Systematic profiling of short tandem repeats in the cattle genome

Liu, George

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309
Systematic profiling of short tandem repeats in the cattle genome

Thursday, July 21, 2016: 11:30 AM

Grand Ballroom I (Salt Palace Convention Center)

George E Liu , Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD

Lingyang Xu , Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD

Ryan Haasl , University of Wisconsin – Platteville, Platteville, WI

Jiajie Sun , South China Agricultural University, Guangzhou, China

Yang Zhou , Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD

Derek M. Bickhart , Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD

JunYa Li , Institute of Animal Science of Chinese Academy of Agricultural Sciences, Beijing, China, Beijing, China

Jiuzhou Song , University of Maryland, Animal Science and Avian, College Park, MD

Tad Sonstegard , Recombinetics, Inc., St Paul, MN

Curt P VanTassell , Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD

Harris Lewin , University of California, Davis, Department of Evolution and Ecology, David, CA

Abstract Text: Short tandem repeats (STRs), or microsatellites (MS), are genetic variants with repetitive 2–6 base pair motifs in many genomes. Using high-throughput sequencing and experimental validations, we systematically profiled STRs in five Holsteins. We identified a total of 60,106 microsatellites and generated the first high-resolution STR map, representing a substantial pool of polymorphism in cattle. We observed significant STR overlaps with RefSeq genes and quantitative trait loci (QTL). We performed evolutionary and population genetic analyses using over 20,000 common dinucleotide STRs. Besides corroborating the well-established positive correlation between allele size and variance in allele size, these analyses also identified dozens of outlier STRs based on two anomalous relationships that counter expected characteristics of neutral evolution. And one STR locus overlaps with a significant region of a summary statistic designed to detect STR-related selection. Additionally, we showed that only 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 tagged by SNPs in the cattle genome, likely due to STR's distinct mutation mechanism and elevated polymorphism. This study provides the foundation for future STR-based studies of cattle genome evolution and selection.

Keywords: cattle genome, short tandem repeat (STR), whole genome sequencing (WGS)

309 Systematic profiling of short tandem repeats in the cattle genome

Meeting Information

309
Systematic profiling of short tandem repeats in the cattle genome