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

Rachel S. Meyer, Jae Young Choi, Michelle Sanches, Anne Plessis, Jonathan Flowers, Junrey Amas, Katherine Dorph, Annie Barretto, Briana Gross, Dorian Q. Fuller, Isaac Kofi Bimpong, Marie Noelle Ndjiondjop, Khaled M. Hazzouri, Glenn B. Gregorio, Michael Purugganan

Research output: Contribution to journalArticle

Abstract

African rice (Oryza glaberrima Steud.) is a cereal crop species closely related to Asian rice (Oryza sativa L.) but was independently domesticated in West Africa ∼3,000 years ago. African rice is rarely grown outside sub-Saharan Africa but is of global interest because of its tolerance to abiotic stresses. Here we describe a map of 2.32 million SNPs of African rice from whole-genome resequencing of 93 landraces. Population genomic analysis shows a population bottleneck in this species that began ∼13,000–15,000 years ago with effective population size reaching its minimum value ∼3,500 years ago, suggesting a protracted period of population size reduction likely commencing with predomestication management and/or cultivation. Genome-wide association studies (GWAS) for six salt tolerance traits identify 11 significant loci, 4 of which are within ∼300 kb of genomic regions that possess signatures of positive selection, suggesting adaptive geographical divergence for salt tolerance in this species.

Original languageEnglish (US)
JournalNature Genetics
DOIs
StateAccepted/In press - Aug 8 2016

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Single Nucleotide Polymorphism
Salt-Tolerance
Population Density
Metagenomics
Western Africa
Africa South of the Sahara
Genome-Wide Association Study
Domestication
Oryza
Genome
Population

ASJC Scopus subject areas

  • Medicine(all)
  • Genetics

Cite this

Domestication history and geographical adaptation inferred from a SNP map of African rice. / Meyer, Rachel S.; Choi, Jae Young; Sanches, Michelle; Plessis, Anne; Flowers, Jonathan; Amas, Junrey; Dorph, Katherine; Barretto, Annie; Gross, Briana; Fuller, Dorian Q.; Bimpong, Isaac Kofi; Ndjiondjop, Marie Noelle; Hazzouri, Khaled M.; Gregorio, Glenn B.; Purugganan, Michael.

In: Nature Genetics, 08.08.2016.

Research output: Contribution to journalArticle

Meyer, RS, Choi, JY, Sanches, M, Plessis, A, Flowers, J, Amas, J, Dorph, K, Barretto, A, Gross, B, Fuller, DQ, Bimpong, IK, Ndjiondjop, MN, Hazzouri, KM, Gregorio, GB & Purugganan, M 2016, 'Domestication history and geographical adaptation inferred from a SNP map of African rice', Nature Genetics. https://doi.org/10.1038/ng.3633
Meyer, Rachel S. ; Choi, Jae Young ; Sanches, Michelle ; Plessis, Anne ; Flowers, Jonathan ; Amas, Junrey ; Dorph, Katherine ; Barretto, Annie ; Gross, Briana ; Fuller, Dorian Q. ; Bimpong, Isaac Kofi ; Ndjiondjop, Marie Noelle ; Hazzouri, Khaled M. ; Gregorio, Glenn B. ; Purugganan, Michael. / Domestication history and geographical adaptation inferred from a SNP map of African rice. In: Nature Genetics. 2016.
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