Domestication history and geographical adaptation inferred from a SNP map of African rice

Nature Genetics

Volumn 48, Issue 9, 2016, Pages 1083-1088

  Meyer, Rachel S ^a,b   Choi, Jae Young ^a   Sanches, Michelle ^a   Plessis, Anne ^a   Flowers, Jonathan M ^a,b   Amas, Junrey ^c   Dorph, Katherine ^a   Barretto, Annie ^c   Gross, Briana ^d   Fuller, Dorian Q ^e   Bimpong, Isaac Kofi ^f   Ndjiondjop, Marie Noelle ^g   Hazzouri, Khaled M ^b   Gregorio, Glenn B ^c   Purugganan, Michael D ^a,b  

^a NEW YORK UNIVERSITY   (United States)

^b NEW YORK UNIVERSITY ABU DHABI   (United Arab Emirates)

^c INTERNATIONAL RICE RESEARCH INSTITUTE   (Philippines)

^d UNIVERSITY OF MINNESOTA DULUTH   (United States)

^e UNIVERSITY COLLEGE LONDON   (United Kingdom)

^f Centre du riz pour l'Afrique Senegal   (Senegal)

^g AFRICA RICE CENTER AFRICARICE   (Benin)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; AFRICAN; ARTICLE; BOTTLENECK POPULATION; CONTROLLED STUDY; DOMESTICATION; EFFECTIVE POPULATION SIZE; GENE EXPRESSION; GENE SEQUENCE; GENETIC DISTANCE; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; GEOGRAPHICAL VARIATION (SPECIES); LANDRACE; NONHUMAN; ORYZA GLABERRIMA; PHENOTYPIC VARIATION; PLANT CHROMOSOME; PLANT GENETICS; PLANT GENOME; PLANT SEED; POPULATION SIZE; POPULATION STRUCTURE; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; RICE; SALT STRESS; SALT TOLERANCE; SEEDLING; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES CULTIVATION; ACCLIMATIZATION; CROP; GENETICS; GEOGRAPHY; ORYZA; PLANT GENE; POPULATION GENETICS;

ACCLIMATIZATION; CROPS, AGRICULTURAL; DOMESTICATION; GENES, PLANT; GENETICS, POPULATION; GENOME, PLANT; GENOME-WIDE ASSOCIATION STUDY; GEOGRAPHY; ORYZA; POLYMORPHISM, SINGLE NUCLEOTIDE; SALT-TOLERANCE;

EID: 84981287712     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3633     Document Type: Article

References (67)

