M. S. Abbas, Genetically engineered (modified) crops (Bacillus thuringiensis crops) and the world controversy on their safety, Egyptian Journal of Biological Pest Control, vol.28, issue.1, p.52, 2018.

G. Acquaah, Breeding self-pollinated species, pp.281-312, 2007.

N. Ahmad and Z. Mukhtar, Genetic manipulations in crops: Challenges and opportunities, Genomics, vol.109, issue.5, pp.494-505, 2017.

W. G. Alexander, D. Peris, B. T. Pfannenstiel, D. A. Opulente, M. Kuang et al., Efficient engineering of marker-free synthetic allotetraploids of Saccharomyces, Fungal Genetics and Biology, vol.89, pp.10-17, 2016.

Z. Ali, M. M. Mahfouz, and S. Mansoor, CRISPR-TSKO: A tool for tissue-specific genome editing in plants, Trends in Plant Science, vol.25, issue.2, pp.123-126, 2020.

A. Alok, S. Sharma, J. Kumar, S. Verma, and H. Sood, Engineering in plant genome using Agrobacterium: Progress and future, Metabolic engineering for bioactive compounds, pp.91-111, 2017.

L. R. Andrade, M. B. Sousa, E. J. Oliveira, M. D. Resende, and C. F. Azevedo, Cassava yield traits predicted by genomic selection methods, PLoS One, vol.14, issue.11, 2019.

A. V. Anzalone, P. B. Randolph, J. R. Davis, A. A. Sousa, L. W. Koblan et al., Search-and-replace genome editing without double-strand breaks or donor DNA, Nature, vol.576, issue.7785, pp.149-157, 2019.

D. M. Arias and L. H. Rieseberg, Gene flow between cultivated and wild sunflowers, Theoretical and Applied Genetics, vol.89, issue.6, pp.655-660, 1994.

A. Aznar, C. Chalvin, P. M. Shih, M. Maimann, B. Ebert et al., Gene stacking of multiple traits for high yield of fermentable sugars in plant biomass, Biotechnology for Biofuels, vol.11, issue.1, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02001358

U. Babar, M. A. Nawaz, U. Arshad, M. T. Azhar, R. M. Atif et al., Transgenic crops for the agricultural improvement in Pakistan: A perspective of environmental stresses and the current status of genetically modified crops, GM Crops & Food, vol.11, issue.1, pp.1-29, 2020.

S. S. Bharat, S. Li, J. Li, L. Yan, and L. Xia, Base editing in plants: Current status and challenges, The Crop Journal, vol.8, issue.3, pp.384-395, 2019.

K. E. Bushley and B. G. Turgeon, Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships, BMC Evolutionary Biology, vol.10, issue.1, p.26, 2010.

D. Byerlee and H. J. Dubin, Crop improvement in the CGIAR as a global success story of open access and international collaboration, International Journal of the Commons, vol.4, pp.452-480, 2009.

T. C. Cairns, C. Nai, and V. Meyer, How a fungus shapes biotechnology: 100 years of Aspergillus niger research, Fungal Biology and Biotechnology, vol.5, issue.1, p.13, 2018.

E. Callaway, V. J. Carrión, J. Perez-jaramillo, V. Cordovez, V. Tracanna et al., Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome, Science, vol.560, issue.6465, pp.606-612, 2018.

N. P. Castañeda-Álvarez, C. K. Khoury, H. A. Achicanoy, V. Bernau, H. Dempewolf et al., Global conservation priorities for crop wild relatives, Nature Plants, vol.2, issue.4, p.16022, 2016.

. Cbd, Convention on Biological Diversity, 1992.

H. Chen and Y. Lin, Promise and issues of genetically modified crops, Current Opinion in Plant Biology, vol.16, issue.2, pp.255-260, 2013.

K. Chen, Y. Wang, R. Zhang, H. Zhang, and C. Gao, CRISPR/Cas genome editing and precision plant breeding in agriculture, Annual Review of Plant Biology, vol.70, issue.1, pp.667-697, 2019.

