Carbon Chemist

Tag: Agriculture

  • How genetically modified crops could feed us and help safeguard nature

    How genetically modified crops could feed us and help safeguard nature

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    AYBGY1 GM crops biohazard warning maize

    Genetically modified maize

    Nick Gregory/Alamy

    I have never been a supporter of Brexit, except for one thing: it has allowed the UK to break free from the damaging straitjacket of European Union agricultural policy, including its prohibition on genetically modified crops. I have always believed this was based more on sentiment than science. In post-Brexit Britain, science has won.

    Last year, the Genetic Technology (Precision Breeding) Act came into force, allowing the development of gene-edited crops and animals in England. This isn’t quite GM, which allows for the insertion of genes from other species, rather than gene editing’s approach…

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  • Promises and challenges of crop translational genomics

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  • McCabe, E. R. B. Translational genomics in medical genetics. Genet. Med. 4, 468–471 (2002).

    Article 
    PubMed 

    Google Scholar     

  • Zeggini, E., Gloyn, A. L., Barton, A. C. & Wain, L. V. Translational genomics and precision medicine: moving from the lab to the clinic. Science 365, 1409–1413 (2019).

    Article 
    ADS 
    PubMed 

    Google Scholar     

  • Salentijn, E. M. J. et al. Plant translational genomics: from model species to crops. Mol. Breed. 20, 1–13 (2007).

    Article 

    Google Scholar     

  • Cannon, S. B., May, G. D. & Jackson, S. A. Three sequenced legume genomes and many crop species: rich opportunities for translational genomics. Plant Physiol. 151, 970–977 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Ronald, P. C. Lab to farm: applying research on plant genetics and genomics to crop improvement. PLoS Biol. 12, e1001878 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Sun, Y., Shang, L., Zhu, Q.-H., Fan, L. & Guo, L. Twenty years of plant genome sequencing: achievements and challenges. Trends Plant Sci. 27, 391–401 (2022).

    Article 
    PubMed 

    Google Scholar     

  • Bennetzen, J. L. & Ma, J. The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis. Curr. Opin. Plant Biol. 6, 128–133 (2003).

    Article 
    PubMed 

    Google Scholar     

  • Carlson, E. A. H. J. Muller’s contributions to mutation research. Mutat. Res. 752, 1–5 (2013).

    Article 
    ADS 
    PubMed 

    Google Scholar     

  • Simmonds, N. W. Bandwagons I Have Known. Tropical Agriculture Association Newsletter December 1991, 7–10 (Tropical Agriculture Association International, 1991).

  • Davey, J. W. et al. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet. 12, 499–510 (2011).

    Article 
    ADS 
    PubMed 

    Google Scholar     

  • Schneeberger, K. et al. SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Nat. Methods 6, 550–551 (2009).

    Article 
    PubMed 

    Google Scholar     

  • Yu, J. et al. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38, 203–208 (2006).

    Article 
    PubMed 

    Google Scholar     

  • Rhie, A. et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature 592, 737–746 (2021).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Alkan, C., Coe, B. P. & Eichler, E. E. Genome structural variation discovery and genotyping. Nat. Rev. Genet. 12, 363–376 (2011).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Ho, S. S., Urban, A. E. & Mills, R. E. Structural variation in the sequencing era. Nat. Rev. Genet. 21, 171–189 (2020).

    Article 
    PubMed 

    Google Scholar     

  • Lei, L. et al. Plant pan-genomics comes of age. Annu. Rev. Plant Biol. 72, 411–435 (2021).

    Article 
    PubMed 

    Google Scholar     

  • Orlando, L. et al. Ancient DNA analysis. Nat. Rev. Methods Primers 1, 14 (2021).

    Article 

    Google Scholar     

  • Tanksley, S. D., Young, N. D., Paterson, A. H. & Bonierbale, M. W. RFLP mapping in plant breeding: new tools for an old science. Bio/Technology 7, 257–264 (1989).


    Google Scholar     

  • Rafalski, J. A. Association genetics in crop improvement. Curr. Opin. Plant Biol. 13, 174–180 (2010).

    Article 
    PubMed 

    Google Scholar     

  • Bernardo, R. Bandwagons I, too, have known. Theor. Appl. Genet. 129, 2323–2332 (2016).

    Article 
    PubMed 

    Google Scholar     

  • Holland, J. B. Genetic architecture of complex traits in plants. Curr. Opin. Plant Biol. 10, 156–161 (2007).

    Article 
    PubMed 

    Google Scholar     

  • Korte, A. & Farlow, A. The advantages and limitations of trait analysis with GWAS: a review. Plant Methods 9, 29 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Distelfeld, A., Li, C. & Dubcovsky, J. Regulation of flowering in temperate cereals. Curr. Opin. Plant Biol. 12, 178–184 (2009).

    Article 
    PubMed 

    Google Scholar     

  • Comadran, J. et al. Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley. Nat. Genet. 44, 1388–1392 (2012).

    Article 
    PubMed 

    Google Scholar     

  • Cheng, S. et al. Harnessing landrace diversity empowers wheat breeding. Nature 632, 823–831 (2024).

  • Wulff, B. B. & Krattinger, S. G. The long road to engineering durable disease resistance in wheat. Curr. Opin. Biotechnol. 73, 270–275 (2022).

    Article 
    PubMed 

    Google Scholar     

  • Athiyannan, N. et al. Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning. Nat. Genet. 54, 227–231 (2022). A good example of how the recent progress in genome sequencing has made gene isolation easier.

    Article 
    PubMed 

    Google Scholar     

  • Meuwissen, T. H., Hayes, B. J. & Goddard, M. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157, 1819–1829 (2001).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Lin, Z., Hayes, B. J. & Daetwyler, H. D. Genomic selection in crops, trees and forages: a review. Crop Pasture Sci. 65, 1177–1191 (2014).

    Article 

    Google Scholar     

  • Rembe, M., Zhao, Y., Jiang, Y. & Reif, J. C. Reciprocal recurrent genomic selection: an attractive tool to leverage hybrid wheat breeding. Theor. Appl. Genet. 132, 687–698 (2019).

    Article 
    PubMed 

    Google Scholar     

  • Poland, J. & Rutkoski, J. Advances and challenges in genomic selection for disease resistance. Annu. Rev. Phytopathol. 54, 79–98 (2016).

    Article 
    PubMed 

    Google Scholar     

  • Zhou, Y. et al. Graph pangenome captures missing heritability and empowers tomato breeding. Nature 606, 527–534 (2022). Structural variants derived from pangenomes improve the accuracy of quantitative genetic analyses.

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Jensen, S. E. et al. A sorghum practical haplotype graph facilitates genome-wide imputation and cost-effective genomic prediction. Plant Genome 13, e20009 (2020).

    Article 
    PubMed 

    Google Scholar     

  • Seyum, E. G. et al. Genomic selection in tropical perennial crops and plantation trees: a review. Mol. Breed. 42, 58 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Wolfe, M. D. et al. Prospects for genomic selection in cassava breeding. Plant Genome 10, https://doi.org/10.3835/plantgenome2017.03.0015 (2017).

  • Flor, H. H. Current status of the gene-for-gene concept. Annu. Rev. Phytopathol. 9, 275–296 (1971).

    Article 

    Google Scholar     

  • Tamborski, J. & Krasileva, K. V. Evolution of plant NLRs: from natural history to precise modifications. Annu. Rev. Plant Biol. 71, 355–378 (2020).

    Article 
    PubMed 

    Google Scholar     

  • Barragan, A. C. & Weigel, D. Plant NLR diversity: the known unknowns of pan-NLRomes. Plant Cell 33, 814–831 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Moore, J. W. et al. A recently evolved hexose transporter variant confers resistance to multiple pathogens in wheat. Nat. Genet. 47, 1494–1498 (2015).

    Article 
    PubMed 

    Google Scholar     

  • Krattinger, S. G. et al. A putative ABC transporter confers durable resistance to multiple fungal pathogens in wheat. Science 323, 1360–1363 (2009).

    Article 
    ADS 
    PubMed 

    Google Scholar     

  • Ercoli, M. F. et al. Plant immunity: rice XA21-mediated resistance to bacterial infection. Proc. Natl Acad. Sci. USA 119, e2121568119 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Jupe, F. et al. Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. Plant J. 76, 530–544 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Hafeez, A. N. et al. Creation and judicious application of a wheat resistance gene atlas. Mol. Plant 14, 1053–1070 (2021).

