Population Genomics of Crop Domestication: Current State and Perspectives

Cubry, Philippe; Vigouroux, Yves

doi:10.1007/13836_2018_48

Population Genomics of Crop Domestication: Current State and Perspectives

Philippe Cubry³ &
Yves Vigouroux³

Chapter
First Online: 11 September 2018

4687 Accesses
1 Citations

Part of the book series: Population Genomics ((POGE))

Abstract

Genomics has enabled access to unprecedented amounts of genomic and transcriptomic data. Studies of crop domestication have benefited from these datasets for deeper insights into when, where, and how crops were domesticated. Although genomics makes it possible to answer such questions, it also creates new technical and methodological challenges. Such large genomic and transcriptomic datasets provide the opportunity to advance from descriptive to hypothesis testing studies. Several model-based methods are now available to test hypotheses and to trace the history of crops. Studies of gene expression and of ancient DNA are new very active fields which hold great promise. Here, we review some key questions concerning crop domestication and discuss how genomics can help answer these questions and what interesting new approaches could be used in the future. As genomics data continue to become available, domestication studies will advance our knowledge not only of well-known domestication models, such as rice and maize, but also of other currently less widely studied crops. We will then be able to test general hypotheses associated with domestication across species.

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References

Alachiotis N, Pavlidis P. RAiSD detects positive selection based on multiple signatures of a selective sweep and SNP vectors. Commun Biol. 2018;1:79. https://doi.org/10.1038/s42003-018-0085-8.
Article PubMed PubMed Central Google Scholar
Avni R, Nave M, Barad O, Baruch K, Twardziok SO, Gundlach H, Hale I, Mascher M, Spannagl M, Wiebe K, Jordan KW, Golan G, Deek J, Ben-Zvi B, Ben-Zvi G, Himmelbach A, MacLachlan RP, Sharpe AG, Fritz A, Ben-David R, Budak H, Fahima T, Korol A, Faris JD, Hernandez A, Mikel MA, Levy AA, Steffenson B, Maccaferri M, Tuberosa R, Cattivelli L, Faccioli P, Ceriotti A, Kashkush K, Pourkheirandish M, Komatsuda T, Eilam T, Sela H, Sharon A, Ohad N, Chamovitz DA, Mayer KFX, Stein N, Ronen G, Peleg Z, Pozniak CJ, Akhunov ED, Distelfeld A. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science. 2017;357:93–7. https://doi.org/10.1126/science.aan0032.
Article CAS PubMed Google Scholar
Beaumont MA, Zhang W, Balding DJ. Approximate Bayesian computation in population genetics. Genetics. 2002;162:2025–35.
PubMed PubMed Central Google Scholar
Beissinger TM, Wang L, Crosby K, Durvasula A, Hufford MB, Ross-Ibarra J. Recent demography drives changes in linked selection across the maize genome. Nat Plants. 2016;2:16084. https://doi.org/10.1038/nplants.2016.84.
Article PubMed Google Scholar
Bellucci E, Bitocchi E, Ferrarini A, Benazzo A, Biagetti E, Klie S, Minio A, Rau D, Rodriguez M, Panziera A, Venturini L, Attene G, Albertini E, Jackson SA, Nanni L, Fernie AR, Nikoloski Z, Bertorelle G, Delledonne M, Papa R. Decreased nucleotide and expression diversity and modified coexpression patterns characterize domestication in the common bean. Plant Cell. 2014;26:1901–12. https://doi.org/10.1105/tpc.114.124040.
Article CAS PubMed PubMed Central Google Scholar
Berthouly-Salazar C, Mariac C, Couderc M, Pouzadoux J, Floc’h J-B, Vigouroux Y. Genotyping-by-sequencing SNP identification for crops without a reference genome: using transcriptome based mapping as an alternative strategy. Front Plant Sci. 2016;7:777. https://doi.org/10.3389/fpls.2016.00777.
Article PubMed PubMed Central Google Scholar
Brandenburg J-T, Mary-Huard T, Rigaill G, Hearne SJ, Corti H, Joets J, Vitte C, Charcosset A, Nicolas SD, Tenaillon MI. Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts. PLoS Genet. 2017;13:e1006666. https://doi.org/10.1371/journal.pgen.1006666.
Article CAS PubMed PubMed Central Google Scholar
Chen H, Patterson N, Reich D. Population differentiation as a test for selective sweeps. Genome Res. 2010;20:393–402. https://doi.org/10.1101/gr.100545.109.
Article CAS PubMed PubMed Central Google Scholar
Choi JY, Purugganan MD. Multiple origin but single domestication led to Oryza sativa. G3 (Bethesda). 2018;8:797–803. https://doi.org/10.1534/g3.117.300334.
Article Google Scholar
Civáň P, Craig H, Cox CJ, Brown TA. Three geographically separate domestications of Asian rice. Nat Plants. 2015;1:15164. https://doi.org/10.1038/nplants.2015.164.
Article PubMed PubMed Central Google Scholar
Clark RM, Wagler TN, Quijada P, Doebley J. A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nat Genet. 2006;38:594–7. https://doi.org/10.1038/ng1784.
Article CAS PubMed Google Scholar
Clotault J, Thuillet A-C, Buiron M, De Mita S, Couderc M, Haussmann BIG, Mariac C, Vigouroux Y. Evolutionary history of pearl millet (Pennisetum glaucum [L.] R. Br.) and selection on flowering genes since its domestication. Mol Biol Evol. 2012;29:1199–212. https://doi.org/10.1093/molbev/msr287.
Article CAS PubMed Google Scholar
Cornille A, Gladieux P, Smulders MJM, Roldán-Ruiz I, Laurens F, Le Cam B, Nersesyan A, Clavel J, Olonova M, Feugey L, Gabrielyan I, Zhang X-G, Tenaillon MI, Giraud T. New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties. PLoS Genet. 2012;8:e1002703. https://doi.org/10.1371/journal.pgen.1002703.
Article CAS PubMed PubMed Central Google Scholar
Cornille A, Giraud T, Smulders MJM, Roldán-Ruiz I, Gladieux P. The domestication and evolutionary ecology of apples. Trends Genet. 2014;30:57–65. https://doi.org/10.1016/j.tig.2013.10.002.
Article CAS PubMed Google Scholar
Csilléry K, Blum MGB, Gaggiotti OE, François O. Approximate Bayesian computation (ABC) in practice. Trends Ecol Evol (Amst). 2010;25:410–8. https://doi.org/10.1016/j.tree.2010.04.001.
Article Google Scholar
Cubry P, Tranchant-Dubreuil C, Thuillet AC, Monat C, Ndjiondjop MN, Labadi K, Cruaud C, Engelen S, Scarcelli N, Rhoné B, Burgarella C, Dupuy C, Larmande P, Wincker P, François O, Sabot F, Vigouroux Y. The rise and fall of African rice cultivation revealed by analysis of 246 new genomes. Curr Biol. 2018;28(14):2274–2282.e6.
Article CAS PubMed Google Scholar
da Fonseca RR, Smith BD, Wales N, Cappellini E, Skoglund P, Fumagalli M, Samaniego JA, Carøe C, Ávila-Arcos MC, Hufnagel DE, Korneliussen TS, Vieira FG, Jakobsson M, Arriaza B, Willerslev E, Nielsen R, Hufford MB, Albrechtsen A, Ross-Ibarra J, Gilbert MTP. The origin and evolution of maize in the Southwestern United States. Nat Plants. 2015;1:14003. https://doi.org/10.1038/nplants.2014.3.
Article PubMed Google Scholar
Dixon LE, Greenwood JR, Bencivenga S, Zhang P, Cockram J, Mellers G, Ramm K, Cavanagh C, Swain SM, Boden SA. TEOSINTE BRANCHED1 regulates inflorescence architecture and development in bread wheat (Triticum aestivum). Plant Cell. 2018;30:563–81. https://doi.org/10.1105/tpc.17.00961.
Article CAS PubMed PubMed Central Google Scholar
Doebley J, Lukens L. Transcriptional regulators and the evolution of plant form. Plant Cell. 1998;10:1075–82.
Article CAS PubMed PubMed Central Google Scholar
Doebley J, Stec A. Genetic analysis of the morphological differences between maize and teosinte. Genetics. 1991;129:285–95.
CAS PubMed PubMed Central Google Scholar
Doebley J, Stec A, Wendel J, Edwards M. Genetic and morphological analysis of a maize-teosinte F2 population: implications for the origin of maize. Proc Natl Acad Sci U S A. 1990;87:9888–92.
Article CAS PubMed PubMed Central Google Scholar