Y. Chen, J. A. Palta, P. Wu, and K. H. Siddique, Crop root systems and rhizosphere interactions, Plant and Soil, vol.439, issue.1, pp.1-5, 2019.

Y. Chooi and Y. Tang, Navigating the fungal polyketide chemical space: From fenes to molecules, The Journal of Organic Chemistry, vol.77, issue.22, pp.9933-9953, 2012.

J. Collemare and M. F. Seidl, Chromatin-dependent regulation of secondary metabolite biosynthesis in fungi: Is the picture complete?, FEMS Microbiology Reviews, vol.43, issue.6, pp.591-607, 2019.

J. Crossa, P. Pérez-rodríguez, J. Cuevas, O. Montesinos-lópez, D. Jarquín et al., Genomic selection in plant breeding: Methods, models, and perspectives, Trends in Plant Science, vol.22, issue.11, pp.961-975, 2017.

J. W. Davey, P. A. Hohenlohe, P. D. Etter, J. Q. Boone, J. M. Catchen et al., Genome-wide genetic marker discovery and genotyping using next-generation sequencing, Nature Reviews Genetics, vol.12, issue.7, pp.499-510, 2011.

W. Decaestecker, R. A. Buono, M. L. Pfeiffer, N. Vangheluwe, J. Jourquin et al., CRISPR-TSKO: A technique for efficient mutagenesis in specific cell types, tissues, or organs in arabidopsis, The Plant Cell, vol.31, issue.12, pp.2868-2887, 2019.

E. Deltcheva, K. Chylinski, C. M. Sharma, K. Gonzales, Y. Chao et al., CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III, Nature, issue.7340, pp.602-607, 2011.

H. Dempewolf, G. Baute, J. Anderson, B. Kilian, C. Smith et al., Past and future use of wild relatives in crop breeding, Crop Science, vol.57, issue.3, pp.1070-1082, 2017.

H. Dempewolf, R. J. Eastwood, L. Guarino, C. K. Khoury, J. V. Müller et al., Adapting agriculture to climate change: A global initiative to collect, conserve, and use crop wild relatives. Agroecology and Sustainable Food Systems, vol.38, pp.369-377, 2014.

H. Deng, R. Gao, X. Liao, and Y. Cai, CRISPR system in filamentous fungi: Current achievements and future directions, Gene, vol.627, pp.212-221, 2017.

, Luxembourg: Publications Office of the European Union, 2001.

M. E. Dulloo, Complementary conservation actions, Crop wild relatives. A manual of in situ conservation, pp.275-294, 2011.

M. E. Dulloo, Maintaining diversity of plant genetic eesources as a basis for food security, Encyclopedia of food security and sustainability, vol.3, pp.54-63, 2019.

M. E. Dulloo, J. E. Rege, M. Ramirez, A. G. Drucker, S. Padulosi et al., Conserving agricultural biodiversity for use in sustainable food systems, Mainstreaming agrobiodiversity in sustainable food systems: Scientific foundations for an Agrobiodiversity, pp.103-139, 2017.

J. G. Ellis, E. S. Lagudah, W. Spielmeyer, and P. N. Dodds, The past, present and future of breeding rust resistant wheat, Frontiers in Plant Science, vol.5, p.641, 2014.

N. C. Ellstrand, Born to run"? not necessarily: Species and trait bias in persistent free-living transgenic plants, Frontiers in Bioengineering and Biotechnology, vol.88, issue.6, 2018.

D. T. Endresen, Predictive association between trait data and ecogeographic data for Nordic barley landraces, Crop Science, vol.50, issue.6, 2010.

D. Eriksson, R. Custers, K. Edvardsson-björnberg, S. O. Hansson, K. Purnhagen et al., Options to reform the European Union legislation on GMOs: Scope and definitions, Trends in Biotechnology, vol.38, issue.3, pp.231-234, 2020.

M. Ermakova, F. R. Danila, R. T. Furbank, and S. Caemmerer, On the road to C4 rice: Advances and perspectives, The Plant Journal, vol.101, issue.4, pp.940-950, 2020.

