High-throughput genotyping methods have increased the analytical power to study complex traits but high cost has remained a barrier for large scale use in animal improvement. We have adapted genotyping-by-sequencing (GBS) used in plants for genotyping 47 animals representing 7 taurine and indicine breeds of cattle from the US and Africa. Genomic DNA was digested with different enzymes, ligated to adapters containing one of 48 unique bar codes and sequenced by the Illumina HiSeq 2000. PstI was the best enzyme producing 1.4 million unique reads per animal and initially identifying a total of 63,697 SNPs. After removal of SNPs with call rates of less than 70%, 51,414 SNPs were detected throughout all autosomes with an average distance of 48.1 kb, and 1,143 SNPs on the X chromosome at an average distance of 130.3 kb, as well as 191 on unmapped contigs. If we consider only the SNPs with call rates of 90% and over, we identified 39,751 on autosomes, 850 on the X chromosome and 124 on unmapped contigs. Of these SNPs, 28,843 were not tightly linked to other SNPs. Average marker density per autosome was highly correlated with chromosome size (coefficient of correlation = −0.798, r² = 0.637) with higher density in smaller chromosomes. Average SNP call rate was 86.5% for all loci, with 53.0% of the loci having call rates >90% and the average minor allele frequency being 0.212. Average observed heterozygosity ranged from 0.046–0.294 among individuals, and from 0.064–0.197 among breeds, with Brangus showing the highest diversity as expected. GBS technique is novel, flexible, sufficiently high-throughput, and capable of providing acceptable marker density for genomic selection or genome-wide association studies at roughly one third of the cost of currently available genotyping technologies.

If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (N_e) than from populations with a small N_e. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in seven countries in Africa, South East Asia and South America using a high-density single-nucleotide polymorphism/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500 bp to 59 kb, as well as 10,107 flanking, biallelic single-nucleotide polymorphisms. Overall, CNVs were rare, small, and skewed toward low frequency variants, consistent with the deleterious model. Relative to African and South East Asian populations, CNVs were significantly more common in South America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an F_ST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g., DNA helicase and three conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen.