Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima). Issue 9 (18th April 2014)

• Record Type: Journal Article
• Authors: Nabholz, Benoit; Sarah, Gautier; Sabot, François; Ruiz, Manuel; Adam, Hélène; Nidelet, Sabine; Ghesquière, Alain; Santoni, Sylvain; David, Jacques; Glémin, Sylvain
• Is Part Of: Molecular ecology. Volume 23:Issue 9(2014)
• Page Start: 2210
• Page End: 2227
• Publication Date: 2014-04-18
• Subjects: Molecular ecology -- Periodicals; Molecular population biology -- Periodicals; 576
• DOI: 10.1111/mec.12738
• Languages: English
• ISSNs: 0962-1083

Abstract

<abstract abstract-type="main" id="mec12738-abs-0001"> <title>Abstract</title> <p>The African cultivated rice (<italic>Oryza glaberrima</italic>) was domesticated in West Africa 3000 years ago. Although less cultivated than the Asian rice (<italic>O. sativa</italic>), <italic>O. glaberrima</italic> landraces often display interesting adaptation to rustic environment (e.g. drought). Here, using RNA‐seq technology, we were able to compare more than 12 000 transcripts between 9 <italic>O. glaberrima, </italic> 10 wild <italic>O. barthii</italic> and one <italic>O. meridionalis</italic> individuals. With a synonymous nucleotide diversity π<sub>s</sub> = 0.0006 per site, <italic>O. glaberrima</italic> appears as the least genetically diverse crop grass ever documented. Using approximate Bayesian computation, we estimated that <italic>O. glaberrima</italic> experienced a severe bottleneck during domestication. This demographic scenario almost fully accounts for the pattern of genetic diversity across <italic>O. glaberrima</italic> genome as we detected very few outliers regions where positive selection may have further impacted genetic diversity. Moreover, the large excess of derived nonsynonymous substitution that we detected suggests that the <italic>O. glaberrima</italic> population suffered from the 'cost of domestication'. In addition, we used this genome‐scale data set to demonstrate that (i) <italic>O. barthii</italic> genetic diversity is positively correlated with recombination rate and negatively with gene density, (ii) expression level is negatively correlated with evolutionary constraint, and (iii) one region on chromosome 5 (position 4–6 Mb) exhibits a clear signature of introgression with a yet unidentified <italic>Oryza</italic> species. This work represents the first genome‐wide survey of the African rice genetic diversity and paves the way for further comparison between the African and the Asian rice, notably regarding the genetics underlying domestication traits.</p> </abstract>