, Voluntary Guidelines for the Conservation and Sustainable Use of Farmers' Varieties/Landraces, 2017.

. Fao, . Ifad, W. Unicef, and . Who, The state of food security and nutrition in the world 2017. FAO, Rome: Building resilience for peace and food security, 2017.

A. R. Fernie and J. Yan, De novo domestication: An alternative route toward new crops for the future, Molecular Plant, vol.12, issue.5, pp.615-631, 2019.

R. J. Frandsen, P. Khorsand-jamal, K. T. Kongstad, M. Nafisi, R. M. Kannangara et al., , 2018.

, Heterologous production of the widely used natural food colorant carminic acid in Aspergillus nidulans, Scientific Reports, vol.8, issue.1, p.12853

M. Friedmann, A. Asfaw, N. Anglin, L. Becerra-lopez-lavalle, R. Bhattacharjee et al., , 2018.

, Genomics-assisted breeding in the CGIAR research program on roots, tubers and bananas (RTB). Agriculture, 8, p.89

G. Fritsche, Breeding Agaricus bisporus at the mushroom experimental station, Mushroom Journal, vol.122, pp.49-53, 1983.

L. Fürtges, S. Obermaier, W. Thiele, S. Foegen, and M. Müller, Diversity in fungal intermolecular phenol coupling of polyketides: Regioselective laccase-based systems, ChemBioChem, vol.20, issue.15, pp.1928-1932, 2019.

P. Gallusci, Z. Dai, M. Génard, A. Gauffretau, N. Leblanc-fournier et al., Epigenetics for plant improvement: Current knowledge and modeling avenues, Trends in Plant Science, vol.22, issue.7, pp.610-623, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01559716

R. M. García-sánchez, M. Parra-quijano, S. Greene, and J. M. Iriondo, Predictive characterisation identifies global sources of acyanogenic germplasm of a key forage species, Crop and Pasture Science, vol.70, issue.6, pp.546-554, 2019.

N. Gilbert, Case studies: A hard look at GM crops, Nature Biotechnol, vol.497, pp.24-26, 2013.

J. M. González-camacho, L. Ornella, P. Pérez-rodríguez, D. Gianola, S. Dreisigacker et al., Applications of machine learning methods to genomic selection in breeding wheat for rust resistance, The Plant Genome, vol.11, issue.2, p.170104, 2018.

M. Govindaraj, M. Vetriventhan, and M. Srinivasan, Importance of genetic diversity assessent in crop plants and its recent advances: An overview of its analystical perspectives, Genetics Research International, 2014.

P. K. Gupta, H. S. Balyan, V. Gahlaut, G. Saripalli, B. Pal et al., Hybrid wheat: Past, present and future, Theoretical and Applied Genetics, vol.132, issue.9, pp.2463-2483, 2019.

C. J. Harvey, M. Tang, U. Schlecht, J. Horecka, C. R. Fischer et al., HEx: A heterologous expression platform for the discovery of fungal natural products, Science Advances, vol.4, issue.4, p.5459, 2018.

E. L. Heffner, M. E. Sorrells, and J. Jannink, Genomic selection for crop improvement, Crop Science, vol.49, issue.1, pp.1-12, 2009.

J. C. Henrikson, A. R. Hoover, P. M. Joyner, and R. H. Cichewicz, A chemical epigenetics approach for engineering the in situ biosynthesis of a cryptic natural product from Aspergillus niger, Organic & Biomolecular Chemistry, vol.7, issue.3, pp.435-438, 2009.

J. M. Hickey, T. Chiurugwi, I. Mackay, W. Powell, J. M. Hickey et al., Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery, Nature Genetics, vol.49, issue.9, pp.1297-1303, 2017.

L. T. Hickey, A. Hafeez, H. Robinson, S. A. Jackson, S. C. Leal-bertioli et al., Breeding crops to feed 10 billion, Nature Biotechnology, vol.37, issue.7, pp.744-754, 2019.

