recombinational landscape and population genomics of caenorhabditis elegans人口重组景观和秀丽隐杆线虫的基因组.pdfVIP

Recombinational Landscape and Population Genomics of Caenorhabditis elegans Matthew V. Rockman1,2,3,4*, Leonid Kruglyak 1,2,5* 1 Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America, 2 Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America, 3 Department of Biology, New York University, New York, New York, United States of America, 4 Center for Genomics and Systems Biology, New York University, New York, New York, United States of America, 5 Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America Abstract Recombination rate and linkage disequilibrium, the latter a function of population genomic processes, are the critical parameters for mapping by linkage and association, and their patterns in Caenorhabditis elegans are poorly understood. We performed high-density SNP genotyping on a large panel of recombinant inbred advanced intercross lines (RIAILs) of C. elegans to characterize the landscape of recombination and, on a panel of wild strains, to characterize population genomic patterns. We confirmed that C. elegans autosomes exhibit discrete domains of nearly constant recombination rate, and we show, for the first time, that the pattern holds for the X chromosome as well. The terminal domains of each chromosome, spanning about 7% of the genome, exhibit effectively no recombination. The RIAILs exhibit a 5.3-fold expansion of the genetic map. With median marker spacing of 61 kb, they are a powerful resource for mapping quantitative trait loci in C. elegans. Among 125 wild isolates, we identified only 41 distinct haplotypes. The patterns of genotypic similarity suggest that some presumed wild strains are laboratory contaminants. The Hawaiian strain, CB4856, exhibits genetic isolatio