Recombination maps for Latino populations based on ancestry inference. S. Shringarpure1, D. Wegmann2, C. Gignoux1, B. Maples1, A. Ferrer-Admetlla2, A. Moreno-Estrada1, K. Sandoval1, C. Eng3, S. Huntsman3, A. Ko4,5, T. Tusie-Luna6,7, C. Aguilar-Salinas6, P. Pajukanta4,5, D. Torgerson3, E. Burchard3, J. Below8, B. Pasaniuc4, S. Gravel10, J. Novembre9, C. Bustamante1 1) Genetics Department, Stanford University, Stanford, CA, USA; 2) Department of Biology, University of Fribourg, Fribourg, Switzerland,; 3) Bioengineering, University of California, San Francisco, San Francisco, CA, USA; 4) Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA; 5) Molecular Biology Institute, UCLA, Los Angeles, USA; 6) Instituto Nacional de Ciencias Médicas y Nutrición, Salvador Zubiran,Mexico City, Mexico; 7) Instituto de Investigaciones Biomédicas de la UNAM, Mexico City, Mexico; 8) School of Public Health, University of Texas, Houston, TX, USA; 9) Department of Human Genetics, University of Chicago, Chicago, IL, USA; 10) Human Genetics, McGill University, Montreal, Canada.

   Accurate estimation of recombination rates is important for studying recombination and its effect on genetic variation. We construct the largest high-resolution recombination map for Latino populations from more than 12,000 individuals of Mexican and Puerto Rican ancestry. Our recombination map inference leverages the recent admixture of African, European and Native American ancestries in the Americas to detect approximately 7.5 million recombination events. At coarse scales, the Latino recombination map correlates well with the European and African recombination maps (r2=0.95 with the HapMap CEU map and 0.85 with the HapMap YRI genetic map at the 1 Mb scale) but shows considerable differentiation at fine scales (r2=0.34 with the CEU map and r2=0.39 with the YRI map at the 10 kb scale). Using estimates of average admixture proportions from the source populations and the European and African recombination maps, we also infer a recombination map specific to Native American populations. In addition, we also construct population-specific recombination maps for Mexicans and Puerto Ricans to study the effect of different Native American ancestral contributions to these populations. Our results provide a useful resource for studying recombination and genetic variation in Latinos and Native Americans.

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