by-chromosome basis. The results have been published in the journal Nature.
Field bean is one of the earliest domesticated crops. It was part of the Neolithic crop package that the first farmers took with them when they left the Fertile Crescent. In the 21st century, nutritional quality remains a key breeding objective: new field bean varieties should have low levels of the alkaloid glycosides vicin and convicin, as well as tannins. In addition, essential amino acids should be better matched to human nutritional needs, while phytates and protease inhibitors should be reduced in the seed to improve nutrient bioavailability. Care should be taken not to alter seed size and compromise pest resistance while improving yield stability.
Using a high-quality genome sequence of common bean, the research team shows that it has grown to a massive 13 Gb due to an imbalance between the rates of amplification and elimination of retrotransposons. They have accomplished the technical feat of assembling the giant chromosome 1, which at 3.3 billion base pairs is as large as the entire human genome. Genes and recombination events are evenly distributed across the chromosomes, and the gene space is remarkably compact considering the size of the genome, although copy number varies significantly due to tandem duplications. "To demonstrate the practical application of genome sequencing, we are developing a test for targeted genotyping and using high-resolution genome-wide association analysis to decipher the genetic basis of seed size and umbilical color," says Dr. Murukarthick Jayakodi, head of the Independent Working Group on Grain Legume Genomics at IPK and lead author of the study.
Breeders can now address the complex challenges made possible by genomic resources and insights. The reference genome will facilitate the rapid introduction of new traits into elite material and enable powerful and broadly applicable mapping approaches. "Our comprehensive genome-wide annotation now sheds light on these effects and adds an important component to genome-based breeding," says Dr. Murukarthick Jayakodi. Together with the identification of target genes, this opens up the possibility of gene cloning. "The resources presented provide a genome-based breeding platform for common bean that will enable breeders and geneticists to accelerate the improvement of sustainable protein production in Mediterranean, subtropical and northern temperate agro-ecological zones," emphasizes the IPK researcher.