Genome-wide patterns of nucleotide polymorphism in domesticated rice. Export

@article{citeulike:6097411, abstract = {Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models to explain contemporary patterns of polymorphisms in rice, including a (i) selectively neutral population bottleneck model, (ii) bottleneck plus migration model, (iii) multiple selective sweeps model, and (iv) bottleneck plus selective sweeps model. We find that a simple bottleneck model, which has been the dominant demographic model for domesticated species, cannot explain the derived nucleotide polymorphism site frequency spectrum in rice. Instead, a bottleneck model that incorporates selective sweeps, or a more complex demographic model that includes subdivision and gene flow, are more plausible explanations for patterns of variation in domesticated rice varieties. If selective sweeps are indeed the explanation for the observed nucleotide data of domesticated rice, it suggests that strong selection can leave its imprint on genome-wide polymorphism patterns, contrary to expectations that selection results only in a local signature of variation.}, author = {Caicedo, Ana L. and Williamson, Scott H. and Hernandez, Ryan D. and Boyko, Adam and Fledel-Alon, Adi and York, Thomas L. and Polato, Nicholas R. and Olsen, Kenneth M. and Nielsen, Rasmus and McCouch, Susan R. and Bustamante, Carlos D. and Purugganan, Michael D.}, citeulike-article-id = {6097411}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pgen.0030163}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17907810}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17907810}, doi = {10.1371/journal.pgen.0030163}, issn = {1553-7404}, journal = {PLoS genetics}, keywords = {domestication, genetics, population, rice}, month = {September}, number = {9}, pages = {1745--1756}, posted-at = {2009-11-11 11:33:22}, priority = {2}, title = {Genome-wide patterns of nucleotide polymorphism in domesticated rice.}, url = {http://dx.doi.org/10.1371/journal.pgen.0030163}, volume = {3}, year = {2007} }

TY - JOUR ID - citeulike:6097411 L3 - citeulike-article-id:6097411 N2 - Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models to explain contemporary patterns of polymorphisms in rice, including a (i) selectively neutral population bottleneck model, (ii) bottleneck plus migration model, (iii) multiple selective sweeps model, and (iv) bottleneck plus selective sweeps model. We find that a simple bottleneck model, which has been the dominant demographic model for domesticated species, cannot explain the derived nucleotide polymorphism site frequency spectrum in rice. Instead, a bottleneck model that incorporates selective sweeps, or a more complex demographic model that includes subdivision and gene flow, are more plausible explanations for patterns of variation in domesticated rice varieties. If selective sweeps are indeed the explanation for the observed nucleotide data of domesticated rice, it suggests that strong selection can leave its imprint on genome-wide polymorphism patterns, contrary to expectations that selection results only in a local signature of variation. IS - 9 JF - PLoS genetics SN - 1553-7404 EP - 1756 TI - Genome-wide patterns of nucleotide polymorphism in domesticated rice. VL - 3 SP - 1745 KW - domestication KW - genetics KW - population KW - rice AU - Caicedo, Ana AU - Williamson, Scott AU - Hernandez, Ryan AU - Boyko, Adam AU - Fledel-Alon, Adi AU - York, Thomas AU - Polato, Nicholas AU - Olsen, Kenneth AU - Nielsen, Rasmus AU - McCouch, Susan AU - Bustamante, Carlos AU - Purugganan, Michael PY - 2007/09// UR - http://dx.doi.org/10.1371/journal.pgen.0030163 ER -