Ancient genomes reveal early Andean farmers selected common beans while preserving diversity.
Journal
Nature plants
ISSN: 2055-0278
Titre abrégé: Nat Plants
Pays: England
ID NLM: 101651677
Informations de publication
Date de publication:
02 2021
02 2021
Historique:
received:
19
10
2019
accepted:
04
01
2021
pubmed:
10
2
2021
medline:
28
4
2021
entrez:
9
2
2021
Statut:
ppublish
Résumé
All crops are the product of a domestication process that started less than 12,000 years ago from one or more wild populations
Identifiants
pubmed: 33558754
doi: 10.1038/s41477-021-00848-7
pii: 10.1038/s41477-021-00848-7
doi:
Types de publication
Historical Article
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
123-128Commentaires et corrections
Type : ErratumIn
Références
Diamond, J. Evolution, consequences and future of plant and animal domestication. Nature 418, 700–707 (2002).
pubmed: 12167878
doi: 10.1038/nature01019
Purugganan, M. D. Evolutionary insights into the nature of plant domestication. Curr. Biol. 29, 705–714 (2019).
doi: 10.1016/j.cub.2019.05.053
Meyer, R. S. & Purugganan, M. D. Evolution of crop species: genetics of domestication and diversification. Nat. Rev. Genet. 14, 840–852 (2013).
pubmed: 24240513
doi: 10.1038/nrg3605
Doebley, J. F., Gaut, B. S. & Smith, B. D. The molecular genetics of crop domestication. Cell 127, 1309–1321 (2006).
doi: 10.1016/j.cell.2006.12.006
pubmed: 17190597
Van de Wouw, M., Kik, C., van Hintum, T., van Treuren, R. & Visser, B. Genetic erosion in crops: concept, research results and challenges. Plant Genet. Resour. 8, 1–15 (2010).
doi: 10.1017/S1479262109990062
Babiker, E. M. et al. Mapping resistance to the Ug99 race group of the stem rust pathogen in a spring wheat landrace. Theor. Appl. Genet. 128, 605–612 (2015).
pubmed: 25599859
doi: 10.1007/s00122-015-2456-6
Dale, J. et al. Transgenic Cavendish bananas with resistance to Fusarium wilt tropical race 4. Nat. Commun. 8, 1496 (2017).
pubmed: 29133817
pmcid: 5684404
doi: 10.1038/s41467-017-01670-6
Esquinas-Alcázar, J. Protecting crop genetic diversity for food security: political, ethical and technical challenges. Nat. Rev. Genet. 6, 946–953 (2005).
pubmed: 16341075
doi: 10.1038/nrg1729
Gepts, P. Plant genetic resources conservation and utilization. Crop Sci. 46, 2278–2292 (2006).
doi: 10.2135/cropsci2006.03.0169gas
Beissinger, T. M. et al. Recent demography drives changes in linked selection across the maize genome. Nat. Plants 2, 16084 (2016).
pubmed: 27294617
doi: 10.1038/nplants.2016.84
Hyten, D. L. et al. Impacts of genetic bottlenecks on soybean genome diversity. Proc. Natl Acad. Sci. USA 103, 16666–16671 (2006).
pubmed: 17068128
pmcid: 1624862
doi: 10.1073/pnas.0604379103
Fuller, D. Q. et al. Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record. Proc. Natl Acad. Sci. USA 111, 6147–6152 (2014).
pubmed: 24753577
pmcid: 4035951
doi: 10.1073/pnas.1308937110
Khush, G. S. Green revolution: the way forward. Nat. Rev. Genet. 2, 815–822 (2001).
pubmed: 11584298
doi: 10.1038/35093585
Fu, Y. B. Understanding crop genetic diversity under modern plant breeding. Theor. Appl. Genet. 128, 2131–2142 (2015).
pubmed: 26246331
pmcid: 4624815
doi: 10.1007/s00122-015-2585-y
Bevan, M. W. et al. Genomic innovation for crop improvement. Nature 543, 346–354 (2017).
