Dataset Information

Genome-wide detection of copy number variations in polled yak using the Illumina BovineHD BeadChip.

ABSTRACT: BACKGROUND:Copy number variations (CNVs), which are genetic variations present throughout mammalian genomes, are a vital source of phenotypic variation that can lead to the development of unique traits. In this study we used the Illunima BovineHD BeadChip to conduct genome-wide detection of CNVs in 215 polled yaks. RESULTS:A total of 1066 CNV regions (CNVRs) were detected with a total length of 181.6?Mb, comprising ~?7.2% of the bovine autosomal genome. The size of these CNVRs ranged from 5.53?kb to 1148.45?kb, with an average size of 170.31?kb. Eight out of nine randomly chosen CNVRs were successfully validated by qPCR. A functional enrichment analysis of the CNVR-associated genes indicated their relationship to a number of molecular adaptations that enable yaks to thrive at high altitudes. One third of the detected CNVRs were mapped to QTLs associated with six classes of economically important traits, indicating that these CNVRs may play an important role in variations of these traits. CONCLUSIONS:Our genome-wide yak CNV map may thus provide valuable insights into both the molecular mechanisms of high altitude adaptation and the potential genomic basis of economically important traits in yak.

SUBMITTER: Jia C

PROVIDER: S-EPMC6518677 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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Publications

Genome-wide detection of copy number variations in polled yak using the Illumina BovineHD BeadChip.

Jia Congjun C Wang Hongbo H Li Chen C Wu Xiaoyun X Zan Linsen L Ding Xuezhi X Guo Xian X Bao Pengjia P Pei Jie J Chu Min M Liang Chunnian C Yan Ping P

BMC genomics 20190514 1

<h4>Background</h4>Copy number variations (CNVs), which are genetic variations present throughout mammalian genomes, are a vital source of phenotypic variation that can lead to the development of unique traits. In this study we used the Illunima BovineHD BeadChip to conduct genome-wide detection of CNVs in 215 polled yaks.<h4>Results</h4>A total of 1066 CNV regions (CNVRs) were detected with a total length of 181.6 Mb, comprising ~ 7.2% of the bovine autosomal genome. The size of these CNVRs ran ...[more]

PMID: 31088363

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Project description:BACKGROUND: In recent years, genome-wide association studies have successfully uncovered single-nucleotide polymorphisms (SNPs) associated with complex traits such as diseases and quantitative phenotypes. These variations account for a small proportion of heritability. With the development of high throughput techniques, abundant submicroscopic structural variations have been found in organisms, of which the main variations are copy number variations (CNVs). Therefore, CNVs are increasingly recognized as an important and abundant source of genetic variation and phenotypic diversity. RESULTS: Analyses of CNVs in the genomes of three sheep breeds were performed using the Ovine SNP50 BeadChip array. A total of 238 CNV regions (CNVRs) were identified, including 219 losses, 13 gains, and six with both events (losses and gains), which cover 60.35 Mb of the sheep genomic sequence and correspond to 2.27% of the autosomal genome sequence. The length of the CNVRs on autosomes range from 13.66 kb to 1.30 Mb with a mean size of 253.57 kb, and 75 CNVRs events had a frequency > 3%. Among these CNVRs, 47 CNVRs identified by the PennCNV overlapped with the CNVpartition. Functional analysis indicated that most genes in the CNVRs were significantly enriched for involvement in the environmental response. Furthermore, 10 CNVRs were selected for validation and 6 CNVRs were further experimentally confirmed by qPCR. In addition, there were 57 CNVRs overlapped in our new dataset and other published ruminant CNV studies. CONCLUSIONS: In this study, we firstly constructed a sheep CNV map based on the Ovine SNP50 array. Our results demonstrated the differences of two detection tools and integration of multiple algorithms can enhance the detection of sheep genomic structure variations. Furthermore, our findings would be of help for understanding the sheep genome and provide preliminary foundation for carrying out the CNVs association studies with economically important phenotypes of sheep in the future.

Dataset Information

Genome-wide detection of copy number variations in polled yak using the Illumina BovineHD BeadChip.

Publications

Genome-wide detection of copy number variations in polled yak using the Illumina BovineHD BeadChip.

Similar Datasets

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