Doebley J, Stec A, Gustus C. Teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics. 1995;141:333–46.
CAS PubMed PubMed Central Google Scholar
Doebley J, Stec A, Hubbard L. The evolution of apical dominance in maize. Nature. 1997;386:485–8. https://doi.org/10.1038/386485a0.
Article CAS PubMed Google Scholar
Doebley JF, Gaut BS, Smith BD. The molecular genetics of crop domestication. Cell. 2006;127:1309–21. https://doi.org/10.1016/j.cell.2006.12.006.
Article CAS PubMed Google Scholar
Durvasula A, Hoffman PJ, Kent TV, Liu C, Kono TJY, Morrell PL, Ross-Ibarra J. angsd-wrapper: utilities for analysing next-generation sequencing data. Mol Ecol Resour. 2016;16:1449–54. https://doi.org/10.1111/1755-0998.12578.
Article CAS PubMed Google Scholar
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 2011;6:e19379. https://doi.org/10.1371/journal.pone.0019379.
Article CAS PubMed PubMed Central Google Scholar
Excoffier L, Dupanloup I, Huerta-Sánchez E, Sousa VC, Foll M. Robust demographic inference from genomic and SNP data. PLoS Genet. 2013;9:e1003905. https://doi.org/10.1371/journal.pgen.1003905.
Article CAS PubMed PubMed Central Google Scholar
Eyre-Walker A, Keightley PD. The distribution of fitness effects of new mutations. Nat Rev Genet. 2007;8:610–8. https://doi.org/10.1038/nrg2146.
Article CAS PubMed Google Scholar
Ferrer-Admetlla A, Liang M, Korneliussen T, Nielsen R. On detecting incomplete soft or hard selective sweeps using haplotype structure. Mol Biol Evol. 2014;31:1275–91. https://doi.org/10.1093/molbev/msu077.
Article CAS PubMed PubMed Central Google Scholar
François O, Blum MGB, Jakobsson M, Rosenberg NA. Demographic history of European populations of Arabidopsis thaliana. PLoS Genet. 2008;4:e1000075. https://doi.org/10.1371/journal.pgen.1000075.
Article CAS PubMed PubMed Central Google Scholar
Garud NR, Messer PW, Buzbas EO, Petrov DA. Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps. PLoS Genet. 2015;11:e1005004. https://doi.org/10.1371/journal.pgen.1005004.
Article CAS PubMed PubMed Central Google Scholar
Gerbault P, Allaby RG, Boivin N, Rudzinski A, Grimaldi IM, Pires JC, Vigueira CC, Dobney K, Gremillion KJ, Barton L, Arroyo-Kalin M, Purugganan MD, de Casas RR, Bollongino R, Burger J, Fuller DQ, Bradley DG, Balding DJ, Richerson PJ, Gilbert MTP, Larson G, Thomas MG. Storytelling and story testing in domestication. Proc Natl Acad Sci U S A. 2014;111:6159–64. https://doi.org/10.1073/pnas.1400425111.
Article CAS PubMed PubMed Central Google Scholar
Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 2009;5:e1000695. https://doi.org/10.1371/journal.pgen.1000695.
Article CAS PubMed PubMed Central Google Scholar
Handley LJL, Manica A, Goudet J, Balloux F. Going the distance: human population genetics in a clinal world. Trends Genet. 2007;23:432–9. https://doi.org/10.1016/j.tig.2007.07.002.
Article CAS PubMed Google Scholar
Hein J, Schierup M, Wiuf C. Gene genealogies, variation and evolution: a primer in coalescent theory. Oxford: Oxford University Press; 2004.
Google Scholar
Hermisson J, Pennings PS. Soft sweeps and beyond: understanding the patterns and probabilities of selection footprints under rapid adaptation. Methods Ecol Evol. 2017;8:700–16. https://doi.org/10.1111/2041-210X.12808.
Article Google Scholar
Heun M, Schäfer-Pregl R, Klawan D, Castagna R, Accerbi M, Borghi B, Salamini F. Site of einkorn wheat domestication identified by DNA fingerprinting. Science. 1997;278:1312–4. https://doi.org/10.1126/science.278.5341.1312.
Article CAS Google Scholar
Hu M, Lv S, Wu W, Fu Y, Liu F, Wang B, Li W, Gu P, Cai H, Sun C, Zhu Z. The domestication of plant architecture in African rice. Plant J. 2018;94:661–9. https://doi.org/10.1111/tpj.13887.
Article CAS PubMed Google Scholar
