TY - JOUR
T1 - The rice paradox
T2 - Multiple origins but single domestication in Asian Rice
AU - Choi, Jae Young
AU - Platts, Adrian E.
AU - Fuller, Dorian Q.
AU - Hsing, Yue Ie
AU - Wing, Rod A.
AU - Purugganan, Michael D.
AU - Kim, Yuseob
N1 - Publisher Copyright:
© The Author 2017.
PY - 2017/4/1
Y1 - 2017/4/1
N2 - The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara. Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O. rufipogon was O. sativa ssp. japonica, occurring at ∼13.1-24.1 ka, which is an order of magnitude older then the earliest archeological date of domestication. This date is consistent, however, with the expansion of O. rufipogon populations after the Last Glacial Maximum ∼18 ka and archeological evidence for early wild rice management in China. We also show that there is significant gene flow from japonica to both indica (∼17%) and aus (∼15%), which led to the transfer of domestication alleles from early-domesticated japonica to proto-indica and proto-aus populations. Our results provide support for a model in which different rice subspecies had separate origins, but that de novo domestication occurred only once, in O. sativa ssp. japonica, and introgressive hybridization from early japonica to proto-indica and proto-aus led to domesticated 'md'ica and aus rice.
AB - The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara. Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O. rufipogon was O. sativa ssp. japonica, occurring at ∼13.1-24.1 ka, which is an order of magnitude older then the earliest archeological date of domestication. This date is consistent, however, with the expansion of O. rufipogon populations after the Last Glacial Maximum ∼18 ka and archeological evidence for early wild rice management in China. We also show that there is significant gene flow from japonica to both indica (∼17%) and aus (∼15%), which led to the transfer of domestication alleles from early-domesticated japonica to proto-indica and proto-aus populations. Our results provide support for a model in which different rice subspecies had separate origins, but that de novo domestication occurred only once, in O. sativa ssp. japonica, and introgressive hybridization from early japonica to proto-indica and proto-aus led to domesticated 'md'ica and aus rice.
KW - Adaptation
KW - Crop species
KW - Gene flow
KW - Introgressive hybridization
UR - http://www.scopus.com/inward/record.url?scp=85018527934&partnerID=8YFLogxK
U2 - 10.1093/molbev/msx049
DO - 10.1093/molbev/msx049
M3 - Article
C2 - 28087768
AN - SCOPUS:85018527934
SN - 0737-4038
VL - 34
SP - 969
EP - 979
JO - Molecular Biology and Evolution
JF - Molecular Biology and Evolution
IS - 4
ER -