B. Hu, W. Wang, S. Ou, J. Tang, H. Li et al., Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies, Nature Genetics, vol.47, issue.7, pp.834-838, 2015.

K. Hua, J. Zhang, J. R. Botella, C. Ma, F. Kong et al., Perspectives on the application of genome-editing technologies in crop breeding, Molecular Plant, vol.12, issue.8, pp.1047-1059, 2019.

D. Jaganathan, K. Ramasamy, G. Sellamuthu, S. Jayabalan, and G. Venkataraman, CRISPR for crop improvement: An update review, Frontiers in Plant Science, issue.985, p.9, 2018.

P. Jorasch, The global need for plant breeding innovation, Transgenic Research, vol.28, issue.2, pp.81-86, 2019.

B. Kang, J. Yun, S. Kim, Y. Shin, J. Ryu et al., Precision genome engineering through adenine base editing in plants, Nature Plants, vol.4, issue.7, pp.427-431, 2018.

S. A. Kautsar, K. Blin, S. Shaw, J. C. Navarro-muñoz, B. R. Terlouw et al., MIBiG 2.0: a repository for biosynthetic gene clusters of known function, Nucleic Acids Research, vol.48, issue.D1, pp.454-458, 2019.

W. Klümper and M. Qaim, A meta-analysis of the impacts of genetically modified crops, PLoS One, vol.9, issue.11, 2014.

S. L. Knowles, H. A. Raja, A. J. Wright, A. M. Lee, L. K. Caesar et al., Mapping the fungal battlefield: Using in situ chemistry and deletion mutants to monitor interspecific chemical interactions between fungi, Frontiers in Microbiology, vol.10, p.285, 2019.

A. C. Komor, Y. B. Kim, M. S. Packer, J. A. Zuris, and D. R. Liu, Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage, Nature, vol.533, issue.7603, pp.420-424, 2016.

S. Kumar, A. Palve, C. Joshi, and R. K. Srivastava, Crop biofortification for iron (Fe), zinc (Zn) and vitamin A with transgenic approaches, Heliyon, vol.5, issue.6, p.1914, 2019.

T. Kyndt, D. Quispe, H. Zhai, R. Jarret, M. Ghislain et al., The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: An example of a naturally transgenic food crop, Proceedings of the National Academy of Sciences, vol.112, issue.18, pp.5844-5849, 2015.

S. Laird, R. Wynberg, M. Rourke, F. Humphries, M. R. Muller et al., Rethink the expansion of access and benefit sharing, Science, vol.367, issue.6483, pp.1200-1202, 2020.

Z. H. Lemmon, N. T. Reem, J. Dalrymple, S. Soyk, K. E. Swartwood et al., Rapid improvement of domestication traits in an orphan crop by genome editing, Nature Plants, vol.4, issue.10, pp.766-770, 2018.

B. Lenaerts, B. C. Collard, and M. Demont, Review: Improving global food security through accelerated plant breeding, Plant Science, vol.287, p.110207, 2019.

D. Li and H. W. Pritchard, The science and economics of ex situ plant conservation, Trends in Plant Science, vol.14, issue.11, pp.614-621, 2009.

Y. Li, S. Li, K. Thodey, I. Trenchard, A. Cravens et al., Complete biosynthesis of noscapine and halogenated alkaloids in yeast, Proceedings of the National Academy of Sciences, vol.115, issue.17, pp.3922-3931, 2018.

Y. Liang, A. Eudes, S. Yogiswara, B. Jing, V. T. Benites et al., A screening method to identify efficient sgRNAs in Arabidopsis, used in conjunction with cell-specific lignin reduction, Biotechnology for Biofuels, vol.12, issue.1, p.130, 2019.

U. Liu, E. Breman, T. A. Cossu, and S. Kenney, The conservation value of germplasm stored at the Millennium Seed Bank, Royal Botanic Gardens, Kew. UK. Biodiversity and Conservation, vol.27, issue.6, pp.1347-1386, 2018.