Huang X, Kurata N, Wei X, Wang Z-X, Wang A, Zhao Q, Zhao Y, Liu K, Lu H, Li W, Guo Y, Lu Y, Zhou C, Fan D, Weng Q, Zhu C, Huang T, Zhang L, Wang Y, Feng L, Furuumi H, Kubo T, Miyabayashi T, Yuan X, Xu Q, Dong G, Zhan Q, Li C, Fujiyama A, Toyoda A, Lu T, Feng Q, Qian Q, Li J, Han B. A map of rice genome variation reveals the origin of cultivated rice. Nature. 2012;490:497–501. https://doi.org/10.1038/nature11532.
Article CAS PubMed PubMed Central Google Scholar
Hufford MB, Xu X, van Heerwaarden J, Pyhäjärvi T, Chia J-M, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, Lai J, Morrell PL, Shannon LM, Song C, Springer NM, Swanson-Wagner RA, Tiffin P, Wang J, Zhang G, Doebley J, McMullen MD, Ware D, Buckler ES, Yang S, Ross-Ibarra J. Comparative population genomics of maize domestication and improvement. Nat Genet. 2012;44:808–11. https://doi.org/10.1038/ng.2309.
Article CAS PubMed PubMed Central Google Scholar
Jaenicke-Després V, Buckler ES, Smith BD, Gilbert MTP, Cooper A, Doebley J, Pääbo S. Early allelic selection in maize as revealed by ancient DNA. Science. 2003;302:1206–8. https://doi.org/10.1126/science.1089056.
Article CAS PubMed Google Scholar
Kofler R, Langmüller AM, Nouhaud P, Otte KA, Schlötterer C. Suitability of different mapping algorithms for genome-wide polymorphism scans with Pool-Seq data. G3. 2016;6:3507–15. https://doi.org/10.1534/g3.116.034488.
Article CAS PubMed PubMed Central Google Scholar
Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T, Yano M. An SNP caused loss of seed shattering during rice domestication. Science. 2006;312:1392–6. https://doi.org/10.1126/science.1126410.
Article CAS PubMed Google Scholar
Korneliussen TS, Albrechtsen A, Nielsen R. ANGSD: analysis of next generation sequencing data. BMC Bioinformatics. 2014;15:356. https://doi.org/10.1186/s12859-014-0356-4.
Article PubMed PubMed Central Google Scholar
Kremling KAG, Chen S-Y, Su M-H, Lepak NK, Romay MC, Swarts KL, Lu F, Lorant A, Bradbury PJ, Buckler ES. Dysregulation of expression correlates with rare-allele burden and fitness loss in maize. Nature. 2018;555:520–3. https://doi.org/10.1038/nature25966.
Article CAS PubMed Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9. https://doi.org/10.1038/nmeth.1923.
Article CAS PubMed PubMed Central Google Scholar
Lemmon ZH, Bukowski R, Sun Q, Doebley JF. The role of cis regulatory evolution in maize domestication. PLoS Genet. 2014;10:e1004745. https://doi.org/10.1371/journal.pgen.1004745.
Article CAS PubMed PubMed Central Google Scholar
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 2013. arXiv:1303.3997 [q-bio].
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009;25:1754–60. https://doi.org/10.1093/bioinformatics/btp324.
Article CAS PubMed PubMed Central Google Scholar
Li H, Durbin R. Inference of human population history from individual whole-genome sequences. Nature. 2011;475:493–6. https://doi.org/10.1038/nature10231.
Article CAS PubMed PubMed Central Google Scholar
Li C, Zhou A, Sang T. Rice domestication by reducing shattering. Science. 2006;311:1936–9. https://doi.org/10.1126/science.1123604.
Article CAS PubMed Google Scholar
Li R, Yu C, Li Y, Lam T-W, Yiu S-M, Kristiansen K, Wang J. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009;25:1966–7. https://doi.org/10.1093/bioinformatics/btp336.
Article CAS PubMed Google Scholar
Lin Z, Li X, Shannon LM, Yeh C-T, Wang ML, Bai G, Peng Z, Li J, Trick HN, Clemente TE, Doebley J, Schnable PS, Tuinstra MR, Tesso TT, White F, Yu J. Parallel domestication of the Shattering1 genes in cereals. Nat Genet. 2012;44:720–4. https://doi.org/10.1038/ng.2281.
Article CAS PubMed PubMed Central Google Scholar
Liu X, Fu Y-X. Exploring population size changes using SNP frequency spectra. Nat Genet. 2015;47:555–9. https://doi.org/10.1038/ng.3254.
Article CAS PubMed PubMed Central Google Scholar
