Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level

Short tandem repeats (STRs), or microsatellites, are genetic variants with repetitive 2–6 base pair motifs in many mammalian 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 dairy cattle. We observed significant STRs overlap with functional 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, our results showed that only 57.1% of STRs located within SNP-based linkage disequilibrium (LD) blocks whereas the other 42.9% were out of blocks. 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.

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“…2011; Lee et al. 2013); KLHL1 is involved in poor sperm motility in Holstein–Friesian bulls (Shin et al. 2014; Hering et al.…”

Section: Resultsmentioning

confidence: 99%

Systematic profiling of short tandem repeats in the cattle genome

Haasl

Sun

et al. 2016

Genome Biol Evol

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“…Hanwoo cattle, having been bred primarily for beef production, exhibit breed‐specific CNVs covering a number of genes, such as Rho GTPase activating protein 10 ( ARHGAP10 ) , AT‐rich interactive domain 2 ( ARID2 ), Ca++‐dependent secretion activator 2 ( CADPS2 ), cadherin‐related 23 ( CDH23 ), GRB2‐associated binding protein 1 ( GAB1 ), leucine‐rich repeat kinase 2 ( LRRK2 ) and mitogen‐activated protein kinase kinase kinase kinase 3 ( MAP4K3 ), which are involved in neuromuscular development and protein modification pathways that are important for muscle development and hence beef production (Shin et al . ). Biological processes, metabolic functions, cellular components and proteins that may play a role in tropical adaptation and have been reported as being significantly over‐represented by CNV genes identified in cattle are shown in Table .…”

Section: Copy Number Variationsmentioning

confidence: 97%

“…Shin et al . () reported 23 genes involved in nervous transmission, neuron motion and neurogenesis to be covered by deletion CNVs in both beef and dairy breeds. These pathways are considered important in bovine domestication that, to a large extent, is determined by an animal's adaptive ability (Jensen ).…”

Section: Copy Number Variationsmentioning

confidence: 99%

Tropically adapted cattle of Africa: perspectives on potential role of copy number variations

et al. 2015

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Africa is host to diverse and locally adapted cattle breeds that are expected to survive the harsh and extreme tropical environments associated with diseases and parasite infections, heat stress and episodes of feed and water scarcity. Genomic copy number variations (CNVs) are considered to be primary role players in cattle breed formation and adaptation where isolation and genetic drift together with subsequent mutations have created an enormous diversity of local populations. CNVs are modifications in DNA structure comprising deletions, duplications and insertions that are >1 kb in size. Despite attracting much attention, the frequency and pattern of bovine CNV events, especially in African cattle breeds, are for the most part largely unknown. Characterization of genetic variation in the indigenous cattle of Africa will be a vital step toward dissecting the molecular mechanisms underlying phenotypic variation and local adaptation. This review therefore aims to describe the current knowledge regarding bovine CNVs and the implications and potentials they encompass for dissecting genetic adaptation and the genotypic skeleton of tropical African cattle populations.

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“…Such is the case of double muscling in cattle (12, 13). This technology has been successfully used to identify genetic variants that cause differences in productivity of milk (14, 15), muscling (15, 16), and fertility (17). Combining GWAS with high-throughput sequencing procedures will enable the identification of unknown causative genetic variants that could improve productivity of cattle.…”

Section: Introductionmentioning

confidence: 99%

A Review of Selected Genes with Known Effects on Performance and Health of Cattle

Casas

Kehrli

2016

Front. Vet. Sci.

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There are genetic conditions that influence production in dairy and beef cattle. The objective of this review was to describe relevant genetic conditions that have been associated with productivity and health in cattle. Genes or genomic regions that have been identified as a candidate for the condition will be included, and the genetic basis of the condition will be defined. Genes and genetic conditions included in this review are bovine leukocyte adhesion deficiency, deficiency of the uridine monophosphate synthase, bovine chronic interstitial nephritis, horn development, myostatin, complex vertebral malformation, leptin, osteopetrosis, apoptosis peptide activating factor 1, chondrodysplastic dwarfism, caseins, calpastatin, umbilical hernia, lactoglobulin, citrullinemia, cholesterol deficiency, prions, thyroglobulin, diacylglycerol acyltransferase, syndactyly, maple syrup urine disease, slick hair, Factor XI deficiency, and μ-Calpain. This review is not meant to be comprehensive, and relevant information is provided to ascertain genetic markers associated with the conditions.

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Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level

Cited by 51 publications

References 107 publications

Systematic profiling of short tandem repeats in the cattle genome

Systematic profiling of short tandem repeats in the cattle genome

Tropically adapted cattle of Africa: perspectives on potential role of copy number variations

A Review of Selected Genes with Known Effects on Performance and Health of Cattle

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