While the domestication history of Asian rice has been extensively studied, details of the evolution of African rice remain elusive. The inner Niger delta has been suggested as the center of origin but molecular data to support this hypothesis is lacking. Here, we present a comprehensive analysis of the evolutionary and domestication history of African rice. By analyzing whole genome re-sequencing data from 282 individuals of domesticated African rice Oryza glaberrima and its progenitor O. barthii, we hypothesize a non-centric (i.e. multiregional) domestication origin for African rice. Our analyses showed genetic structure within O. glaberrima that has a geographical association. Furthermore, we have evidence that the previously hypothesized O. barthii progenitor populations in West Africa have evolutionary signatures similar to domesticated rice and carried causal domestication mutations, suggesting those progenitors were either mislabeled or may actually represent feral wild-domesticated hybrids. Phylogeographic analysis of genes involved in the core domestication process suggests that the origins of causal domestication mutations could be traced to wild progenitors in multiple different locations in West and Central Africa. In addition, measurements of panicle threshability, a key early domestication trait for seed shattering, were consistent with the gene phylogeographic results. We suggest seed non-shattering was selected from multiple genotypes, possibly arising from different geographical regions. Based on our evidence, O. glaberrima was not domesticated from a single centric location but was a result of diffuse process where multiple regions contributed key alleles for different domestication traits.
ngsAdmix ancestry proportion
ngsAdmix results estimating ancestry proportions from K=2 to K=9 for all 282 samples.
ngsAdmix.zip
O. rufipogon genome aligned to O. barthii or O. glaberrima
O. rufipogon reference genome sequence was aligned to O. barthii or O. glaberrima reference genome. For every O. barthii or O. glaberrima coordinate was converted into O. rufipogon sequence resulting in a O. barthii-ized or O. glaberrima-ized O. rufipogon genome sequence. Not alignable regions were indicated as 'N'.
Oruf_outgroup_genome.zip
Haplotype Network
Phased vcf file for the genes sh1, sh4, and PROG1 region. Data used to estimate the haplotype network.
HaploNetwork.zip
ngsCovar PCA result
Genotype likelihood based PCA analysis of O. glaberrima population.
ngsCovar.zip
Phylogenomic and phylogenetic tree plotted with iTol
Newick format trees for genome-wide and the 3 domestication genes. Tree can be visualized on iTol (http://itol.embl.de) and colored using the supplied itol file.
ngsDist.zip
Pairwise Fst values
All pairwise genome-wide Fst values calculated using ANGSD.
ANGSD_FST.zip
Theta and related population genetics statistics
Genome-wide theta and related population genetics statistics calculated using ANGSD.
ANGSD_THETA.zip
LD statistics
LD values calculated using PLINK for each genetic group.
r2mean_1000bin.txt
Genotypes surrounding domestication gene
File used to visualize the SNPs (genotypes) surroinding domestication gene of interest.
HAPLOTYPE_VIEW.zip
Binary plink file for silhouette score filtered individuals
Binary plink files used for treemix study. Contains individuals and their SNPs after implementing the silhouette score based filtering.
SilhouetteScoreFilteredGroup.zip
Filtered VCF file used in study (chr1) - glaberrima as reference genome
O. glaberrima reference genome based SNP calls. Filtering process described in paper.
chr1.final.recode.vcf.gz
Filtered VCF file used in study (chr2) - glaberrima as reference genome
O. glaberrima reference genome based SNP calls. Filtering process described in paper.
chr2.final.recode.vcf.gz
Filtered VCF file used in study (chr3) - glaberrima as reference genome
O. glaberrima reference genome based SNP calls. Filtering process described in paper.
chr3.final.recode.vcf.gz
Filtered VCF file used in study (chr4) - glaberrima as reference genome
O. glaberrima reference genome based SNP calls. Filtering process described in paper.
chr4.final.recode.vcf.gz
Filtered VCF file used in study (chr5) - glaberrima as reference genome
O. glaberrima reference genome based SNP calls. Filtering process described in paper.
chr5.final.recode.vcf.gz
Filtered VCF file used in study (chr6) - glaberrima as reference genome
O. glaberrima reference genome based SNP calls. Filtering process described in paper.
chr6.final.recode.vcf.gz
Filtered VCF file used in study (chr7) - glaberrima as reference genome
O. glaberrima reference genome based SNP calls. Filtering process described in paper.
chr7.final.recode.vcf.gz
Filtered VCF file used in study (chr8) - glaberrima as reference genome
O. glaberrima reference genome based SNP calls. Filtering process described in paper.
chr8.final.recode.vcf.gz
Filtered VCF file used in study (chr9) - glaberrima as reference genome
O. glaberrima reference genome based SNP calls. Filtering process described in paper.
chr9.final.recode.vcf.gz
Filtered VCF file used in study (chr10) - glaberrima as reference genome
O. glaberrima reference genome based SNP calls. Filtering process described in paper.
chr10.final.recode.vcf.gz
Filtered VCF file used in study (chr11) - glaberrima as reference genome
O. glaberrima reference genome based SNP calls. Filtering process described in paper.
chr11.final.recode.vcf.gz
Filtered VCF file used in study (chr12) - glaberrima as reference genome
O. glaberrima reference genome based SNP calls. Filtering process described in paper.
chr12.final.recode.vcf.gz
Filtered VCF file used in study (chr1) - barthii as reference genome
O. barthii reference genome based SNP calls. Filtering process described in paper.
chr1.final.recode.vcf.gz
Filtered VCF file used in study (chr2) - barthii as reference genome
O. barthii reference genome based SNP calls. Filtering process described in paper.
chr2.final.recode.vcf.gz
Filtered VCF file used in study (chr3) - barthii as reference genome
O. barthii reference genome based SNP calls. Filtering process described in paper.
chr3.final.recode.vcf.gz
Filtered VCF file used in study (chr4) - barthii as reference genome
O. barthii reference genome based SNP calls. Filtering process described in paper.
chr4.final.recode.vcf.gz
Filtered VCF file used in study (chr5) - barthii as reference genome
O. barthii reference genome based SNP calls. Filtering process described in paper.
chr5.final.recode.vcf.gz
Filtered VCF file used in study (chr6) - barthii as reference genome
O. barthii reference genome based SNP calls. Filtering process described in paper.
chr6.final.recode.vcf.gz
Filtered VCF file used in study (chr7) - barthii as reference genome
O. barthii reference genome based SNP calls. Filtering process described in paper.
chr7.final.recode.vcf.gz
Filtered VCF file used in study (chr8) - barthii as reference genome
O. barthii reference genome based SNP calls. Filtering process described in paper.
chr8.final.recode.vcf.gz
Filtered VCF file used in study (chr9) - barthii as reference genome
O. barthii reference genome based SNP calls. Filtering process described in paper.
chr9.final.recode.vcf.gz
Filtered VCF file used in study (chr10) - barthii as reference genome
O. barthii reference genome based SNP calls. Filtering process described in paper.
chr10.final.recode.vcf.gz
Filtered VCF file used in study (chr11) - barthii as reference genome
O. barthii reference genome based SNP calls. Filtering process described in paper.
chr11.final.recode.vcf.gz
Filtered VCF file used in study (chr12) - barthii as reference genome
O. barthii reference genome based SNP calls. Filtering process described in paper.
chr12.final.recode.vcf.gz