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The giant diploid faba genome unlocks variation in a global protein crop.

Murukarthick JayakodiAgnieszka A GoliczJonathan KreplakLavinia Ioana FecheteDeepti AngraPetr BednářElesandro BornhofenHailin ZhangRaphael BoussageonSukhjiwan KaurKwok CheungJana ČížkováHeidrun GundlachAsis HallabBaptiste ImbertGabriel Keeble-GagnèreAndrea KoblížkováLucie KobrlováPetra KrejčíTroels W MouritzenPavel NeumannMarcin NadziejaLinda Kærgaard NielsenPetr NovákJihad OrabiSudharsan PadmarasuTom Robertson-Shersby-HarvieLaura Ávila RobledilloAndrea SchiemannJaakko TanskanenPetri TörönenAhmed O WarsameAlexander H J WittenbergAxel HimmelbachGrégoire AubertPierre-Emmanuel CourtyJaroslav DolezelLiisa U HolmLuc L JanssHamid KhazaeiJiří MacasMartin MascherPetr SmýkalRod J SnowdonNils SteinFrederick L StoddardJens StougaardNadim TayehAna M TorresBjörn UsadelIngo SchubertDonal Martin O'SullivanAlan H SchulmanStig Uggerhøj Andersen
Published in: Nature (2023)
Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity 1 . However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value 2 . Faba bean (Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.
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