    Article 
    PubMed 

    Google Scholar     

  • Guo, Y. et al. Population genomics of Puccinia graminis f.sp. tritici highlights the role of admixture in the origin of virulent wheat rust races. Nat. Commun. 13, 6287 (2022).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Seong, K. & Krasileva, K. V. Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses. Nat. Microbiol. 8, 174–187 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Förderer, A. et al. A wheat resistosome defines common principles of immune receptor channels. Nature 610, 532–539 (2022).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Zhao, Y.-B. et al. Pathogen effector AvrSr35 triggers Sr35 resistosome assembly via a direct recognition mechanism. Sci. Adv. 8, eabq5108 (2022).

    Article 
    ADS 
    MathSciNet 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Ma, S. et al. Direct pathogen-induced assembly of an NLR immune receptor complex to form a holoenzyme. Science 370, eabe3069 (2020).

    Article 
    PubMed 

    Google Scholar     

  • Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Frankel, O. H. Genetic conservation: our evolutionary responsibility. Genetics 78, 53–65 (1974).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Altieri, M. A. & Merrick, L. In situ conservation of crop genetic resources through maintenance of traditional farming systems. Econ. Bot. 41, 86–96 (1987).

    Article 

    Google Scholar     

  • Meilleur, B. A. & Hodgkin, T. In situ conservation of crop wild relatives: status and trends. Biodivers. Conserv. 13, 663–684 (2004).

    Article 

    Google Scholar     

  • Marden, E., Sackville Hamilton, R., Halewood, M. & McCouch, S. International agreements and the plant genetics research community: a guide to practice. Proc. Natl Acad. Sci. USA 120, e2205773119 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Mascher, M. et al. Genebank genomics bridges the gap between the conservation of crop diversity and plant breeding. Nat. Genet. 51, 1076–1081 (2019).

    Article 
    PubMed 

    Google Scholar     

  • Sansaloni, C. et al. Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints. Nat. Commun. 11, 4572 (2020).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Schulthess, A. W. et al. Genomics-informed prebreeding unlocks the diversity in genebanks for wheat improvement. Nat. Genet. 54, 1544–1552 (2022). Genomics helps to bridge the gap between the conservation of plant genetic resources and practical breeding.

    Article 
    PubMed 

    Google Scholar     

  • Milner, S. G. et al. Genebank genomics highlights the diversity of a global barley collection. Nat. Genet. 51, 319–326 (2019).

    Article 
    PubMed 

    Google Scholar     

  • Romay, M. C. et al. Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biol. 14, R55 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Wang, W. et al. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature 557, 43–49 (2018).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • McCouch, S. R., McNally, K. L., Wang, W. & Sackville Hamilton, R. Genomics of gene banks: a case study in rice. Am. J. Bot. 99, 407–423 (2012).

    Article 
    PubMed 

    Google Scholar     

  • De Beukelaer, H., Davenport, G. F. & Fack, V. Core Hunter 3: flexible core subset selection. BMC Bioinformatics 19, 203 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Yu, X. et al. Genomic prediction contributing to a promising global strategy to turbocharge gene banks. Nat. Plants 2, 16150 (2016).

    Article 
    PubMed 

    Google Scholar     

  • Bhullar, N. K., Street, K., Mackay, M., Yahiaoui, N. & Keller, B. Unlocking wheat genetic resources for the molecular identification of previously undescribed functional alleles at the Pm3 resistance locus. Proc. Natl Acad. Sci. USA 106, 9519–9524 (2009).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Milne, R. J. et al. The wheat Lr67 gene from the Sugar Transport Protein 13 family confers multipathogen resistance in barley. Plant Physiol. 179, 1285–1297 (2019).

    Article 
    PubMed 

    Google Scholar     

  • Risk, J. M. et al. The wheat Lr34 gene provides resistance against multiple fungal pathogens in barley. Plant Biotechnol. J. 11, 847–854 (2013).

    Article 
    PubMed 

    Google Scholar     

  • Luo, M. et al. A five-transgene cassette confers broad-spectrum resistance to a fungal rust pathogen in wheat. Nat. Biotechnol. 39, 561–566 (2021).

    Article 
    PubMed 

    Google Scholar     

  • Wulff, B. B. & Moscou, M. J. Strategies for transferring resistance into wheat: from wide crosses to GM cassettes. Frontiers Plant Sci. 5, 692 (2014).

    Article 

    Google Scholar     

  • Athiyannan, N. et al. Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning. Nat. Genet. 54, 227–231 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Wang, Y. et al. An unusual tandem kinase fusion protein confers leaf rust resistance in wheat. Nat. Genet. 55, 914–920 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Cavalet-Giorsa, E. et al. Origin and evolution of the bread wheat D genome. Nature https://doi.org/10.1038/s41586-024-07808-z (2024).

  • Cardi, T. et al. CRISPR/Cas-mediated plant genome editing: outstanding challenges a decade after implementation. Trends Plant Sci. 28, 1144–1165 (2023).

    Article 
    PubMed 

    Google Scholar     

  • Watson, A. et al. Speed breeding is a powerful tool to accelerate crop research and breeding. Nat. Plants 4, 23–29 (2018).

    Article 
    ADS 
    PubMed 

    Google Scholar     

  • Cha, J.-K. et al. Speed vernalization to accelerate generation advance in winter cereal crops. Mol. Plant 15, 1300–1309 (2022).

    Article 
    PubMed 

    Google Scholar     

  • Mascher, M. et al. A chromosome conformation capture ordered sequence of the barley genome. Nature 544, 427–433 (2017).

    Article 
    ADS 
    PubMed 

    Google Scholar     

  • The International Wheat Genome Sequencing Consortium. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361, eaar7191 (2018). In the past, large international consortia were needed to assemble reference sequences of large crop genomes.

    Article 

    Google Scholar     

  • Jayakodi, M. et al. The barley pan-genome reveals the hidden legacy of mutation breeding. Nature 588, 284–289 (2020).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Zhou, Y. et al. Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice. Nat. Commun. 14, 1567 (2023).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Przewieslik-Allen, A. M. et al. The role of gene flow and chromosomal instability in shaping the bread wheat genome. Nat. Plants 7, 172–183 (2021).

    Article 
    PubMed 

    Google Scholar     

  • van Rengs, W. M. J. et al. A chromosome scale tomato genome built from complementary PacBio and Nanopore sequences alone reveals extensive linkage drag during breeding. Plant J. 110, 572–588 (2022).

    Article 
    PubMed 

    Google Scholar     

  • Wendler, N. et al. Bulbosum to go: a toolbox to utilize Hordeum vulgare/bulbosum introgressions for breeding and beyond. Mol. Plant 8, 1507–1519 (2015).

    Article 
    PubMed 

    Google Scholar     

  • Mieulet, D. et al. Unleashing meiotic crossovers in crops. Nat. Plants 4, 1010–1016 (2018). Single genes can have large effects on the recombination landscape.

    Article 
    PubMed 

    Google Scholar     

  • Rönspies, M., Dorn, A., Schindele, P. & Puchta, H. CRISPR–Cas-mediated chromosome engineering for crop improvement and synthetic biology. Nat. Plants 7, 566–573 (2021).

    Article 
    PubMed 

    Google Scholar     

  • Schmidt, C. et al. Changing local recombination patterns in Arabidopsis by CRISPR/Cas mediated chromosome engineering. Nat. Commun. 11, 4418 (2020).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Schwartz, C. et al. CRISPR–Cas9-mediated 75.5-Mb inversion in maize. Nat. Plants 6, 1427–1431 (2020).

    Article 
    PubMed 

    Google Scholar     

  • Bartlett, M. E., Moyers, B. T., Man, J., Subramaniam, B. & Makunga, N. P. The power and perils of de novo domestication using genome editing. Annu. Rev. Plant Biol. 74, 727–750 (2023).

    Article 
    PubMed 

    Google Scholar     

  • Yu, H. & Li, J. Breeding future crops to feed the world through de novo domestication. Nat. Commun. 13, 1171 (2022).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Hanak, T., Madsen, C. K. & Brinch-Pedersen, H. Genome editing-accelerated re-domestication (GEaReD)—a new major direction in plant breeding. Biotechnol. J. 17, 2100545 (2022).

    Article 

    Google Scholar     

  • Zhang, S. et al. Sustained productivity and agronomic potential of perennial rice. Nat. Sust. 6, 28–38 (2023).

    Article 

    Google Scholar     

  • Singh, D., Buhmann, A. K., Flowers, T. J., Seal, C. E. & Papenbrock, J. Salicornia as a crop plant in temperate regions: selection of genetically characterized ecotypes and optimization of their cultivation conditions. AoB Plants 6, plu071 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Lenser, T. & Theißen, G. Molecular mechanisms involved in convergent crop domestication. Trends Plant Sci. 18, 704–714 (2013).