T. Lonhienne, M. D. Garcia, G. Pierens, M. Mobli, A. Nouwens et al., Structural insights into the mechanism of inhibition of AHAS by herbicides, Proceedings of the National Academy of Sciences, vol.115, issue.9, pp.1945-1954, 2018.

M. Mackay and K. Street, Focused identification of germplasm strategy -FIGS, 2004.

. Cereals, Proceedings of the 54th Australian Cereal Chemistry Conference and the 11th Wheat Breeders' Assembly, pp.138-141, 2004.

V. Melbourne, Australia: Cereal Chemestry Division, Royal Australian Chemical Institute

J. Martin-laffon, M. Kuntz, and A. E. Ricroch, Worldwide CRISPR patent landscape shows strong geographical biases, Nature Biotechnology, vol.37, issue.6, pp.613-620, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02148307

D. J. Mattern, V. Valiante, F. Horn, L. Petzke, and A. A. Brakhage, Rewiring of the austinoid biosynthetic pathway in filamentous fungi, 2017.

, ACS Chemical Biology, vol.12, issue.12, pp.2927-2933

N. Maxted, D. Hunter, and R. O. Ortiz-rios, Plant genetic conservation, 2020.

B. R. Mcfadden and S. J. Smyth, Perceptions of genetically engineered technology in developed areas, Trends in Biotechnology, vol.37, issue.5, p.6, 2018.

J. Mcphetres, B. T. Rutjens, N. Weinstein, and J. A. Brisson, Modifying attitudes about modified foods: Increased knowledge leads to more positive attitudes, Journal of Environmental Psychology, vol.64, pp.21-29, 2019.

T. H. Meuwissen, B. J. Hayes, and M. E. Goddard, Prediction of total genetic value using genome-wide dense marker maps, Genetics, vol.157, issue.4, pp.1819-1829, 2001.

R. S. Meyer and M. D. Purugganan, Evolution of crop species: Genetics of domestication and diversification, Nature Reviews Genetics, vol.14, issue.12, pp.840-852, 2013.

S. Michel, C. Kummer, M. Gallee, J. Hellinger, C. Ametz et al., Improving the baking quality of bread wheat by genomic selection in early generations, Theoretical and Applied Genetics, vol.131, issue.2, pp.477-493, 2018.

S. G. Milner, M. Jost, S. Taketa, E. R. Mazón, A. Himmelbach et al., Genebank genomics highlights the diversity of a global barley collection, Nature Genetics, vol.51, issue.2, pp.319-326, 2019.

K. Mochida, S. Koda, K. Inoue, T. Hirayama, S. Tanaka et al., Computer vision-based phenotyping for improvement of plant productivity: A machine learning perspective, 2018.

. Gigascience, , vol.8

K. Morel, E. Revoyron, M. San-cristobal, and P. V. Baret, Innovating within or outside dominant food systems? Different challenges for contrasting crop diversification strategies in Europe, PLoS One, vol.15, issue.3, 2020.
URL : https://hal.archives-ouvertes.fr/hal-02536917

J. A. Napier, R. Olsen, and D. R. Tocher, Update on GM canola crops as novel sources of omega-3 fish oils, National Academies of Sciences Engineering and Medicine, vol.17, issue.4, pp.703-705, 2016.

, Genetically engineered crops: Experiences and prospects, pp.29-46, 2016.

J. C. Navarro-muñoz and J. Collemare, Evolutionary histories of Type III polyketide synthases in fungi, Frontiers in Microbiology, vol.10, 2020.

R. Nelson, T. Wiesner-hanks, R. Wisser, and P. Balint-kurti, Navigating complexity to breed disease-resistant crops, Nature Reviews Genetics, vol.19, issue.1, pp.21-33, 2018.

A. Nicolia, A. Manzo, F. Veronesi, and D. Rosellini, An overview of the last 10 years of genetically engineered crop safety research, Critical Reviews in Biotechnology, vol.34, issue.1, pp.77-88, 2014.

