##### PUB RECORD #####
## 10.1038/s41586-023-05791-5  36890232  PMC10033403  Jayakodi, Golicz et al., 2023  "Jayakodi M, Golicz AA, Kreplak J, Fechete LI, Angra D, Bednář P, Bornhofen E, Zhang H, Boussageon R, Kaur S, Cheung K, Čížková J, Gundlach H, Hallab A, Imbert B, Keeble-Gagnère G, Koblížková A, Kobrlová L, Krejčí P, Mouritzen TW, Neumann P, Nadzieja M, Nielsen LK, Novák P, Orabi J, Padmarasu S, Robertson-Shersby-Harvie T, Robledillo LÁ, Schiemann A, Tanskanen J, Törönen P, Warsame AO, Wittenberg AHJ, Himmelbach A, Aubert G, Courty PE, Doležel J, Holm LU, Janss LL, Khazaei H, Macas J, Mascher M, Smýkal P, Snowdon RJ, Stein N, Stoddard FL, Stougaard J, Tayeh N, Torres AM, Usadel B, Schubert I, O'Sullivan DM, Schulman AH, Andersen SU. The giant diploid faba genome unlocks variation in a global protein crop. Nature. 2023 Mar;615(7953):652-659. doi: 10.1038/s41586-023-05791-5. Epub 2023 Mar 8. PMID: 36890232; PMCID: PMC10033403." ##

PMID- 36890232
OWN - NLM
STAT- MEDLINE
DCOM- 20230331
LR  - 20230403
IS  - 1476-4687 (Electronic)
IS  - 0028-0836 (Print)
IS  - 0028-0836 (Linking)
VI  - 615
IP  - 7953
DP  - 2023 Mar
TI  - The giant diploid faba genome unlocks variation in a global protein crop.
PG  - 652-659
LID - 10.1038/s41586-023-05791-5 [doi]
AB  - 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.
CI  - (c) 2023. The Author(s).
FAU - Jayakodi, Murukarthick
AU  - Jayakodi M
AUID- ORCID: 0000-0003-2951-0541
AD  - Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 
      Seeland, Germany.
FAU - Golicz, Agnieszka A
AU  - Golicz AA
AUID- ORCID: 0000-0002-9711-4826
AD  - Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany.
FAU - Kreplak, Jonathan
AU  - Kreplak J
AD  - Agroecologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne 
      Franche-Comte, Dijon, France.
FAU - Fechete, Lavinia I
AU  - Fechete LI
AUID- ORCID: 0000-0002-8502-9210
AD  - Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 
      Denmark.
FAU - Angra, Deepti
AU  - Angra D
AD  - School of Agriculture, Policy and Development, University of Reading, Reading, 
      UK.
FAU - Bednar, Petr
AU  - Bednar P
AUID- ORCID: 0000-0001-7070-6015
AD  - Department of Analytical Chemistry, Faculty of Science, Palacky University, 
      Olomouc, Czech Republic.
FAU - Bornhofen, Elesandro
AU  - Bornhofen E
AUID- ORCID: 0000-0002-7447-6226
AD  - Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus C, 
      Denmark.
FAU - Zhang, Hailin
AU  - Zhang H
AUID- ORCID: 0000-0001-8757-9905
AD  - Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 
      Seeland, Germany.
FAU - Boussageon, Raphael
AU  - Boussageon R
AUID- ORCID: 0000-0002-5858-8105
AD  - Agroecologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne 
      Franche-Comte, Dijon, France.
FAU - Kaur, Sukhjiwan
AU  - Kaur S
AUID- ORCID: 0000-0003-3972-7058
AD  - Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, 
      Australia.
FAU - Cheung, Kwok
AU  - Cheung K
AUID- ORCID: 0000-0002-3418-3840
AD  - School of Agriculture, Policy and Development, University of Reading, Reading, 
      UK.
FAU - Cizkova, Jana
AU  - Cizkova J
AUID- ORCID: 0000-0001-7787-1849
AD  - Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the 
      Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech 
      Republic.
FAU - Gundlach, Heidrun
AU  - Gundlach H
AUID- ORCID: 0000-0002-6757-0943
AD  - Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research 
      Center for Environmental Health, Neuherberg, Germany.
FAU - Hallab, Asis
AU  - Hallab A
AD  - IBG-4 Bioinformatics Forschungszentrum Julich, Julich, Germany.
AD  - Bingen Technical University of Applied Sciences, Bingen, Germany.
FAU - Imbert, Baptiste
AU  - Imbert B
AUID- ORCID: 0000-0002-8229-8693
AD  - Agroecologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne 
      Franche-Comte, Dijon, France.