    Article 
    PubMed 

    Google Scholar     

  • Larson, S. et al. Genome mapping of quantitative trait loci (QTL) controlling domestication traits of intermediate wheatgrass (Thinopyrum intermedium). Theor. Appl. Genet. 132, 2325–2351 (2019).

    Article 
    PubMed 

    Google Scholar     

  • Stetter, M. G., Gates, D. J., Mei, W. & Ross-Ibarra, J. How to make a domesticate. Curr. Biol. 27, R896–R900 (2017).

    Article 
    PubMed 

    Google Scholar     

  • Abbo, S. et al. Plant domestication versus crop evolution: a conceptual framework for cereals and grain legumes. Trends Plant Sci. 19, 351–360 (2014).

    Article 
    PubMed 

    Google Scholar     

  • Fuller, D. Q. Contrasting patterns in crop domestication and domestication rates: recent archaeobotanical insights from the Old World. Ann. Bot. 100, 903–924 (2007).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Lemmon, Z. H. et al. Rapid improvement of domestication traits in an orphan crop by genome editing. Nat. Plants 4, 766–770 (2018). Agronomically relevant traits in a minor crop were improved by targeted mutagenesis.

    Article 
    PubMed 

    Google Scholar     

  • Li, T. et al. Domestication of wild tomato is accelerated by genome editing. Nat. Biotechnol. 36, 1160–1163 (2018).

    Article 

    Google Scholar     

  • Fernie, A. R. & Yan, J. De novo domestication: an alternative route toward new crops for the future. Mol. Plant 12, 615–631 (2019).

    Article 
    PubMed 

    Google Scholar     

  • Bevan, M. W. et al. Genomic innovation for crop improvement. Nature 543, 346–354 (2017).

    Article 
    ADS 
    PubMed 

    Google Scholar     

  • Khoury, C. K. et al. Crop genetic erosion: understanding and responding to loss of crop diversity. New Phytol. 233, 84–118 (2022).

    Article 
    PubMed 

    Google Scholar     

  • Brown, W. L. Genetic diversity and genetic vulnerability—an appraisal. Econ. Bot. 37, 4–12 (1983).

    Article 

    Google Scholar     

  • Mayer, M. et al. Discovery of beneficial haplotypes for complex traits in maize landraces. Nat. Commun. 11, 4954 (2020).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Stephan, W. Genetic hitchhiking versus background selection: the controversy and its implications. Philos. Trans. R. Soc. B 365, 1245–1253 (2010).

    Article 

    Google Scholar     

  • Yang, J. et al. Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize. PLoS Genet. 13, e1007019 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Wang, L. et al. The interplay of demography and selection during maize domestication and expansion. Genome Biol. 18, 215 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Lozano, R. et al. Comparative evolutionary genetics of deleterious load in sorghum and maize. Nat. Plants 7, 17–24 (2021).

    Article 
    PubMed 

    Google Scholar     

  • Liu, Q., Zhou, Y., Morrell, P. L. & Gaut, B. S. Deleterious variants in Asian rice and the potential cost of domestication. Mol. Biol. Evol. 34, 908–924 (2017).

    PubMed 

    Google Scholar     

  • Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6, 80–92 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Ng, P. C. & Henikoff, S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 31, 3812–3814 (2003).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Khan, A. W. et al. Super-pangenome by Integrating the wild side of a species for accelerated crop improvement. Trends Plant Sci. 25, 148–158 (2019).

    Article 
    PubMed 

    Google Scholar     

  • Gao, H. et al. The landscape of tolerated genetic variation in humans and primates. Science 380, eabn8153 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Ramstein, G. P. & Buckler, E. S. Prediction of evolutionary constraint by genomic annotations improves functional prioritization of genomic variants in maize. Genome Biol. 23, 183 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Wallace, J. G., Rodgers-Melnick, E. & Buckler, E. S. On the road to breeding 4.0: unraveling the good, the bad, and the boring of crop quantitative genomics. Annu. Rev. Genet. 52, 421–444 (2018).

    Article 
    PubMed 

    Google Scholar     

  • Roze, D. A simple expression for the strength of selection on recombination generated by interference among mutations. Proc. Natl Acad. Sci. USA 118, e2022805118 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Gabriel, W., Lynch, M. & Bürger, R. Muller’s ratchet and mutational meltdowns. Evolution 47, 1744–1757 (1993).

    Article 
    PubMed 

    Google Scholar     

  • Naeem, M., Demirel, U., Yousaf, M. F., Caliskan, S. & Caliskan, M. E. Overview on domestication, breeding, genetic gain and improvement of tuber quality traits of potato using fast forwarding technique (GWAS): a review. Plant Breed. 140, 519–542 (2021).

    Article 

    Google Scholar     

  • Jansky, S. H. et al. Reinventing potato as a diploid inbred line–based crop. Crop Sci. 56, 1412–1422 (2016).

    Article 

    Google Scholar     

  • ter Steeg, E. M. S., Struik, P. C., Visser, R. G. F. & Lindhout, P. Crucial factors for the feasibility of commercial hybrid breeding in food crops. Nat. Plants 8, 463–473 (2022).

    Article 
    PubMed 

    Google Scholar     

  • Zhou, Q. et al. Haplotype-resolved genome analyses of a heterozygous diploid potato. Nat. Genet. 52, 1018–1023 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Sun, H. et al. Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar. Nat. Genet. 54, 342–348 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Tang, D. et al. Genome evolution and diversity of wild and cultivated potatoes. Nature 606, 535–541 (2022). Initial analysis of a genus-wide pangenome of potato and its wild relatives.

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Zhang, C. et al. The genetic basis of inbreeding depression in potato. Nat. Genet. 51, 374–378 (2019).

    Article 
    PubMed 

    Google Scholar     

  • Wu, Y. et al. Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding. Cell 186, 2313–2328.e2315 (2023).

    Article 
    PubMed 

    Google Scholar     

  • Ye, M. et al. Generation of self-compatible diploid potato by knockout of S-RNase. Nat. Plants 4, 651–654 (2018).

    Article 
    PubMed 

    Google Scholar     

  • Mascher, M., Jayakodi, M. & Stein, N. The reinvention of potato. Cell Res. 31, 1144–1145 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Servin, B., Martin, O. C., Mézard, M. & Hospital, F. Toward a theory of marker-assisted gene pyramiding. Genetics 168, 513–523 (2004).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Hurni, S. et al. The powdery mildew resistance gene Pm8 derived from rye is suppressed by its wheat ortholog Pm3. Plant J. 79, 904–913 (2014).

    Article 
    PubMed 

    Google Scholar     

  • Cordell, H. J. Epistasis: what it means, what it doesn’t mean, and statistical methods to detect it in humans. Hum. Mol. Genet. 11, 2463–2468 (2002).

    Article 
    PubMed 

    Google Scholar     

  • Soyk, S. et al. Bypassing negative epistasis on yield in tomato imposed by a domestication gene. Cell 169, 1142–1155.e1112 (2017).

    Article 
    PubMed 

    Google Scholar     

  • Soyk, S., Benoit, M. & Lippman, Z. B. New horizons for dissecting epistasis in crop quantitative trait variation. Annu. Rev. Genet. 54, 287–307 (2020).

    Article 
    PubMed 

    Google Scholar     

  • Jiang, Y., Schmidt, R. H., Zhao, Y. & Reif, J. C. A quantitative genetic framework highlights the role of epistatic effects for grain-yield heterosis in bread wheat. Nat. Genet. 49, 1741–1746 (2017).

    Article 
    PubMed 

    Google Scholar     

  • Bouché, F., Lobet, G., Tocquin, P. & Périlleux, C. FLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana. Nucleic Acids Res. 44, D1167–D1171 (2016).

    Article 
    PubMed 

    Google Scholar     

  • Chen, D., Yan, W., Fu, L.-Y. & Kaufmann, K. Architecture of gene regulatory networks controlling flower development in Arabidopsis thaliana. Nat. Commun. 9, 4534 (2018).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Ahsan, A. et al. Identification of epistasis loci underlying rice flowering time by controlling population stratification and polygenic effect. DNA Res. 26, 119–130 (2018).

    Article 
    PubMed Central 

    Google Scholar     

  • Mathew, B., Léon, J., Sannemann, W. & Sillanpää, M. J. Detection of epistasis for flowering time using Bayesian multilocus estimation in a barley MAGIC population. Genetics 208, 525–536 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Durand, E. et al. Flowering time in maize: linkage and epistasis at a major effect locus. Genetics 190, 1547–1562 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Padmarasu, S., Himmelbach, A., Mascher, M. & Stein, N. In situ Hi-C for plants: an improved method to detect long-range chromatin interactions. Methods Mol. Biol. 1933, 441–472 (2019).