J. C. Nielsen, S. Grijseels, S. Prigent, B. Ji, J. Dainat et al., Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species, Nature Microbiology, vol.2, issue.6, p.17044, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02629382

Q. Niu, S. Wu, Y. Li, X. Yang, P. Liu et al., Expanding the scope of CRISPR/Cas9-mediated genome editing in plants using an xCas9 and Cas9-NG hybrid, Journal of Integrative Plant Biology, vol.62, issue.4, pp.398-402, 2020.

E. Pellegrino, S. Bedini, M. Nuti, and L. Ercoli, Impact of genetically engineered maize on agronomic, environmental and toxicological traits: A meta-analysis of 21 years of field data, Scientific Reports, vol.8, issue.1, p.3113, 2018.

B. T. Pfannenstiel and N. P. Keller, On top of biosynthetic gene clusters: How epigenetic machinery influences secondary metabolism in fungi, Biotechnology Advances, vol.37, issue.6, p.107345, 2019.

S. Pironon, T. Etherington, J. Borrell, N. Kühn, M. Macias-fauria et al., Potential adaptive strategies for 29 sub-Saharan crops under future climate change, Nature Climate Change, vol.9, issue.10, pp.758-763, 2019.

T. Prescott, J. Wong, B. Panaretou, E. Boa, A. Bond et al., Useful fungi, State of the world's fungi 2018 report, pp.24-31, 2018.

M. Z. Prodhan, M. T. Hasan, M. M. Chowdhury, M. S. Alam, M. L. Rahman et al., Bt eggplant (Solanum melongena L.) in Bangladesh: Fruit production and control of eggplant fruit and shoot borer (Leucinodes orbonalis Guenee), effects on non-target arthropods and economic returns, PLoS One, vol.13, issue.11, p.205713, 2018.

Y. Rebets, E. Brötz, B. Tokovenko, and A. Luzhetskyy, , 2014.

, Actinomycetes biosynthetic potential: How to bridge in silico and in vivo, Journal of Industrial Microbiology & Biotechnology, vol.41, issue.2, pp.387-402

M. Roell and M. D. Zurbriggen, The impact of synthetic biology for future agriculture and nutrition, Current Opinion in Biotechnology, vol.61, pp.102-109, 2020.

S. Romano, S. A. Jackson, S. Patry, and A. D. Dobson, Extending the "One Strain Many Compounds" (OSMAC) principle to marine microorganisms, Marine Drugs, vol.16, issue.7, p.244, 2018.

J. Romeis and M. Meissle, Stacked Bt proteins pose no new eisks to nontarget arthropods, Trends in Biotechnology, vol.38, issue.3, pp.234-236, 2020.

P. Ronald, Plant genetics, sustainable agriculture and global food security, Genetics, vol.188, issue.1, pp.11-20, 2011.

N. Ruiz-lopez, R. P. Haslam, J. A. Napier, and O. Sayanova, Successful high-level accumulation of fish oil omega-3 long-chain polyunsaturated fatty acids in a transgenic oilseed crop, The Plant Journal, vol.77, issue.2, pp.198-208, 2014.

J. Rutkoski, R. P. Singh, J. Huerta-espino, S. Bhavani, J. Poland et al., Genetic gain from phenotypic and genomic selection for quantitative resistance to stem rust of wheat, The Plant Genome, vol.8, issue.2, pp.1-10, 2015.

J. Savoie, M. Foulongne-oriol, G. Barroso, and P. Callac, 1 Genetics and genomics of cultivated mushrooms, application to breeding of agarics, Agricultural Applications. The Mycota (A comprehensive treatise on fungi as experimental systems for basic and applied research), vol.11, pp.3-33, 2013.

R. H. Schlegel, History of plant breeding, 2018.

V. Schroeckh, K. Scherlach, H. Nützmann, E. Shelest, W. Schmidt-heck et al., Intimate bacterial-fungal interaction triggers biosynthesis of archetypal polyketides in Aspergillus nidulans, Proceedings of the National Academy of Sciences, vol.106, issue.34, pp.14558-14563, 2009.

T. Searchinger, R. Waite, C. Hanson, J. Ranganathan, P. Dumas et al., Creating a sustainable food future: A menu of solutions to feed nearly 10 billion people by 2050 (Final report, 2019.