Liu Q, Zhou Y, Morrell PL, Gaut BS. Deleterious variants in Asian rice and the potential cost of domestication. Mol Biol Evol. 2017;34:908–24. https://doi.org/10.1093/molbev/msw296.
Article CAS PubMed Google Scholar
Lu J, Tang T, Tang H, Huang J, Shi S, Wu C-I. The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication. Trends Genet. 2006;22:126–31. https://doi.org/10.1016/j.tig.2006.01.004.
Article CAS PubMed Google Scholar
Lukens L, Doebley J. Molecular evolution of the teosinte branched gene among maize and related grasses. Mol Biol Evol. 2001;18:627–38. https://doi.org/10.1093/oxfordjournals.molbev.a003843.
Article CAS PubMed Google Scholar
Lunter G, Goodson M. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res. 2011;21:936–9. https://doi.org/10.1101/gr.111120.110.
Article CAS PubMed PubMed Central Google Scholar
Magwa RA, Zhao H, Yao W, Xie W, Yang L, Xing Y, Bai X. Genomewide association analysis for awn length linked to the seed shattering gene qSH1 in rice. J Genet. 2016;95:639–46.
Article CAS PubMed Google Scholar
Makino T, Rubin C-J, Carneiro M, Axelsson E, Andersson L, Webster MT. Elevated proportions of deleterious genetic variation in domestic animals and plants. Genome Biol Evol. 2018;10:276–90. https://doi.org/10.1093/gbe/evy004.
Article CAS PubMed PubMed Central Google Scholar
Mariac C, Scarcelli N, Pouzadou J, Barnaud A, Billot C, Faye A, Kougbeadjo A, Maillol V, Martin G, Sabot F, Santoni S, Vigouroux Y, Couvreur TLP. Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies. Mol Ecol Resour. 2014;14:1103–13. https://doi.org/10.1111/1755-0998.12258.
Article CAS PubMed Google Scholar
Matsuoka Y, Vigouroux Y, Goodman MM, Sanchez GJ, Buckler E, Doebley J. A single domestication for maize shown by multilocus microsatellite genotyping. Proc Natl Acad Sci U S A. 2002;99:6080–4. https://doi.org/10.1073/pnas.052125199.
Article CAS PubMed PubMed Central Google Scholar
Meyer RS, Purugganan MD. Evolution of crop species: genetics of domestication and diversification. Nat Rev Genet. 2013;14:840–52. https://doi.org/10.1038/nrg3605.
Article CAS PubMed Google Scholar
Meyer RS, Choi JY, Sanches M, Plessis A, Flowers JM, Amas J, Dorph K, Barretto A, Gross B, Fuller DQ, Bimpong IK, Ndjiondjop M-N, Hazzouri KM, Gregorio GB, Purugganan MD. Domestication history and geographical adaptation inferred from a SNP map of African rice. Nat Genet. 2016;48:1083–8. https://doi.org/10.1038/ng.3633.
Article CAS PubMed Google Scholar
Molina J, Sikora M, Garud N, Flowers JM, Rubinstein S, Reynolds A, Huang P, Jackson S, Schaal BA, Bustamante CD, Boyko AR, Purugganan MD. Molecular evidence for a single evolutionary origin of domesticated rice. Proc Natl Acad Sci U S A. 2011;108:8351–6. https://doi.org/10.1073/pnas.1104686108.
Article PubMed PubMed Central Google Scholar
Moreira PA, Mariac C, Scarcelli N, Couderc M, Rodrigues DP, Clement CR, Vigouroux Y. Chloroplast sequence of treegourd (Crescentia cujete, Bignoniaceae) to study phylogeography and domestication. Appl Plant Sci. 2016;4:1600048. https://doi.org/10.3732/apps.1600048.
Article Google Scholar
Moreira PA, Aguirre-Dugua X, Mariac C, Zekraoui L, Couderc M, Rodrigues DP, Casas A, Clement CR, Vigouroux Y. Diversity of treegourd (Crescentia cujete) suggests introduction and prehistoric dispersal routes into Amazonia. Front Ecol Evol. 2017a;5:150. https://doi.org/10.3389/fevo.2017.00150.
Article Google Scholar
Moreira PA, Mariac C, Zekraoui L, Couderc M, Rodrigues DP, Clement CR, Vigouroux Y. Human management and hybridization shape treegourd fruits in the Brazilian Amazon Basin. Evol Appl. 2017b;10:577–89. https://doi.org/10.1111/eva.12474.
Article CAS Google Scholar
Moyers BT, Morrell PL, McKay JK. Genetic costs of domestication and improvement. J Hered. 2018;109:103–16. https://doi.org/10.1093/jhered/esx069.