    Article 
    PubMed 

    Google Scholar     

  • Liu, L. et al. Enhancing grain-yield-related traits by CRISPR–Cas9 promoter editing of maize CLE genes. Nat. Plants 7, 287–294 (2021).

    Article 
    PubMed 

    Google Scholar     

  • Aguirre, L., Hendelman, A., Hutton, S. F., McCandlish, D. M. & Lippman, Z. B. Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size. Science 382, 315–320 (2023). On the molecular genetics of regulatory variation in tomato.

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Boyle, E. A., Li, Y. I. & Pritchard, J. K. An expanded view of complex traits: from polygenic to omnigenic. Cell 169, 1177–1186 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Zhao, L. et al. Integrative analysis of reference epigenomes in 20 rice varieties. Nat. Commun. 11, 2658 (2020).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Han, T. et al. An epigenetic basis of inbreeding depression in maize. Sci. Adv. 7, eabg5442 (2021).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Thiel, J. et al. Transcriptional landscapes of floral meristems in barley. Sci. Adv. 7, eabf0832 (2021).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Zhang, T.-Q., Chen, Y., Liu, Y., Lin, W.-H. & Wang, J.-W. Single-cell transcriptome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root. Nat. Commun. 12, 2053 (2021).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Watt, M. et al. Phenotyping: new windows into the plant for breeders. Annu. Rev. Plant Biol. 71, 689–712 (2020).

    Article 
    PubMed 

    Google Scholar     

  • Araus, J. L. et al. Crop phenotyping in a context of global change: what to measure and how to do it. J. Integr. Plant Biol. 64, 592–618 (2022).

    Article 
    PubMed 

    Google Scholar     

  • Sweet, D. D., Tirado, S. B., Springer, N. M., Hirsch, C. N. & Hirsch, C. D. Opportunities and challenges in phenotyping row crops using drone-based RGB imaging. Plant Phenome J. 5, e20044 (2022).

    Article 

    Google Scholar     

  • Barker, J. et al. Development of a field-based high-throughput mobile phenotyping platform. Comput. Electron. Agric. 122, 74–85 (2016).

    Article 

    Google Scholar     

  • Araus, J. L. & Cairns, J. E. Field high-throughput phenotyping: the new crop breeding frontier. Trends Plant Sci. 19, 52–61 (2014).

    Article 
    PubMed 

    Google Scholar     

  • Heuermann, M. C., Knoch, D., Junker, A. & Altmann, T. Natural plant growth and development achieved in the IPK PhenoSphere by dynamic environment simulation. Nat. Commun. 14, 5783 (2023).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Perez de Souza, L., Alseekh, S., Scossa, F. & Fernie, A. R. Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research. Nat. Methods 18, 733–746 (2021).

    Article 
    PubMed 

    Google Scholar     

  • Dubin, M. J. et al. DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation. eLife 4, e05255 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Nica, A. C. & Dermitzakis, E. T. Expression quantitative trait loci: present and future. Philos. Trans. R. Soc. B 368, 20120362 (2013).

    Article 

    Google Scholar     

  • Monroe, J. G. et al. Mutation bias reflects natural selection in Arabidopsis thaliana. Nature 602, 101–105 (2022).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Araus, J. L., Kefauver, S. C., Zaman-Allah, M., Olsen, M. S. & Cairns, J. E. Translating high-throughput phenotyping into genetic gain. Trends Plant Sci. 23, 451–466 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Hu, Y. & Schmidhalter, U. Opportunity and challenges of phenotyping plant salt tolerance. Trends Plant Sci. 28, 552–566 (2023).

    Article 
    PubMed 

    Google Scholar     

  • Reynolds, M. et al. Breeder friendly phenotyping. Plant Sci. 295, 110396 (2020).

    Article 
    PubMed 

    Google Scholar     

  • Awada, L., Phillips, P. W. B. & Smyth, S. J. The adoption of automated phenotyping by plant breeders. Euphytica 214, 148 (2018).

    Article 

    Google Scholar     

  • Papoutsoglou, E. A., Athanasiadis, I. N., Visser, R. G. F. & Finkers, R. The benefits and struggles of FAIR data: the case of reusing plant phenotyping data. Sci. Data 10, 457 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Papoutsoglou, E. A. et al. Enabling reusability of plant phenomic datasets with MIAPPE 1.1. New Phytol. 227, 260–273 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Selby, P. et al. BrAPI—an application programming interface for plant breeding applications. Bioinformatics 35, 4147–4155 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Bell, G., Hey, T. & Szalay, A. Beyond the data deluge. Science 323, 1297–1298 (2009).

    Article 
    PubMed 

    Google Scholar     

  • Jones, J. W. et al. Brief history of agricultural systems modeling. Agric. Syst. 155, 240–254 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Chenu, K. et al. Contribution of crop models to adaptation in wheat. Trends Plant Sci. 22, 472–490 (2017).

    Article 
    PubMed 

    Google Scholar     

  • De Souza, A. P. et al. Soybean photosynthesis and crop yield are improved by accelerating recovery from photoprotection. Science 377, 851–854 (2022).

    Article 
    ADS 
    PubMed 

    Google Scholar     

  • Habier, D., Fernando, R. L. & Garrick, D. J. Genomic BLUP decoded: a look into the black box of genomic prediction. Genetics 194, 597–607 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Hammer, G., Messina, C., Wu, A. & Cooper, M. Biological reality and parsimony in crop models—why we need both in crop improvement! in silico Plants 1, diz010 (2019).

    Article 

    Google Scholar     

  • Roeder, A. H. K. et al. Fifteen compelling open questions in plant cell biology. Plant Cell 34, 72–102 (2021). A collection of thought-provoking perspectives on future directions in basic plant science.

    Article 
    PubMed Central 

    Google Scholar     

  • Alexandratos, N. & Bruinsma, J. World agriculture towards 2030/2050: the 2012 revision. ESA Working Paper 12-03 (FAO, 2012).

  • Roser, M. Breaking out of the Malthusian trap: How pandemics allow us to understand why our ancestors were stuck in poverty. Our World in Data https://ourworldindata.org/breaking-the-malthusian-trap (2020).

  • Ritchie, H., Rosado P. & Roser, M. Hunger and Undernourishment. Our World in Data https://ourworldindata.org/hunger-and-undernourishment (2023).

  • Ghazal, H. et al. Plant genomics in Africa: present and prospects. Plant J. 107, 21–36 (2021).

    Article 
    PubMed 

    Google Scholar     

  • Jamnadass, R. et al. Enhancing African orphan crops with genomics. Nat. Genet. 52, 356–360 (2020).

    Article 
    PubMed 

    Google Scholar     

  • VanBuren, R. et al. Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff. Nat. Commun. 11, 884 (2020).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Wang, M. et al. Improved assembly and annotation of the sesame genome. DNA Res. 29, dsac041 (2022).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Qi, W. et al. The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features. GigaScience 11, giac028 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar     

  • Kuon, J.-E. et al. Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars. BMC Biol. 17, 75 (2019).

    Article 
    PubMed 

    Google Scholar     

  • Varshney, R. K. et al. Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics. Biotechnol. Adv. 31, 1120–1134 (2013).

    Article 
    PubMed 

    Google Scholar     

  • Mboowa, G., Sserwadda, I. & Aruhomukama, D. Genomics and bioinformatics capacity in Africa: no continent is left behind. Genome 64, 503–513 (2021).

    Article 
    PubMed 

    Google Scholar     

  • Santantonio, N. et al. Strategies for effective use of genomic information in crop breeding programs serving Africa and South Asia. Frontiers Plant Sci 11, 353 (2020).

    Article 

    Google Scholar     

  • Poore, J. & Nemecek, T. Reducing food’s environmental impacts through producers and consumers. Science 360, 987–992 (2018). This paper presents strong arguments for why environmental concerns matter to everyone, including plant breeders.

    Article 
    ADS 
    PubMed 

    Google Scholar     

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  • California Can Slake the Thirst of Its Farms by Storing Water Underground

    California Can Slake the Thirst of Its Farms by Storing Water Underground

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    For example, two winters’ worth of snow followed by intense heat created a flood risk in 2023. State officials decided to release water from Lake Oroville and other reservoirs across Southern California and the Central Valley. Although this helped prevent flooding and sent water downstream, many Californians were upset that the fresh water was being wasted. In attempts to reduce overflow releases, water agencies and irrigation districts made recharge basins to capture precipitation. But it wasn’t enough. Constant overpumping and a changing climate leave aquifers depleted to this day.

    Their natural recharge process—precipitation accumulating as surface water that percolates through the soil to recharge groundwater aquifers—can also be disrupted by urbanization or impervious covers like pavement, said Bruk Berhanu, a senior researcher in water efficiency and reuse at the Pacific Institute.