pubmed: 28300107
doi: 10.1038/nature22011
Bitocchi, E. et al. Mesoamerican origin of the common bean (Phaseolus vulgaris L.) is revealed by sequence data. Proc. Natl Acad. Sci. USA 109, E788–E796 (2012).
pubmed: 22393017
pmcid: 3325731
doi: 10.1073/pnas.1108973109
Schmutz, J. et al. A reference genome for common bean and genome-wide analysis of dual domestications. Nat. Genet. 46, 707–713 (2014).
pubmed: 24908249
pmcid: 7048698
doi: 10.1038/ng.3008
Bitocchi, E. et al. Beans (Phaseolus ssp.) as a model for understanding crop evolution. Front. Plant Sci. 8, 722 (2017).
pubmed: 28533789
pmcid: 5420584
doi: 10.3389/fpls.2017.00722
Winkel, T. et al. Discontinuities in quinoa biodiversity in the dry Andes: an 18-century perspective based on allelic genotyping. PLoS ONE 13, e0207519 (2018).
pubmed: 30517116
pmcid: 6281180
doi: 10.1371/journal.pone.0207519
Fages, A. et al. Tracking five millennia of horse management with extensive ancient genome time series. Cell 177, 1419–1435 (2019).
pubmed: 31056281
pmcid: 6547883
doi: 10.1016/j.cell.2019.03.049
Rendón-Anaya, M. et al. Genomic history of the origin and domestication of common bean unveils its closest sister species. Genome Biol. 18, 60 (2017).
pubmed: 28356141
pmcid: 5370463
doi: 10.1186/s13059-017-1190-6
Allaby, R. G., Ware, R. L. & Kistler, L. A re-evaluation of the domestication bottleneck from archaeogenomic evidence. Evol. Appl. 12, 29–37 (2019).
pubmed: 30622633
doi: 10.1111/eva.12680
Castañeda-Álvarez, N. P. et al. Global conservation priorities for crop wild relatives. Nat. Plants 2, 16022 (2016).
pubmed: 27249561
doi: 10.1038/nplants.2016.22
Pochettino, M. L. & Scattolin, M. C. Identificación y significado de frutos y semillas carbonizados de sitios arqueológicos de la ladera occidental del Aconquija, Prov. Catamarca, Rca. Argentina. Rev. Mus. La Plata, Antropol. 9, 169–181 (1991).
Singh, S. P., Gepts, P. & Debouck, D. G. Races of common bean (Phaseolus vulgaris, Fabaceae). Econ. Bot. 45, 379–396 (1991).
doi: 10.1007/BF02887079
Williams, V. I. Formaciones sociales en el noroeste argentino: variabilidad prehispánica en el surandino durante el Periodo de Desarrollos Regionales y el estado Inca. Rev. Haucaypata 9, 62–76 (2015).
Núñez, L. & Nielsen, A. E. En Ruta: Arquelogía, Historia y Etnografía del Tráfico Surandino (Encuentro Grupo Editor, 2011).
Da Fonseca, R. R. et al. The origin and evolution of maize in the southwestern United States. Nat. Plants 1, 14003 (2015).
pubmed: 27246050
doi: 10.1038/nplants.2014.3
Dubos, C. et al. MYB transcription factors in Arabidopsis. Trends Plant Sci. 15, 573–581 (2010).
pubmed: 20674465
doi: 10.1016/j.tplants.2010.06.005
Rau, D. et al. Genomic dissection of pod shattering in common bean: mutations at non‐orthologous loci at the basis of convergent phenotypic evolution under domestication of leguminous species. Plant J. 97, 693–714 (2019).
pubmed: 30422331
doi: 10.1111/tpj.14155
Saitoh, K., Onishi, K., Mikami, I., Thidar, K. & Sano, Y. Allelic diversification at the C (OsC1) locus of wild and cultivated rice: nucleotide changes associated with phenotypes. Genetics 168, 997–1007 (2004).