Article PubMed Google Scholar
Nabholz B, Sarah G, Sabot F, Ruiz M, Adam H, Nidelet S, Ghesquière A, Santoni S, David J, Glémin S. Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima). Mol Ecol. 2014;23:2210–27. https://doi.org/10.1111/mec.12738.
Article CAS PubMed Google Scholar
Nakagome S, Alkorta-Aranburu G, Amato R, Howie B, Peter BM, Hudson RR, Rienzo AD. Estimating the ages of selection signals from different epochs in human history. Mol Biol Evol. 2016;33:657–69. https://doi.org/10.1093/molbev/msv256.
Article CAS PubMed Google Scholar
Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, Bustamante C. Genomic scans for selective sweeps using SNP data. Genome Res. 2005;15:1566–75. https://doi.org/10.1101/gr.4252305.
Article CAS PubMed PubMed Central Google Scholar
Ohta T. Near-neutrality in evolution of genes and gene regulation. Proc Natl Acad Sci U S A. 2002;99:16134–7. https://doi.org/10.1073/pnas.252626899.
Article CAS PubMed PubMed Central Google Scholar
Paterson AH, Lin YR, Li Z, Schertz KF, Doebley JF, Pinson SR, Liu SC, Stansel JW, Irvine JE. Convergent domestication of cereal crops by independent mutations at corresponding genetic loci. Science. 1995;269:1714–8. https://doi.org/10.1126/science.269.5231.1714.
Article CAS PubMed Google Scholar
Peter BM, Slatkin M. Detecting range expansions from genetic data. Evolution. 2013;67:3274–89. https://doi.org/10.1111/evo.12202.
Article PubMed PubMed Central Google Scholar
Peter BM, Slatkin M. The effective founder effect in a spatially expanding population. Evolution. 2015;69:721–34. https://doi.org/10.1111/evo.12609.
Article PubMed PubMed Central Google Scholar
Poncet V, Martel E, Allouis S, Devos M, Lamy F, Sarr A, Robert T. Comparative analysis of QTLs affecting domestication traits between two domesticated x wild pearl millet (Pennisetum glaucum L., Poaceae) crosses. Theor Appl Genet. 2002;104:965–75. https://doi.org/10.1007/s00122-002-0889-1.
Article CAS PubMed Google Scholar
Pourkheirandish M, Hensel G, Kilian B, Senthil N, Chen G, Sameri M, Azhaguvel P, Sakuma S, Dhanagond S, Sharma R, Mascher M, Himmelbach A, Gottwald S, Nair SK, Tagiri A, Yukuhiro F, Nagamura Y, Kanamori H, Matsumoto T, Willcox G, Middleton CP, Wicker T, Walther A, Waugh R, Fincher GB, Stein N, Kumlehn J, Sato K, Komatsuda T. Evolution of the grain dispersal system in barley. Cell. 2015;162:527–39. https://doi.org/10.1016/j.cell.2015.07.002.
Article CAS PubMed Google Scholar
Przeworski M. Estimating the time since the fixation of a beneficial allele. Genetics. 2003;164:1667–76.
PubMed PubMed Central Google Scholar
Purugganan MD, Fuller DQ. The nature of selection during plant domestication. Nature. 2009;457:843–8. https://doi.org/10.1038/nature07895.
Article CAS PubMed Google Scholar
Ray N, Currat M, Foll M, Excoffier L. SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination. Bioinformatics. 2010;26:2993–4. https://doi.org/10.1093/bioinformatics/btq579.
Article CAS PubMed Google Scholar
Sabeti PC, Reich DE, Higgins JM, Levine HZP, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, Ackerman HC, Campbell SJ, Altshuler D, Cooper R, Kwiatkowski D, Ward R, Lander ES. Detecting recent positive selection in the human genome from haplotype structure. Nature. 2002;419:832–7. https://doi.org/10.1038/nature01140.
Article CAS PubMed Google Scholar
Sarah G, Homa F, Pointet S, Contreras S, Sabot F, Nabholz B, Santoni S, Sauné L, Ardisson M, Chantret N, Sauvage C, Tregear J, Jourda C, Pot D, Vigouroux Y, Chair H, Scarcelli N, Billot C, Yahiaoui N, Bacilieri R, Khadari B, Boccara M, Barnaud A, Péros J-P, Labouisse J-P, Pham J-L, David J, Glémin S, Ruiz M. A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives. Mol Ecol Resour. 2017;17:565–80. https://doi.org/10.1111/1755-0998.12587.
Article CAS PubMed Google Scholar