    The study suggests more managed aquifer recharge (MAR) infrastructure is needed to adequately catch large amounts of water in short time periods and avoid similar water-loss situations.

    MAR is an intentional method of recharging aquifers, especially those at low levels. Already commonly implemented in California, MAR infrastructure includes conveyance structures that redistribute water to dehydrated locations, and injection—spraying water on land or, the more costly option, directly infusing water in wells.

    Yet, to ensure an effective recharge of the aquifers, more monitoring and measurement is required. “Through 2014, growers were not required to monitor or report any withdrawals or injections to aquifers,” said Schwabe.

    Regardless, California has more monitoring practices than other states mainly because water availability is not as big a concern elsewhere, said Berhanu. Monitoring standards vary by state and region. Regulations for urban areas differ from agricultural or industrial areas. Based on Berhanu’s work assessing the country’s volumetric potential for water use efficiency at the municipal level, he found that “there is no federal regulatory framework for monitoring or reporting. In a lot of cases, water supplies aren’t even metered.”

    Even in areas that did have regulations, the reports were often infrequent or incomplete; the UC Riverside researchers are working on expanding the few accurate monitoring systems put in place in Southern California by proactive growers.

    Additionally, the study proposes voluntary water markets where farmers with a surplus of water can trade it to another farmer in need. It’s a win-win process: The selling farmer makes extra profit and the other gets much-needed water. “With prices based on scarcity plus delivery costs, such a marketplace would have incentives for storage and efficient use,” Schwabe said in a press release.

    Berhanu added that water-trading markets can work in some areas but not in others. “It needs a very strong governance framework to make sure all of the players are playing according to the rules.” The process will need to have improved monitoring practices, transparent data, and clear external costs, he said. “The more decentralized you get with how these transactions are being made, it becomes very difficult to coordinate the overall watershed-scale system benefits.”

    The study also mentions the value of reusing wastewater. Historically, wastewater has been treated to an environmental safety standard then released into the ocean or groundwater system. Over time, natural processes will clean it. Instead of waiting for the environment to purify it, water treatment facilities can repurpose the wastewater for irrigation, commercial use, or recharging purposes.

    As of 2023, water treatment plants can purify wastewater so well that people can drink it. “At some point, the water that we use will become someone else’s water for drinking or irrigation,” said Berhanu. Whether wastewater is for drinking or recharging aquifers, California plants are expanding their operations to include recycling methods so they can produce a sufficient supply.

    “The overall volume of water in the world doesn’t really change. We need to shift our thinking from looking at how much water is available at one point of time to trying to better integrate our practices with the entire water cycle,” said Berhanu.

    The study goes on to mention numerous efficiency-based and management solutions, like sustainable farming practices, land repurposing, and desalination to help the agriculture industry adjust.

    “Now is the time to think about possibilities and opportunities for collaboration across agriculture, municipalities, and the environment to invest in smart investments that capture more water and put it in the ground,” said Schwabe.

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  • Green ammonia production process could revolutionise farming

    Green ammonia production process could revolutionise farming

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    A breakthrough technique using liquid metal to produce green ammonia could drastically cut carbon emissions associated with the global production of this essential chemical.

    Researchers from RMIT University have developed a low-energy method that could pave the way for a sustainable green ammonia production process, which is vital for both agriculture and clean energy.

    Ammonia’s dual role in food and energy production

    Ammonia plays a crucial part in the global economy, primarily used in fertilisers to grow much of the world’s food supply.

    It also serves as a critical player in the clean energy sector as a carrier for hydrogen, a promising alternative fuel.

    Despite its importance, traditional ammonia production comes at a significant environmental cost. Current methods consume over 2% of the world’s energy and contribute nearly 2% of global carbon emissions.

    The widely-used Haber-Bosch process, developed over a century ago, is highly energy-intensive, requiring extreme heat and pressure to split nitrogen and hydrogen into ammonia. However, new research offers a greener alternative, potentially revolutionising ammonia production.

    Greener alternative reduces energy consumption

    Led by Dr Karma Zuraiqi, a research fellow at RMIT University, the team has developed an innovative approach that slashes energy consumption and emissions.

    Their method uses 20% less heat and requires 98% less pressure compared to the traditional Haber-Bosch process. The breakthrough findings demonstrate the effectiveness of this low-energy approach in producing ammonia without sacrificing efficiency.

    “Ammonia production worldwide is currently responsible for twice the emissions of Australia. If we can improve this process and make it less energy-intensive, we can make a large dent in carbon emissions,” said Zuraiqi.

    This new technique could significantly reduce the carbon footprint associated with ammonia production, offering a more sustainable solution to meet global demands.

    Liquid metal catalysts: The key to efficiency

    The RMIT team is at the forefront of research into liquid metal catalysts for various applications, including ammonia production, carbon capture, and energy generation.

    Catalysts are materials that accelerate chemical reactions without being consumed in the process, and in this case, liquid metal catalysts have unlocked new possibilities for green ammonia production.

    The researchers created ‘nano planets’, tiny droplets of liquid metal containing copper and gallium, which function as catalysts in the reaction.

    These nano planets, with their hard crust and liquid core, efficiently break apart nitrogen and hydrogen to form ammonia.

    The combination of copper and gallium proved to be more effective together than either metal used alone, with gallium facilitating nitrogen splitting and copper aiding in hydrogen breakdown.

    “Copper and gallium separately had both been discounted as poor catalysts for ammonia production, yet together they do the job extremely well,” explained RMIT Professor Torben Daeneke.

    This synergy between the two metals offers a cost-effective and abundant alternative to the precious metals, such as ruthenium, used in conventional processes.

    Upscaling and future potential

    While the traditional Haber-Bosch process is only feasible in large industrial settings, the RMIT team’s green ammonia method has the potential to be scaled for both large-scale and decentralised production.

    This flexibility could lead to small-scale green ammonia production at renewable energy sites like solar farms, reducing transportation costs and emissions even further.

    In addition to its applications in fertiliser production, this green ammonia technology could play a crucial role in the hydrogen economy.

    Converting hydrogen into ammonia makes it safer and easier to transport. However, if ammonia produced through traditional methods is used as a hydrogen carrier, emissions could increase, counteracting the benefits of hydrogen as a clean energy source.

    While the laboratory results are promising, the next challenge is scaling the green ammonia production method for industrial use. The team is now working to design a system that can operate at even lower pressures, making it more practical for a variety of industries.

    This innovative approach to green ammonia production could be a game-changer in reducing emissions and driving the shift toward cleaner energy sources, making the future of ammonia both greener and more sustainable.

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  • why pristine wilderness is a human-made myth

    why pristine wilderness is a human-made myth

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    Nature’s Ghosts: The World We Lost and How to Bring it Back Sophie Yeo HarperNorth (2024)

    A century ago, the world’s first ‘wilderness area’ was established in the Gila Mountains of southern New Mexico, by the forester Aldo Leopold. He wasn’t concerned with preserving ancient wildlands or resurrecting a memory of the Pleistocene epoch. He wanted hunters to be able to take a two-week backpacking trip without encountering a road. Out of such pragmatic sentiments — and decades before the US Congress offered protections — grew a system of more than 800 wilderness areas on federal lands in the United States. Hundreds more have since sprung up worldwide.

    The wilderness is widely seen as a place untrammelled by human activities. Not so, argues journalist Sophie Yeo in Nature’s Ghosts. Advocating lyrically for rebuilding a diverse natural world, she recognizes that, however wild a region might seem, human activities have left a mark in even the most isolated regions. People have been a part of nature as long as they’ve been around, coevolving with its ecosystems for millennia.

    Rewilding the planet: how seven artificial islands could help a dying Dutch lake

    Take the English countryside. In A Child’s History of England (1852–54), novelist Charles Dickens perpetuates the narrative that the country was once covered in pristine forests and swamps, on which humans had little imprint until they acquired metal tools. Yeo dissects the deep flaws in this vision.

    Far from eking out an existence on the margins of vast forests, our forebears were reshaping the environment as soon as humans diverged as a species. Spiralling out from her home in England, Yeo explores such transformations by examining fisheries in Finland; restoration of wildwood in the Scottish borders; biodiversity-preservation programmes on small farms in Transylvania, Romania; and farming practices in Denmark and Greenland.

    In Finland, for example, fishers at lake Puruvesi have reclaimed rights to fish using conventional practices in areas that were usurped by the crown and state in the sixteenth century. By rebranding the vendace (Coregonus vandesius) — a small whitefish that was typically destined to be pet food — as a marketable delicacy, the fishers are providing a modern rationale for conserving an ancient landscape and way of life. For half of the year, the fishers drill through the ice and deploy large seine nets to scoop up the vendace from beneath the frozen surface of the lake.

