Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 May;122(5):636-646.
doi: 10.1038/s41437-018-0150-6. Epub 2018 Nov 6.

Diversity of copy number variation in the worldwide goat population

Affiliations

Diversity of copy number variation in the worldwide goat population

Mei Liu et al. Heredity (Edinb). 2019 May.

Abstract

Goats (Capra hircus) are an important farm animal species. Copy number variation (CNV) represents a major source of genomic structural variation. We investigated the diversity of CNV distribution in goats using CaprineSNP50 genotyping data generated by the ADAPTmap Project. We identified 6286 putative CNVs in 1023 samples from 50 goat breeds using PennCNV. These CNVs were merged into 978 CNV regions, spanning ~262 Mb of total length and corresponding to ~8.96% of the goat genome. We then divided the samples into six subgroups per geographic distribution and constructed a comparative CNV map. Our results revealed a population differentiation in CNV across different geographical areas, including Western Asia, Eastern Mediterranean, Alpine & Northern Europe, Madagascar, Northwestern Africa, and Southeastern Africa groups. The results of a cluster heatmap analysis based on the CNV count per individual across different groups was generally consistent with the one generated from the SNP data, likely reflecting the population history of different goat breeds. We sought to determine the gene content of these CNV events and found several important CNV-overlapping genes (e.g. EDNRA, ADAMTS20, ASIP, KDM5B, ADAM8, DGAT1, CHRNB1, CLCN7, and EXOSC4), which are involved in local adaptations such as coat color, muscle development, metabolic processes, osteopetrosis, and embryonic development. Therefore, this research generated an extensive CNV map in the worldwide population of goat, which offers novel insight into the goat genome and its functional annotation.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no conflict of interest.

Figures

Fig. 1
Fig. 1
Boxplot for distributions of CNVs count per autosome across six goat groups. WAS: Western Asia, n = 53; EME: Eastern Mediterranean, n = 195; ANE: Alpine & Northern Europe, n = 103; NWA: Northwestern Africa, n = 182; SEA: Southeastern Africa, n = 412; MAD: Madagascar, n = 78. Each “box” contains a thin horizontal line (25–75% range) and a horizontal black line (median)
Fig. 2
Fig. 2
Genomic distribution and frequencies of CNV regions on autosomes in six groups from the goat ADAPTmap data-set. The tracks from outside to inside are: Northwestern Africa (NWA), Southeastern Africa (SEA), Madagascar (MAD), Alpine & Northern Europe (ANE), Eastern Mediterranean (EME), Western Asia (WAS), respectively. The frequency of CNVR was plotted for the subgroups and only CNVRs contained > = 2 CNV events were used
Fig. 3
Fig. 3
Six diverse goat groups were grouped into clusters in heatmap plots based on the top 5% of CNVRs (26 CNVRs). WAS: Western Asia; EME: Eastern Mediterranean; ANE: Alpine & Northern Europe; NWA: Northwestern Africa; SEA: Southeastern Africa; MAD: Madagascar. The value in the legend of the heatmap is CNV event frequency (CNV count in each CNVR /sample size)
Fig. 4
Fig. 4
PennCNV plot of Log R Ratio for three different status of DGAT1 CNV within CNVR9. a Boxplot for distributions of LRRs of 21 probes within CNVR9. Probes 14 and 15 in the red box were located in DGAT1. The mean and standard deviation were generated by three sample groups with DGAT1 CNV state 1 (cn = 0), 2 (cn = 1) and 5 (cn = 3), respectively. b Scatter plot of LRR for a CNV event harboring DGAT1 (plots in blue box) in three individuals randomly selected. IT_NIC0012, MA_451, and IT_GAR0011 were defined as state1 (cn = 0), state2 (cn = 1), and state5 (cn = 3) by PennCNV, respectively. Only CNVs, spanning at least 3 probes with a standard deviation (SD) of LRR < 0.30, were reported

References

    1. Agerholm JS, McEvoy FJ, Menzi F, Jagannathan V, Drögemüller C. A CHRNB1 frameshift mutation is associated with familial arthrogryposis multiplex congenita in Red dairy cattle. BMC Genom. 2016;17:479. doi: 10.1186/s12864-016-2832-x. - DOI - PMC - PubMed
    1. Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009;19:1655–1664. doi: 10.1101/gr.094052.109. - DOI - PMC - PubMed
    1. Alvarez CE, Akey JM. Copy number variation in the domestic dog. Mamm Genome. 2012;23:144–163. doi: 10.1007/s00335-011-9369-8. - DOI - PubMed
    1. Bentzinger CF, Wang YX, Rudnicki MA. Building muscle: molecular regulation of myogenesis. Cold Spring Harb Perspect Biol. 2012;4:a008342. doi: 10.1101/cshperspect.a008342. - DOI - PMC - PubMed
    1. Bickhart DM, Rosen BD, Koren S, Sayre BL, Hastie AR, Chan S, et al. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nat Genet. 2017;49:643–650. doi: 10.1038/ng.3802. - DOI - PMC - PubMed

Publication types