1. Carney, J.A. Black Rice: The African Origins of Rice Cultivation in the Americas (Harvard University Press, 2002).
2. Linares, O.F. African rice (Oryza glaberrima): history and future potential. Proc. Natl. Acad. Sci. USA 99, 16360-16365 (2002).
3. Wang, M. et al. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat. Genet. 46, 982-988 (2014).
4. Sarla, N. & Mallikarjuna, S.B.P. Oryza glaberrima: a source for improvement of Oryza sativa. Curr. Sci. 89, 955-963 (2005).
5. Agnoun, A. et al. The African rice Oryza glaberrima Steud: knowledge distribution and prospects. Int. J. Biol. 4, 158-180 (2012).
6. Price, A.L. et al. Principal components analysis corrects for stratifcation in genome-wide association studies. Nat. Genet. 38, 904-909 (2006).
7. Kahle, D. & Wickham, H. ggmap: spatial visualization with ggplot2. R J. 5, 144-161 (2013).
8. Falush, D., Stephens, M. & Pritchard, J.K. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164, 1567-1587 (2003).
9. Portères, R. in Papers in African Prehistory (eds. Fage, J.D. & Oliver, R.A.) 43-58 (Cambridge University Press, 1970).
10. Portères, R. in Origins of African Plant Domestication (eds. Harlan, J.R., De Wet, J.M. & Stemler, A.B.) 409-452 (Mouton, 1976).
11. Pickrell, J.K. & Pritchard, J.K. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967 (2012).
12. Tenaillon, M.I., U'Ren, J., Tenaillon, O. & Gaut, B.S. Selection versus demography: a multilocus investigation of the domestication process in maize. Mol. Biol. Evol. 21, 1214-1225 (2004).
13. Caicedo, A.L. et al. Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet. 3, 1745-1756 (2007).
14. Schiffels, S. & Durbin, R. Inferring human population size and separation history from multiple genome sequences. Nat. Genet. 46, 919-925 (2014).
15. Thomas, C.G. et al. Full-genome evolutionary histories of selfng, splitting, and selection in Caenorhabditis. Genome Res. 25, 667-678 (2015).
16. Nabholz, B. et al. Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima). Mol. Ecol. 23, 2210-2227 (2014).
17. Eyre-Walker, A., Gaut, R.L., Hilton, H., Feldman, D.L. & Gaut, B.S. Investigation of the bottleneck leading to the domestication of maize. Proc. Natl. Acad. Sci. USA 95, 4441-4446 (1998).
18. Hyten, D.L. et al. Impacts of genetic bottlenecks on soybean genome diversity. Proc. Natl. Acad. Sci. USA 103, 16666-16671 (2006).
19. Zhu, Q., Zheng, X., Luo, J., Gaut, B.S. & Ge, S. Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol. Biol. Evol. 24, 875-888 (2007).
20. Tjallingii, R. et al. Coherent high-and low-latitude control of the northwest African hydrological balance. Nat. Geosci. 1, 670-675 (2008).
21. Manning, K. & Timpson, A. The demographic response to Holocene climate change in the Sahara. Quat. Sci. Rev. 101, 28-35 (2014).
22. Murray, S.S. in Fields of Change: Progress in African Archaeobotany (ed. Cappers, R.T.J.) 53-62 (Barkhuis, 2007).
23. Zach, B. & Klee, M. Four thousand years of plant exploitation in the Chad Basin of NE Nigeria. II: Discussion on the morphology of caryopses of domesticated Pennisetum and complete catalog of the fruits and seeds of Kursakata. Veg. Hist. Archaeobot. 12, 187-204 (2003).
24. Fuller, D.Q., Nixon, S., Stevens, C.J. & Murray, M.A. in The Archaeology of African Plant Use (eds. Stevens, C., Nixon, S., Murray, M.A. & Fuller, D.Q.) 17-24 (Left Coast Press, 2014).
25. Eichhorn, B. & Neumann, K. in Archaeology of African Plant Use (eds. Stevens, C., Nixon, S., Murray, M.A. & Fuller, D.Q.) (Left Coast Press, 2014).
26. Temudo, M. Planting knowledge, harvesting agro-biodiversity: a case study of Southern Guinea-Bissau rice farming. Hum. Ecol. 39, 301-321 (2011).
27. Carney, J.A. Landscapes of technology transfer: rice cultivation and African continuities. Technol. Cult. 37, 5-35 (1996).
28. International Rice Research Institute. Standard Evaluation System for Rice (International Rice Research Institute, 2014).
29. Matlon, P., Randolph, T. & Guei, R. in Impact of Rice Research (eds. Pingali, P.B. & Hossain, M.) 382-404 (International Rice Research Institute, 1998).
30. Huang, X. et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat. Genet. 42, 961-967 (2010).
31. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575 (2007).
32. Kang, H.M. et al. Variance component model to account for sample structure in genome-wide association studies. Nat. Genet. 42, 348-354 (2010).
