An extensive analysis of the African rice genetic diversity through a global genotyping

Theoretical and Applied Genetics

Volumn 127, Issue 10, 2014, Pages 2211-2223

  Orjuela, Julie ^a   Sabot, François ^a   Chéron, Sophie ^a   Vigouroux, Yves ^a   Adam, Hélène ^a   Chrestin, Harold ^a   Sanni, Kayode ^b,c   Lorieux, Mathias ^a   Ghesquière, Alain ^a  

^a University of Montpellier 2   (France)

^b AFRICA RICE CENTER AFRICARICE   (Benin)

^c AATF   (Kenya)

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; GEOGRAPHICAL DISTRIBUTION;

AFRICAN RICE; BIOTIC STRESS; DIVERSE SPECIES; GENETIC DIVERSITY; GENOTYPING; GEOGRAPHIC ORIGINS; KEY MESSAGE; MISCLASSIFICATIONS;

POPULATION STATISTICS;

PLANT DNA;

AFRICA; CLASSIFICATION; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; GENOTYPE; GEOGRAPHY; HYBRIDIZATION; POPULATION GENETICS; RICE; SINGLE NUCLEOTIDE POLYMORPHISM;

AFRICA; DNA, PLANT; GENETIC VARIATION; GENETICS, POPULATION; GENOTYPE; GEOGRAPHY; HYBRIDIZATION, GENETIC; ORYZA SATIVA; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 84929516845     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-014-2374-z     Document Type: Article

References (41)

