|XU, LINGYANG - CHINESE ACADEMY OF AGRICULTURAL SCIENCES|
|HAASL, RYAN - UNIVERSITY OF WISCONSIN|
|SUN, JIAJIE - SOUTH CHINA AGRICULTURAL UNIVERSITY|
|ZHOU, YANG - NORTHWEST AGRICULTURAL & FORESTRY UNIVERSITY|
|SON, JIUZHOU - UNIVERSITY OF MARYLAND|
|Van Tassell, Curtis - Curt|
|LWEIN, HARRIS - UNIVERSITY OF CALIFORNIA|
|Liu, Ge - George|
Submitted to: Genome Biology and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/21/2016
Publication Date: 10/24/2016
Citation: Xu, L., Haasl, R.J., Sun, J., Zhou, Y., Bickhart, D.M., Son, J., Van Tassell, C.P., Lwein, H.A., Liu, G. 2016. Systematic profiling of bovine short tandem repeats using whole genome sequencing data. Genome Biology and Evolution. 9(1):20-31.
Interpretive Summary: Short tandem repeats (STRs), or microsatellites, are genetic variants underlying quantitaitve trait locus (QTL) mapping in animal genomes. Using whole genome sequencing data, we systematically identified STRs and studied their population genetic properties in cattle. These results fill our knowledge gaps and provide the foundation for future studies of STR's functional role in genome evolution and selection. Farmers, scientist, and policy planners who need improve animal health and production based on genome-enable animal selection will benefit from this study.
Technical Abstract: Short tandem repeats (STRs), or microsatellites, are genetic variants with repetitive motifs of 2–6 base pairs that are abundant in the genomes of pro- and eukaryotic organisms. Using the program lobSTR and whole genome sequencing data, we systematically profiled STR variation in five Holstein cattle. We identified a total of 60,106 microsatellites and generated the first high-resolution STR map in cattle. We observed significant overlaps between STRs and RefSeq genes and between STRs and quantitative trait loci (QTL), revealing STR's potential contributions to phenotypic diversity. We performed preliminary population genetic analysis using the genotypes for over 20,000 dinucleotide microsatellites shared by all five cattle. Our results corroborate the well-established positive correlation between allele size and variance in allele size. However, we also identified dozens of outlier loci based on two anomalous relationships that counter expected characteristics of neutral microsatellite variation. In addition, one STR locus overlaps with a significant region of a summary statistics designed to detect STR-related selection. Moreover, we found that 57.1% of STRs are located within SNP-based linkage disequilibrium (LD) blocks while the other 42.9% are not. Therefore, a substantial number of STRs are not covered by SNPs in the cattle genome, likely due to STR's distinct mutation mechanism and elevated polymorphism. We conclude that STRs represent a substantial pool of polymorphism in the cattle genome, which in some cases may underlie phenotype. This study provides the foundation for future studies of STR's role in cattle genome evolution and selection.