pubmed: 15514070
pmcid: 1448844
doi: 10.1534/genetics.103.018390
Estrada, O., Breen, J., Richards, S. M. & Cooper, A. Ancient plant DNA in the genomic era. Nat. Plants 4, 394–396 (2018).
pubmed: 29915330
doi: 10.1038/s41477-018-0187-9
Brunson, K. & Reich, D. The promise of paleogenomics beyond our own species. Trends Genet. 35, 319–329 (2019).
pubmed: 30954285
doi: 10.1016/j.tig.2019.02.006
Mascher, M. et al. Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley. Nat. Genet. 48, 1089–1093 (2016).
pubmed: 27428749
doi: 10.1038/ng.3611
Ramos-Madrigal, J. et al. Genome sequence of a 5,310-year-old maize cob provides insights into the early stages of maize domestication. Curr. Biol. 26, 3195–3201 (2016).
pubmed: 27866890
doi: 10.1016/j.cub.2016.09.036
Wagner, S. et al. High throughput DNA sequencing of ancient wood. Mol. Ecol. 27, 1138–1154 (2018).
pubmed: 29412519
pmcid: 5896730
doi: 10.1111/mec.14514
Kistler, L. et al. Multiproxy evidence highlights a complex evolutionary legacy of maize in South America. Science 362, 1309–1313 (2018).
pubmed: 30545889
doi: 10.1126/science.aav0207
Smith, O. et al. A domestication history of dynamic adaptation and genomic deterioration in sorghum. Nat. Plants 5, 369–379 (2019).
pubmed: 30962527
doi: 10.1038/s41477-019-0397-9
Lema, V. Non-domesticated cultivation in the Andes: plant management and nurturing in the Argentine northwest. Veg. Hist. Archaeobot. 24, 143–150 (2015).
doi: 10.1007/s00334-014-0494-7
Oliszewski, N. & Babot, P. in Avances y Desafíos Metodológicos en Arqueobotánica: Miradas Consensuadas y Diálogos Compartidos desde Sudamérica (eds Belmar, C. & Lema, V.) 301–324 (Facultad de Patrimonio Cultural y Educaciòn Universidad SEK Chile, 2015).
Schubert, M. et al. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nat. Prot. 9, 1056–1082 (2014).
doi: 10.1038/nprot.2014.063
Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. & Orlando, L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).
pubmed: 23613487
pmcid: 3694634
doi: 10.1093/bioinformatics/btt193
Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinform. 15, 356 (2014).
doi: 10.1186/s12859-014-0356-4
Vieira, F. G., Fumagalli, M., Albrechtsen, A. & Nielsen, R. Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation. Genome Res. 23, 1852–1861 (2013).
pubmed: 23950147
pmcid: 3814885
doi: 10.1101/gr.157388.113
Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).
pubmed: 19648217
pmcid: 2752134
doi: 10.1101/gr.094052.109
Lawson, D. J., Hellenthal, G., Myers, S. & Falush, D. Inference of population structure using dense haplotype data. PLoS Genet. 8, e1002453 (2012).
pubmed: 22291602
pmcid: 3266881
doi: 10.1371/journal.pgen.1002453
Slotte, T. The impact of linked selection on plant genomic variation. Brief. Funct. Genomics 13, 268–275 (2014).
pubmed: 24759704
pmcid: 4110415
doi: 10.1093/bfgp/elu009
Renaut, S. & Rieseberg, L. H. The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops. Mol. Biol. Evol. 32, 2273–2283 (2015).
pubmed: 25939650
doi: 10.1093/molbev/msv106
Beissinger, T. M. et al. Recent demography drives changes in linked selection across the maize genome. Nat. Plants 2, 16084 (2016).
pubmed: 27294617
doi: 10.1038/nplants.2016.84
Huang, D. W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).
doi: 10.1038/nprot.2008.211