Q. Shan and D. F. Voytas, Editing plant genes one base at a time, Nature Plants, vol.4, issue.7, pp.412-413, 2018.

Z. Shimatani, S. Kashojiya, M. Takayama, R. Terada, T. Arazoe et al., Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion, Nature Biotechnology, vol.35, issue.5, pp.441-443, 2017.

M. Singh, K. Shwet, and V. Sharma, Status and trends in world mushroom production-I, Mushroom Research, vol.26, issue.1, pp.1-20, 2017.

N. Singh, S. Wu, W. J. Raupp, S. Sehgal, S. Arora et al., Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions, Scientific Reports, vol.9, issue.1, p.650, 2019.

E. Skellam, Strategies for engineering natural product biosynthesis in fungi, Trends in Biotechnology, vol.37, issue.4, pp.416-427, 2018.

P. Smýkal, M. N. Nelson, J. D. Berger, and E. J. Von-wettberg, The impact of genetic changes during crop domestication, Agronomy, vol.8, issue.7, p.119, 2018.

C. Steiniger, S. Hoffmann, A. Mainz, M. Kaiser, K. Voigt et al., Harnessing fungal nonribosomal cyclodepsipeptide synthetases for mechanistic insights and tailored engineering, Chemical Science, vol.8, issue.11, pp.7834-7843, 2017.

A. A. Stierle, D. B. Stierle, D. Decato, N. D. Priestley, J. B. Alverson et al., The Berkeleylactones, antibiotic macrolides from fungal coculture, Journal of Natural Products, vol.80, issue.4, pp.1150-1160, 2017.

M. Stöckli, B. I. Morinaka, G. Lackner, A. Kombrink, R. Sieber et al., Bacteria-induced production of the antibacterial sesquiterpene lagopodin B in Coprinopsis cinerea, Molecular Microbiology, vol.112, issue.2, pp.605-619, 2019.

J. J. Stocks, C. L. Metheringham, W. J. Plumb, S. J. Lee, L. J. Kelly et al., Genomic basis of European ash tree resistance to ash dieback fungus, Nature Ecology & Evolution, vol.3, issue.12, pp.1686-1696, 2019.

K. Street, M. Mackay, E. Zuev, N. Kaul, M. El-bouhssini et al., Ditg-arstastflgcIAahhhnV 2008. Diving into the genepool -a rational system to access specific traits from large germplasm collections, 2014.

S. Taghavi-namin, M. Esmaeilzadeh, M. Najafi, T. B. Brown, and J. O. Borevitz, Deep phenotyping: Deep learning for temporal phenotype/genotype classification, Plant Methods, vol.14, issue.1, p.66, 2018.

M. Tester and P. Langridge, Breeding technologies to increase crop production in a changing world, Science, vol.327, issue.5967, pp.818-822, 2010.

I. Thormann, Applying FIGS to crop wild relatives and landraces in Europe, Crop Wild Relative, vol.8, p.1, 2012.

I. Thormann, M. Parra-quijano, D. T. Endresen, M. L. Rubio-teso, J. M. Iriondo et al., Predictive characterization of crop wild relatives and landraces, 2014.

I. Thormann, M. Parra-quijano, M. L. Rubio-teso, D. T. Endresen, S. Dias et al., Enhancing Crop Genepool Use: Capturing Wild Relative and Landrace Diversity for Crop Improvement: CAB International UK, pp.64-77, 2016.

S. Tian, L. Jiang, X. Cui, J. Zhang, S. Guo et al., Engineering herbicide-resistant watermelon variety through, 2018.

, CRISPR/Cas9-mediated base-editing, Plant Cell Reports, vol.37, issue.9, pp.1353-1356

S. Trachsel, S. M. Kaeppler, K. M. Brown, and J. P. Lynch, Shovelomics: High throughput phenotyping of maize (Zea mays L.) root architecture in the field, Plant and Soil, vol.341, issue.1, pp.75-87, 2011.