Scarcelli N, Mariac C, Couvreur TLP, Faye A, Richard D, Sabot F, Berthouly-Salazar C, Vigouroux Y. Intra-individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it? Mol Ecol Resour. 2016;16:434–45. https://doi.org/10.1111/1755-0998.12462.
Article CAS PubMed Google Scholar
Schiffels S, Durbin R. Inferring human population size and separation history from multiple genome sequences. Nat Genet. 2014;46:919–25. https://doi.org/10.1038/ng.3015.
Article CAS PubMed PubMed Central Google Scholar
Schrider DR, Kern AD. S/HIC: robust identification of soft and hard sweeps using machine learning. PLoS Genet. 2016;12:e1005928. https://doi.org/10.1371/journal.pgen.1005928.
Article CAS PubMed PubMed Central Google Scholar
Schrider DR, Kern AD. Soft sweeps are the dominant mode of adaptation in the human genome. Mol Biol Evol. 2017;34:1863–77. https://doi.org/10.1093/molbev/msx154.
Article CAS PubMed PubMed Central Google Scholar
Sedlazeck FJ, Rescheneder P, von Haeseler A. NextGenMap: fast and accurate read mapping in highly polymorphic genomes. Bioinformatics. 2013;29:2790–1. https://doi.org/10.1093/bioinformatics/btt468.
Article CAS PubMed Google Scholar
Skotte L, Korneliussen TS, Albrechtsen A. Estimating individual admixture proportions from next generation sequencing data. Genetics. 2013;195:693–702. https://doi.org/10.1534/genetics.113.154138.
Article CAS PubMed PubMed Central Google Scholar
Smith J, Coop G, Stephens M, Novembre J. Estimating time to the common ancestor for a beneficial allele. Mol Biol Evol. 2018;35:1003–17. https://doi.org/10.1093/molbev/msy006.
Article CAS PubMed PubMed Central Google Scholar
Studer A, Zhao Q, Ross-Ibarra J, Doebley J. Identification of a functional transposon insertion in the maize domestication gene tb1. Nat Genet. 2011;43:1160–3. https://doi.org/10.1038/ng.942.
Article CAS PubMed PubMed Central Google Scholar
Swarts K, Gutaker RM, Benz B, Blake M, Bukowski R, Holland J, Kruse-Peeples M, Lepak N, Prim L, Romay MC, Ross-Ibarra J, Sanchez-Gonzalez JJ, Schmidt C, Schuenemann VJ, Krause J, Matson RG, Weigel D, Buckler ES, Burbano HA. Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America. Science. 2017;357:512–5. https://doi.org/10.1126/science.aam9425.
Article CAS PubMed Google Scholar
Ta KN, Sabot F, Adam H, Vigouroux Y, De Mita S, Ghesquière A, Do NV, Gantet P, Jouannic S. miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species. Rice (N Y). 2016;9:10. https://doi.org/10.1186/s12284-016-0082-9.
Article CAS Google Scholar
Tajima F. The amount of DNA polymorphism maintained in a finite population when the neutral mutation rate varies among sites. Genetics. 1996;143:1457–65.
CAS PubMed PubMed Central Google Scholar
Tan L, Li X, Liu F, Sun X, Li C, Zhu Z, Fu Y, Cai H, Wang X, Xie D, Sun C. Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet. 2008;40:1360–4. https://doi.org/10.1038/ng.197.
Article CAS PubMed Google Scholar
Tenaillon MI, U’Ren J, Tenaillon O, Gaut BS. Selection versus demography: a multilocus investigation of the domestication process in maize. Mol Biol Evol. 2004;21:1214–25. https://doi.org/10.1093/molbev/msh102.
Article CAS PubMed Google Scholar
Terhorst J, Kamm JA, Song YS. Robust and scalable inference of population history from hundreds of unphased whole genomes. Nat Genet. 2017;49:303–9. https://doi.org/10.1038/ng.3748.
Article CAS PubMed Google Scholar
Tong W, Kim T-S, Park Y-J. Rice chloroplast genome variation architecture and phylogenetic dissection in diverse Oryza species assessed by whole-genome resequencing. Rice. 2016;9:57. https://doi.org/10.1186/s12284-016-0129-y.
Article PubMed PubMed Central Google Scholar
Vavilov NI, Vavylov MI, Vavílov NÍ, Dorofeev VF. Origin and geography of cultivated plants. Cambridge: Cambridge University Press; 1992.
Google Scholar