33. Yang, T. et al. The role of a potassium transporter OsHAK5 in potassium acquisition and transport from roots to shoots in rice at low potassium supply levels. Plant Physiol. 166, 945-959 (2014).
34. Horie, T. et al. Rice sodium-insensitive potassium transporter, OsHAK5, confers increased salt tolerance in tobacco BY2 cells. J. Biosci. Bioeng. 111, 346-356 (2011).
35. Chen, H., Patterson, N. & Reich, D. Population differentiation as a test for selective sweeps. Genome Res. 20, 393-402 (2010).
36. Weir, B.S. & Cockerham, C.C. Estimating F-statistics for the analysis of population structure. Evolution 38, 1358-1370 (1984).
37. Lewontin, R.C. & Krakauer, J. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74, 175-195 (1973).
38. Sahi, C., Singh, A., Blumwald, E. & Grover, A. Beyond osmolytes and transporters: novel plant salt-stress tolerance-related genes from transcriptional profling data. Physiol. Plant. 127, 1-9 (2006).
39. Ruan, S.L. et al. Proteomic identifcation of OsCYP2, a rice cyclophilin that confers salt tolerance in rice (Oryza sativa L.) seedlings when overexpressed. BMC Plant Biol. 11, 34 (2011).
40. Allaby, R.G., Fuller, D.Q. & Brown, T.A. The genetic expectations of a protracted model for the origins of domesticated crops. Proc. Natl. Acad. Sci. USA 105, 13982-13986 (2008).
41. Fuller, D.Q. Contrasting patterns in crop domestication and domestication rates: recent archaeobotanical insights from the Old World. Ann. Bot. 100, 903-924 (2007).
42. Wilcox, G. in Biodiversity in Agriculture: Domestication, Evolution, and Sustainability (eds. Gepts, P. et al.) 92-109 (Cambridge University Press, 2012).
43. DePristo, M.A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011).
44. McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
45. Flowers, J.M. et al. Whole-genome resequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii. Plant Cell 27, 2353-2369 (2015).
46. Hazzouri, K.M. et al. Whole genome re-sequencing of date palms yields insights into diversifcation of a fruit tree crop. Nat. Commun. 6, 8824 (2015).
47. 1118; iso-2; iso-3. Fly (Austin) 6, 80-92 (2012).
48. Korneliussen, T.S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinformatics 15, 356 (2014).
49. Earl, D.A. & vonHoldt, B.M. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4, 359-361 (2012).
50. Jakobsson, M. & Rosenberg, N.A. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23, 1801-1806 (2007).
51. Rosenberg, N. Distruct: a program for the graphical display of population structure. Mol. Ecol. Notes 4, 137-138 (2004).
52. Gronau, I., Hubisz, M.J., Gulko, B., Danko, C.G. & Siepel, A. Bayesian inference of ancient human demography from individual genome sequences. Nat. Genet. 43, 1031-1034 (2011).
53. Tamura, K. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739 (2011).
54. Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
55. Gaut, B.S., Morton, B.R., McCaig, B.C. & Clegg, M.T. Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc. Natl. Acad. Sci. USA 93, 10274-10279 (1996).
56. Pearson, G., Ayers, S. & Eberhard, D. Relative salt tolerance of rice during germination and early seedling development. Soil Sci. 102, 151-156 (1966).
57. Gregorio, G.B., Senadhira, D. & Mendoza, R.D. Screening Rice for Salinity Tolerance IRRI Discussion Paper Series 22 (IRRI, 1997).
58. + exclusion and allele mining of HKT1;5 in Oryza sativa and O. glaberrima: many sources, many genes, one mechanism? BMC Plant Biol. 13, 32 (2013).
59. R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2015).
60. Wu, J. et al. Physical maps and recombination frequency of six rice chromosomes. Plant J. 36, 720-730 (2003).
61. Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156-2158 (2011).
62. Turner, S.D. qqman: an R package for visualizing GWAS results using QQ and Manhattan plots. Preprint at bioRxiv http://dx.doi.org/10.1101/005165 (2014).
63. Kersey, P.J. et al. Ensembl Genomes 2016: more genomes, more complexity. Nucleic Acids Res. 44 D1, D574-D580 (2016).
64. Untergasser, A. et al. Primer3-new capabilities and interfaces. Nucleic Acids Res. 40, e115 (2012).
65. Thornton, B. & Basu, C. Real-time PCR (qPCR) primer design using free online software. Biochem. Mol. Biol. Educ. 39, 145-154 (2011).
66. Fischer, G. et al. Global Agro-ecological Zones Assessment for Agriculture (IASA and FAO, 2008).
67. Fritz, S. et al. Cropland for sub-Saharan Africa: a synergistic approach using fve land cover data sets. Geophys. Res. Lett. 38, L04404 (2011).