FAU - Keeble-Gagnere, Gabriel
AU  - Keeble-Gagnere G
AD  - Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, 
      Australia.
FAU - Koblizkova, Andrea
AU  - Koblizkova A
AD  - Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, 
      Ceske Budejovice, Czech Republic.
FAU - Kobrlova, Lucie
AU  - Kobrlova L
AUID- ORCID: 0000-0001-9024-7717
AD  - Department of Botany, Faculty of Science, Palacky University, Olomouc, Czech 
      Republic.
FAU - Krejci, Petra
AU  - Krejci P
AUID- ORCID: 0000-0002-4653-1195
AD  - Department of Analytical Chemistry, Faculty of Science, Palacky University, 
      Olomouc, Czech Republic.
FAU - Mouritzen, Troels W
AU  - Mouritzen TW
AUID- ORCID: 0000-0003-0558-1425
AD  - Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 
      Denmark.
FAU - Neumann, Pavel
AU  - Neumann P
AUID- ORCID: 0000-0001-6711-6639
AD  - Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, 
      Ceske Budejovice, Czech Republic.
FAU - Nadzieja, Marcin
AU  - Nadzieja M
AUID- ORCID: 0000-0002-6643-8019
AD  - Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 
      Denmark.
FAU - Nielsen, Linda Kaergaard
AU  - Nielsen LK
AUID- ORCID: 0000-0003-3215-9481
AD  - Sejet Planteforaedling, Horsens, Denmark.
FAU - Novak, Petr
AU  - Novak P
AUID- ORCID: 0000-0002-5068-9681
AD  - Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, 
      Ceske Budejovice, Czech Republic.
FAU - Orabi, Jihad
AU  - Orabi J
AD  - Nordic Seed, Odder, Denmark.
FAU - Padmarasu, Sudharsan
AU  - Padmarasu S
AUID- ORCID: 0000-0003-3125-3695
AD  - Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 
      Seeland, Germany.
FAU - Robertson-Shersby-Harvie, Tom
AU  - Robertson-Shersby-Harvie T
AD  - School of Agriculture, Policy and Development, University of Reading, Reading, 
      UK.
FAU - Robledillo, Laura Avila
AU  - Robledillo LA
AD  - Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, 
      Ceske Budejovice, Czech Republic.
FAU - Schiemann, Andrea
AU  - Schiemann A
AD  - Nordic Seed, Odder, Denmark.
FAU - Tanskanen, Jaakko
AU  - Tanskanen J
AD  - Natural Resources Institute Finland (Luke), Helsinki, Finland.
FAU - Toronen, Petri
AU  - Toronen P
AD  - Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
FAU - Warsame, Ahmed O
AU  - Warsame AO
AUID- ORCID: 0000-0002-9281-0443
AD  - School of Agriculture, Policy and Development, University of Reading, Reading, 
      UK.
FAU - Wittenberg, Alexander H J
AU  - Wittenberg AHJ
AUID- ORCID: 0000-0002-0482-2592
AD  - KeyGene, Wageningen, The Netherlands.
FAU - Himmelbach, Axel
AU  - Himmelbach A
AD  - Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 
      Seeland, Germany.
FAU - Aubert, Gregoire
AU  - Aubert G
AUID- ORCID: 0000-0002-1867-5730
AD  - Agroecologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne 
      Franche-Comte, Dijon, France.
FAU - Courty, Pierre-Emmanuel
AU  - Courty PE
AD  - Agroecologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne 
      Franche-Comte, Dijon, France.
FAU - Dolezel, Jaroslav
AU  - Dolezel J
AUID- ORCID: 0000-0002-6263-0492
AD  - Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the 
      Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech 
      Republic.
FAU - Holm, Liisa U
AU  - Holm LU
AUID- ORCID: 0000-0002-7807-2966
AD  - Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
FAU - Janss, Luc L
AU  - Janss LL
AUID- ORCID: 0000-0001-9804-1529
AD  - Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus C, 
      Denmark.
FAU - Khazaei, Hamid
AU  - Khazaei H
AUID- ORCID: 0000-0002-5202-8764
AD  - Natural Resources Institute Finland (Luke), Helsinki, Finland.
FAU - Macas, Jiri
AU  - Macas J
AUID- ORCID: 0000-0003-0829-1570
AD  - Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, 
      Ceske Budejovice, Czech Republic.
FAU - Mascher, Martin
AU  - Mascher M
AUID- ORCID: 0000-0001-6373-6013
AD  - Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 
      Seeland, Germany.
AD  - German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 
      Leipzig, Germany.
FAU - Smykal, Petr
AU  - Smykal P
AUID- ORCID: 0000-0002-6117-8510
AD  - Department of Botany, Faculty of Science, Palacky University, Olomouc, Czech 
      Republic.