    Ghosts of environments past

    Weaving into her narrative an understanding of ecological niches, previous biodiversity crises and the deep environmental legacy of Roman farming, Yeo demonstrates the fallacy of trying to return the environment to any point in the past, whether that be pre-Roman Great Britain or Pleistocene Europe. Most continents — save for Africa, where large animals live on, and Antarctica, the surface of which has long been buried under kilometres of ice — are, as Yeo puts it, “haunted by the ghosts of the megafauna” that disappeared in the past 50,000 years, yet left an imprint on soil nutrients or made holes in ecological communities.

    Brown bison rides through columns of steam at Yellowstone National Park's Grand Prismatic Spring, Wyoming.

    A bison in Wyoming.Credit: Paolo Picciotto/REDA&CO/UIG/Getty

    She recounts how certain sharks in the Kiribati archipelago, white-tailed eagles (Haliaeetus albicilla) in Wales and beavers in California were regarded more as myth than reality, until careful work confirmed that those species once thrived in these regions. Those that remain often have to adapt to humans’ presence. The replacement of Bison antiquus in North America by Bison bison, or the succession of modern cattle from aurochs (Bos primigenius) in Europe, were marked by notable reductions in body size after centuries of evolving, interbreeding and hunting.

    The ecological legacies of human activities are pervasive and often subtle. Each environment has a history and preserves a record of its past. Part of Yeo’s mission is to show how these ghostly records should inform decisions about how best to recover some of nature’s past diversity as humanity moves towards a warmer and more uncertain future.

    How to keep wildcats wild: ancient DNA offers fresh insights

    An important point in her account is that there is no pristine baseline, devoid of human activity, to which restorers might retreat. For example, the woodland around the French commune of Thuilley-aux-Groseilles seems to be a remnant of an old-growth forest. But the enrichment of soils from Roman agriculture is evident in its plant communities, with buttercups prominent around houses and enclosures, and the broad-leaved helleborine (Epipactis helleborine) found in remoter areas.

    Yeo concludes that “the natural world has drifted so far from its origins that we no longer know what counts as natural”. It is impossible to establish what an area of land would have looked like or how it would have functioned before humans.

    Stuck in the present

    Yeo identifies three challenges for efforts to turn back history. First, as with the difficulty of identifying past white-tailed eagles in Wales, conservators often do not even know what is missing in an ecosystem, much less how they once worked. Second, climate change renders moot any effort to return ecosystems to how they were during, say, the seventeenth century, let alone the Pleistocene — and future conditions will differ from those now or in the past. Third, there are too many humans on the planet to leave substantial parts of it untouched.

    Green landscape with white-tailed Eagle Observatory on three wooden posts.

    White-tailed eagles (Haliaeetus albicilla) on a reserve in Wales.Credit: Getty

    I am all in favour of continuing to repair the ecosystems of the Rocky Mountains in North America, by rebuilding populations of American bison, wolves, mountain lions (Puma concolor) and grizzly bears (Ursus arctos horribilis). But encounters with humans often end badly for these animals, imposing practical limitations to their reintroduction.

    Whereas people in low- or middle-income countries most affected by climate change and environmental degradation stand to gain the most from the restorations described by Yeo, the majority don’t have the luxury of considering rejuvenating nature. Although Yeo does not consider environmental justice and economic inequality as deeply as one might wish, she does recognize that the growing human population limits the opportunities for rebuilding now-vanished landscapes.

    These animals are racing towards extinction. A new home might be their last chance

    Yeo asserts that properly understanding the past can be a key to building a richer future, not by trying to rewind the tape of history to some pre-human idyll, but by reinvigorating the natural world in a way that is sustainable and enriches lives. This does not require humans to be banished from wild places.

    Yeo views nature as “fragile but tenacious”. Her vision is close to Leopold’s a century ago. After the Gila Wilderness was established, he realized that wilderness must be more than a refuge for hunters; the wolves and mountain lions that hunters killed were essential to functioning ecosystems.

    Nature’s Ghosts underscores how people have more choices than they realize when it comes to crafting a better future. The book rejects as false the dichotomy between urbanization and economic growth or untrammelled wilderness. Enriching landscapes and healthy ecosystems can coexist with building modern economies. But achieving this goal requires a deep knowledge of what has been lost and an appreciation for the resilience of species in the face of environmental tumult. Importantly, it requires acceptance that, although the future will not be a simulacrum of the past, a future with richer biodiversity is attainable.

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  • Beyond Meat Is Stalling in the US. Europe Could Be Another Story

    Beyond Meat Is Stalling in the US. Europe Could Be Another Story

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    The plant-based meat industry is in a bad place. Sales in the US fell last year as the pandemic-era enthusiasm for vegan burgers and sausages continued to wane. Beyond Meat, once the darling of the plant-based boom and the first one of its cohort to go public, in 2019, has become a cautionary tale about the tough road ahead for similar companies.

    Beyond Meat announced mixed results for the second quarter of 2024. Revenue was down 8.8 percent, and sales volumes declined by 14 percent compared to the second quarter of 2023, but the margin the company made on each of its products was up.

    “We are encouraged by many of the results we see this quarter, results that demonstrate clear progress against our 2024 plan and our longer-term goal of profitable operations,” Beyond Meat CEO Ethan Brown told investors in an earnings call Wednesday.

    In 2023, Beyond’s revenue declined by 18 percent, to $343.4 million—which was above the low market expectations—but it also reported $82.7 million in losses. In the US, sales declined by 32.3 percent. So far, the company hasn’t rebounded, announcing a weak first quarter with revenue down by 18 percent again, to $75.6 million, as it continued to be hit by underwhelming demand from the US.

    Europe has been one of the brighter spots for Beyond over the past couple of years. In 2023, the company’s international sales grew while sales in the US sharply declined. In the UK, McDonald’s has sold McPlant burgers with Beyond Meat patties since fall 2021, while a similar partnership in the US didn’t get beyond the trial stage.

    Although Beyond reported declining sales internationally as well, on the most recent earnings call, chief financial officer Lubi Kutua said that the company was focused on widening its distribution in Europe. “We’re starting from a very small base in the EU,” Kutua said. “We just don’t have that large of a presence out in Europe at the moment.”

    Faced with difficult decisions in its path toward profitability, one investor predicted during an earnings call in February that the “center of gravity” of Beyond’s business was likely to shift to international markets. Brown did not directly address that point in the February call but conceded that, in his opinion, the conversation in the US around plant-based meats had been “politicized” and “clouded with this misinformation.” Plant-based meat has been pitted against animal meat in the US’s culture war.

    The entire plant-based industry has been affected by a fickle customer base. Rival Impossible Foods, which is targeting a “liquidity event” to raise capital in a move that could see it IPO or consider a sale to another company, has decided to rebrand itself to increase its appeal to meat eaters. Meanwhile, other vegan brands like Nowadays, Meatless Farm, and VBites have gone bust.

    Plant-based meats shouldn’t be counted out altogether, says Chris DuBois, an executive vice president at the analyst firm Circana. “It’s still a billion-dollar category, and that’s a big deal.”

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  • Production and formulation of biofertilisers and biopesticides

    Production and formulation of biofertilisers and biopesticides

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    The EXCALIBUR project explores the complexities of biofertiliser and biopesticide production, analysing the advantages of two production processes and identifying areas of improvement to facilitate scaling up and widespread adoption.

    Plant-beneficial microorganisms (both biofertilisers and biocontrol agents) are increasingly recognised as a sustainable alternative to chemical fertilisers due to their numerous benefits for agriculture, the environment, and human health.

    One of the most cited definitions of biofertilisers was described by Malusa and Vassilev ten years ago: A biofertiliser could be defined as the formulated product containing one or more microorganisms that enhance the nutrient status (and the growth and yield) of plants by either replacing soil nutrients and/or by making nutrients more available to plants and/or by increasing plant access to nutrients. It should be noted that this definition differentiates biofertilisation from biological control.

    While the emphasis of biofertilisation is on the effects of plant beneficial microorganisms that improve plant growth, stress tolerance and quality, biocontrol agents reduce/suppress plant pathogens partially or completely by producing metabolically inhibitory substances or, indirectly, by increasing the natural resistance of the plant. Both terms are not specific and do not differentiate between bacteria, fungi, and other organisms that have plant growth-promoting or biological control capacity.

    The multifunctional properties of microorganisms should be mentioned, which can exert plant-growth-promoting and biocontrol activity simultaneously. From both scientific and practical points of view, the production and widespread adoption of biofertilisers face several bottlenecks that need to be addressed to fully realise their potential benefits.