S. R. Tracy, K. A. Nagel, J. A. Postma, H. Fassbender, A. Wasson et al., Crop improvement from phenotyping roots: Highlights reveal expanding opportunities, Trends in Plant Science, vol.25, issue.1, pp.105-118, 2020.

V. Valiante, D. J. Mattern, A. Schüffler, F. Horn, G. Walther et al., Discovery of an extended austinoid biosynthetic pathway in Aspergillus calidoustus, ACS Chemical Biology, vol.12, issue.5, pp.1227-1234, 2017.

J. Van-heerwaarden, D. Ortega-del-vecchyo, E. R. Alvarez-buylla, and M. R. Bellon, New genes in traditional seed systems: Diffusion, detectability and persistence of transgenes in a maize metapopulation, PLoS One, vol.7, issue.10, pp.46123-46123, 2012.

K. P. Voss-fels, A. Stahl, and L. T. Hickey, Q&A: Modern crop breeding for future food security, BMC Biology, vol.17, issue.1, p.18, 2019.

X. Wang, Y. Xu, Z. Hu, and C. Xu, Genomic selection methods for crop improvement: Current status and prospects, The Crop Journal, vol.6, issue.4, pp.330-340, 2018.

O. T. Westengen, S. Jeppson, and L. Guarino, Global ex-situ crop diversity conservation and the Svalbard Global Seed Vault: Assessing the current status, PLoS One, vol.8, issue.5, pp.64146-64146, 2013.

C. Williams, A. Walsh, V. Vaglica, A. Sirakaya, M. Da-silva et al., Conservation Policy: Helping or hindering science to unlock properties of plants and fungi, People, Planet, vol.2, issue.5, pp.535-545, 2020.

E. T. Wurtzel, C. E. Vickers, A. D. Hanson, A. H. Millar, M. Cooper et al., Revolutionizing agriculture with synthetic biology, Nature Plants, vol.5, issue.12, pp.1207-1210, 2019.

S. V. Wyse and J. B. Dickie, Predicting the global incidence of seed desiccation sensitivity, Journal of Ecology, vol.105, issue.4, pp.1082-1093, 2017.

J. Xu, C. Jiang, Z. Zhang, W. Ma, and Y. Guo, Recent progress regarding the bioactivities, biosynthesis and synthesis of naturally occurring resorcinolic macrolides, Acta Pharmacologica Sinica, vol.35, issue.3, pp.316-330, 2014.

Y. Xu, T. Zhou, S. Zhang, P. Espinosa-artiles, L. Wang et al., Diversity-oriented combinatorial biosynthesis of benzenediol lactone scaffolds by subunit shuffling of fungal polyketide synthases, Proceedings of the National Academy of Sciences, vol.111, issue.34, pp.12354-12359, 2014.

T. Yamato, A. Handa, T. Arazoe, M. Kuroki, A. Nozaka et al., Single crossover-mediated targeted nucleotide substitution and knock-in strategies with CRISPR/Cas9 system in the rice blast fungus, Scientific Reports, vol.9, issue.1, 2019.

H. Zhang, Y. Li, and J. Zhu, Developing naturally stress-resistant crops for a sustainable agriculture, Nature Plants, vol.4, issue.12, pp.989-996, 2018.

Y. Zhang, A. A. Malzahn, S. Sretenovic, and Y. Qi, The emerging and uncultivated potential of CRISPR technology in plant science, Nature Plants, vol.5, issue.8, pp.778-794, 2019.

Y. Zhang, K. Massel, I. D. Godwin, and C. Gao, Applications and potential of genome editing in crop improvement, Genome Biology, vol.19, issue.1, p.210, 2018.

C. Zhao, Y. Zhang, J. Du, X. Guo, W. Wen et al., Crop phenomics: Current status and perspectives, Frontiers in Plant Science, vol.10, 2019.

I. Ziamtsov and S. Navlakha, Machine learning approaches to improve three basic plant phenotyping tasks using three-dimensional point clouds, Plant Physiology, vol.181, issue.4, pp.1425-1440, 2019.