FAU - Snowdon, Rod J
AU  - Snowdon RJ
AUID- ORCID: 0000-0001-5577-7616
AD  - Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany.
FAU - Stein, Nils
AU  - Stein N
AUID- ORCID: 0000-0003-3011-8731
AD  - Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 
      Seeland, Germany.
AD  - Center of Integrated Breeding Research (CiBreed), Georg-August-University, 
      Gottingen, Germany.
FAU - Stoddard, Frederick L
AU  - Stoddard FL
AUID- ORCID: 0000-0002-8097-5750
AD  - Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.
AD  - Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland, Cordoba, 
      Spain.
FAU - Stougaard, Jens
AU  - Stougaard J
AD  - Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 
      Denmark.
FAU - Tayeh, Nadim
AU  - Tayeh N
AD  - Agroecologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne 
      Franche-Comte, Dijon, France.
FAU - Torres, Ana M
AU  - Torres AM
AUID- ORCID: 0000-0002-2907-4287
AD  - Instituto Andaluz de Investigacion y Formacion Agraria, Pesquera, Alimentaria y 
      de la Produccion Ecologica (IFAPA), Area de Mejora y Biotecnologia, Centro 
      Alameda del Obispo, Cordoba, Spain.
FAU - Usadel, Bjorn
AU  - Usadel B
AUID- ORCID: 0000-0003-0921-8041
AD  - IBG-4 Bioinformatics Forschungszentrum Julich, Julich, Germany.
AD  - Institute for Biological Data Science, CEPLAS, Heinrich Heine University 
      Dusseldorf, Dusseldorf, Germany.
FAU - Schubert, Ingo
AU  - Schubert I
AD  - Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 
      Seeland, Germany.
FAU - O'Sullivan, Donal Martin
AU  - O'Sullivan DM
AUID- ORCID: 0000-0003-4889-056X
AD  - School of Agriculture, Policy and Development, University of Reading, Reading, 
      UK. d.m.osullivan@reading.ac.uk.
FAU - Schulman, Alan H
AU  - Schulman AH
AUID- ORCID: 0000-0002-4126-6177
AD  - Natural Resources Institute Finland (Luke), Helsinki, Finland. 
      alan.schulman@helsinki.fi.
AD  - Institute of Biotechnology, University of Helsinki, Helsinki, Finland. 
      alan.schulman@helsinki.fi.
AD  - Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland, Cordoba, 
      Spain. alan.schulman@helsinki.fi.
FAU - Andersen, Stig Uggerhoj
AU  - Andersen SU
AUID- ORCID: 0000-0002-1096-1468
AD  - Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 
      Denmark. sua@mbg.au.dk.
LA  - eng
GR  - BB/P023509/1/BB_/Biotechnology and Biological Sciences Research Council/United 
      Kingdom
PT  - Journal Article
DEP - 20230308
PL  - England
TA  - Nature
JT  - Nature
JID - 0410462
RN  - 0 (DNA, Satellite)
RN  - 0 (Plant Proteins)
RN  - 0 (Retroelements)
SB  - IM
MH  - Chromosomes, Plant/genetics
MH  - *Crops, Agricultural/genetics/metabolism
MH  - *Diploidy
MH  - DNA Copy Number Variations/genetics
MH  - DNA, Satellite/genetics
MH  - Gene Amplification/genetics
MH  - Genes, Plant/genetics
MH  - *Genetic Variation/genetics
MH  - *Genome, Plant/genetics
MH  - Genome-Wide Association Study
MH  - *Genomics
MH  - Geography
MH  - *Plant Breeding/methods
MH  - *Plant Proteins/genetics/metabolism
MH  - Recombination, Genetic
MH  - Retroelements/genetics
MH  - Seeds/anatomy & histology/genetics
MH  - *Vicia faba/anatomy & histology/genetics/metabolism
PMC - PMC10033403
COIS- The authors declare no competing interests.
EDAT- 2023/03/09 06:00
MHDA- 2023/03/25 06:00
CRDT- 2023/03/08 23:18
PHST- 2022/09/23 00:00 [received]
PHST- 2023/02/03 00:00 [accepted]
PHST- 2023/03/09 06:00 [pubmed]
PHST- 2023/03/25 06:00 [medline]
PHST- 2023/03/08 23:18 [entrez]
AID - 10.1038/s41586-023-05791-5 [pii]
AID - 5791 [pii]
AID - 10.1038/s41586-023-05791-5 [doi]
PST - ppublish
SO  - Nature. 2023 Mar;615(7953):652-659. doi: 10.1038/s41586-023-05791-5. Epub 2023 
      Mar 8.