Vigouroux Y, McMullen M, Hittinger CT, Houchins K, Schulz L, Kresovich S, Matsuoka Y, Doebley J. Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proc Natl Acad Sci U S A. 2002;99:9650–5. https://doi.org/10.1073/pnas.112324299.
Article CAS PubMed PubMed Central Google Scholar
Vitti JJ, Grossman SR, Sabeti PC. Detecting natural selection in genomic data. Annu Rev Genet. 2013;47:97–120. https://doi.org/10.1146/annurev-genet-111212-133526.
Article CAS PubMed Google Scholar
Wang H, Nussbaum-Wagler T, Li B, Zhao Q, Vigouroux Y, Faller M, Bomblies K, Lukens L, Doebley JF. The origin of the naked grains of maize. Nature. 2005;436:714–9. https://doi.org/10.1038/nature03863.
Article CAS PubMed PubMed Central Google Scholar
Wang L, Beissinger TM, Lorant A, Ross-Ibarra C, Ross-Ibarra J, Hufford MB. The interplay of demography and selection during maize domestication and expansion. Genome Biol. 2017;18:215. https://doi.org/10.1186/s13059-017-1346-4.
Article CAS PubMed PubMed Central Google Scholar
Wang RL, Stec A, Hey J, Lukens L, Doebley J. The limits of selection during maize domestication. Nature. 1999;398:236–9. https://doi.org/10.1038/18435.
Article CAS PubMed Google Scholar
Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S, Wu Z, Li M, Zheng T, Fuentes RR, Zhang F, Mansueto L, Copetti D, Sanciangco M, Palis KC, Xu J, Sun C, Fu B, Zhang H, Gao Y, Zhao X, Shen F, Cui X, Yu H, Li Z, Chen M, Detras J, Zhou Y, Zhang X, Zhao Y, Kudrna D, Wang C, Li R, Jia B, Lu J, He X, Dong Z, Xu J, Li Y, Wang M, Shi J, Li J, Zhang D, Lee S, Hu W, Poliakov A, Dubchak I, Ulat VJ, Borja FN, Mendoza JR, Ali J, Li J, Gao Q, Niu Y, Yue Z, Naredo MEB, Talag J, Wang X, Li J, Fang X, Yin Y, Glaszmann J-C, Zhang J, Li J, Hamilton RS, Wing RA, Ruan J, Zhang G, Wei C, Alexandrov N, McNally KL, Li Z, Leung H. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature. 2018;557:43–9. https://doi.org/10.1038/s41586-018-0063-9.
Article CAS PubMed PubMed Central Google Scholar
Win KT, Yamagata Y, Doi K, Uyama K, Nagai Y, Toda Y, Kani T, Ashikari M, Yasui H, Yoshimura A. A single base change explains the independent origin of and selection for the nonshattering gene in African rice domestication. New Phytol. 2017;213:1925–35. https://doi.org/10.1111/nph.14290.
Article CAS PubMed Google Scholar
Wu W, Liu X, Wang M, Meyer RS, Luo X, Ndjiondjop M-N, Tan L, Zhang J, Wu J, Cai H, Sun C, Wang X, Wing RA, Zhu Z. A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication. Nat Plants. 2017;3:17064. https://doi.org/10.1038/nplants.2017.64.
Article CAS PubMed Google Scholar
Xie Q, Li N, Yang Y, Lv Y, Yao H, Wei R, Sparkes DL, Ma Z. Pleiotropic effects of the wheat domestication gene Q on yield and grain morphology. Planta. 2018;247:1089–98. https://doi.org/10.1007/s00425-018-2847-4.
Article CAS PubMed Google Scholar

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Institut de Recherche pour le développement, Université de Montpellier, Montpellier, France
Philippe Cubry & Yves Vigouroux

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Philippe Cubry
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Correspondence to Yves Vigouroux .

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Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB, Canada
Om P. Rajora

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Cubry, P., Vigouroux, Y. (2018). Population Genomics of Crop Domestication: Current State and Perspectives. In: Rajora, O. (eds) Population Genomics. Population Genomics. Springer, Cham. https://doi.org/10.1007/13836_2018_48

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DOI: https://doi.org/10.1007/13836_2018_48
Published: 11 September 2018
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-04587-6
Online ISBN: 978-3-030-04589-0
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