    Over recent years, after a long period of isolation, selection, and characterisation of plant-beneficial microorganisms, the main lines of research have been oriented to optimising the fermentation processes for the production of high-quality and large volumes of biomass/spores and their further formulation.

    It is also important to study and analyse the whole biotechnological chain for fertiliser/biocontrol production, as all its parts are interdependent. This is particularly true for fermentation formulation and even storage-application processes and procedures.

    Identifying challenges

    The production and widespread adoption of biofertilisers face several bottlenecks that need to be addressed to fully realise their potential benefits. Some of the main challenges at the production level are scaling up laboratory technologies, the cost of production, and quality control. Compared to chemical fertilisers, biofertilisers need special equipment, selected, cheap, available substrates, and controlled, optimised conditions for microbial growth.

    Further, scaling up the process should maintain the viability and safety of the selected microorganism and its efficacy while avoiding contamination and strain variability, bearing in mind the dual nature (opportunistic pathogenicity) of the majority of soil microorganisms.

    More research is needed to identify and develop microbial strains that interact stable and effectively with plant/soil systems and optimise their production and formulation.

    Two production processes

    What we know is that the production process could be carried out in solid-state or submerged conditions. Many research groups work on just one of these production options.

    However, it would be of great benefit for biotechnological companies producing plant-beneficial microorganisms to have the possibility of production mode selection. Therefore, if the strain is able to grow and develop a sufficient amount of biomass/spores in solid-state and submerged conditions, it could be better to offer two production schemes.

    Both processes offer specific advantages and disadvantages, which are well known in general, although they produce different bioproducts on different media and use different microorganisms. Solid-state fermentation and submerged liquid fermentation differently affect microbial growth and microbial metabolic activity, and – in some cases – the control and management of the overall microbial development in both processes are environmentally dependent.

    For example, in the H2020 project EXCALIBUR (grant number 817946), we found that a simple medium buffering increases the growth of Paenibacillus polymyxa in conditions of liquid-submerged fermentation (unpublished results). However, the same strain showed higher spore formation in solid-state compared to spore formation in submerged fermentation, with the number of CFU/ml always depending on the type of the solid substrate.

    Our experience confirmed the results of other authors, namely that solid-state fermentation is advantageous compared to the submerged process. It offers an easier final formulation combined with product viability after longer periods of storage.

    On the other hand, liquid-submerged fermentation is easier to control and can more rapidly produce the desired biomass and/or plant-beneficial microbial metabolites. Liquid-medium-based agitated processes provide many advantages compared to solid substrate-based fermentations.

    One of the main advantages is the homogenous distribution of both nutrients and oxygen in the bioreactor. In a liquid-agitated bioprocess, manipulation of the environmental conditions followed by the respective microbial behaviour changes is easier. In the field of microbial production, there are still many unexploited biotechnological schemes. For example, the fed-batch mode of fermentation, which is used in some biotechnological small- and large-scale processes, has not been tested in the production of many biofertilisers and biocontrol microorganisms.

    Similarly, processes with immobilised cells, biomass recycling, and continuous fermentations are not applied in this field, although they offer a number of technological and economic advantages. Here, we should mention the fact that microbial live cells are usually attached to surfaces or immobilised within soil particles, and some of the above processes can rely on these cell properties.

    Fermentation and commercial opportunities

    The mode of fermentation, to a great extent, determines the mode of formulation and the type of commercial product. The final products of solid-state fermentation consist of:

    • The solid, partially degraded particles, usually lignocellulosic waste materials, which in many cases serve simultaneously as a support and substrate.
    • Microbial biomass (including spores) in the form of more or less well-developed mycelium layer or bacterial cells within the substrate pores and/or on their surface.
    • Metabolites are produced during the fermentation process with plant-beneficial properties.

    After drying and milling, this material could be used directly as a commercial product. Another possibility is to separate the spores of the post-fermentation material and, after mixing with solid cell-viability-enhancing protectors, can be used in soil-plant systems. The third option is to extract the metabolite part of the mixture and form a cell-free product. While the first two options are well known, the third one is still in its infancy.

    However, we believe that the development of cell-free microbial plant-beneficial metabolite-based formulations is the future of bio-based agriculture for many reasons.

    The main one is the lack of necessity of a cell- or spore-based formulate for further adaptation and development in a soil-plant system. Fermentation liquid free of cells contains many metabolites, some of which could stimulate the growth and activity of other microorganisms in soil or in bioreactors.

    Interchanging metabolites and specific growth substances is a natural process within a given microbial community in a highly complex medium such as soil, which contains millions of microorganisms in small volumes. This process also affects phenomena such as quorum sensing, biofilm formation, and interactions between plants and beneficial (or pathogenic) autochthonous/introduced microorganisms.

    Therefore, introducing metabolite-containing cell-free post-fermentation liquid could be a challenge as well and needs additional studies.

    Gel-based formulates

    Another very attractive technique for the formulation is the macro- and micro-encapsulation of cells and spores of plant-beneficial microorganisms, particularly of double, triple, and multiple microbial gel-based formulates, which could also include phyto- or microbial stimulants.

    In general, gel-entrapped biological systems offer many advantages, such as better survival during storage and slow release of their content in the soil while protecting it from harsh soil conditions. Additionally, the advantage is that they could also be used in fermentation processes to produce the above-mentioned metabolites or mineral fertilisers if we can use microorganisms, which solubilise insoluble mineral-bearing materials.

    An important feature of plant-beneficial microorganisms is their abiotic and biotic stress-fighting capabilities. This is another complex issue that depends on the mode of microbial production and formulation in soil-plant systems. Analysing the results we obtained in this line of the multinational project EXCALIBUR, it appeared that the microorganisms feel better and are more efficient in an immobilised state.

    Understanding and evaluating impact

    The effect of microbial formulates on the belowground biological diversity and functions should be better addressed.

    In fact, even though a number of microbial-based products are commercially available worldwide, a challenge to fostering the broad-field application of microbial-based products relates to the fact that their beneficial traits are not always consistently expressed under field cultivation conditions. The interactions between plants and beneficial microorganisms are complex, and the mechanisms that regulate the plant-soil-microorganisms system remain largely to be discovered.

    This is particularly relevant when comparing results from experiments that are carried out in vitro in the laboratory and in situ under greenhouse and complex agricultural conditions. The mechanisms underlying the fate and persistence of bioinoculants in soil can result from the sum of multiple variables and, therefore, be difficult to understand and predict.

    Bioinocula released into soil often result in transient loads of the microbial strain/s that generally fade away with time. Thus, it is logical to assume that persisting microbial inoculants will have a more prolonged impact than short-lived inoculants. Given the supposed transitory survival of bioinocula, many scientists and practitioners assume that soil microbial inoculants would have negligible effects on the autochthonous soil microbial communities.

    However, the quick disappearance of inoculum in the soil does not necessarily imply a lack of long-lasting changes in the soil resident community. For example, Rhizobium inoculation to promote soybean productivity significantly influenced the bacterial community in the crop rhizosphere and the fungal community.

    Furthermore, the introduction of non-pathogenic Escherichia coli into soil shifted the niche structure of resident bacterial communities, leading to changes in the relative abundances of significant soil bacterial genera, such as Bacillus, Pseudomonas, Burkholderia, and Bradyrhizobium.

    The survival of microbial inoculants in soil also depends on the soil’s native microbiota: It is high when the autochthonous microbial community’s diversity is low and vice versa.

    However, the importance of evaluating the impact of inoculation in a temporal context should be kept in mind since the effects might change over time. For example, most of the studies addressing the impact of microbial inoculants on soil native communities measured the effects only over a short period after inoculation, usually within the vegetative season.

    In most cases, the inoculation led to changes in the structure of the resident communities, but it remains unclear whether the impact could persist for a more extended time, thus indicating the actual resilience capacity after the disturbance.

    Future outlook

    Due to the importance of the microbiome, the underlying communication and interaction mechanisms between the microbiomes and the environment require better knowledge, which has to expand our current holistic concept, acknowledging that biotic (plants and animals) and environmental (soil, water, and air) microbiomes form an interactive network that can impact the assembly and the functions of holobionts of all living organisms within an ecosystem.

    Fermentation and formulation approaches that exploit co-cultivation methods, use of wastes as substrates, and synergic interactions between strains represent a perspective strategy to boost the commercial production of microbial consortia that can overcome environmental stresses compared to single strains, thus assuring a lower risk of field failures.

    Moreover, the potential multifunctionality of many beneficial strains might represent an additional opportunity to develop innovative microbial-based products, though regulatory issues may contrast their commercial application.

