PMC:4502373 / 10067-11192 JSONTXT

{"project":"2_test","denotations":[{"id":"25931611-19846765-43349741","span":{"begin":229,"end":233},"obj":"19846765"},{"id":"25931611-19930592-43349742","span":{"begin":250,"end":254},"obj":"19930592"},{"id":"25931611-20927341-43349743","span":{"begin":256,"end":260},"obj":"20927341"},{"id":"25931611-17701901-43349744","span":{"begin":408,"end":412},"obj":"17701901"},{"id":"25931611-19846765-43349745","span":{"begin":836,"end":840},"obj":"19846765"},{"id":"25931611-19390634-43349746","span":{"begin":861,"end":865},"obj":"19390634"},{"id":"25931611-19200528-43349747","span":{"begin":976,"end":980},"obj":"19200528"}],"text":"In total, 1106 animals of 55 breeds were genotyped with an Illumina BovineSNP50 chip assay (Supporting Information, Table S1, Table S2). Information regarding DNA samples and SNP genotypes were previously reported (Decker et al. 2009; Gautier et al. 2009, 2010). The duplicate samples across multiple datasets of cattle were identified and removed based on an IBS matrix computed using PLINK (Purcell et al. 2007). The IBS matrix estimates the genetic relationship based on genome-wide SNPs similarity. A quality control was implemented to retain SNPs that can be mapped on UMD3.1 bovine assembly and have minor allele frequency (MAF) ≥0.01 (Table S3). Ancestral and derived allelic phases of these SNPs were determined based on information on several closely related out-group species, including bison, buffalo, and yak (Decker et al. 2009; Matukumalli et al. 2009). Imputation of missing genotypes and haplotype phasing were performed with BEAGLE 3.3 (Browning and Browning 2009). Analyses of signatures of selection for European and African cohorts were performed using polymorphic and phased SNPs within each cattle type."}