1. Albar L, Ndjiondjop M-N, Esshak Z, Berger A, Pinel A, Jones M et al (2003) Fine genetic mapping of a gene required for Rice yellow mottle virus cell-to-cell movement. Theor Appl Genet 107:371–378
2. Barry MB, Pham JL, Noyer JL, Billot C, Courtois B, Ahmadi N (2007) Genetic diversity of the two cultivated rice species (O. sativa & O. glaberrima) in Maritime Guinea. Evidence for interspecific recombination. Euphytica 154:127–137
3. Bezançon G (1993) Le riz cultivé d’origine Africaine Oryza glaberrima Steud, et les formes sauvages et adventices apparentées: diversité, relations génétiques et domestication
4. Billot C, Droc G, Courtois B, Farouk A, Ahmadi N, Clément G et al (2007) HaplOryza—SNP analysis of the genetic diversity along the rice genome. http://www.generationcp.org/communications/programme-publications/project-briefs/doc_download/78-2006-executive-summaries
5. Dramé KN, Sanchez I, Gregorio G, Ndjiondjop M-N (2011) Suitability of a selected set of simple sequence repeats (SSR) markers for multiplexing and rapid molecular characterization of African rice (Oryzaglaberrima Steud.). Afr J Biotechnol 10:6675–6685
6. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620
7. Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolut Bioinform Online 1:47–50
8. Garavito A, Guyot R, Lozano J, Gavory F, Samain S, Panaud O et al (2010) A genetic model for the female sterility barrier between Asian and African cultivated rice species. Genetics 185:1425–1440
9. Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryzasativa L. Genetics 169:1631–1638
10. Glaszmann JC (1988) Geographic pattern of variation among Asian native rice cultivars (Oryza sativa L.) based on fifteen isozyme loci. Genome 30(5):782–792
11. Gridley HE, Jones MP, Wopereis-Pura M (2002) Development of new rice for Africa (NERICA) and participatory varietal selection. In: Breeding rainfed rice for drought-prone environments: integrating conventional and participatory plant breeding in South and Southeast Asia: proceedings of a DFID Plant Sciences Research Programme/IRRI Conference, pp 12–15
12. Gutiérrez AG, Carabalí SJ, Giraldo OX, Martínez CP, Correa F, Prado G et al (2010) Identification of a Rice stripe necrosis virus resistance locus and yield component QTLs using Oryzasativa × O. glaberrima introgression lines. BMC Plant Biol 10:6
13. He Z, Zhai W, Wen H, Tang T, Wang Y, Lu X et al (2011) Two evolutionary histories in the genome of rice: the roles of domestication genes. PLoS Genet 7:e1002100
14. Huang P, Molina J, Flowers JM, Rubinstein S, Jackson SA, Purugganan MD et al (2012) Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view. Mol Ecol 21:4593–4604
15. Li H, Durbin R (2009) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760
16. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N et al (2009) The sequence alignment/Map format and SAMtools. Bioinformatics 25:2078–2079
17. Li Z-M, Zheng X-M, Ge S (2011) Genetic diversity and domestication history of African rice (Oryzaglaberrima) as inferred from multiple gene sequences. Theor Appl Genet 123:21–31
18. Linares OF (2002) African rice (Oryzaglaberrima): history and future potential. Proc Natl Acad Sci 99:16360–16365
19. Liu Q, Guo Y, Li J, Long J, Zhang B, Shyr Y (2012) Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data. BMC Genom 13:S8
20. Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA 101:12404–12410
21. Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10–12
22. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A et al (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303
23. Milne I, Shaw P, Stephen G, Bayer M, Cardle L, Thomas WTB et al (2010) Flapjack–graphical genotype visualization. Bioinformatics 26:3133–3134
24. Murray SS (2004) Searching for the origins of African rice domestication. Antiquity 78
25. Nabholz B, Sarah G, Sabot F, Ruiz M, Adam H, Nidelet S, Ghesquière A, Santoni S, David J, Glemin S (2014) Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (O. glaberrima). Mol Ecol. doi:10.1111/mec.12738
26. Nuijten E, van Treuren R, Struik PC, Mokuwa A, Okry F, Teeken B et al (2009) Evidence for the emergence of new rice types of interspecific hybrid origin in West African farmers’ fields. PLoS ONE 4:e7335
27. Orjuela J, Thiémélé D, Kolade O, Chéron S, Ghesquière A, Albar L (2013) A recessive resistance to Rice yellow mottle virus is associated with a rice homolog of the CPR5 gene, a regulator of active defence mechanisms. Mol Plant Microbe Interact 26(12):1455–1463
28. Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Genetic diversity of cultivated tropical plants, pp 43–76
29. Portères R (1962) Primary cradles of agriculture in the African continent. J Afr Hist 3:195–210
30. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
31. Rousset F, Raymond M (1995) Testing heterozygote excess and deficiency. Genetics 140:1413–1419
32. Sano Y (1990) The genic nature of gamete eliminator in rice. Genetics 125:183–191
33. Second G (1982) Origin of the genic diversity of cultivated rice (Oryza spp.): study of the polymorphism scored at 40 isozyme loci. Jpn J Genet 57:25–57
34. Semon M, Nielsen R, Jones MP, McCouch SR (2005) The population structure of African cultivated rice Oryza glaberrima (Steud.): evidence for elevated levels of linkage disequilibrium caused by admixture with O. sativa and ecological adaptation. Genetics 169:1639–1647
35. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
36. Thiémélé D, Boisnard A, Ndjiondjop M-N, Chéron S, Séré Y, Aké S et al (2010) Identification of a second major resistance gene to Rice yellow mottle virus, RYMV2, in the African cultivated rice species, O. glaberrima. Theor Appl Genet 121:169–179
37. Thomson MJ, Zhao K, Wright M, McNally KL, Rey J, Tung C-W et al (2011) High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform. Mol Breed 29:875–886
38. Vaughan DA, Kadowaki K, Kaga A, Tomooka N (2005) On the phylogeny and biogeography of the genus oryza. Breed Sci 55:113–122
39. Vaughan DA, Lu B-R, Tomooka N (2008) The evolving story of rice evolution. Plant Sci 174:394–408
40. Zhao K, Tung C-W, Eizenga GC, Wright MH, Ali ML, Price AH et al (2011) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2:467
41. Zhu Q, Zheng X, Luo J, Gaut BS, Ge S (2007) Multilocus analysis of nucleotide variation of Oryzasativa and its wild relatives: severe bottleneck during domestication of rice. Mol Biol Evol 24:875–888