genome-wide patterns of nucleotide polymorphism in domesticated rice在驯化水稻全基因组核苷酸多态性模式.pdfVIP

Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice 1[¤a 2[ 2 2 2¤b 2 Ana L. Caicedo , Scott H. Williamson , Ryan D. Hernandez , Adam Boyko , Adi Fledel-Alon , Thomas L. York , 3 1¤c 2¤d 3 2* Nicholas R. Polato , Kenneth M. Olsen , Rasmus Nielsen , Susan R. McCouch , Carlos D. Bustamante , Michael D. Purugganan1,4,5* 1 Department of Genetics, North Carolina State University, Raleigh, North Carolina, United States of America, 2 Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America, 3 Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America, 4 Department of Biology, New York University, New York, New York, United States of America, 5 Center for Comparative Functional Genomics, New York University, New York, New York, United States of America 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