    Contributors

    Nikolay Vassilev
    Department of Chemical Engineering
    University of Granada (Spain)

    Maria Vassileva
    Department of Chemical Engineering
    University of Granada (Spain)

    Dr Stefano Mocali, PhD
    Researcher
    EXCALIBUR project Coordinator
    CREA-AA, Florence (Italy)
    https://www.crea.gov.it/en/web/agricoltura-e-ambiente/

    Please note, this article will also appear in the 19th edition of our quarterly publication.

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  • The Fight to Save Florida’s Oranges

    The Fight to Save Florida’s Oranges

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    “We need more time,” said Rezazadeh. Growers in St. Lucie County started using the antibiotic last year. “There are some hopes that we keep the trees alive until we find a cure.”

    The state’s total citrus acreage suffered a massive blow in the 1990s when an eradication program for canker disease, then the industry’s biggest foe, resulted in the culling of hundreds of thousands of trees on private properties. In the years since citrus greening took hold, the ripple effects of the blight have compounded with an ever-present barrage of hurricanes, floods, and drought threatening growers.

    Hurricanes do more than uproot trees, scatter fruit, and shake trees so violently it can take them years to recover. Torrential rain and flooding can inundate groves and deplete the soil of oxygen. Diseased trees face particular risk because illness often impacts their roots, weakening them. Ray Royce, executive director of Highlands County Citrus Growers Association, likens it to a preexisting medical condition.

    “I’m an old guy. I get a cold, or I get sick, it’s harder for me to recover at 66 than it was at 33. If I had some underlying health issues, it’s even harder,” he said. “Greening is kind of this negative underlying health condition that makes anything else that happens to the tree, that stresses that tree, just further magnified.”

    It doesn’t help that climate change is bringing insufficient rainfall, higher temperatures, and record-setting dry seasons, leaving soils with less water. A lack of precipitation has also dried up wells and canals in some of the state’s most productive regions. All of this can reduce yields and cause fruit to drop prematurely.

    Of course, healthy trees have a higher chance of withstanding such threats. But the tenacity of strong groves is being tested, and once-minor events like a short freeze can be enough to end any already on the verge of demise.

    “We all of a sudden had a little bit of a run of bad luck. We had a hurricane. Then after the hurricane, we had a freeze,” said Royce. “Now we’ve just gone through a drought which will no doubt negatively impact the crop for next year. And so we, in a way, need to catch a couple of good breaks and have a few good years where we’re getting the right amount of moisture, where we don’t have hurricanes, or freezes, that are negatively impacting trees.”

    Human-induced climate change means that the respite Royce desperately hopes for is improbable. In fact, forecasters expect this to be the most active hurricane season in recorded history. Researchers have also found that warming will increase the pressures of plant diseases, like greening, in crops worldwide.

    Although “almost every tree in Florida” is afflicted with the disease, and the reality of warming temperatures spreading pathogens is a growing concern, the state’s citrus producing days are far from over, said Tim Widmer, a plant pathologist who specializes in crop diseases and plant health. “We don’t have the solution yet,” he said. “But there are things that look very, very promising.” A windfall of funding has been devoted to the hunt for answers to a befuddling problem. Florida’s legislature earmarked $65 million in the 2023-2024 budget to support the industry, while the 2018 federal farm bill included $25 million annually, for the length of the bill, toward combating the disease.

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  • Crushed rocks and fertiliser switches can cut nitrous oxide from farms

    Crushed rocks and fertiliser switches can cut nitrous oxide from farms

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    Spreading rock dust on fields can sequester carbon and reduce nitrous oxide emissions

    SO-Photography/Alamy Stock Photo

    Spreading crushed basalt on cropland and using special fertilisers that stop nitrogen loss could cut global agricultural emissions of a potent planet-warming gas by 25 per cent.

    Nitrous oxide is a greenhouse gas with 270 times more warming power than carbon dioxide. Global emissions have risen by 40 per cent in the past 40 years. Agriculture is a major driver, due to increased use of nitrogen-based fertilisers and growing livestock numbers.

    Microbes in the soil convert ammonium from fertilisers and animal waste into nitrate and release nitrous oxide in the process. Chemical compounds that hamper this process, called nitrification inhibitors, can be added to fertilisers to reduce nitrous oxide emissions. Spreading basalt rock dust on soils, a technique known as enhanced rock weathering (ERW), can also help by making the soil more alkaline.

    But as well as being a planet-warming pollutant, nitrous oxide emissions also have a complex relationship with the ozone layer, in some circumstances aiding its recovery. It has therefore proved difficult to find the best approach to mitigate nitrous oxide emissions without inadvertently harming the ozone layer.

    To address this, Maria Val Martin at the University of Sheffield, UK, and her colleagues modelled the impact of widespread use of both ERW and nitrification inhibitors on nitrous oxide emissions and the ozone layer, under two different climate scenarios.

    They found a “moderate” approach, in which ERW is deployed in key regions around the world, and where most farmers except the poorest use nitrification inhibitors, could lower nitrous oxide emissions from agriculture by 25 per cent. Overall nitrous oxide emissions would be cut by 5 per cent. These gases also come from combustion engines and industry.

    What’s more, up to 2 gigatonnes of additional carbon would be sequestered in the soil thanks to the ERW, and there would be no harm to the ozone layer under both scenarios, says Val Martin.

    “We get the [carbon] sequestration from enhanced rock weathering; we have the decrease in nitrous oxide, which is 300 times more powerful than CO2, so we have the climate benefit from reducing nitrous oxide emissions. And then we safeguard the ozone layer,” she says.

    Deploying nitrous oxide reduction efforts on this scale would cost billions of dollars. Using ERW to sequester carbon will cost $80-180 per tonne of CO2, according to previous studies, with reduction in nitrous oxide emissions a “free” co-benefit of carbon sequestration, according to Val Martin. Using nitrification inhibitors costs around $28-45 per hectare, and to cover 600 million hectares, as modelled in the study, would cost $17-27 billion annually. That area is around an eighth of all farmland.

    Nevertheless, Val Martin says the scenario is deliberately cautious in its ambition, so it could be deployed in the real world. “With this work, what we wanted to do is come up with a scenario that could be realistic. So if governments want to mitigate nitrous oxide, they can do it with [these] strategies that we have in place.”

    Parv Suntharalingam at the University of East Anglia, UK, says new strategies to curb nitrous oxide emissions are urgently required, and the study is especially valuable for its focus on curbing emissions without harming the ozone layer.

    Topics:

    • agriculture/
    • greenhouse gas emissions

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  • Why ‘open source’ AIs could be anything but, the derailment risks of long freight trains, and breeding better wheat

    Why ‘open source’ AIs could be anything but, the derailment risks of long freight trains, and breeding better wheat

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    Download the Nature Podcast 26 June 2024

    In this episode:

    00:31 How open are ‘open source’ AI systems?

    Many of the large language models powering AI systems are described as ‘open source’ but critics say this is a misnomer, with restricted access to code and training data preventing researchers from probing how these systems work. Although the definition of open source in AI models is yet to be agreed, advocates say that ‘full’ openness is crucial in efforts to make AI accountable. New research has ranked the openness of different systems, showing that despite claims of ‘openness’ many companies still don’t disclose a lot of key information.

    Nature News: Not all ‘open source’ AI models are actually open: here’s a ranking

    06:12 Why longer freight trains are more prone to derailment

    In the US, there are no federal limits on the length of a freight train, but as companies look to run longer locomotives, questions arise about whether they are at greater risk of derailment. To find out, a team analysed data on accidents to predict the chances of longer trains coming off the tracks. They showed that replacing two 50-car freight trains with one 100-car train raises the odds of derailment by 11%, with the chances increasing the longer a train gets. Although derailments are uncommon, this could change as economic pressures lead the freight industry to experiment with ever-longer trains.

    Scientific American: Longer and Longer Freight Trains Drive Up the Odds of Derailment

    11:44 How historic wheat could give new traits to current crops

    Genes from century-old wheat varieties could be used to breed useful traits into modern crops, helping them become more disease tolerant and reducing their need for fertilizer. Researchers sequenced the genomes of hundreds of historic varieties of wheat held in a seed collection from the 1920s and ’30s, revealing a huge amount of genetic diversity unseen in modern crops. Plant breeding enabled the team to identify some of the areas of the plants’ genomes responsible for traits such as nutritional content and stress tolerance. It’s hoped that in the long term this knowledge could be used to improve modern varieties of wheat.

    Science: ‘Gold mine’ of century-old wheat varieties could help breeders restore long lost traits

    Subscribe to Nature Briefing, an unmissable daily round-up of science news, opinion and analysis free in your inbox every weekday.

    Never miss an episode. Subscribe to the Nature Podcast on Apple Podcasts, Spotify, YouTube Music or your favourite podcast app. An RSS feed for the Nature Podcast is available too.

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